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Old 01/03/2016, 09:09 PM   #2501
Dfee
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Quote:
Originally Posted by Billybatz9 View Post
What nitrate target should I be aiming for?

If you had sps this will be an issue I'm sure. I don't have sps and I got mine up to 20-40 ppm.


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Old 01/03/2016, 09:16 PM   #2502
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Originally Posted by karimwassef View Post
I got a coral life turbo twist 12x because it's compact. It's 36W, so I have to pass the water very slowly (200gph) through it.

If I were to do it again, I'd go with a 110W with a much higher flow rate.

Karim, you used this small uv on that huge system of yours? I just read that build thread yesterday actually. Really cool setup!

I guess uv is the only thing I haven't tried and what I'll buy next. I still cannot get rid of the dustings of Dino on glass and power heads. Most annoying is how my corals are affected. Zoas barely come out. Everything else struggling but not as bad as Zoas.


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Old 01/03/2016, 09:20 PM   #2503
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Originally Posted by Dfee View Post
Karim, you used this small uv on that huge system of yours? I just read that build thread yesterday actually. Really cool setup!

I guess uv is the only thing I haven't tried and what I'll buy next. I still cannot get rid of the dustings of Dino on glass and power heads. Most annoying is how my corals are affected. Zoas barely come out. Everything else struggling but not as bad as Zoas.
My zoas open, but they don't grow like they should be


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Old 01/03/2016, 09:23 PM   #2504
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Originally Posted by Billybatz9 View Post
My zoas open, but they don't grow like they should be

Yeah, my Dino's aren't even on coral or rock. Finally got my nitrates up. No idea about po4. I guess it's low po4 or some other element I'm missing by not doing water changes.


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Old 01/03/2016, 09:32 PM   #2505
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It's not about the UV by itself. That's why most people give up on it.

UV must be used in combination with lights out and very slow flow based on the power.

Also, I used heavy and wet skimming to export the dead dinos killed by the UV... and carbon to remove the chemical biproduct.

Then I added a lot of new life and fed it with phyto.

and then I fed heavily but used scrubbers and GFO to keep the water full of food, but low in waste.


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Old 01/03/2016, 09:33 PM   #2506
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Originally Posted by Dfee View Post
Karim, you used this small uv on that huge system of yours? I just read that build thread yesterday actually. Really cool setup!

I guess uv is the only thing I haven't tried and what I'll buy next. I still cannot get rid of the dustings of Dino on glass and power heads. Most annoying is how my corals are affected. Zoas barely come out. Everything else struggling but not as bad as Zoas.
Thanks. I was skeptical of the size of the UV, and it took a few days for the results to start showing...


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Old 01/04/2016, 06:56 AM   #2507
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Happy New Year, everyone.

Sorry for disappearing, but it wasn't for lack of interest in the subject matter -- rather the opposite, actually. I've been off doing more homework, starting with an interlibrary loan request for a book on the evolutionary history of marine primary producers. After I read it, I spent some time following up on some of the papers cited in it that looked interesting, but which weren't particularly relevant to the topic at hand (this guy is my new hero). Having fallen well behind the thread by then, I hit a runtime problem: the longer I was off doing my own thing, the more there was to catch up with.

Let's start with skimmate dosing. Some good questions have been asked since I last popped up and I'll try to answer a few of them along the way, but that's the obvious old business, and addressing it gives me an avenue to lead you guys into what's going to be a very lengthy science lecture about dinos, corals, bacteria, and algae in general... I apologize up front for the length of this write-up, which is cosmically longer and more science-y than my earlier posts on this topic -- so much so that I'm going to have to break it up into several separate posts because RC has a 25,000 character limit. Yikes! But as I said before, wrestling with O. ovata brings us about as close to the cutting edge of science as reefers are ever likely to get, and investigating this over the last few months proved to be the necessary motivation and correct angle of attack to at last bring my mental model of how reefs function into the 21st Century. I like to regard my experience of this hobby as playing "catch up with the scientists", and I found all the cool scientists hanging out in a Venn diagram where evolutionary biology intersects with the microbial loop and biogeochemical cycling. It's a party. You guys should totally check it out, and this is my best attempt to sketch out a map that will get you there.

Long story short (and vastly oversimplified) the bacteria associated with toxic dinoflagellates can kill corals, and the bacteria associated with healthy corals and other macrofauna can kill toxic dinos, including O. ovata.

I doubt this is a happy coincidence. It looks like an evolved defense against benthic dinoflagellates. Corals have lived alongside dinos for at least 228 million years, when the first dinoflagellate cysts show up in the fossil record, so obviously they've had lots of time to work the problem. That's undoubtedly what Montireef stumbled onto when he dumped skimmate into his tank: healthy corals release mucus loaded with coral-friendly bacteria; coral mucus is colloidal and its chemical backbone is a polypeptide, making it highly skimmable; the coral-friendly bacteria weaponized Montireef's skimmate and knocked back his dino bloom.

So if you are sufficiently geeky to ride this ride, go pee, maybe swing by the fridge, and settle in. Software updates always take a while, but BONUS!!! Along the way: sponges. I know -- exciting, right?

Okay, everybody ready? Off we go...


Quote:
Originally Posted by DNA
Yesterday morning I started to add the content of my skimmer back to the tank after having sat there for a week.
I drained the wet part from the skimmer in 3 doses 3 hours apart to make sure it was not too much of a shock to the fish.
I can't say I like the smell of sulfur in the morning, but it didn't seem to have any effect on the fishes.
Sulfide is generated by anaerobic bacterial respiration. Under the "millions of microscopic rafts of colloidal organic carbon" theory of probiotic skimmate dosing, the presence of anaerobes would reduce the potential effectiveness of skimmate dosing against a dino bloom because they'd die (or, if aerotolerant, go dormant) as soon as they hit oxygenated water.


Quote:
Originally Posted by DNA
Since corals are showing a little color it could be that the corals are hosting a new type of dinos.
I suppose it's possible, but it seems unlikely that corals of different species would all accept new symbiotes at the same time, and the dinos Montireef reported finding in his skimmate, oxyrrhis marina, would not be of any use to corals because they're heterotrophic and from the wrong genus. In fact, they're a well known "out group" in genetic reconstructions of dinoflagellate family trees and are thought to be a basal lineage that predates the evolution of mixotrophic dinos.


Quote:
12/30/2014, 10:41 AM #557
Montireef
Yes, my system was too ULNS and noticed important bacterial growth in the skimmate so I dumped the whole cup. Corals got very happy and extended polyps.
Did you see anything like that, DNA? Polyp extension is often a reaction to nighttime hypoxia in the wild, but in our tanks, that's typically feeding behavior. That would suggest there's food in the water, which would be a simpler explanation for improved color than swapping in a new species of dinos. And we know corals eat bacteria...


Quote:
Originally Posted by The Coral Probiotic Hypothesis
Three of the most abundant organic compounds in the sea, cellulose, agar and chitin, are degraded by bacteria but not by eukaryotes. After the bacteria degrade these compounds and multiply, some of these bacteria may serve as food for the coral animal. Thus, coral bacteria can allow corals to obtain energy from a complex mixture of polymers. In addition to having an enormous genetic potential to produce degradative enzymes, the relative amounts of different coral degradative bacteria can change rapidly as the nutrient source changes.
...so it's not much of a stretch to conclude that corals would be interested in bits of colloidal organic carbon with bacteria growing on them. That's pretty much what their mucus is, actually.

BTW -- fun science fact: nitrogen is required for the synthesis of chitin (poly-N-acetyl-D-glucosamine), the protein used to form the exoskeletons of, among other things, pods. And corals eat pods.


Quote:
Originally Posted by DNA
The results are in.
After 5 days the dinos are just going on with their daily lives as usual.
If fact I've got slightly more of them right now than last 12 months.

This means we can't say that recycled skimmate will help with a dino problem.
We also can't say it's useless until several others try this out.
Well, that's very disappointing. I suggest trying again with fresh skimmate, as that's what Montireef indicated he used.


Quote:
Originally Posted by Quiet_Ivy
Day 3 adding week-old skimmate collected in a jar back to my tank.

Good news: Got here this morning and Whoah! 90% of the cyano is gone!

Bad news: big dino outbreak, I see the harder brown circular spots on the glass and some have developed strings since yesterday morning. Hermit crab is ok. Corals ok except for my hammer which sucked all its polyps in and looks very cranky.
That correlates with DNA's experience, so it looks like good data to me... Week old skimmate makes dinos worse.

Since both you and DNA reported dino growth, the simplest explanation for these failures is that week-old skimmate is dino food, either indirectly by providing organic carbon to feed the heterotrophic bacteria the dinos are farming, directly by providing bacteria to feed the dinos themselves, or both at the same time. Your dinos were fruitful and multiplied, and they ate all the cyano.

To think about how this went wrong, I needed information, so something I had been avoiding had to be faced up to: I knew from the beginning that I should've looked into the known bacterial associates of O. lenticularis to see what they had in common, but I also knew this would be rather time consuming and only relevant to O. ovata to the extent that I could get away with reasoning by inference, so I had no idea if it would be time well spent or not... But with DNA and Quiet_Ivy reporting failure, I was curious to find out if there were any bacteria that would do well in anoxic or hypoxic skimmate, so I bit the bullet.

And sure enough, there was a pattern. It looked like O. lenticularis favors a class of bacteria called gamma-proteobacteria, many of which are facultative anaerobes, but Old School lab techniques are biased towards detecting gamma-proteobacteria because they generally grow readily on agar in petri dishes, so that could be an artifact. Happily, a more recent paper that examined the microbiome of two strains of O. lenticularis using genetic tools capable of detecting bacteria that can't be cultured confirmed that these dinos consort with gamma-proteobacteria, and more intriguingly, they may have an obligate association with another, entirely unrelated species of bacteria.


Quote:
Originally Posted by Bacteria Associated with Toxic Clonal Cultures of the Dinoflagellate Ostreopsis lenticularis
O. lenticularis, as well as other toxic dinoflagellates, have been reported to have bacterial species associated to them. Aeromonas, Alteromonas, Bacillus, Cytophaga, Flavobacterium, Moraxella, Pseudomonas, Roseobacter, and Vibrio are the bacterial genera most frequently associated with toxic dinoflagellates. ...

A total of 127 sequences (62 sequences from clone no. 302 and 65 from clone no. 303) were generated and analyzed phylogenetically...these clusters were grouped within two major bacterial clades that included: Proteobacteria (alpha and gamma) and the CFB complex. Previous studies have shown that bacterial communities associated with different toxic dinoflagellates are also restricted to these two bacterial phyla. From this analysis, we found that both O. lenticularis clones have nine bacterial species associated to them, two of which where common to both dinoflagellate clones. These bacterial species were studied further because they may represent organisms persistently and specifically associated to the dinoflagellate. The first bacterial species, represented by clusters 302T-1 and 303T-9 (100% homology), belongs to the CFB complex (referred to as CFB 302T-1 from now on) and is the most predominant organism constituting 51% and 47% of the sequences from clone no. 302 and clone no. 303, respectively. The second organism, a gamma-Proteobacterium represented by clusters 302T-9 and 303T-2 (100% homology), constitutes 19% and 15% of the sequences from clone no. 302 and clone no. 303, respectively.

The persistent and specific association of these bacterial species was further tested... The results show that the gamma-Proteobacterium was not present in the new O. lenticularis clones. ... The 16S rRNA gene from CFB 302T-1 did not amplify from total bacterial DNA isolated from a clonal culture of a free living dinoflagellate Cochlodinium polykricoides also established from southwestern Puerto Rico. Considering that CFB 302T-1 was present in clonal cultures established a decade after the original clones used in this study and that it was not present in C. polykricoides, we conclude that this organism has a persistent and apparently specific association with O. lenticularis. ...

These two 16S rRNA sequences share 99% identity to each other, but were only 95% similar to the closest GenBank match (AM040105), suggesting that both these clusters represent a new VBNC [viable but non-culturable] bacterial species belonging to the genus Bacteroides
This is puzzling... Bacteroides are found in anoxic marine sediments, but they're generally regarded as anaerobic gut bacteria -- or that, at any rate, is clearly where most of the grant money is ATM. They do have a tendency to produce useful chemicals like vitamins B-12 and K that make them potential symbiotes, and it has been speculated that endosymbiotic bacteria are supplying dinoflagellates with B-12, but bacteroides are not what one would expect to find in association with a primary producer that releases oxygen when the sun shines. The author seems to be aware of this, as the "family tree" published in that paper emphasizes a more tenuous connection between CFB 302T-1 and bacteria from the genus cytophaga (a 90% hit, below the 93% similarity that's taken to indicate two bacteria are probably from the same genus), which consists of aerobic bacteria that fill a similar ecological niche as bacteroides. Indeed, in the original version of this paper (a master's thesis from 2006) the bacteria are unambiguously described as a cytophaga species -- the 95% hit on AM040105 is acknowledged but otherwise ignored. Reading between the lines, I can't help but suspect that the student's faculty advisor was similarly suspicious of the hit on AM040105: CFB 302T-1 can't really be a bacteroides! Hmmm... Best go with the second-best match, instead.

But on the other hand, an obligate association with anaerobic bacteria might make sense for benthic dinos, and it would explain why sulfurous skimmate is dino chow... After all, in the absence of water-pumping infauna like worms and shrimp that toxic benthic dinos would drive off or kill, typically only the top 5-10 mm (call it a quarter to half an inch) of reef sands in the wild are oxygenated; and it's well known that diatoms and other single-celled organisms on tidal flats migrate as much as several centimeters into the sand at low tide to protect themselves from UV light and dessication, so it may be that strong swimmers like dinos routinely dive into hypoxic or anoxic sand in search of a meal. In fact, bacteroides are capable of breaking down and consuming the ostis' cellulose armor, so cultivating an aerotolerant bacteroides that goes dormant in the presence of oxygen would be a good way for ostis to keep their food from eating them while they're swimming around on the nightly hunt or looking for someplace to establish a new bacteria farm.

Additionally, dinoflagellates are unique among oxygenic photosynthesizers in that the vast majority of mixotrophic dinos use form II rubisco, and that version of the 4 billion year old enzymatic flywheel that primary producers use to fix carbon is associated with anoxygenic photosynthesis and photoheterotrophy. Dinos stole the genes for it from bacteria and made it work, presumably because it's fast, and being able to rapidly fix carbon is obviously a useful trait for a primary producer. In fact, it has been argued that stealing genes from bacteria is dinos' raison d'etre -- their nuclei store DNA in a weird way that's not quite eukaryotic and not quite prokaryotic, so much so that they were hypothesized decades ago to be descended from an ancient "missing link" organism halfway between bacteria and eukaryotes, but that didn't pan out. Apparently, the reason dinos store their DNA this way is to make it easier to insert bacterial DNA into their own genomes. Stealing and hoarding DNA would explain why dinos have oversized genomes, and they're so freakishly good at it that they made form II rubisco work where it has no business being: inside a eukaryotic, oxygenic primary producer. If they can do that, I wouldn't put it past benthic dinos to have acquired genes that help them survive foraging expeditions in anoxic environments, so maybe O. lenticularis really does have an obligate association with a bacteroides species.

Google Scholar couldn't find many useful papers about benthic bacteroides in marine sediments and reef sands. They're part of the normal benthic anaerobic community, but most of the current research into bacteroides in the marine environment concerns sewage outflows from coastal cities and fecal bacteria contaminating beaches and near-shore waters, which BTW ostreopsis dinos are negatively correlated with in the Mediterranean... If ostis actually do heart bacteroides, it's apparently an aerotolerant marine species that they're into, not an intestinal species we're flushing into the oceans.

GenBank is open the public -- our tax dollars at work! -- so I searched for AM040105 and found that it's an uncultured Bacteroidetes first detected in the sands of tidal flats in the North Sea. The paper in which it was described is behind a paywall, but the abstract is available and points towards "the Cytophaga/Flavobacterium group" aka the Cytophaga-Flavobacterium-Bacteroides (CFB) group. The sands AM040105 were found in are described as well oxygenated, but on the other hand, aerotolerant anaerobes tied into the sulfur cycle were detected in significant numbers -- maybe there are aerotolerant bacteroides present, as well, or maybe there are anoxic microenvironments in biofilms growing on buried detritus where bacteroides can thrive.

So not much help there, but we know AM040105 is a marine Bacteroidetes, and so is CFB 302T-1 as the CFB group is now the phylum Bacteroidetes. To have narrowed it down even that much is useful.


Quote:
Originally Posted by Ecology of marine Bacteroidetes: a comparative genomics approach
Members of the phylum Bacteroidetes are the most abundant group of bacteria in the ocean after Proteobacteria and Cyanobacteria. They account for a significant fraction of marine bacterioplankton especially in coastal areas, where they represent between 10% and 30% of the total bacterial counts. They are globally distributed in a variety of marine environments such as coastal, offshore, sediments and hydrothermal vents.

The better known members of the Bacteroidetes are specialized in processing polymeric organic matter, particularly in the mammalian gut (for example, Bacteroides spp.) or in soils (Cytophaga). In aquatic habitats, Bacteroidetes are abundant during and following algal blooms, showing a preference for consuming polymers rather than monomers. In the oceans, the main lifestyle of Bacteroidetes is assumed to be attachment to particles and degradation of polymers. ... Thus, Bacteroidetes likely have a different life strategy to that of other marine bacteria such as Alphaproteobacteria and Cyanobacteria. The latter are photoautotrophs, while marine Alphaproteobacteria (at least the most abundant ones) are aerobic heterotrophs that preferentially use monomers and live suspended in the water column. If the preference of Bacteroidetes for polymers and an existence attached to surfaces could be confirmed, their role in the carbon cycle of the oceans would be complementary to that of the other two groups. ...

The number of peptidases and GHs [glycoside hydrolases, enzymes that break down high molecular weight polysaccharides like cellulose] increased with the size of the genome in all bacteria. Most Bacteroidetes had more of these enzymes than the average bacterium, irrespectively of the genome size. This is one of the major observations showing the dedicated role of marine Bacteroidetes as polymer degraders. ...

A striking observation was that marine Bacteroidetes had many more peptidases than GHs. This was not the case for the non-marine Bacteroidetes examined. This strongly suggests a specialization of marine Bacteroidetes on the degradation of proteins, which is consistent with experimental studies using microautoradiography. ...

These indices show that not only do these bacteria have more peptidases than GHs, but that there is a larger diversity of the former. Thus, the conclusion that protein degradation is the main speciality of marine Bacteroidetes is robust.
So regardless of whether the obligate association O. lenticularis has is with an anaerobic bacteroides or an aerobic cytophaga or from some other genus entirely, we know it's a marine Bacteroidetes and thus have a good idea of what ecological niche it fills.

The assertion that proteobacteria are planktonic and Bacteroidetes colonize detritus isn't wrong but should not be taken as gospel. Bacteroidetes have an unusually large number of genes for making adhesion proteins that facilitate sticking to stuff which indicates that this is an important aspect of their biology, but they're also found among the plankton, and proteobacteria have genes for adhesion proteins, too, and are found growing on marine snow. Similarly, proteobacteria tend to consume labile organic carbon and Bacteroidetes specialize in breaking down and consuming very large organic molecules, but there are proteobacteria that can consume high molecular weight polysaccharides like cellulose, lignin, and chitin, and Bacteroidetes can consume the simple sugars that polysaccharides are made from (for example, cellulose is made from polymerized glucose -- hence "polysaccharide").

The observation that Bacteroidetes play a complementary role in the marine carbon cycle to cyano and proteobacteria is very interesting, as Bacteroidetes and proteobacteria normally dominate communities of marine heterotrophic bacteria. Cyano makes organic carbon, and diazotrophic cyano is protein-rich because it can fix nitrogen (...broadly speaking, nitrogen consumption indicates protein synthesis and growth, while phosphorous consumption indicates the synthesis of genetic material and reproduction), while proteobacteria and Bacteroidetes respectively specialize in metabolizing labile organic carbon and recalcitrant organic carbon -- or as we hobbyists would see it, that's a primary producer and a CUC. So that raises an interesting question about the bacterial community around O. lenticularis: Is there a similar bacterial CUC associated with dinos?

CONTINUED...


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Old 01/04/2016, 07:12 AM   #2508
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Operating under the assumption that CFB 302T-1 is actually a cytophaga species, not a bacteroides, because that looks like the best lead we have, the genera of bacteria associated with O. lenticularis are...

--

AEROMONAS: Gamma-proteobacteria. Ubiquitous gram-negative rods. Facultative anaerobes. Saprophytic, meaning they participate in the decomposition of organic matter. One of the most common genera of bacteria found in salt and fresh water and frequently associated with diseases in fish, amphibians, reptiles, and birds. Considered a potentially serious emerging pathogen in humans. Aeromonas hydrophila can be fatal, and the genus is generally regarded as toxic and pathogenic (if you Google them, you'll get a lot of information about drinking water).

ALTEROMONAS: Gamma-proteobacteria related to Pseudomonas. Species have been repeatedly shuffled in and out of this genus in recent decades as a result of improved analytic techniques, and apparently there are currently only 8 of these aerobic and facultatively anaerobic gram-negative curved rods with single flagella. Happily, it seems none of them are pathogenic. Found in marine sediments and one species lives in seafloor hot springs, but mostly planktonic. One species is reportedly very good at hoovering up labile (very low molecular weight) dissolved organic carbon and is often associated with phyto blooms in NSW. Others are saprophytic -- an alternomonas species is among the bioluminescent bacteria that colonize marine snow, making it glow in hopes that it will be seen sinking through the darkness and eaten, giving the bacteria access to the nutrient-rich environment in a fish's intestines.

coryneform bacteria: "Coryneform" literally means "club-shaped" and apparently refers to unidentified bacteria cultured in the experiment from the '80s.

CYTOPHAGA: Ubiquitous gram-negative rods. This genus was massively reorganized on the basis of genetic evidence about 15 years ago, tearing it down to just two species -- Cytophaga hutchinsonii and C. aurantiaca -- and reassigning the other cytophagas to new genera. Formerly part of the CFB group, which no longer really exists but you still see references to it in the literature, cytophaga actually groups in a clade with the genus flexibacter, which was also torn down to the type species a while back and rebuilt on the basis of genetic evidence... Up until about 2005 or '06, there are bunches of papers about the Cytophaga-Flavobacterium Bacteroidetes group, aka the Cytophaga-Flavobacterium-Bacteroides group, or the Cytophaga-Flavobacterium/Flexibacter-Bacteroides group, or the Flexibacter–Bacteroides–Cytophaga phylum, or simply the Flavobacteriaceae, and several other names before it all shook out and settled on the classes Cytophagia, Flavobacteria, Bacteroidia, and Sphingobacteria of the phylum Bacteroidetes, representing an estimated 7000 different species, over half of them Flavobacteria which are easily recognizable by the large clocks they wear as necklaces. It's hard to tell what information from older studies of cytophaga from the CFB days is applicable to modern marine cytophaga, and further complicating matters from our POV, cytophaga are generally considered soil bacteria as the type species of the genus, C. hutchinsonii, was isolated from soil. Marine cytophaga had a reputation in some quarters as algicidal bacteria because they could consume macroalgal cell wall and structural polysaccharides like xylan, mannan, and cellulose, but on the other hand, one of the new genera into which old cytophaga species were moved is cellulophaga ("cellulose eater") -- yet C. hutch can grow using cellulose as its only source of organic carbon... Since O. ovata is epiphytic and can kill macroalgae, cytophaga would be plausible food bacteria for them if they were associated with disease and mortality in macro, and indeed I found some recent studies comfirming that marine cytophaga are among the bacteria associated with decaying phyto blooms and may opportunistically attack macroalgae. The genus' reputation is intact. Interestingly, cytophaga can consume lipids, and lipids + polysaccharides = lipopolysaccharides = bacterial cell wall proteins. An obligate association between ostis and a species of cytophaga bacteria thus makes sense on some level, as cytophaga look like excellent candidates for the CUC on the dinos' bacteria farms, and since they constitute about half the bacteria present in vitro, cytophaga sp. is also the obvious candidate for being the ostis' preferred food bacteria.

ERYTHROBACTER: Gram-negative non-motile aerobic alpha-proteobacteria. Erythrobacter are anoxygenic photoheterotrophs related to purple photosynthetic bacteria. Most commonly found in eutrophic coastal waters. Not all species make bacteriochlorophyll, and there was no mention of pigmented bacteria in either of the papers on the bacteria associated with O. lenticularis, so I would guess that whatever species of erythrobacter was present wasn't photoheterotrophic (...intuitively, it seems like benthic dinos shouldn't like photoheterotrophs because they're competing for the same real estate, but it makes sense that photoheterotrophs like dinos because they can swim and use this ability to stay in the light).

FLAVOBACTERIUM: Ubiquitous gram-negative rods of the phylum Bacteroidetes. Type genus of the family Flavobacteriaceae of the class Flavobacteria. Saprophytes that can consume carbohydrates, amino acids, proteins, and polysaccharides, but cannot consume alcohols, organic acids, hydrocarbons, and aromatics. Some species are pathogenic in FW but not in SW, and the genus likely evolved in FW and adapted to the marine environment. Marine pathogenic flavos afflict macroalgae as well as fish. Flavos are widely associated with phyto blooms, especially green algaes, in both FW and marine ecosystems, and they're often found in the benthic bacterial community though generally are not present in large numbers. Officially, flavos are aerobic, but poking around on Google Scholar suggests that at least some of them are facultative anaerobes -- even F. columnare, the cause of cotton mouth in FW fish, is described as aerobic but can reduce NO3 and release sulfide, both of which suggest the ability to use terminal electron receptors other than oxygen (...nitrate and sulfur are the classic fallbacks that you see over and over in facultative anaerobes: they go with NO3 because nitrate reduction works in marginally anoxic/micro-oxic conditions and NO3 yields the most energy of all the anaerobic terminal electron receptors, and they stick with sulfur because sulfur reduction is viable in full-on anoxia, and it's "Old Reliable" -- their aerobic metabolism was bolted onto biochemical machinery inherited from anaerobic ancestors, and the old system still works).

MESORHIZOBUM: Alpha-proteobacteria. Gram-negative facultative anaerobes generally considered soil bacteria, where they form symbiotic relationships with plants from the legume family and trade fixed nitrogen for organic carbon. Mesorhizobum species have been found in association with both terrestrial and marine worms. Can break down and consume cellulose and lignin, but none of the species in this genus is known to cause disease or even be an opportunistic pathogen in plants or algae.

NOCARDIA: Gram-positive rods of the class Actinobacteria. Saprophytic facultative anaerobes found in water and soil rich in organic matter (...the word for this in Science is "copiotrophic" -- copiotrophy is to heterotrophs as eutrophy is to autotrophs -- I think the root is the Latin "copi" meaning abundance, not the Greek "copros" meaning feces, but amusingly, for hobbyists it would make sense either way). Known to be very common in FW aquariums and a normal part of the intestinal microflora of tropical FW fish. Considered pathogenic in humans but with low virulence. Marine species can infect fish and mammals. Nocardia infections thought to be introduced through fish meal in high-protein feed pellets are a common problem for aquaculture operations, which I mention because this could be a vector that affects hobbyists, as well.

PSEUDOMONAS: Gamma-proteobacteria. Gram-negative flagellated rods found in soil and all aquatic environments. Formerly thought to be aerobic but now considered "metabolically diverse". Saprophytic, and terrestrial species are often found in association with plant roots, trading nutrients for carbohydrates and amino acids. Aquatic species are generally regarded as non-pathogenic or opportunistic pathogens that infect organisms with compromised immune systems. Psuedomonas fluorescens has been used as a probiotic treatment by aquaculturists to protect fish from bacteria and fungi with mixed success -- it seems to prevent vibriosis, for example, but not infection by aeromonas.

ROSEOBACTER: Alpha-proteobacteria. Gram-negative flagellated heterotrophs. Named for the color of bacteriochlorophyll-a made by photoheterotrophic species, which were the first to be discovered. Not all roseobacters are photoheterotrophs, but some that don't make bacteriochlorophyll carry the genes for it and can be induced to do so by exposing them to lower salinity levels, which tracks with the general observation that photoheterotrophs tend to be most common in eutrophic, turbid coastal waters such as bays and estuaries where salinity levels are often lower than NSW.

THALASSOMONAS: Gamma-proteobacteria. Aerobic gram-negative halophilic flagellated rods found only in SW. Can break down gelatin, casein, starch and lecithin, but not alginate or agar. The type species of the genus, Thalassomonas viridans, was isolated from oysters and first described in 2001.

VIBRIO: Gamma-proteobacteria. Facultative anaerobes and aggressive practitioners of chemical warfare that typically dominate copiotrophic environments. Vibrio are common in marine sediments and also in the water column as bacterioplankton, where many species are adapted to an oligotrophic environment in the open ocean. Vibrio are part of the normal intestinal population of healthy fish, people, and other animals, and a few of the same species (and also others) are lethal pathogens. Of those that cause disease in humans, the best known is V. cholerae, the cause of cholera. Pathogenic vibrio are a major problem in the marine environment; fewer pathogenic species are known in FW. At least two pathogenic species (Vibrio harveyi and V. splendidus) luminesce upon reaching some critical population density, causing sick shrimp to glow so predators can easily find them and the bacteria will gain access to the copiotrophic environment inside a fish. Some vibrio bacteria like to live on pods, perhaps to take advantage of the organic carbon released by feeding (pods are messy eaters) and other biological processes, or perhaps because some species of vibrio can grow using chitin as their only source of organic carbon. Vibrio spp. were the second-most-common bacteria associated with O. lenticularis and are thus also candidates for being their food bacteria (amphidinium carterae as well as two species of prorocentrum dinos have been reported preying on vibrio parahaemolyticus, a human pathogen -- but on the other hand, these same bacteria are algicidal towards another dino, cochlodinium polykrikoides...).

ULVIBACTER: Gram-negative aerobic non-motile rods of the phylum Bacteroidetes and the family Flavobacteriaceae. These bacteria are marine and require Na+ sodium ions for growth. Only six species are known from this genus, which groups in a clade with genera populated by ex-cytophagas, including the genus cellulophaga. The type species, U. littoralis, was first described in 2004 after being isolated from the epiphytic community of the frondose green macroalgae Ulva fenestrata. Ulvibacters tend to bloom during the early stages of decay in phyto blooms, so their association with O. lenticularis is probably opportunistic.

--

So not only are proteobacteria and Bacteroidetes present, but they're pretty much all that's present... The only break from the pattern is nocardia, an Actinobacteria reported in 1989 but not 2006. While several of the gamma-pros are facultative anaerobes that might do well in standing water as bacterial respiration draws down oxygen levels, a protein skimmer looks tailor-made to create heaven for Bacteroidetes. It may be that anaerobic bacteroides, which as marine Bacteroidetes are adapted to metabolize recalcitrant proteins, are the main beneficiaries as the O2 level drops in stored skimmate.

Saprophytic bacteria are logical partners for benthic dinos, as they feed on detritus, which of course is in plentiful supply in most DT sand beds, and are exactly the sort of P-rich bacteria that dinos would need to eat to get all the phosphorous they require and still have some left over with which to recruit diazotrophic cyano. Additionally, there's a metabolic pathway that allows some heterotrophic bacteria to break down large, recalcitrant organic carbon molecules that are normally too large for their enzymes to work on, but they need labile organic carbon to make it work. In other words, the small DOC molecules the dinos exude may allow some of their associated bacteria to break up very large molecules and get at organic carbon (and other nutrients, as well, but for heterotrophic bacteria it's mostly about the carbon) they wouldn't ordinarily have access to. That's why carbon dosing is good for water clarity, incidentally.

But what really caught my eye when I was first looking into this was the association between O. lenticularis and vibrio bacteria. What if O. ovata is buddies with vibrio, too? That would be an Axis of Evil -- I mean, there are a lot of toxic dinos in the sea, and there are plenty of pathogenic bacteria out there, too, but O. ovata teaming up with vibrio would be like Lex Luthor teaming up with Sauron. It's pretty much a worst case scenario.

And it also totally makes sense. As hobbyists, our basic understanding of how dinos do business is that they kill everything and hoover up the nutrients that are released as stuff decays, and the bacteria associated with Ostreopsis lenticularis are consistent with this model. Ostis, perhaps in combination with vibrio and other potentially pathogenic bacteria, can kill benthic fauna and algae; saprophytic bacteria then feed on the deceased; and the ostis feed on the bacteria (...note, however, that this is an idealized model, and it's surely not so tidy IRL -- check out this paper to get some idea of the potential complexities of dino-centric food webs, and it also bears mentioning that ostis probably have a "long tail" of biodiversity in the bacteria associated with them, but the laboratory techniques for identifying these bacteria, which by definition are only present in small numbers, are still pretty new and apparently haven't been used on dinos yet). The same dynamic would work for O. ovata, and the similarities the two species share, in habitat preferences and external characteristics and the fact that they're toxic dinoflagellates from the same genus, suggest they have essentially the same lifestyle and perhaps even similar bacterial partners. But like I said, I can only get away with this kind of thinking to the extent that I can reason by inference, so I went looking for evidence to provide some theoretical support for such intuitive leaps...


Quote:
Originally Posted by Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum
A total of 61 distinct bacteria spanning three phyla were cultured from the seven strains of G. catenatum. Thirty (49%) of the bacterial strains were affiliated with the Alphaproteobacteria... Thirteen (21%) isolates were affiliated with the Gammaproteobacteria... The remaining isolates came from two phyla, the Bacteroidetes (26%) and the high G+C% Gram-positive Actinobacteria (3%) [...note that the nocardia bacteria reported with O. lenticularis in 1989 are gram-positive actinobacteria]. ... The abundance of Gammaproteobacteria and Bacteroidetes in G. catenatum cultures averaged 5 and 4% respectively. ...

A number of the bacterial strains isolated were phylogenetically closely related to one another, while having originated from G. catenatum cultures from different parts of the world. ... Another distinct group was a specific clade of Roseobacter/Roseovarius-like strains that originated from G. catenatum cultures isolated from the sea areas as separate as Australia, Korea, Japan and Spain. In addition, many strains were also closely related to bacteria identified in association with other dinoflagellates such as the Paralytic Shellfish Toxin producing Alexandrium tamarense, Alexandrium lusitanicum and Alexandrium affine, the diarrhetic shellfish poisoning (DSP) Prorocentrum lima, and the non-toxic dinoflagellate Scrippsiella trochoidea. These similarities were especially evident among the dinoflagellate-derived strains belonging to the Rhodobacteraceae and Alteromonadaceae families. ...

In summary, the Alphaproteobacteria dominated the strains isolated, and an individual Alphaproteobacteria (Rhodobacteraceae) was always the most numerically abundant bacterium present in each culture. Half of all of the Alphaproteobacteria isolated were capable of a mode of photosynthetic growth, termed AAP [aerobic anoxygenic photosynthesis]. The second trend was for there to be cultivable oligotrophic and/or hydrocarbon-degrading Gammaproteobacteria present in almost all of the cultures. And thirdly, one or more cultivable isolates belonging within the Flexibacteraceae or Flavobacteriaceae families of the Bacteroidetes were always present in each culture.

The bacterial flora of G. catenatum generally mirrors that found associated with other dinoflagellates, being dominated by the Alphaproteobacteria (principally the Rhodobacteraceae -- frequently referred to as Roseobacter clade). For example, 50% of all phylotypes identified in four Pfiesteria sp. cultures were affiliated with the Alphaproteobacteria, with the Rhodobacteraceae Rg. algicola and Hyphomonas jannaschiana-like bacteria among the most numerous of these phylotypes. Rhodobacteraceae were also a dominant feature of the bacterial flora associated with the DSP-producing dinoflagellate P. lima, and from which the association Rg. algicola was originally described. The bacterial flora of Alexandrium spp. and S. trochoidea cultures were also dominated by Alphaproteobacteria, with the Roseobacter clade dominating both the cultivable species and ribotype clones identified. Like G. catenatum, members of the Alteromonadaceae (Marinobacter and Alteromonas) were consistently identified in other dinoflagellate cultures.

The high incidence of Alphaproteobacteria associated with algae does not appear to be restricted to the dinoflagellates, as Alphaproteobacteria, primarily Rhodobacteraceae, were always identified in association with each of six different species of diatom culture. Bacterial culture from the domoic acid-producing pennate diatoms, Pseudo-nitzschia multiseries, Pseudo-nitzschia seriata and non-toxic Pseudo-nitzschia delicatissima, consistently identified one or more Alphaproteobacteria associated with each of these cultures.

A striking feature of the bacterial flora of G. catenatum was the high degree of genetic similarity of members of the Alpha- and Gammaproteobacteria (Rhodobacteraceae and the Alteromonadaceae, respectively) compared to other dinoflagellates, particularly the PST-producing genus Alexandrium. ...

The similarities of bacterial flora across different dinoflagellates have two potential explanations. Firstly, there are selective mechanisms operating in laboratory cultures that favour genera from within the Rhodobacteraceae and Gammaproteobacteria...

The second explanation for the similarities in the bacterial community across G. catenatum cultures and with other dinoflagellates is that the bacteria from these groups may be of specific importance to the growth and physiology of dinoflagellate cells. Bacterial mineralisation of the algal extracellular products and phytodetritus is recognised as being an important part of the 'microbial loop', re-supplying algal cells with readily utilisable forms of C, N and P. The supply of vitamins, chelated iron by bacterially produced siderophores, or the production of cytokinins are examples where bacterially produced factors have been shown to stimulate algal growth. It may also be that the aerobic photoheterotrophs (AAP) identified in this study, which dominated the cultivable bacterial flora of G. catenatum cultures, may have a role in contributing energy to G. catenatum growth. ...

Three reports have identified specific bacteria as key components of the bacterial flora associated with the stimulation of dinoflagellate growth. ... Importantly, these bacteria belong to the two bacterial families consistently encountered in G. catenatum and other dinoflagellate bacterial communities.
Translated from the Science, that means there's a dinoflagellate holobiont (...actually, this paper is about bacteria and thus establishes that there's a dinoflagellate microbiome, but as noted above, IRL there's a fairly complex micro-ecosystem associated with dinos, and since I'm not a scientist and can freely point out the obvious in public, I'm just gonna go ahead and call it: there's a dinoflagellate holobiont). These guys were talking about pelagic dinos, not benthic species, but if multiple species of dinoflagellates across different genera have similar bacterial communities associated with them, then there's probably a benthic dinoflagellate holobiont, as well.

And it's obviously significant that the bacteria associated with O. lenticularis are essentially the same as those associated with pelagic dinos: alpha-pros, gamma-pros, and Bacteroidetes; and the alpha-pros in O. lenticularis' microbiome include potential photoheterotrophs (erythrobacter and roseobacter); even the exception to the pattern is a gram-positive actinobacteria. That's a strong correlation. The primary difference is which among these groups is dominant, as alpha-pros are numerically dominant in the pelagic dino holobiont, while the bacteria reported with O. lenticularis were about 50% cytophaga (or bacteroides) which are Bacteroidetes, followed by gamma-pros, and alpha-pros were the least numerous group. This suggests that the benthic dinoflagellate microbiome is a version of the pelagic dino microbiome with the bacterial CUC adapted to a different environment, which is further circumstantial evidence supporting the notion that there's substantial similarity between the bacterial populations associated with O. lenticularis and O. ovata.

CONTINUED...


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Old 01/04/2016, 07:31 AM   #2509
34cygni
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Gamma-proteobacteria, including vibrio, are common in marine sediments and often numerically dominant in the top centimeter or two of oxygenated sediments, where most saprophytic activity takes place -- benthic dinos would pretty much have to make friends with them to be benthic. Further, gamma- and epsilon-proteobacteria are the dominant sulfur oxidizing bacteria in marine sediments. Sulfur is the terminal electron receptor of choice for a great many anaerobes, and to give you an idea of how important that is, your preferred terminal electron receptor is oxygen... You breathe oxygen, they breathe sulfur.

Before O2 was made widely available by the evolution of cyanobacteria 2.7 billion years ago, bacteria got by for more than a billion years using other electron receptors like iron and nitrogen, but sulfur, which has five oxidation states ranging from +2 (sulfate) to -2 (sulfide), was the terminal electron receptor of choice for most bacteria, so much so that microbiologists sometimes refer to the ancient, anoxic biosphere as "the sulfur Earth". And much as plants turn CO2 back into O2, something has to close the sulfur cycle and turn sulfide back into sulfate. This happens all by itself if sulfide is exposed to oxygen, and capturing the energy released by the chemical reactions involved is an easy way for bacteria to make a living. Lots of them do it, or at least have the genes for it and can do it if the opportunity presents itself. Back before O2 was around and this ecological niche didn't yet exist, anaerobic sulfur oxidizers evolved to use sulfide as an electron donor and make SO4 using oxygen from CO2, but they're phototrophs and can only do this if there's light available. Sulfide accumulation can be highly problematic for anaerobic communities in deep water because it readily reacts with iron and hydrogen and can cause bacterial ecosystems to grind to a halt by locking up these key electron donors (...the word for this in Science is "euxinia" -- if you like to geek out on this stuff, search Google Scholar for Canfield ocean and "Canfield ocean", and if you're looking for a new apocalypse to worry about, search regular Google for Canfield ocean). Partnering with sulfur oxidizing bacteria seems like a good idea for benthic dinos, as they make a living, and possibly also make food for the dinos, off the waste products of anaerobic and facultatively anaerobic bacteria (sulfide) and the dinos (oxygen).

Partnering with cytophaga, on the other hand, looks downright suicidal for thecate dinoflagellates with cellulose armor like O. lenticularis or O. ovata, as the type species of the genus, Cytophaga hutchinsonii, can subsist on cellulose without any other source of organic carbon. Ostis no doubt have a biochemical trick or two up their sleeves to keep themselves from being eaten, and it may be that in copiotrophic sediments, cytophaga can be "bribed" with labile organic carbon because that's what they need to get at the tough stuff. But there are probably limits to whatever ostis are doing to protect themselves from cytophaga on their bacteria farms, as algicidal bacteria are known to play a key role in ending red tides and other algae blooms, and I've read about symbiotic bacteria turning on algae and actually releasing algicidal chemicals when they detect signs of weakness due to age or viral infection or lack of nutrients... Such highly opportunistic, "Curse your sudden but inevitable betrayal!" type partnerships may be common between algae and bacteria, and this could explain why dino blooms sometimes mysteriously go away when hobbyists decide to leave them alone and let nature take its course.

It's also interesting that cytophaga are apparently dominant in the bacterial community associated with ostis rather than alpha-proteobacteria, which are dominant in the pelagic dino holobiont, or gamma-pros, which are generally dominant among benthic saprophytic communities. I was unable to find any sort of broad-based information that might indicate what a "normal" population of bacteria in marine sediments on a healthy reef should look like, but FWIW I found a breakdown of bacterial DNA in sand from the Great Barrier Reef:

gamma-proteobacteria 29.4%
bacteroidetes/CFB group 20.4%
epsilon-proterobacteria 13.6%
planctomycetaceae 7.7%
alpha-proteobacteria 6.8%
verrucomicrobiaceae 6.8%
cyanobacteria 5.4%
acidobacteriaceae 2.7%

Contrast this diversity with the bacterial community associated with O. lenticularis...


Quote:
Originally Posted by Bacteria Associated with Toxic Clonal Cultures of the Dinoflagellate Ostreopsis lenticularis
A library consisting of partial 16S rRNA sequences (~500 bp) was constructed from total bacterial DNA extracted from O. lenticularis (clones no. 302 and no. 303). A total of 127 sequences (62 sequences from clone no. 302 and 65 from clone no. 303) were generated and analyzed phylogenetically. ... Based on BLASTN comparisons, these clusters were grouped within two major bacterial clades that included: Proteobacteria (alpha and gamma) and the CFB complex. Previous studies have shown that bacterial communities associated with different toxic dinoflagellates are also restricted to these two bacterial phyla.
This collapse in bacterial biodiversity appears to be real because observations in NSW confirm that alpha-pros, gamma-pros, and Bacteroidetes are associated with dinos, but it could be an artifact of in vitro cultures... There was an experiment with small corals taken from the Red Sea, placed in 2 liter fishbowls, and maintained with water changes every three days, and the bacterial community in the coral mucus shifted to just proteobacteria (alphas, betas, and gammas) and Bacteroidetes/CFBs. As noted above, proteobacteria and bacteroidetes normally dominate marine heterotrophic bacterial communities, and the reason for this is that they share essentially the same biochemical system for quorum sensing. This doesn't mean they can all automatically talk to one another, but because the underlying machinery is the same, it's easy (as these things go) for them to acquire the ability to sense the presence of and even communicate with another species so they can coordinate their actions and cooperate in the organization and defense of the biofilms they live in -- or so they can detect and fight it out with another species competing for the same ecological niche.


Quote:
Originally Posted by The effect of quorum-sensing blockers on the formation of marine microbial communities and larval attachment
The tested QS blockers caused changes in bacterial density and bacterial community structure... The groups most affected by QS blockers were Alphaproteobacteria, Gammaproteobacteria and the Cytophagales [which in the context of this paper from 2006 means Bacteroidetes]. ...

Although bacteria are unicellular organisms, they can control their growth and population densities. In order to achieve this, bacteria have evolved a regulatory mechanism named quorum sensing (QS) that consists of exuded info-chemicals that activate or de-activate target bacterial genes responsible for cell division and adhesion and, thus, control biofilm formation and composition. Biofilm formation, in turn, can control many processes at surfaces, for example the uptake or release of compounds by host organisms, bacterial virulence for the host, and biocorrosion. The process of QS is based on the production and release of low-molecular-weight signal molecules (often called autoinducers). The extracellular concentration of QS molecules reflects the population density of the producing organism. Bacteria can perceive and react to such signal molecules, allowing the whole cell population to initiate a concerted action once a critical population density has been reached. ...

A genomic database analysis has indicated that such interspecies communication possibly occurs throughout the Eubacteria. The QS-producing bacteria are highly diverse and fall within a large number of species among Alpha-, Beta- and Gammaproteobacteria which are dominant in tropical waters. In contrast to Gram-negative bacteria, Gram-positive bacteria exude peptides as signal molecules. QS signals produced by bacteria may also show transphyletic effects and induce algal spore attachment. ...

Many marine organisms, such as the red alga Delisea pulchra and the bacterium Aeromonas veronii, use QS blockers to control epibiotic biofilm formation. Delisea pulchra produces furanones that interfere with bacterial AHLs [a class of signaling molecules called N-acetyl homoserine lactones] and inhibit the growth of Gram-negative bacteria as well as the settlement of invertebrate larvae. At the same time, it is possible to propose that QS blockers can control larval settlement indirectly by regulating the microbial community structure of biofilms and the density of bacteria...
Remember those vibrio bacteria that make prawns glow in the dark? That's quorum sensing in action. The vibrio don't want to kill the prawns because other bacteria would take over during decomposition, so they've evolved to stop short of that and light up, instead, to make sick animals even easier prey.

Eukaryotes, including prawns, are able to eavesdrop on and participate in the quorum sensing conversations of some bacteria, allowing them to select for and interact with their obligate bacterial symbionts. Current science suggests that obligate symbiotic associations between a specific species of bacteria and a larger host organism like a dinoflagellate or coral polyp or fish or person are rare in the sense that host organisms do not select for their entire microbiome but only a handful of keystone species within it. Other bacteria associated with any particular organism may serve functionally as symbiotes in that they're rendering some biochemically important service for their host, but they can in fact be replaced with other species competing for the same niche. This plasticity in the microbiomes associated with host organisms is adaptive, like corals being able to swap out their zoox for a new symbiodinium species to adapt to warmer water.

The manipulation of specific QS and QQ ("quorum quenching") chemicals by host organisms allows them to establish required relationships with key bacterial symbiotes, and the selection of those particular bacteria is the foundation that defines the overall structure of the hosts' microbiomes -- symbiotes have a good thing going, and they don't want any pathogens to foul things up, so they only tolerate commensal bacteria that won't harm them or their host. There are also other mechanisms hosts use to influence the population of bacteria that grow on and in them, including an organism's immune system, of course, as well as chemical defenses that function within individual cells and tissue types, and structuring the overall mix of organic carbon they exude so as to give a competitive advantage to their preferred bacteria (...mother's milk is structured to do exactly this in the digestive tracts of babies, for example, and formula contains small amounts of exotic sugars in a comparatively ham-fisted effort to imitate this effect). But bacteria reproduce, and thus evolve, so much more quickly than corals and fish and people that these countermeasures would eventually, inevitably be beaten. The host's symbiotic and commensal bacteria are thus the keystone of the whole operation -- especially for reef-building stony corals, which seem to have no innate immune systems (...in contrast, extracts of branching and soft corals have been shown to have antibacterial effects).

As a result, when the fishbowl corals were put back where they came from in the Red Sea, instead of being overwhelmed by opportunistic bacteria, their mucus bacteria populations returned to normal and matched other healthy corals in the area. Corals are constantly exposed to bacteria from the water column and the food they capture, and they (and every marine organism) solved the problem of living in bacteria soup by establishing a microbiome that selects for commensal bacteria. In fact, corals seem to be able to selectively attract certain types of bacteria from the water. For example, coral mucus effectively traps picocyanobacteria -- in recent years, scientists have become aware of a vast and diverse population of picoplankton eking out a living in the clear waters of the "nutrient desert" in the open ocean, and corals tap into this invisible nutrient pool by capturing super-tiny cyano that drifts onto reefs. This is apparently another adaptation corals have made to obtain nitrogen in the oligotrophic reef environment.

So if dinos exert selective pressures on the bacterial communities associated with them -- and in fact, that's something I would expect dinos to be particularly good at because, as noted, stealing DNA from bacteria is kinda their thing -- then the obvious question is whether ostis use their toxins or exude some other chemicals to shift the saprophytic bacteria population in the sand to favor cytophaga, or if a bloom begins by taking advantage of conditions that naturally favor the dominance of cytophaga (...it does happen in the wild, but not often). From what I can determine, eutrophy generally favors the dominance of gamma-pros and flavobacteria among benthic saprophytes, presumably because flavos are geared towards consuming macromolecules made by green algae. If so, that would be good news for phyto dosers, as adding green phyto would be a selective pressure that wants to tilt the Bacteroidetes population in the sand from cytophaga to flavobacteria, which would not be good news for ostis.

There have been efforts to connect O. ovata blooms to eutrophic conditions, especially since they began to show up along the southern coast of Europe in the Mediterranean and Adriatic Seas -- like hobbyists, scientists generally seem to regard dinos simply as algae and want to tie them to certain nutrient conditions. However, nobody has been successful in identifying conditions that might trigger an ostreopsis bloom, and in fact the idea that osti blooms are associated with elevated nutrient levels was pretty well refuted by the documentation of a major O. ovata bloom in the shallow and generally nutrient-poor waters around a small, isolated, uninhabited group of islands in the equatorial mid-Atlantic.


Quote:
Originally Posted by Ostreopsis cf. ovata (Dinophyta) bloom in an equatorial island of the Atlantic Ocean
The Archipelago of Saint Paul's Rocks consists of a remote group of ten small islands... Only the biggest island has low vegetation and the area is subjected to severe sea and wind conditions. The area provides shelter for many species of seabirds, fish, crustaceans as well as insects and is important as feeding and reproductive area for various migratory species. The waters in the area are oligotrophic but upwelling events caused by the interaction between oceanic currents and the submarine relief may happen. The region is considered strategic to the development of industrial fisheries, although there are recent reports of negative impacts of this activity (overfishing) in the area. Koening and Oliveira (2009) reported that dinoflagellates represent 82% of the total number of microphytoplankton species in the area and the cyanobacterium Trichodesmium thiebautii is distinguished by its frequency and dominance. ...

In the present study, a bloom of O. ovata is reported in an oceanic area where the only identifiable anthropogenic impact would be apparently the industrial fishing activity. ... As a comparison, along Rio de Janeiro, at the southeastern subtropical Brazilian coast, O. ovata has been found in bloom densities in an area subjected to coastal upwelling, distant from heavy freshwater discharge from rivers and not eutrophic. At other more eutrophic areas, subjected to anthropogenic impacts (such as treated sewage discharge), the species has not been found in bloom densities. ... The question raised is if O. ovata blooms are singular for not being associated to eutrophic conditions, in contrast to most other harmful species.

Moreover, studies with O. cf. ovata laboratory cultures have shown that the species develops aberrant cell shape when grown in full media (L2), what is reverted when cells are transferred to a less concentrated (L2/2) medium. This same pattern was observed in cultures of Ostreopsis siamensis when grown in GSe and f/2 medium. According to those authors, increased nitrate and phosphate concentrations impeded the growth of O. siamensis and caused aberrant cell shape. ...the massive abundance of O. ovata at Saint Paul's Rocks, located 1000 km away off the main continental landmass and not inhabited is, controversially, an indication that eutrophication is possibly not playing a part in stimulating blooms of this species.
Fun science fact: Trichodesmium thiebautii is a common species of diazotrophic cyanobacteria in both the Atlantic and Pacific Oceans that's known to be able to rapidly fix nitrogen. If you have cyano associated with a persistent bloom of O. ovata and access to a microscope, please take a look at your cyano and see if it could be tricho -- this might be an obligate association, or it might be O. ovata recruiting whatever species of cyano was handy.

I found it very interesting that O. ovata took over this isolated reef complex and wondered what Saint Paul's Rocks might have in common with our aquaria...

There isn't a lot of information on the reef ecology of the Archipelago of Saint Peter and Saint Paul, aka Saint Paul's Rocks, because it's one of the smallest and most isolated reefs in the world, being as it is way the hell out in the middle of the Atlantic Ocean. Geologically, the islands are unusual in that they're an exposed high point in the mid-oceanic ridge, and though officially a national park of Brazil, there are no regulations on fishing in the area, and the archipelago is regarded by marine biologists as a "paper park" -- a protected area on paper, but not in fact. The area has been heavily fished since the 1950s, so the local ecology has been trashed to the point where reef sharks are locally extinct (...the word for this in Science is "extirpation", incidentally). That is, the sharks' prey species were fished out, so the sharks starved -- in the 1970s, they were so numerous that scientists reported losing fish they caught for examination to hungry sharks. By the turn of the century, no more reef sharks, just the occasional pelagic specimen wandering in from the open ocean.

I recognize this phenomenon from reading Coral Reefs in the Microbial Seas a few years ago. The same pattern of events has been identified on reefs all over the world: overfishing depletes the population of fish on a reef; released from grazing pressure by the lack of herbivores, algae grows like crazy and takes over the reef; DOC released by algae triggers the growth of pathogenic bacteria that kill reef corals; along the way, sharks disappear because there aren't enough fish around to support a population of apex predators. However, the model does not predict a successional stage in which a dying reef is taken over by benthic dinos... What's so special about this tiny, rocky reef out in the middle of nowhere that 10 years after the sharks died off, 80% of the phyto was dinoflagellates and O. ovata owned the place?

Well, I'm thinking it's copiotrophy -- if eutrophy favors flavos, perhaps copiotrophy favors cytophaga (...or bacteroides, or whatever bacteria ostis are eating). This appears to be consistent with the sole identified environmental impact on Saint Paul's Rocks: "industrial fishing". Large fishing vessels nowadays are floating factories that can process and freeze tons of fish every day. This generates large volumes of waste -- offal, basically, as well as bycatch -- that of course is dumped into the sea. This waste is a food resource for seabirds and, perversely, fish. So the archipelago is probably occasionally contaminated by plumes of proteinaceous waste consisting of uneaten food and fish poo. Sound familiar? Plus, it crossed my mind that waste plumes from factory fishing vessels might be seeding the sands with dino-friendly bacteria in a sort of reverse Montireef Protocol...

And there was something else that jumped out at me:


Quote:
Originally Posted by Ostreopsis cf. ovata (Dinophyta) bloom in an equatorial island of the Atlantic Ocean
The Saint Paul's Rocks is an oceanic area with a number of endemic species and low functional redundancy relative to coastal sites. As an example, herbivorous fishes such as acanthurids [tangs] and scarids [parrotfish], which are commonly found in tropical reef areas, are functionally absent there. This role is performed by abundant pomacentrids [damsels] and balistids [triggerfish].
The fact that the ecosystem of Saint Paul's Rocks is half-broken due to missing species is also a noteworthy parallel with our tanks (and our tanks will always have this problem, I expect -- no reefer in his right mind would want a bumphead parrotfish even if he had a DT big enough to support one, for example) but it caught my eye that triggerfish were called out as herbivores, as even the algae-eating, reef-safe trigs in the aquarium trade are pretty aggressive predators on small crustaceans like pods and shrimp. If triggerfish are especially abundant in the waters off Saint Paul's Rocks, grazing pressure from them might be holding down the pod population, which in turn would reduce the grazing pressure that should be holding down the dino population. And shrimp and benthic pods are detrivores, so a shortage of them could reduce the efficiency with which the reef sands process detritus -- think of it as the difference between a Shimek-compliant DSB and a DT SSB.

By the time a plume of waste from a factory fishing operation hit the reef, it would be diluted and heavily worked over by bacteria. Whatever settled on the reef would be largely recalcitrant, partially degraded, high molecular weight proteins.

Now have a look at this:


Quote:
Originally Posted by Google Scholar
Gradients of coastal fish farm effluents and their effect on coral reef microbes
M Garren, S Smriga, F Azam - Environmental microbiology, 2008 - Wiley Online Library
... For example, Cytophaga gene sequences were associated with high-molecular-weight dissolved ... and colleagues (2005), other studies in the region found that benthic sediments near suspended ... libraries of different origin (ie coral, feces or water bacterial communities) (Table 4 ...
Cited by 34 Related articles All 4 versions Cite Save
Emphasis mine. A paper from 2008 is borderline but should be recent enough that the authors are referring to the modern, post-reorganization cytophaga genus, especially given that they're talking about gene sequences. However, that paper is behind a paywall... So close, yet so far!

CONTINUED...


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Old 01/04/2016, 07:45 AM   #2510
34cygni
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But that has to be "For example, Cytophaga gene sequences were associated with high-molecular-weight dissolved organic carbon", and given the title of the paper, it's not too difficult to infer what sort of DOC stimulates cytophaga growth... But I still went and looked up the abstract, natch:


Quote:
Originally Posted by Gradients of coastal fish farm effluents and their effect on coral reef microbes
Coastal milkfish (Chanos chanos) farming may be a source of organic matter enrichment for coral reefs in Bolinao, Republic of the Philippines. Interactions among microbial communities associated with the water column, corals and milkfish feces can provide insight into the ecosystem's response to enrichment. Samples were collected at sites along a transect that extended from suspended milkfish pens into the coral reef. Water was characterized by steep gradients in the concentrations of dissolved organic carbon (70-160 uM), total dissolved nitrogen (7-40 uM), chlorophyll a (0.25-10 ug/l), particulate matter (106-832 ug/l), bacteria (5 x 10^5 - 1 x 10^6 cells/ml) and viruses (1-7 x 10^7 cells/ml) that correlated with distance from the fish cages. Particle-attached bacteria, which were observed by scanning laser confocal microscopy, increased across the gradient from < 0.1% to 5.6% of total bacteria at the fish pens. Analyses of 16S rRNA genes by denaturing gradient gel electrophoresis and environmental clone libraries revealed distinct microbial communities for each sample type. Coral libraries had the greatest number of phyla represented (range: 6-8) while fish feces contained the lowest number (3). Coral libraries also had the greatest number of 'novel' sequences (defined as < 93% similar to any sequence in the NCBI nt database; 29% compared with 3% and 5% in the feces and seawater libraries respectively). Despite the differences in microbial community composition, some 16S rRNA sequences co-occurred across sample types including Acinetobacter sp. and Ralstonia sp. Such patterns raise the question of whether bacteria might be transported from the fish pens to corals or if microenvironments at the fish pens and on the corals select for the same phylotypes. Understanding the underlying mechanisms of effluent-coral interactions will help predict the ability of coral reef ecosystems to resist and rebound from organic matter enrichment.
Milkfish are widely aquacultured in tropical Asia and normally feed on phyto and pods in the wild, but farmed fish are fed high-protein pellets or even given chopped-up fish and chicken guts as supplemental feed.

That's as close to a smoking gun as I can manage: ostis are associated with cyotphaga, and cytophaga are associated with recalcitrant high molecular weight dissolved organic carbon from high-protein fish poo. If flavos are the Bacteroidetes adapted to consume the remains of green algae, then marine cytophaga may be on the other end of the spectrum: a hardcore protein specialist. It looks like the ecological niche they fill is eating what's left after other bacteria have eaten all the good stuff, plus as noted they can consume bacterial cell walls, so when the good stuff runs out, cytophaga can eat the dead bacteria, too. Cytophaga are the CUC for the CUC for the CUC, if you will. That might explain this...


Quote:
12/30/2015, 10:59 PM #2421
karimwassef
Yes. I had dry rock too.

It's a key ingredient IMO.
Quote:
12/31/2015, 05:17 AM #2429
DNA
They survey I did with Monty blew my dry rock theory off the table, but it's still a likely factor in the equation.
The good stuff dies when LR dries, and the rock remains moist long enough for decomposition to begin, so it's covered in partly-degraded proteins and dead bacteria. Cytophaga heaven.

And being the CUC of last resort tracks with cytophaga being able to consume keratin, a highly recalcitrant protein found in turtle shells, hooves, feathers, fur, and your hair, tongue, skin, and fingernails -- and, interestingly, feather meal is sometimes used as a cheap source of protein in fish food pellets and can constitute up to 5-10% of milkfish feed pellets. And there are a lot of birds nesting on Saint Paul's Rocks, which presumably means a lot of feathers end up in the water... Hmmm... Are there any known inputs of keratin in our systems? That would be an interesting correlation.

But I keep thinking about all the detritus that comes out when you stir a sand bed. All that indigestible detritus... It's been through several different creatures, probably some of them more than once, and still the bacteria haven't been able to break it down. That's the very definition of recalcitrant organic carbon, and that's what gets buried in a shallow DT sand bed that's stirred by macrofauna. Indeed, burying that stuff is really pretty much the point of DT SSBs. That's why nobody wants to acknowledge that DT SSBs are a broken implementation of Shimek's DSB tech -- an automated landfill burying detritus that settles to the bottom of a DT seems rather ingenious and is undeniably convenient. Out of sight, out of mind.

I gather many hobbyists are under the impression that burying detritus in a DT SSB feeds beneficial denitrifying bacteria. As should be apparent by now, nothing could be further from the truth. Bacteria that specialize in denitrification are just one small part of a diverse population, and they tend to limit themselves. The less NO3 there is available, the less effectively denitrifiers can compete for organic carbon. That's why LR and Old School UGF setups won't zero out NO3 by themselves, for example, and that's why DyMiCo filters, which are built to maintain the proper redox conditions to favor denitrifying bacteria, have to inject labile DOC directly into the sand bed to help them do their job. Same thing with sulfur denitrators: as NO3 levels get low, flow through the media has to be increased to counteract the dropoff in efficiency that results from the denitrifying bacteria being at a competitive disadvantage. And because denitrifying bacteria live in the transition zone where hypoxia becomes anoxia, aerobic and facultatively aerobic saprophytes, including vibrio, get first crack at any labile organic carbon that reaches the substrate. (...I suspect this is why a lot of hobbyists have trouble keeping shrimp, incidentally: benthic livestock in general, and especially animals that like to root around in the sand looking for tasty morsels to eat, are directly exposed not only to high levels of potentially pathogenic bacteria but also to chemicals released by the bacterial decomposition of detritus, such as ammonia and weak organic acids, that stress shrimp and make them vulnerable to opportunistic infections. The same thing happens in wild populations of lobsters where the benthic sediments are enriched with organic matter from river discharges and algae blooms, for example, and it's a common problem with aquacultured shrimp, as well. Chitinolytic -- chitin-disassembling -- bacteria associated with black spot/brown spot disease include species from the genera aeromonas, pseudomonas, flavobacterium, and vibrio... Ring any bells? Many vibrio species show chemotaxis towards chitin, including V. cholerae, and as noted some can grow using chitin as their only source of organic carbon.)


Quote:
Originally Posted by natas
My Dino disappear at night much like everyone else. My understanding here is that they go into the water column at night. How do we explain how they always end up in the same place the next morning? I literally have spots on the sand that show no Dino. The spots that are showing disappear at night and look the same (sometimes bigger) the next morning.
Dinos return to the same spots every morning because that's where the food is. The sand bed bacteria are not a single, uniform community but rather a patchwork distribution of competing populations that shift in accordance with the available food in any particular spot, and I hypothesize that the spots where cytophaga become dominant are the spots where ostreopsis dinos set up shop. Indeed, it may be enough that cytophaga becomes dominant among the bacteroidetes/CFB group bacteria without displacing gamma-pros as the numerically dominant group overall... In any event, once the dinos have seized a piece of ground and established a bacteria farm there, they do their best to hold on to it, and if the dino population grows, their bacteria farms have to grow, too.


Quote:
Originally Posted by DNA
Did one more of those wonderful and elaborate tests of mine.
I placed a square plastic on the sandbed and left it there for couple of days.

Yesterday I removed it and today I have a perfect square free of dinos, but edged by dense mat of dinos.
Cool!

Covering the sand would cause it to remain anoxic, which would give obligate and aerotolerant anaerobes an advantage over facultative anaerobes. The shift in the bacteria population destroyed that part of the ostis' bacteria farm -- no food, no dinos. Either the dinos' food bacteria are dead, or they're reduced in numbers too much to support a bloom on the sand above, or they've thrown in their lot with their fellow heterotrophs and will no longer refrain from eating dinos. And if you used transparent plastic, it may be that the phototrophic niche in the surface layer of the sand has been taken over by photoheterotrophs. If you left a transparent piece of plastic in place long enough, I suspect you'd eventually see cyano growing on the sand, as many species are facultative anaerobes and can use sulfur as a terminal electron receptor at night.

While they may only be able to get their farms started by opportunistically exploiting a cytophaga-dominated benthic bacterial community, if the benthic dino holobiont includes vibrio, that could explain how they kill corals...


Quote:
Originally Posted by Regulation of microbial populations by coral surface mucus and mucus-associated bacteria
Caribbean populations of the elkhorn coral Acropora palmata have declined due to environmental stress, bleaching, and disease. Potential sources of coral mortality include invasive microbes that become trapped in the surface mucus and thrive under conditions of increased coral stress. In this study, mucus from healthy A. palmata inhibited growth of potentially invasive microbes by up to 10-fold. ... This result suggests that coral mucus plays a role in the structuring of beneficial coral-associated microbial communities and implies a microbial contribution to the antibacterial activity described for coral mucus. ...

This study shows that mucus collected from Acropora palmata has antibiotic activity against (1) Gram-positive and Gram-negative bacteria, (2) a number of potentially invasive microbes (including microbes from Florida Keys canal water, African dust, and surrounding sea water), and (3) a pathogen implicated in white pox disease of A. palmata. This result suggests that healthy A. palmata employ a biochemical mechanism for disease resistance that may act as a primary defense against pathogens. In contrast, mucus collected from A. palmata during a period of increased water temperature did not show significant antibiotic activity against the same suite of sources and tester strains, suggesting that the protective mechanism employed by A. palmata is lost when temperatures increase. ...

Collectively, these results suggest that coral mucus provides a hostile environment for some bacteria and a nurturing environment for others, illustrating that the mucus plays an important role in structuring microbial communities on the coral surface. ...

The antibiotic properties of coral mucus, and the potential for mucus to select a discrete set of commensal bacteria, were lost at increased temperatures during a bleaching event. Mucus was taken from corals sustained at a mean daytime sea surface temperature of 28 to 30C for 2 mo prior to collection. Vibrios were the predominant species cultured from the mucus of apparently healthy Acropora palmata tissue during this event. Vibrios were also predominant in the water column during this period, representing 85% of the cultured isolates. Less than 2% of bacteria isolated from the surface of A. palmata during this period produced antibiotic activity. These findings illustrate a temporal shift in the protective qualities of coral mucus, and a composition shift from beneficial bacteria to vibrio dominance under conditions of increased temperature. Vibrios present during this event included those involved in temperature dependent bleaching of corals, such as Vibrio shiloi and V. coralyticus as well as numerous vibrios known to be opportunistic to other marine organisms. ... However, as mucus was collected from apparently healthy coral tissue, and not bleached tissue, this provides evidence that a community shift to vibrio dominance may occur prior to zooxanthellae loss.
Vibrio bad. But other bacteria good.

So I went looking for them...


Quote:
Originally Posted by Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica
The inhibitory properties of the microbial community of the coral mucus from the Mediterranean coral Oculina patagonica were examined. Out of 156 different colony morphotypes that were isolated from the coral mucus, nine inhibited the growth of Vibrio shiloi, a species previously shown to be a pathogen of this coral. An isolate identified as Pseudoalteromonas sp. was the strongest inhibitor of V. shiloi. Several isolates, especially one identified as Roseobacter sp., also showed a broad spectrum of action against the coral pathogens Vibrio coralliilyticus and Thallassomonas loyana, plus nine other selected Gram-positive and Gram-negative bacteria. Inoculation of a previously established biofilm of the Roseobacter strain with V. shiloi led to a 5-log reduction in the viable count of the pathogen within 3 h, while inoculation of a Pseudoalteromonas biofilm led to complete loss of viability of V. shiloi after 3 h. These results support the concept of a probiotic effect on microbial communities associated with the coral holobiont.

Coral bleaching is caused by disturbance of the mutual symbiotic relationship between algae (zooxanthellae) within the tissues of the coral animal. The symbiosis can be disrupted due to a range of external environmental physical and toxic stressors, which can act either alone or together. In addition to these widely accepted factors in coral bleaching, the hypothesis that bacterial infection may also trigger bleaching was developed as a result of the study of interactions observed since 1997 between the coral Oculina patagonica and the bacterium Vibrio shiloi. Oculina patagonica is an invasive species of the eastern Mediterranean Sea, first recorded in 1993. The infection and bleaching of O. patagonica by V. shiloi was first described by Kushmaro et al. (1996, 1997) and shown to be temperature dependent; it does not occur at 16–20C, but is stimulated at temperatures above 25C. ... Once in the coral tissue, the pathogen multiplies and produces extracellular toxins that block photosynthesis, bleach and lyse the zooxanthellae. In addition to the zooxanthellae, the tissue of healthy corals and their secreted mucus layer supports a diverse community of other microorganisms, including bacteria, archaea, fungi, and viruses. Since 2004, it has not been possible to recover V. shiloi from healthy or diseased corals. Ainsworth et al. (2008) confirmed the absence of V. shiloi during the annual bleaching event in 2005. ... A possible explanation for this disappearance was suggested in the Coral Probiotic Hypothesis proposed by Reshef et al. (2006) and developed by Rosenberg et al. (2007). This proposes that the abundance and types of microorganisms associated with corals change in response to global environmental changes such as temperature, allowing the coral to adapt to new conditions by altering its population of specific symbiotic bacteria. ...

Several strains of bacteria cultured from O. patagonica showed antagonistic activities towards a range of marine and terrestrial pathogens, with 5.8% of the isolates active against V. shiloi, the former bleaching pathogen of this coral. Previous studies have shown similar Alpha- and Betaproteobacteria to be present in healthy O. patagonica. Similarly, Ritchie (2006) found that almost 20% of the cultured bacteria from the Acropora palmata coral in the Caribbean displayed antibiotic activity, including towards the causative agent of white pox disease. Not surprisingly, when the antibiotic producers that were isolated from O. patagonica mucus were tested against each other, no inhibition occurred, suggesting that the strains isolated could be resistant to these antagonistic mechanisms, and therefore may be better adapted to life in the mucus. ...

The bacteria had different strengths and spectra of activity against the various test bacteria, suggesting that the microbial interactions in the mucus are diverse and complicated. The Roseobacter isolate had the broadest range of activity and inhibited a range of terrestrial and marine pathogens. There are numerous reports of antibiotic production by bacteria belonging to the Roseobacter clade. Bruhn et al. (2005) and Rao et al. (2005, 2006) demonstrated the selective advantages that members of the Roseobacter clade have in colonizing the surface of algae and outcompeting previously established biofilms. ... The strongest inhibitor of V. shiloi and the other coral pathogens tested was the strain JNM12, identified as Pseudoalteromonas. This genus is known to produce a range of bioactive compounds and strain JNM12 shows red-brown pigmentation of its colonies, which has previously been associated with antibiotic production. ...

Both cells and culture supernatants of Pseudoalteromonas JNM12 and Roseobacter JNM14 inhibited the growth of V. shiloi. ...

Our results support the conclusions of Ritchie (2006) that coral mucus and its associated microorganisms play an important role in promoting beneficial microbial communities. From the experiments performed here, it is clear that different coral bacteria may contribute differently to the protection of the coral. It is unlikely that one or two coral mucus isolates can fully explain the development of immunity to a disease, but a 'cocktail' of bacteria with different antibiotic properties could together prevent infection by a pathogen such as V. shiloi.
Roseobacter?!? That name has come up more than once in association with toxic dinoflagellates...


Quote:
Originally Posted by Bacteria Associated with Toxic Clonal Cultures of the Dinoflagellate Ostreopsis lenticularis
Aeromonas, Alteromonas, Bacillus, Cytophaga, Flavobacterium, Moraxella, Pseudomonas, Roseobacter, and Vibrio are the bacterial genera most frequently associated with toxic dinoflagellates.
Quote:
Originally Posted by Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum
The bacterial flora of G. catenatum generally mirrors that found associated with other dinoflagellates, being dominated by the Alphaproteobacteria (principally the Rhodobacteraceae -- frequently referred to as Roseobacter clade)
...but if they can protect corals, clearly that deserves a closer look.


Quote:
Originally Posted by Production of Antibacterial Compounds and Biofilm Formation by Roseobacter Species Are Influenced by Culture Conditions
Bacterial communities associated with marine algae are often dominated by members of the Roseobacter clade... Nine of 14 members of the Roseobacter clade, of which half were isolated from cultures of the dinoflagellate Pfiesteria piscicida, produced antibacterial compounds. ... We hypothesize that the ability to produce antibacterial compounds that principally inhibit non-Roseobacter species, combined with an enhancement in biofilm formation, may give members of the Roseobacter clade a selective advantage and help to explain the dominance of members of this clade in association with marine algal microbiota. ...

Several studies have found that members of the Roseobacter clade inhibit other bacteria, and this may contribute to their dominance among alga-associated bacteria. ... Indeed particle-associated members of the Roseobacter clade are 13 times more likely to produce antimicrobial compounds than are free-living members. Furthermore, while growing in a biofilm, a member of the Roseobacter clade was able to prevent the growth of other bacteria on surfaces. ...

None of the Roseobacter clade strains tested were sensitive to filtered culture supernatants containing the antibacterial activity produced by either Silicibacter sp. strain TM1040 [a laboratory strain of roseobacter isolated from the toxic dinoflagellate Pfisteria piscicida] or Phaeobacter strain 27-4 [a roseobacter that produces an antibiotic called tropodithietic acid, or TDA, and is used as a probiotic in marine aquaculture]. This is in contrast to the non-Roseobacter marine species tested, many of which were sensitive to the filtered supernatant. Vibrio anguillarum 90-11-287, Pseudomonas elongate, "Spongiobacter nickelotolerans," environmental and clinical strains of Vibrio cholerae, V. coralliilyticus, V. shiloi, and a Halomonas sp. (all members of the gamma-Proteobacteria) were sensitive to the compound(s). ...

Vibrio coralliilyticus and V. shiloi are important coral pathogens causing coral bleaching, and both were inhibited by Silicibacter sp. strain TM1040 and Phaeobacter strain 27-4. The coral polyp is protected by a mucus layer that is populated by alpha-Proteobacteria group bacteria, and bacteria taxonomically related to Silicibacter sp. strain TM1040 are associated with corals. One may therefore hypothesize that Roseobacter species play a role in preventing coral bleaching, and, indeed, antibacterial activity in coral extracts which inhibit members of the Vibrionaceae has been detected, supporting this hypothesis.
It has been at the back of my mind since Day 1 that the dinos-as-farmers hypothesis needs a villain -- or a hero, from our perspective. That is to say, if the dinos are defending their farms to keep them from being overrun by unfriendly bacteria, what bacteria are they trying to keep out?

Or to put it another way: What bacteria were in Montireef's skimmate when he nuked his dino bloom?

Bacteria that don't seem to get along well with gamma-proteobacteria, especially vibrio, and which are known for invading and outcompeting existing biofilms look like awfully good candidates for the active ingredient in the Montireef Protocol.

CONTINUED...


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Old 01/04/2016, 08:01 AM   #2511
34cygni
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But on the other hand, they're known associates of toxic dinos and apparently part of the benthic dino holobiont -- a real bummer for me, as the easy story here would be, "Ostis like vibrio, and rosies don't like vibrio; therefore, rosies don't like ostis." So I tried to figure out if there was a common element to the association of Roseobacter Clade bacteria with dinos and corals, which of course have dinoflagellate endosymbionts...


Quote:
Originally Posted by Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides
In this study, we examine microbial communities of early developmental stages of the coral Porites astreoides... Bacteria are associated with the ectoderm layer in newly released planula larvae, in 4-day-old planulae, and on the newly forming mesenteries surrounding developing septa in juvenile polyps after settlement. Roseobacter clade-associated (RCA) bacteria and Marinobacter sp. are consistently detected in specimens of P. astreoides spanning three early developmental stages, two locations in the Caribbean and 3 years of collection. ... The results are the first evidence of vertical transmission (from parent to offspring) of bacteria in corals. The results also show that at least two groups of bacterial taxa, the RCA bacteria and Marinobacter, are consistently associated with juvenile P. astreoides against a complex background of microbial associations, indicating that some components of the microbial community are long-term associates of the corals and may impact host health and survival. ...

The Rhodobacterales sequences in this study primarily represent the RCA group of bacteria. ... Roseobacter is an abundant and diverse genus in seawater communities, notably in coral reef habitats and coral mucus, and Roseobacter are among the first bacterial associates acquired from seawater by larvae of the Pacific spawning coral Pocillopora meandrina. Other RCA bacteria have been shown to exhibit antibacterial activity against known marine pathogens. Many RCA bacteria engage in associations with dinoflagellates in the marine environment and in laboratory culture. On the basis of the prevalence of chemotaxis toward dimethylsulfoniopropionate, a dinoflagellate metabolite, among RCA bacteria, it has been hypothesized that some RCA bacteria detected in corals are associated with Symbiodinium spp., though it is unknown whether this interpartner communication results in a fitness benefit to the Symbiodinium or to the coral host. Though RCA bacteria in some corals may provide potential benefits to the coral holobiont, other RCA strains have been found to be pathogenic, implicated in coral black band disease and juvenile oyster disease. Ribotypes identified in the clone libraries are affiliated (98–99% sequence similiarity) with RCA sequences derived from disease bands in the coral Siderastrea siderea and Thalassomonas sp. and Rhodobacter sp. (94–99% sequence similarity) associated with disease bands in other corals.
Emphasis mine.

Dimethylsulfoniopropionate, eh? Okay, obviously that needs to be looked into, but first and foremost, the link to BBD can't be ignored. What's the difference between rosies that protect corals and rosies that kill corals?


Quote:
Originally Posted by Microbial community composition of black band disease on the coral host Siderastrea siderea from three regions of the wider Caribbean
Microbial communities associated with black band disease (BBD) on colonies of the reef building coral Siderastrea siderea from reefs in 3 regions of the wider Caribbean were studied... All of the clone libraries were dominated by Alphaproteobacteria and contained sequences associated with bacteria of the sulfur cycle... Additionally, all clone libraries had sequence types of bacteria associated with toxin producing dinoflagellates. These sequences were most abundant in a sewage impacted reef site in St. Croix, which also had the highest prevalence of BBD-infected colonies. ... We propose that with degrading water quality (i.e. increasing nutrients) certain proteobacteria thrive and increase BBD virulence. ...

BBD, first reported in the 1970s, is characterized by a dark, migrating band which moves across a living coral colony completely lysing coral tissue and often killing the entire colony in a matter of months. It is most accurately described as a horizontally migrating, cyanobacterial-dominated, sulfide-rich microbial mat but is unique in that it is pathogenic to corals and is motile. Thus far, in addition to the dominant cyanobacteria, sulfate-reducing bacteria (in particular Desulfovibrio spp.), sulfide-oxidizing bacteria, numerous heterotrophic bacteria, and fungi have been reported in the BBD community. Members of all of these groups have been proposed as primary pathogens; however, few have been isolated into culture and Koch’s postulates have not been fulfilled for any of them. The fulfillment of Koch's postulates has classically been the 'gold standard' for verifying that a suspected microbial pathogen is responsible for a specific disease. ...

A total of 26 clone sequences, from all 3 regions, were related (96-99% similarity by BLAST analysis) to bacteria associated with paralytic shellfish toxin (PST) producing dinoflagellates. [...among bacteria, the rule of thumb is that >=97% genetic similarity is probably the same species; 93-96% is probably another species from the same genus] ... Twelve sequences from all 3 regions were closely related (98-99% similarity by BLAST analysis) to an uncultured Alphaproteobacterium (AJ294357) associated with the toxic dinoflagellate Alexandrium. ... Five sequences, 3 from the Bahamas, one from the Florida Keys, and one from St. Croix were closely related (94-97% similarity) to the Alphaproteobacterium (AF260726) associated with the toxic dinoflagellate Alexandrium tamarense, with this identification confirmed by phylogenetic analysis. In Clone Libraries A and F, 2 sequences (DQ446084, and EF123311, respectively) were closely related (98% similarity) to an Alphaproteoacterium (AY701434) associated with the toxic dinoflagellate Gymnodinium catenatum. Phylogenetic analysis confirmed that the 2 sequences were closely related to the Hyphomonas group of bacteria, some members of which are associated with toxic dinoflagellates. In the clone library from the polluted St. Croix site (F), a sequence (DQ644019) was related (98% similarity) to a Bacteroidetes bacterium (AY701462) associated with a toxic dinoflagellate. ...

Any specific role in the BBD community of the dominant Alpha-proteobacteria is not yet known. Because they are not well represented in healthy coral mucus and coral tissue, it is worth noting the abundance of Roseobacter clade members in BBD samples. ... A recent study showed that many of the Roseobacter species produce antibacterial compounds that inhibit non-Roseobacter species, which may contribute to the dominance of members of this clade in diverse environments, including BBD. ...

It may be that degraded water quality is causing a shift within the population of Alpha-proteobacteria to the more toxic representatives of this group. ...

Two previous molecular studies of the BBD community detected sequences matching Roseovarius crassostreae, the bacterial pathogen associated with JOD [juvenile oyster disease -- interestingly, this is the only pathogenic rosie I've found mention of aside from the ones involved with BBD]. In the present study this sequence was again found in a large number (15) of clones, with sequence homologies of 94 to 97%, from the Bahamas and St. Croix sites. ...

Sequence types matching bacteria associated with toxic dinoflagellates were observed in the clone libraries from all 3 geographic regions and have been reported previously by our group from Bahamas samples. These sequences were not observed in the healthy SML [surface mucus layer] of samples of the same coral colonies. The present study showed their consistent presence in all the BBD samples examined, irrespective of the sampling location.
If life were like the movies, this would be the turning point in the narrative when I have a crucial flash of insight: "By Jove, if bacteria associated with toxic dinos can kill corals, then it just might be that bacteria associated with healthy corals can kill. Toxic. Dino. Flagellates. To the Sciencemobile!"

But that's not how it works in the real world (...nor, alas, do I have a Sciencemobile). In the real world, I bumbled around for weeks trying to puzzle through this, discarding several theories along the way that didn't pan out for one reason or another, and even when I thought I had the answer, it still took a couple of months to write this up because more than once I tugged on a loose thread during fact-checking and a chunk of the thing unraveled and had to be put back together a little bit differently. For example, sorting out what the heck was going on with the CFB group and in particular the genus cytophaga took like two weeks all by itself... So even though you already know where I'm going with all this, I'm taking you there the long way around because that's the scenic route.

I read another paper on BBD from 2006 and was able to identify a rosie in uninfected coral mucus that produces a well-known antibacterial and antifungal compound called tropodithietic acid (TDA), but this species was not present in the BBD biofilm, and two of the BBD rosies were species known not to produce TDA. And another paper I read indicated that most TDA synthesis in vitro appeared to occur at the water's surface in stagnant cultures -- TDA synthesis is known to be energy-intensive, so it's likely that producing significant amounts of it requires enough oxygen for the bacteria to run entirely in aerobic mode. If there really are beneficial rosies in skimmate, that could explain why Montireef's fresh skimmate was dino death but week-old skimmate is dino chow: as bacterial respiration draws down dissolved O2, the coral-friendly rosies don't have enough oxygen to make TDA and thus lose the battle for dominance in biofilms growing on colloidal detritus in the skimmer cup. Perhaps TDA-making rosies are one of the keystone species corals recruit to maintain a friendly bacteria population in their mucus...

At any rate, there's still this dimethylsulfoniopropionate that dinos make and which attracts rosies. That doesn't look like a clue so much as a big, flashing, polychromatic neon arrow.

Dimethylsulfoniopropionate, aka DMSP, is produced by a great many different species of algae and is the single most common organic sulfur compound in NSW. Dinos and coccolithophores, in particular, are known to make a lot of DMSP for some reason -- even a few heterotrophic dinos have been shown to make the stuff.

Making DMSP on an industrial scale is a serious problem for a dino bloom because DMSP and/or its breakdown product DMS serve as chemotactic cues for a vast variety of species, ranging from many different species of bacteria (including vibrios and other gamma-pros as well as rosies) and protists all the way up the food chain to fish, penguins, and seals. It seems like freakin' everything in the ocean can detect and home in on DMSP, DMS, or both -- including pods, though DMSP may also deter pods from feeding... AFAIK the jury's still out on whether producing lots of DMSP is a net plus or minus for dinos on the getting-eaten-by-pods problem, but I'm guessing the latter, as DMSP production by dinos must be an obligate physiological process or they'd stop making so darn much of it, so if DMSP is a problem for pods, it's a problem they've had millions of years to solve. Pods can evolve resistance to dino toxins (some pods have been shown to concentrate dino toxins from red tides and pass them up the food chain) so why not DMSP? And BTW, not only symbiodinium dinos but coral polyps themselves make DMSP, so coral mucus is full of the stuff.

In other words, corals are pod magnets. Neat.

And corals are also vibrio magnets. In fact, there's N-acetyl-D-glucosamine (the monomers from which chitin is assembled) in coral mucus, which is not so neat.

So now the big, flashing, polychromatic neon arrow is surrounded by chase lights, flanked by dancing girls, and skylined by fireworks.

Nobody really knows why dinos make so much DMSP. It has several potential uses, including osmoregulation, deterring grazers, helping to protect photosynthesis machinery from being damaged by the oxygen it produces, and DMSP has been shown to inhibit the attachment of some bacteria to macroalgae, notably cytophaga which specialize in consuming high molecular weight organic carbon and thus are likely opportunistic pathogens that can exploit any existing damage or infection. You'd think DMSP would do the same for dinos, so perhaps DMSP is one of the biochemical tricks ostis use to keep their food from eating them.

The most convincing theory I found about DMSP is that synthesizing it consumes organic carbon and two sulfide ions, the fully reduced form of sulfur. So basically, DMSP is where primary producers dump excess photosynthate and sulfide when they're nutrient-limited and/or their biological processes are being impeded by the accumulation of sulfide, which is necessary for the synthesis of the amino acids cysteine and methionine but is also toxic and highly reactive, so you can't just leave it sitting around. This would explain why dinos make a lot of DMSP, as mixotrophic organisms that get most of their nutrients by eating bacteria would end up with surplus sulfur (...and it may also explain why heterotrophic dinos have been observed to steal plastids from their prey but only keep them a short time, sometimes less than an hour, before digesting them). And fun science fact: coccolithophores, which also produce relatively high levels of DMSP, are also mixotrophic. That DMSP is biologically useful in a variety of ways is just how evolution works -- if you need to make an organic sulfur compound as a sink for excess sulfide and fixed carbon, picking a molecule that's good for something would give you a competitive advantage.

The garbage can hypothesis for the synthesis of DMSP finds indirect support from another paper on BBD that I read...


Quote:
Originally Posted by Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea
We found the BBD-associated microbial communities to be highly diverse compared to the SML [surface mucus layer] communities. High bacterial diversity associated with BBD has been reported previously for four different species of corals (M. annularis, M. cavernosa, D. strigosa, and C. natans) in studies that used molecular methods. The present study, which investigated a fifth BBD host coral (S. siderea), also revealed much variability in the species composition in BBD, even between two black band-diseased colonies of the same species on the same reef. A large percentage of members of Rhodobacterales (alpha-proteobacteria) were observed in our BBD clone libraries, in particular, members of the Roseobacter spp. The Roseobacter clade is one of the major marine groups and comprises more than 20% of the coastal bacterioplankton community. ... A reason for the numerical abundance of these bacteria in association with black band-diseased corals has yet to be elucidated.

Members of the alpha-proteobacteria that are associated with toxin-producing dinoflagellates and the Juvenile Oyster Disease-causing bacterium Roseovarius crassostreae (Rhodobacterales, alpha-proteobacteria) were observed in our BBD clone libraries. Other important members of the alpha-proteobacteria, Sulfitobacter sp. strain ARCTIC-P49 and Sulfitobacter pontiacus, were also observed in our BBD clone libraries. The presence of S. pontiacus in BBD-associated corals has been reported previously. Members of the Sulfitobacter genus have been reported to be involved in oxidation of sulfite, which would be important in the active sulfuretum present in BBD. As in the previous studies, we detected sulfate-reducing bacteria in (one of) our BBD clone libraries. ... In contrast to the earlier studies, we did not find any sulfate-reducing bacteria in the SML of apparently healthy tissue (although the other studies analyzed samples of the tissue and not the SML).
This study suggests that coral mucus selects against sulfate-reducing bacteria while acknowledging that other studies have detected such bacteria in coral tissue, meaning that the coral polyps themselves contain or live alongside sulfate reducers that release sulfide at night when oxygen is in short supply. In other words, it looks like corals make DMSP in part to detoxify the sulfide released by their symbiotic and commensal bacteria when the polyps go hypoxic at night and the bacteria are forced to use sulfur as a terminal electron receptor (...changing from aerobic to anaerobic isn't a strict either/or thing with facultative anaerobes -- they'll use whatever oxygen they can get and rely on their anaerobic metabolism to whatever extent they have to). To avoid making this problem any worse than it already is, the bacteria in surface mucus layer select against bacteria that will release still more sulfide, potentially smothering the polyps.

Okay, so now we've got the dinos' side of what's going on with DMSP, but there's still the question of why rosies are attracted to the stuff...

The Roseobacter Bacteria Clade are a sprawling, highly diverse subset of the alpha-proteobacteria that are found in virtually every marine environment from sea ice to black smokers. According to the most recent information I was able to access, the RBC currently includes more than 50 genera and thousands of species, most of which are known only by genetic fragments from shotgun sequencing of bacterial DNA in seawater. They're most common in coastal environments and cooler waters and seem to be least common in the Sargasso Sea, probably because it's too ULNS -- they like a bit of eutrophy -- and the seaweed apparently doesn't like them very much. Rosies tend to dominate algal bacterial communities in the marine environment, and they're typically among the first bacteria to colonize exposed surfaces in NSW and start forming biofilms (...perhaps because of TDA-making species). The name is an historical artifact describing the color of bacteriochlorophyll-a, as the first roseobacter species to be discovered was among the earliest known aerobic anoxygenic phototrophic bacteria. This turns out to be an important niche: it's now believed that anoxygenic phototrophy accounts for as much as 10% of the solar energy captured by marine plankton. Some rosies are photoautotrophs but others lack the genes for fixing carbon and are photoheterotrophic. One study of phototrophy in the RBC found that not all the rosies that carried the genes for bacteriochlorophyll-a were actually making the stuff. Interestingly, some of those that weren't could be induced to do so by reducing salinity, which tracks with photoheterotrophic bacteria in general being common in turbid estuaries where the salinity is often lower than NSW.

The defining feature of the RBC is that rosies store an unusually large amount of DNA in distinct structures called plasmids that are separate from their chromosomes and can be readily passed from one bacterium to another. Bacteria use plasmids to store and circulate particularly useful bits of DNA, allowing them to add new, special-purpose DNA to the genes that they start out with so they can do something they weren't previously able to do, and rosies are particularly keen on sharing genes with each other. All bacteria do this -- a classic example is vibrio cholerae, which normally isn't pathogenic but becomes lethally so if upgraded with the right DNA. It's called "lateral gene transfer" or "horizontal gene transfer" and seriously messes with the heads of paleomicrobiologists trying to work out the origins and evolution of bacteria and archaea. And it's also why there's a rule of thumb that a genetic similarity of 97% indicates that two bacteria are probably members of the same species, when human and chimpanzee genomes are >98% identical (...though on the other hand, the whole concept of a "species" kind of breaks down in a world were genes can be passed around like baseball cards). Bacteria can move DNA across species boundaries in at least three different ways that I'm aware of, but they share genes most readily with other bacteria that live alongside them in the same environment, especially if they're from the same species or genus. Though on the other hand, just because two species are in the same genus doesn't mean they get along -- there's a lot of cutthroat competition among vibrio bacteria, for example, some of which make antibiotics that can kill other vibrios.

In essence, bacteria use distributed storage to address the problem of the limited amount of DNA any one bacterium can contain. Rosies, however, take this to the next level: their winning evolutionary strategy is to continue to share genes even as they evolve away from each other, and the bigger and more diverse the clade becomes, pushing into new environments and bumping up against new competitors, the more interesting bits of DNA they're able to collect, and the more effective their strategy becomes. Each of them has a small part of a vast library of genetic shareware that any of them can use to solve a problem or exploit an opportunity.

There are so many species in the RBC occupying so many different ecological niches that there are bound to be counterexamples to refute any generalization made about them, but broadly speaking, rosies are organoheterotrophic, sulfur-oxidizing facultative anaerobes that can use NO3 and inorganic sulfur as terminal electron receptors. A few are full-on denitrifiers that release N2, and some others have the genes for denitrification but don't seem to use them. Rosies can survive in permanently anoxic sediments, even deep in the heart of the anerobic community several centimeters below the surface, though in substantially reduced numbers compared to the saprophytic zone (the top 1-2 cm or so of eutrophic coastal sediments) where they can comprise as much as 10-15% of the population under favorable conditions.

CONTINUED...


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Old 01/04/2016, 08:36 AM   #2512
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And for rosies, "favorable conditions" typically means access to organic sulfur. Though they have a reputation as ecological generalists because the clade is so diverse and widespread, they seem to specialize in metabolizing organic sulfur, particularly the single most common organic sulfur compound in seawater: DMSP. Lots of bacteria can metabolize DMSP, including gamma-pros like vibrio, but rosies are good at it.


Quote:
Originally Posted by Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico
Members of the alpha-proteobacteria dominated DMSP assimilation, accounting for 35–40% of bacteria assimilating DMSP. Cytophaga-like bacteria and gamma-proteobacteria each accounted for 15–30% of DMSP-assimilating cells. The alpha-proteobacteria accounted for a greater fraction of the DMSP-assimilating community than expected based on their overall abundance, whereas Cytophaga-like bacteria were typically underrepresented in the DMSP-assimilating community. Members of the Roseobacter clade assimilated more DMSP on a per-cell basis than any other group, but they did not account for most of the DMSP assimilation, nor were they always present even when DMSP turnover was high. These results indicate that the biogeochemical flux of dissolved DMSP is mediated by a large and diverse group of heterotrophic bacteria. ...

Concentrations of dissolved DMSP ranged from 1.3 to 5.5 nmol/L at all stations. Although small, the dissolved DMSP pool turned over rapidly, with the turnover time averaging 10 h across all stations. Turnover times, however, varied greatly among environments, ranging from about 2 h in the Gulf of Maine to 28 h in the Sargasso Sea. ...

Large numbers of bacteria participated in the turnover of the dissolved DMSP pool. On average, 48% of the prokaryotic community assimilated DMSP, with the fraction of the total community assimilating DMSP ranging from 32% to 61% among environments. ...

The composition of the DMSP-assimilating community generally resembled the composition of the total bacterial community. Some phylogenetic groups, however, comprised a greater fraction of the DMSP-assimilating community than predicted based on their overall abundance. The alpha-proteobacteria were overrepresented in the DMSP-assimilating community at all stations. For example, alpha-proteobacteria were approximately 24% of the total community in the Sargasso Sea but comprised approximately 40% of the DMSP-assimilating community. In contrast, Cytophaga-like bacteria were slightly underrepresented in three of four stations. For example, Cytophaga-like bacteria were 21% of the total community in the Gulf of Maine, but only composed approximately 16% of the DMSP-assimilating community. Members of the gamma-proteobacteria were not significantly overrepresented in the DMSP-assimilating community. ...

Members of the Roseobacter clade, a subgroup of the alpha-proteobacteria, were detected at both stations in the Gulf of Maine but not in the Sargasso Sea (abundance <5% of total). ... Since almost all Roseobacter cells incorporated DMSP, the Roseobacter clade was overrepresented in the DMSP-assimilating community. ... The fraction of DMSP assimilated by the Roseobacter clade...was more than twofold higher than expected based on their percentage of the DMSP-assimilating community. ... In addition, DMSP-active Roseobacter cells were 32-71% larger than the DMSP-active cells of the entire bacterial community.

The fate of DMSP appears to be largely influenced by microbial metabolism... DMSP can be a carbon and sulfur source for microbial communities or it can be cleaved into DMS, which can impact atmospheric chemistry and global climate. Not all bacteria, though, can cleave DMSP or assimilate it into biomass; few bacteria can do both. The capacity to assimilate DMSP is widespread among members of the Roseobacter clade, and the only bacteria known to both assimilate DMSP and form DMS are members of the Roseobacter clade. This apparent link between phylogeny and metabolic activity led to the hypothesis that the Roseobacter clade plays an important role in the cycling of DMSP. ... In this study, the Roseobacter clade assimilated DMSP to a greater extent than expected based on their abundance, but it did not dominate DMSP assimilation. Instead, we found that bacteria from several phylogenetic groups assimilated DMSP.

Since the Roseobacter clade only accounted for roughly 10% of the DMSP-assimilating community, they appear to be able to better use DMSP on a per-cell basis than other bacteria. Their competitive advantage may be due to a high-capacity uptake system for DMSP. ... The apparent affinity of the Roseobacter clade for DMSP may allow Roseobacter to out-compete other bacteria for DMSP, a potentially significant source of carbon as well as sulfur to bacteria. Since bacterial communities are often limited by carbon, the capacity of the Roseobacter clade to out-compete other bacteria for DMSP might help the Roseobacter clade increase its abundance when concentrations and fluxes of dissolved DMSP are high. This hypothesis is consistent with the observation that the Roseobacter clade is abundant during DMSP-producing algal blooms. ... Members of the Roseobacter clade were found in coastal waters but were not detected in the Sargasso Sea. Despite the absence of Roseobacter, there was still substantial turnover of the dissolved DMSP pool, and a large number of bacteria assimilated DMSP in the Sargasso Sea. Other bacteria, especially other alpha-proteobacteria, were able to fill the niche of the missing Roseobacter clade. ...

The alpha-proteobacteria were consistently overrepresented in the DMSP-assimilating community in the Gulf of Maine and Sargasso Sea, whereas Cytophaga-like bacteria were typically underrepresented. It is surprising to see the same trend in DMSP assimilation in both productive coastal waters (Gulf of Maine) and oligotrophic waters (Sargasso Sea), since the bacterial communities are probably different in these environments and the alpha-proteobacteria and Cytophaga-like bacteria assimilating DMSP in the Gulf of Maine are probably not the same as those assimilating DMSP in the Sargasso Sea. If the bacterial communities did differ substantially among these environments, then our data indicate that there is specialization in DMSP assimilation at the major phylogenetic group level. ...

The capacity to assimilate DMSP is probably common among the major phylogenetic groups because DMSP is a major source of sulfur for bacterial communities, potentially satisfying greater than 90% of the total bacterial sulfur demand. Most DMSP-derived sulfur is incorporated into methionine and cysteine and assimilated into protein during protein synthesis. If DMSP assimilation satisfies virtually all of the bacterial sulfur demand, and all bacteria synthesizing protein need sulfur, then virtually all bacteria synthesizing protein should assimilate DMSP. We found that the DMSP-assimilating community was composed of all major phylogenetic groups...

DMSP-assimilating bacteria were not only diverse, but abundant as well. On average, half of all bacteria assimilated DMSP in the environments investigated. ...DMSP assimilation is indicative of protein synthesis, a process carried out by both dividing and nondividing-yet-active bacteria. ... In addition to their high abundance, DMSP-assimilating bacteria appear to be 40% larger by volume than nonassimilating bacteria on average. ... Data from these three studies indicate that dividing and nondividing-yet-active bacteria are significantly larger than the rest of the bacterial community. ... The large size of DMSP-assimilating cells may make them susceptible to grazing. Micrograzers preferentially graze on large and actively dividing bacteria in marine communities. This selective removal process can affect the composition of the bacterial communities by depressing the abundance of the larger, more active cells. ...

Incorporation of DMSP into bacterial biomass, however, is only one possible fate for DMSP. Other fates, such as the production of DMS and nonvolatile compounds, are also mediated by microbial communities. As with DMSP assimilation, the capacity to produce DMS and nonvolatile compounds from DMSP is not equally distributed among bacterial isolates and may not be equally distributed in natural communities as well. Therefore, the composition of bacterial communities could affect other aspects of DMSP processing in addition to DMSP assimilation.
Well, that explains this:


Quote:
Originally Posted by Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum
The bacterial flora of G. catenatum generally mirrors that found associated with other dinoflagellates, being dominated by the Alphaproteobacteria (principally the Rhodobacteraceae -- frequently referred to as Roseobacter clade)
In fact, rosies suddenly look like candidates for dino chow, given that predators prefer larger, faster-growing bacteria... But in benthic sands full of recalcitrant organic carbon left over from fish poo, cytophaga are probably fat and happy -- especially if they're supplied with labile organic carbon to help them attack the recalcitrant stuff.

As noted, however, cytophaga in the wild has been associated with decaying phyto blooms and sick macro. And some species are considered algicidal...


Quote:
Originally Posted by Algicidial Bacteria from fish culture areas in Bolinao, Pangasinan, Northern Philippines
One of the control techniques in HAB [Harmful Algal Blooms] is the application of biological agent such as algicidal bacteria. ... Genera of some algicidal bacteria have been assigned to Alteromonas, Bacillus, Cellulophaga [the type species of cellulophaga was originally a cytophaga before the big reorganization of that genus], Cytophaga, Flavobacterium, Micrococcus, Planomicrobium, Pseudoalteromonas, Pseudomonas, Saprospira, Vibrio, and Zobelia. ...in this study, bacteria were isolated, identified, and screened for algicidal activity [against alexandrium dinos] and their algicidal activity were verified against...five other dinoflagellate cultures available in the HAB laboratory of UP MSI [University of the Philippines Marine Science Institute] i.e., Pyrodinium bahamense; Alexandium affine; Alexandrium carterae; Gymnodinium catenatum; and Ostreopsis ovata. ...

The confirmatory test using the other dinoflagellate cells showed loss of motility as the initial response to the bacteria. Pyrodinium bahamense and A. affine cells shedded off their thecae during the first few hours of interaction. The chain-forming G. catenatum cells were the first to become non-motile...whereas Amphidinium carterae cells were the least sensitive among the dinoflagellates tested. All dinoflagellate cells tested against the bacteria did not recover and exhibited more lysis [meaning they were visibly dead, as opposed to just no longer moving] as compared to dinoflagellate cells in the control wells which remained motile and unaffected after 24 h of interaction. ...

Interestingly, R. lacuscaerulensis has caused loss of motility to Alexandium spp. just after 1 h of interaction. Ruegeria species are members of the marine Roseobacter clade. Ruegeria spp. acts similarly like Phaeobacter strain 27-4 and produces tropodithietic acid (TDA) and brown pigment and antagonizes Vibrio anguillarum and inhibits other fish pathogenic bacteria in vitro and is also capable of reducing mortality of fish larvae infected with fish pathogenic bacteria.
While black band disease involves rosies associated with toxic dinoflagellates, here at last is evidence that it works both ways: toxic dinos, including O. ovata, are vulnerable to rosies associated with healthy coral and other macrofauna.

In addition to Ruegeria lacuscaerulensis, another TDA-making rosie, Roseobacter gallaeciensis, was identified as having algicidal effects, though it took 6 hours or more to work on Alexandrium dinos. Ruegeria are a genus of rosies that have been identified as possible probiotics due to their association with healthy clams, sea urchins, and sablefish in a marine fish hatchery. Ruegeria also show up in the seaweed microbiome, where they're believed to protect macro with TDA and antifungal compounds. Roseobacter gallaeciensis (now reassigned to the genus Phaeobacter) is ubiquitous in the oligotrophic waters of the eastern Mediterranean and is found in the mucus of healthy Oculina patagonica corals from that area, and it has been used as a probiotic in aquaculture.

I don't know if it's TDA-making rosies, in particular, that will kill toxic dinos, but that's what it looks like ATM. They apparently do this through direct physical contact rather than releasing dino-killing chemicals into the water -- I would guess that TDA allows the rosies (or perhaps other bacteria they're friends with) to get through the dinos' bacterial allies, then they home in on the DMSP released by the dinos, and when they find them, the rosies kill them and eat them. Of course, this makes more rosies that make more TDA, kill more dino-friendly bacteria, and eat more dinos, which makes more rosies that make more TDA... It's a chain reaction of dino doom, which explains why Montireef's bloom collapsed so quickly. (Incidentally, it turns out that rosies don't just make TDA but a suite of very similar molecules -- so much so that scientists have a hard time telling them apart -- and it seems that's how they prevent the emergence of resistance among other bacteria. Ostreopsis ovata also makes a suite of very similar toxins, called ovatoxins. It may be that from their perspective, toxic dinos are making antibiotics to manage their bacteria farms, and the effects these chemicals have on other, larger organisms are just happy evolutionary accidents that give them a competitive advantage.)

Also of interest is that just as some rosies kill corals and some live in their mucus, the same is true for dinos. Ruegeria lacuscaerulensis kills dinos, for example, and Ruegeria algicola's natural habitat is on dinoflagellates. This sort of balkanization of not just the Roseobacter Clade but individual genera within that group, with species showing more loyalty to host organisms than they do to their "cousins" in the same genus, is commonplace because speciation in bacteria is often driven by moving into a new ecological niche. Recall that bacteria share genes through lateral gene transfer most readily with bacteria that live alongside them, sharing the same habitat, and that the overall community structure of commensal bacteria is dictated by the true, obligate symbiotes recruited by the host organism or passed down to it by its parents... Over time, lateral gene transfer from the obligate symbiotes that are always present would dominate the flow of genetic information simply because they're always present. This would be an evolutionary pressure that would tend to lead to the "capture" of bacteria from other species in the broader microbiome as they take in host-friendly genes and tweak the function of existing biochemical machinery to adapt to their environment. By acquiring or improving their ability to detect and emit QS and QQ chemicals used by the obligate symbiotes, for example, or to more efficiently metabolize the particular mix of organic carbon the host makes available, the interests of commensal bacteria would become more closely aligned with the interests of their hosts and their obligate symbiotes. Thus, coral microbiomes not only have the flexibility to bring in new species of bacteria to cope with new threats, such as recruiting algicidal bacteria to defend against dinos, but lateral gene transfer gives the existing community a mechanism to establish a stable relationship with the new recruits, accommodate them in the mucus, and perhaps eventually turn them into stalwart allies.

Thus as I said, I don't think it's a happy coincidence that some of the bacteria living on healthy corals will kill toxic dinos. This looks like an evolved defense against dinoflagellates -- just as Oculina patagonica corals in the Mediterranean recruited bacteria to fight off V. shiloi, for example, ancient corals recruited algicidal bacteria to defend themselves against benthic dinos.


Quote:
Originally Posted by Organic matter release by Red Sea coral reef organisms -- potential effects on microbial activity and in situ O2 availability
Results of the present study showed that all investigated benthic reef organisms released POM (POC and PON) [Particulate Organic Matter, Particlate Organic Carbon, and Particulate Organic Nitrogen] into their surroundings in significant quantities. For corals, this release can account for up to half of the carbon assimilated by their zooxanthellae. ...

The OM [Organic Matter] released by corals stimulates microbial activity generally less than algae-derived OM. Further, corals mainly release POM in the form of coral mucus, which is a transparent exopolymer that is able to trap particles, thereby fulfilling an important role as an energy carrier and nutrient trap in coral reef ecosystems. In contrast, algae release OM that is predominantly in dissolved form, and...algae-derived OM potentially supports a different microbial community. Coral-derived OM can be degraded to some extent by microbes on the coral surface, but this material is mainly (>90%) degraded by the microbial community associated with the reef sands after detachment.
So while corals do eat their mucus to ingest bacteria and detritus, they release *a lot* more mucus than I thought. The release of organic carbon by aquarium corals has been correlated with feeding -- after a delay during which the corals are metabolizing their food, they begin releasing mucus. In the wild, corals feed pretty much constantly, and they release mucus pretty much constantly in order to prevent fouling by sediments and competing organisms, but flow levels are normally high enough to wash the stuff away, so this isn't obvious. Since coral mucus is colloidal organic carbon with a polypeptide backbone, it's pretty much made to be skimmed, which would explain how dino-killing bacteria got into Montireef's skimmate.

But coral mucus flocculates like nobody's business -- most anything drifting in the water tends to stick to it, including other bits of mucus, and in the wild it ends up settling out of the water column fairly quickly, often within a few meters of the coral that released it. The mucus is then biodegraded in the benthic sediments, meaning corals may be constantly seeding reef sands with beneficial dino-killing bacteria to protect themselves.

Unfortunately, even if that's correct, I'm not certain this mechanism would function in a typical DT because the beneficial, coral-friendly bacteria would not be falling on fertile ground. Or perhaps more accurately, the ground is too fertile -- too copiotrophic -- as DT sand beds stirred by macrofauna are full of detritus, while sand on real reefs is full of microfauna that process organic matter into bits small enough for bacteria to consume and recycle back into living biomass. On real reefs, even the sand is comparatively nutrient-poor, and coral mucus and the detritus it snags out of the water column is an important source of organic carbon and other nutrients for bacteria, protists, and miscellaneous fauna living in the sand.

So the obvious question is that if dino bacteria and coral bacteria don't get along, why don't corals react when dino snot gets all over them?

Well, it looks like healthy corals do react, but on the other hand...


Quote:
Originally Posted by Regulation of microbial populations by coral surface mucus and mucus-associated bacteria
However, as mucus was collected from apparently healthy coral tissue, and not bleached tissue, this provides evidence that a community shift to vibrio dominance may occur prior to zooxanthellae loss.
...just because a coral looks healthy, that doesn't mean it actually is. Coral polyps that don't try to protect themselves as they're being overgrown by dinos are probably "immuno-compromised" by a changed bacteria population in their mucus. Their rosies are gone, or perhaps worse have been replaced with the wrong kind of rosies, and some critical chemical signal that the corals need to recognize what's happening and ramp up mucus production to protect themselves isn't being sent. Additionally, synthesizing mucus requires nitrogen (and also sulfur, interestingly -- this looks like it could be another way for coral polyps to do something useful while ridding themselves of excess sulfide, and it may also affect the microbial population of the mucus, as many antibiotics, including TDA, are sulfur-based) which means corals that are starved for N would be unable to defend themselves in this manner.

Note that this suggests the Montireef Protocol could fail because all the corals present have already shifted to an unhealthy bacterial community in their mucus.

Unfortunately, I don't see any easy way for us to know when coral bacteria have shifted away from their normal, healthy complement of species. That would take some fairly serious science -- though on the other hand, nowadays a bright high school student can do fairly serious science along these lines. But there may be visible warning signs that the shift is underway...


Quote:
Originally Posted by Dfee
Why do we think coralline recedes and turns white? Alk, mag, and ca all good. Dino's not necessarily on the parts that turn white
As you might expect, the bacterial population of coralline is coral-friendly.


Quote:
Originally Posted by Induction of Larval Settlement in the Reef Coral Porites astreoides by a Cultivated Marine Roseobacter Strain
Our study revealed that a strain of bacteria (Roseivivax sp. 46E8), representing the Roseobacter clade of alpha-proteobacteria, induces larval settlement in the coral Porites astreoides. This finding adds to the accumulating evidence that Roseobacter-affiliated bacteria play an important role in the larval ecology and survival of early life stages in corals. Bacteria from the Roseobacter clade are among the most abundant bacterial groups in the oceans, and they are important in global biogeochemical cycling. Roseobacter clade bacteria have consistently been detected as abundant members of seawater-associated bacterial communities during reproduction of both brooding and spawning coral colonies, and they are prevalent in larvae, juveniles, and adults of diverse corals. The consistent detection of these taxa in early life stages of diverse corals suggests that they engage in long-term symbioses with corals and may therefore have important functional roles in their coral hosts. Bacteria from the Roseobacter clade have been proposed to defend coral larvae from pathogenic bacteria and provide fixed organic nitrogen to the partner Symbiodinium spp. ...

Although Roseivivax sp. 46E8 caused a significant increase in larval settlement compared to sterile seawater controls, the amount of settlement was less than that in our other experimental treatments with naturally occurring crustose coralline algal biofilms. The "invisible majority" -- bacteria, viruses, and organic matter -- are important drivers of coral reef health and resilience.
I'd bet good money that coralline is the canary in the coral mine signalling that the bacteria population in an aquarium is shifting away from the coral-friendly bunch that we want and towards dino-friendly types. And as I looked into this, I found that the bacteriological warfare going on between corals and dinos is just one aspect of the general competitive struggle for ecological dominance between corals and primary producers.

CONTINUED...


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Old 01/04/2016, 08:37 AM   #2513
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Can You maybe paste that on a blog and post a link on the forum?


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Old 01/04/2016, 08:46 AM   #2514
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Quote:
Originally Posted by Unseen players shape benthic competition on coral reefs
Benthic algae on coral reefs are conventionally grouped into functional groups, including the crustose coralline algae (CCA), macroalgae, and turf algae. Each of these groups contains many different species, each with their own species-specific subtleties. ... CCA are commonly associated with healthy reefs and are generally thought to have positive interactions with corals. ...

Macroalgae are the most commonly studied type of algae regarding coral–algae competition. A variety of different macroalgae species (mostly fleshy algae) have been shown to inhibit coral growth and cause bleaching, hypoxia, and lower photosynthetic efficiency and chlorophyll-a content of symbiotic zooxanthellae along the edge of the coral colony. ...

Turf algae (i.e., 'turfs') are heterogeneous assemblages of short filamentous algae, juvenile macroalgae, and cyanobacteria. Turfs are also home to diverse and essentially uncharacterized eukaryotic and prokaryotic microbial communities, as well as to viruses. The heterogeneity of turf algal assemblages means that they have different effects on corals, although the majority of interactions studied have been negative. Turf algae inhibit coral growth and negatively influence adjacent coral tissue integrity, physiology, and fecundity. ...

Initial studies of coral–algae competition were focused on the physical mechanisms that corals and algae use to damage each other (reviewed by McCook in 2001). Algae employ tactics such as shading and abrasion, and corals respond with mesentery and nematocyst attack. More recent studies have shown that other biological factors change the relative competitive advantage in specific ways. ...

Benthic algae harbor rich microbiota, including a large number of potential pathogens and coral disease-associated microbes. These pathogens may be transmitted to corals during competitive interactions, but different groups of algae have distinct effects on the coral holobiont. Turf algae, for example, are associated with major shifts in the bacterial communities along the coral border, including more potential pathogens and virulence genes. ... By contrast, coral interactions with CCA have a distinct community of bacteria at the interface, but these are not pathogen-like.

One common physiological signature that separates coral–CCA interactions from coral–turf and coral–macroalgae interactions is hypoxia. Both experimentally-initiated and naturally-occurring interactions between corals and turf or macroalgae are hypoxic, whereas coral tissues in contact with CCA remain superoxic. Low oxygen along the coral–algae interaction zone can be alleviated by removal of the alga or by treatment with antibiotics, showing in all experiments to date that hypoxia is the result of microbial activity. Although hypoxia may be the cause of coral mortality, it is highly probable that other so far unidentified pathogenicity and chemical factors are the actual lethal factors in most of the interaction zones, and that hypoxia is a secondary effect of the microbes eating the decaying tissue. ...

The DDAM model is based on experimental and ecological evidence showing that algae (i) release DOM, which (ii) facilitates microbial growth and respiration on the benthos and the water column, particularly that of opportunistic pathogens, which in turn (iii) causes morbidity and mortality of corals. This effect can be mitigated by antibiotics, implicating microbes as a significant factor in algae-mediated coral death. ...

Physical interactions between corals and algae can inflict damage directly on the competitor, potentially freeing space for the attacker to advance. However, physical mechanisms alone, typically tested through the use of plastic mimics, play a relatively minor role in coral–algae competition when compared to the effects of live organisms. This difference is due to the transfer of chemicals and microbes to the competitor. Direct contact between algae and corals, for example, delivers DOM, potential pathogens, and hydrophobic organic matter (including allelochemicals) to the tissue of the competitor. ...

Given that direct and indirect contact between algae and corals can elicit negative influences, it will be important to determine how organic matter (OM) and microbes move between holobionts. Coral reefs are complex physical structures that have a significant influence on the movement of water. Despite often high flow and wave action on coral reefs, net water transport is slow within and directly above the reef. This water also has structure. There is a misconception that flow and advection homogenize the reef water landscape, when in fact the water over a coral reef is a varying, complex landscape that is shaped by the structure of the benthos and the flow of the water interacting with it. From the microbial perspective, every drop of seawater is a heterogeneous mix of gels, strings of organic matter, microscopic particles, and discrete hotspots of microbial and viral activity. It is within these water masses that most coral–algae interaction dynamics occur, but this layer of connectivity on coral reefs is only beginning to be described and visualized.
It's worth noting that carbon dosing has been examined in light of the DDAM model...


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Originally Posted by Advanced Aquarist Feature Article: Total Organic Carbon (TOC) and the Reef Aquarium: an Initial Survey, Part I
Any discussion on the relationship between DOC levels and coral health would be remiss without a digression into the currently popular practice of dosing reef tanks with carbon sources, specifically vodka (= ethanol), sugar, and/or vinegar (see http://glassbox-design.com/2008/achi...perimentation/ for a timely discussion). The logic behind this husbandry technique stems from the speculation that the increase in DOC provided by these chemicals will promote bacterial growth, and this increase in bacterial growth will in turn boost the removal of nitrogen and phosphorus-containing nutrients from the water column. The increased bacterial mass can then be removed by efficient skimming, leading to a net export of undesirable nutrients (N, P) from the aquarium. A standard recipe has been developed by Eric of Glassbox-Design: 200 mL of 80-proof vodka, 50 mL of vinegar, and 1.5 tablespoons sugar, mixed together. The dosing recommendation with this mixture involves starting with 0.1 mL/20-gal per day, and gradually increasing to a maintenance dose of 0.5 mL/20-gal per day. How do these carbon input values compare to the carbon (via carbohydrate) input values of Rohwer? In fact, the Eric/Glassbox-Design protocol is equivalent to raising the aquarium water by about 1.1 ppm of C at the maintenance dose. The Rohwer carbon dosing values that led to coral mortality over a 30-day exposure were in the range 2 - 10 ppm of C. So, it appears that the Eric/Glassbox-Design recipe does not leave much margin for error in dosing levels; overdosing by 2-3X might lead to coral mortality.
Recall that one of the ways that organisms can influence the community composition of bacteria living on them is by controlling the composition of organic carbon that they release. Algae release excess photosynthate when nutrient limited rather than shut down their photosynthesis machinery; but I did not know algae have evolved to release labile DOC constantly, much as I did not know wild corals release mucus more or less constantly, in order to influence the population of their microbiomes. It's a safe bet algae recruits potentially pathogenic (to us and animals we care about) proteobacteria and helps them outcompete potentially pathogenic (to the algae) Bacteroidetes such as cytophaga, which as noted earlier is discouraged from settling on macro by DMSP (...and this may explain why ostis don't reach high population densities when growing epiphytically: their main food bacteria can't grow, so unless they can infect the algae with cytophaga and melt it down, they have to make do with eating vibrio or some other proteobacteria). This is a good example of how host organisms can work the problem from both ends, using the organic carbon they release to both attract and repel bacteria to keep themselves healthy.

The DOC primary producers put into the water has downstream effects on reef microbial communities just as coral mucus does, and causing coralline to die back by shifting its epiphytic community away from coral-friendly bacteria may be one of those effects. The impact of algal DOC on aquarium corals has also been seen -- there was an interesting thread about low-level DDAM effects from algae scrubbers a few years back on Santa Monica's web site (...if the link doesn't work, here's the URL: algae scrubber dot net /forums/archive/index.php/t-1327.html). Primary producers are powering up algae-friendly bacteria with labile DOC just as corals use their mucus to tip the balance of the microbial population in their favor. In other words, the battle for dominance between algae and corals isn't only taking place when individual organisms are bumping up against one another and competing for light and nutrients in the same physical space; they're both trying to remake the entire reef ecosystem from the bottom up.


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Originally Posted by Influence of coral and algal exudates on microbially mediated reef metabolism
Coral reefs, although generally located in oligotrophic environments, are one of the most biodiverse ecosystems on the planet, due largely to their high productivity and efficient nutrient recycling mechanisms. ... Organic material supplied to the ecosystem by benthic primary producers as exudates is thought to play a pivotal role in community-wide transitions on coral reefs. Exudates may serve different ecological functions depending on their origin. Coral exudates may keep valuable resources in oligotrophic reef systems by trapping particles from the water column, which are remineralized by the benthic microbial communities. In contrast, algae derived exudates have been shown to stimulate rapid growth of planktonic microbies and community shifts towards copiotrophic and potentially pathogenic microbial communities in the water column. ...

Previous studies of tropical reef-associated primary producers have shown that all primary producers release a significant portion of their photosynthetically fixed carbon immediately into their environment. It has further been established that fleshy macroalgae and especially small ( < 2 cm) filamentous algal turfs generally have noticeably higher DOC release rates than calcifying primary producers including hermatypic corals. ...

However, counter to expectations, Nelson et al. (2011) demonstrated that in a backreef system dominated by algae rather than corals, DOC concentrations were significantly lower than in the surrounding offshore waters. Other studies incorporating multiple islands in the central Pacific have shown similar patterns where fleshy algal abundance is inversely related to DOC concentrations in the water column. This surprising inverse correlation may be explained by a significantly more heterotrophic microbial metabolism following initially higher availability of algae derived bio-available DOC. A system wide decrease in DOC concentrations could then be the result of (a) increases in the abundance of heterotrophic microbes and, (b) a co-metabolism, which occurs when microbes are given an initial surplus of labile carbon, enabling this bacterial community to utilize refractory carbon sources.

Recent research has shown that macroalgae derived exudates, enriched in the dissolved combined neutral sugar components Fucose and Galactose, facilitate significantly higher rates of bacterioplankton growth and concomitant DOC utilization than coral exudates or untreated seawater. Further, microbial communities growing in different exudates selectively remove different dissolved combined neutral sugar (DCNS) components, whereby the bacterial communities growing on algal exudates have significantly higher utilization rates of the sugar components which were enriched in the respective algal exudates. Analysis of microbial community composition identifies clear differentiation between the communities selected for by algae exudates and those growing on coral exudates or seawater controls. Macroalgae fostered rapid growth of less diverse communities and selected for copiotrophic bacterial populations with more opportunistic pathogens -- so-called "super-heterotrophic" communities. In contrast coral exudates engendered a smaller shift in bacterioplankton community structure and maintained relatively high diversity.

The microbial landscape on tropical reefs, however, is not only restricted to the water column directly adjacent to the reef benthos ( ~ 10^5 - 10^6 / cm^3 ). In addition to microbes associated with benthic macro-organisms ( > 10^7 / cm^2 of surface area), those associated with calcareous reef sands ( ~ 10^9 / cm^3 ) and the vast porous reef structures in the reef matrix may also play a significant role in biogeochemical cycling. Surface associated microbes may carry out multiple ecological functions, such as nitrogen fixation or inhibition of potential pathogens for their host organisms. The benthic microbial communities, living in the reef structure or reef sands, on the other hand have been recognized as important components for the reef community, as they are capable of rapidly reallocating nutrients in the otherwise oligotrophic tropical reef environments. They also may constitute an essential food source for protists and invertebrates, forming the base of benthic food webs. Next to remineralization and redistribution of nutrients, recent studies have emphasized the role of the benthic microbial communities as important primary producers in these ecosystems. ...

In the present study, over a full diurnal cycle, benthic primary producers released about 10% of their daily fixed carbon as DOC in the surrounding waters.

Responses of the associated microbial communities to these exudates varied widely and were dependent on the source of the exudates as well as the habitat that the microbes originated from. ... Further, our results suggest that, with shifts from coral to algae dominated systems, dissolved organic carbon concentrations in the water column will decrease as a result of an elevated heterotrophic microbial community metabolism, congruent with demonstrated DOC depletion in shallow reefs.

Results from the beaker incubations containing either benthic or planktonic microbes and seawater only showed that while the planktonic microbial community was consistently net heterotrophic the benthic microbial community metabolism was net autotrophic due to daytime photosynthesis, producing significantly higher amounts of oxygen during the daylight hours than it consumed over a 24 h period. Scaled volumetrically to the scale of a 3 m deep reef ecosystem, the effects of the respective net autotrophic benthic and net heterotrophic planktonic microbial communities had comparable magnitudes, resulting in a combined neutral net microbial community metabolism with no significant change of DOC and DO values over a whole diurnal cycle.

The introduction of exudates, however, had noticeable and significantly diverging influences on this balanced community metabolism. Coral exudates increased the net planktonic microbial community production, changing the net oxygen production towards an average positive balance during daylight hours. Coral exudates also enhanced the inherently autotrophic character of the microphytobenthos, such that at the reef scale coral exudates overall stimulated net ecosystem productivity...by an increase in bioavailable inorganic nutrients, supplied by heterotrophic remineralization of coral exudates in the biocatalytic reef sands. In contrast, addition of algal exudates, most noticeably exudates derived from turf algae, stimulated heterotrophic oxygen and organic carbon consumption rates by the planktonic and benthic microbial community, mediating an overall shift toward a significantly more heterotrophic microbial community metabolism. ... Our previous study conducted in this reef system demonstrated that exudates from fleshy macroalgae were enriched in specific carbohydrate components and were more labile than exudates derived from corals, fostering rapid but inefficient growth of primarily copiotrophic bacterioplankton in the surrounding water column. By facilitating the remineralization of semi-labile DOC inputs from the open ocean the high carbon demand of inefficient copiotrophic "super-heterotrophs" may be a mechanism fueling the excessive carbon consumption rates estimated here and the subsequent depletion of DOC on reefs dominated by fleshy algae such as the backreef of Mo'orea.

In contrast, the shift towards a net autotrophic metabolism of the collective microbial community stimulated by coral exudates likely compensates for the initially lower photosynthetic oxygen production rates of corals compared to algae. In our estimates this resulted in comparable net oxygen fluxes of the combined community metabolism in coral compared to algae dominated locations. Coral exudates facilitated changes in the microbial community metabolism towards higher primary production rates and led to an overall increase in DOC concentrations (resulting from net coral and microbial DOC release). Together these results suggest that reefs dominated by corals, by stimulating microbial primary production, may maintain comparable net ecosystem productivity to those dominated by fleshy algae, but additionally may maintain elevated levels of potentially labile DOC available for remineralization and recycling by microbial communities.
Benthic microbial primary production is limited to the uppermost couple of mm in reef sands because light doesn't penetrate very far, but on the other hand, what applies to heterotrophic bacteria applies to single-celled primary producers, as well: there's a very large surface area available in that thin layer of sand. Added up, benthic primary production turns out to be quite substantial.


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Originally Posted by Microbial photosynthesis in coral reef sediments (Heron Reef, Australia)
We investigated microphytobenthic photosynthesis at four stations in the coral reef sediments at Heron Reef, Australia. The microphytobenthos was dominated by diatoms, dinoflagellates and cyanobacteria, as indicated by biomarker pigment analysis. Conspicuous algae firmly attached to the sand grains (ca. 100 um in diameter, surrounded by a hard transparent wall) [...note that this sounds a bit like what Quiet_Ivy described as "harder brown circular spots on the glass"] were rich in peridinin, a marker pigment for dinoflagellates, but also showed a high diversity based on cyanobacterial 16S rDNA gene sequence analysis. ... An estimate based on our spatially limited dataset indicates that the microphytobenthic production for the entire reef is in the order of magnitude of the production estimated for corals.
That's a lot of production. From our perspective as hobbyists, that's the engine powering a DSB -- and corals are trying to rev it up with the mucus they shed. Bumping up primary production levels in the sediments would help corals outcompete algae on a broad, reef-wide level because as we hobbyists learned from Dr. Shimek, a healthy and diverse benthic food web releases coral chow into the water column.

While I was looking for papers addressing how organic carbon influences microbial populations on coral reefs, papers on sponges kept coming up. Sponges are weird and ancient creatures, so I couldn't resist checking them out. When I read some recent papers, I discovered that a completely new aspect of reef biology has come to light in the last couple of years, finally bringing the role of sponges into focus. The original paper is behind a paywall, but fortunately for us, Google Scholar found a follow-up paper from another scientist chiming in with an important refinement of the theory...


Quote:
Originally Posted by Sponge waste that fuels marine oligotrophic food webs: a re-assessment of its origin and nature
Sponges are prominent members of coral reefs, where they mediate the transfer of energy and matter through the fluxes of organic carbon and dissolved inorganic nutrients. A new perspective on their trophic role comes from the recent finding by de Goeij et al. (2013) that reef sponges take up most of the dissolved organic matter (DOM) available in the water column before it is transferred away from a reef. The fate of that DOM carbon used by sponges has been a mystery, as respiration requires only about 40% of the total carbon taken up, and the remainder is not converted into detectable growth. de Goeij et al. proposed that DOM energy may be invested in renewing the entire cell layer of choanocytes (monociliated filtration cells) every few hours. The choanocyte renewal would produce a significant outflow of particulate organic matter (POM) rich in carbon and nitrogen that would be rapidly assimilated by a variety of invertebrates, thereby fueling the reef food chain. By this mechanism, sponges are proposed to play a crucial trophic role, fueling food chains of not only coral reefs but also many other oligotrophic marine communities, including caves, varied deep-sea habitats, etc. ...

The TEM [Transmission Electron Microscope] approach reveals that the outgoing POM through which sponges fuel oligotrophic food webs results from more complex cellular processes than mere choanocyte renewal. The squeezing of entire cells with inclusions (spherulous, granular and archaeocyte-like cells) into the excurrent canals and the extrusion of membrane-bound inclusions mediated by the endopinacocytes appears to contribute notably to the outgoing POM. ...

The detected migration of mesohyl cells into the canals appears to be related to the elimination of digestive leftovers (egestion and defecation) and metabolic by-products (excretion), two basic physiological functions only rarely investigated in sponges. As sponges lack organ systems to collect and evacuate products from intra-cellular digestion and metabolism in the deep mesohyl, these waste products are stored in cells that subsequently enter into the outgoing flow, contributing to the POM that exits the sponge. Archaeocyte-like cells, known to have intense phagocytic activity, appear to be engaged in digestion and elimination of refractory leftovers, while spherulous and granular cells appear to be involved in excretion of metabolic by-products. Although many aspects of the physiology of sponges still remain poorly understood, it is clear that many physiological processes of the sponges are based on the ability of these organisms to maintain substantial cell and metabolite traffic through their simple epithelia. Extrusion of spherulous cells through the epithelia of the aquiferous canals of A. cavernicola has previously been documented by Vacelet (1967), who first suggested that it could be a way to eliminate excretory products. Likewise, spherulous cells heavily charged with inclusions have been reported to leave the body of the non-feeding larva of the sister sponge species Aplysina aerophoba. The larva is a lecithotrophic life-cycle stage unable to incorporate particulate food but able to generate metabolic excreta. Therefore, spherulous cells are concluded to be involved in elimination of metabolic by-products that are not related to the digestive process. ...

In the absence of detailed studies on vesicle content, it is assumed that the energetic content of these mesohyl cells -- charged with excretion by-products and digestive leftovers -- is lower than that of the choanocytes. It is worth noting that many of the discarded choanocytes and some archaeocyte-like cells were charged with phagosomes containing undigested food. Consequently, these cells are expected to contribute greatly to the POM transfer of energy to the following steps in the trophic chain. As water pumping and food ingestion are energetically costly processes, it is intriguing that choanocytes that are about to be discarded keep engulfing and start digesting pieces of particulate food that will never contribute to the sponge energy balance because these cells will readily be discarded as POM.
So coral reefs run on sponge poop... I've long had a vague suspicion that a heterotrophic element was missing from a system consisting of a mixotrophic reef tank and an autotrophic sump, but I did not see that coming.

CONTINUED...


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Old 01/04/2016, 09:06 AM   #2515
34cygni
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Sponges having the ability to consume DOC explains why they're taking over Caribbean reefs now that most of the corals are dead and the fish are gone: the sponges are sucking up DOC released by the algae, and they can also capture bacterioplankton growing on labile algal DOC.


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Originally Posted by Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)
Traditionally, sponges were considered to be suspension feeders that efficiently remove bacterio-, phyto-, and even zooplankton from water they actively pump through their filtration systems. However, already in 1974, Reiswig hypothesized that sponges may also retain dissolved organic carbon (DOC), which was later confirmed for several sponges, ranging from tropical to temperate sponge species. These tropical coral reef sponges can take up >90% of the total organic carbon (TOC) as DOC, indicating that they foremost rely on DOC to meet their carbon demand. Since DOC also accounts for >90% of the TOC pool on coral reefs, the ability to utilize this food source may aid certain sponges to thrive under oligotrophic conditions, whereas most other heterotrophic reef organisms are unable to capitalize on this resource. ...

Our results further suggest that...sponges can efficiently take up DOC across a wide range of ambient DOC concentrations. This indicates that these sponges are well adapted to utilize DOC as food source. ...

The ability of sponges to take up and assimilate DOC has been proposed to be crucial to maintain biodiversity and high productivity on tropical coral reefs. In the so-called "sponge loop", analogously to the microbial loop, sponges make energy and nutrients stored in the dissolved organic matter (DOM) pool available to the benthic food web via DOM assimilation and subsequent detritus production by the sponges. Our study now shows that excavating sponges most likely also participate in the sponge loop...

[B]eing suspension feeders, coral-excavating sponges were considered to benefit from elevated concentration of particulate resources, such as phytoplankton and bacteria. However, here we could show that coral-excavating sponges mainly rely on DOC to meet their carbon demand. Thus, an increase in DOC production, or quality, on coral reefs is likely to be beneficial for them. Shifts in the benthic reef community have caused major changes in the production and cycling of organic matter on reefs. Due to anthropogenic disturbances benthic algae are increasing at the expense of scleractinian corals on most coral reefs throughout the Caribbean region. Both, scleractinian corals and benthic algae release a substantial amount of their photosynthetically fixed carbon as organic matter in the surrounding water. However, benthic algae are reported to release more DOM than corals and algal-derived DOM appears to be of a higher quality [meaning more labile]. Sponges, including excavating species, could therefore benefit in two ways from an increase in DOM production and quality due to the shift in benthic communities: (1) directly via uptake of DOM and (2) indirectly by feeding on the heterotrophic planktonic microbial community, which is fueled by the DOM release of benthic algae. several Caribbean reefs and is suggested to become more frequent with increasing reef degradation. Here we could show that the coral-excavating sponges Siphonodictyon sp. and C. delitrix are capable of consuming DOC and mainly rely on DOC to meet their organic carbon demand. This suggests that coral-excavating sponges are likely to benefit from an increase in DOC production and quality as a result of the ongoing coral-algal phase shift.
Coral-excavating sponges are a fairly big deal from an ecological standpoint, as massive stony corals building up and sponges drilling down can create enormous topological complexity on and within reefs. A pit excavated by a sponge is a detritus trap (that's probably why sponges evolved this behavior in the first place) and decaying detritus tends to become acidic. Acid eats away calcareous deposits very quickly, and there are internal currents moving through the porous, heterogeneous reef rock driven by pressure differentials from waves and tides that can pull acidic water into the reef matrix and create complex, highly interconnected networks of small caves and crevices beneath reefs.


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Originally Posted by Endoscopic exploration of Red Sea coral reefs reveals dense populations of cavity-dwelling sponges
Framework cavities are the largest but least explored coral reef habitat. Previous dive studies of caverns, spaces, below plate corals, rubble, and artificial cavities suggest that cavity-dwelling (coelobite) filter-feeders are important in the trophodynamics of reefs. ...

Line transects showed that 26-42% of the projected reef area is riddled by crevices of various sizes. The median opening diameter of only 0.2m renders these crevices inaccessible to visual inspection by divers using conventional technology. We carried out detailed measurements of crevice dimensions with a diver-operated endoscopic video camera... Combining these results with the line transect data yielded a cumulative coelobite living area of 2.5 - 7.4 square meters of crevice wall per square meter of reef. This is a conservative estimate considering the fact that many of the crevices extended beyond the range of the quantitative survey [meaning deeper than the 4 meter limit of the camera's reach], and that the interconnections between anastomosing crevices escaped detection...

Quantitative analysis of 2301 high-resolution images revealed a rich coelobite community covering 2.8 plus-or-minus 0.9 square meters per projected m^2 reef... Coralline algae predominated near the sunlit entrances. Sponges abounded in posterior sections of the crevices, constituting 51-73% of the coelobite cover. The high densities, as well as the dominance of delicate sheet-like growth forms, support the assumption that the distribution and abundance patterns of coral reef sponges are controlled by predators. ...

Current speeds...averaged between 0.9 and 5.5 cm/s. Wash-out experiments with fluorescent dyes featured half-life periods of only 75 plus-or-minus 15 seconds, suggesting complete flushing of cavity waters within a few minutes.

Dye experiments showed that the water flow throught framework crevices was driven by flow speed differences across the bumpy reef surface, much like pressure-induced air flow through termite mounds, where the intake openings are located in troughs near the base and the exhause openings in exposed positions near the crest. As a result, water flow was almost always directed into the crevices, leaving the framework through countless cracks and holes near the elevated parts of the reef.

The largely unidirectional flow pattern allowed us to determine the bulk filtering rate of the coelobite community...

Phytoplankton uptake by the coelobite community [was] equivalent to 22% of the gross community metabolism of the entire reef. Total picoplankton removal, as suggested by the available biomass of bacteria in tropical waters, is probably more than twice this value...

Owing to the long doubling times of phytoplankton and bacteria (6-24 h) relative to the residence time of water over the narrow shelf (1-5 h), most of the picoplankton consumed in the reef originates from offshore, thus constituting a source of new material for the reef ecosystem.

Nutrient enrichments in the cavities suggest intense mineralization of the organic matter by the crevice biota. Nutrient ratios near the Redfield ratio (N:P = 15.5) reflect the planktonic source of the mineralized material, contrasting the higher values reported for intrinsic reef material, for example in lagoonal patch reefs (N:P = 20), pore waters (N:P = 21), or benthic producers (N:P = 30). Stoichiometric conversion of picoplanktonic organic matter to inorganic nutrients (assuming 100% of the ingested food is respired) shows that allochthonous N and P may contribute one-third of the total nutrient flux emanating from the cavities in readily assimilable form (such as ammonia, 42% of N) for corals and algae.
I've known for a while, now, that a coral reef is basically a vast algae scrubber sitting on top of an even bigger bacterial biofilter, and I've seen divers exploring reef caves on TV, but I had no idea there was a full-on cryptic zone underlying the entire reef structure! How cool is that?!? This suggests that the ideal setup for a hobby system would be a reef tank draining into a countercyclically lit display fuge with a Shimek-compliant DSB (...not necessarily in overall volume, but in terms of depth and the absence of counterindicated fauna so as to maintain benthic biodiversity -- at last, an excuse for the marine hobbyist to buy a hex tank!), which drains in turn into a large (ie, spanning the width of the stand for the two tanks above) cryptic sump with LR and a shallow sand bed where sponges consume labile DOC from the nutrient-limited macro and release POC for the corals. Probably wouldn't be hard to accommodate a pelagic (FO or FOWLR) DT downstream of the reef tank by upsizing the display fuge and sump accordingly.

This seems like a good time to mention that carbonate and silicate sands host different bacterial communities -- here's a paper about that, if anyone's interested -- which suggests that a mix of the two will increase bacterial biodiversity, and a cryptic sump would be a good spot to try that as darkness would make life difficult for diatoms. Given that there are other organisms that like silica (radiolarians leap to mind, and about 75% of extant sponge species have siliceous skeletons) that pretty much got kicked in the teeth by the evolution of a primary producer with silicon armor, putting some silica sand in a cryptic zone may benefit benthic biodiversity beyond just bacteria.

Speaking of diatoms -- fun science fact: the earliest fossil evidence of diatoms follows closely upon the evolution of new, faster-growing grasses on land. Scientists think that the increased production of phytoliths (silica crystals plants make in their tissues to discourage herbivores) sped up the terrestrial silicon cycle, resulting in an increased flux of silica into rivers, lakes, and oceans via erosion which led to rising dissolved Si levels and, eventually, diatoms.

Turns out that this sort of feedback between nutrient availability and evolution illuminates the ecological niches of primary producers on a broad level...


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Originally Posted by The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level
Green algae [meaning green phyto in this context] appear to have intermediate values for nitrate uptake parameters and exhibit the velocity-adapted strategy as they have high maximum growth rates and second highest nitrate uptake rates. They have an extremely high affinity for ammonium...

Coccolithophores are well adapted not only to oligotrophic (low nutrient) conditions, but also to high irradiance levels often associated with such conditions [...low nutrient NSW is usually clear because not much grows in it, and what does grow is usually very, very small because small cells can compete more effectively for nutrients -- hence the previously mentioned vast and diverse population of picoplankton eking out a living in the "nutrient desert" of the oligotrophic open ocean]. In contrast, diatoms have low half-saturation constants for irradiance-dependent growth and are generally more adapted to low light characteristic of high nutrient, intense mixing conditions. Thus, phytoplankton nutrient utilization strategies, in conjunction with their responses to physical environment, such as turbulence and light, to a large extent define ecological niches of the two groups. The idea of phytoplankton functional groups associated with different nutrient and turbulence regimes was pioneered by Margalef and elegantly expressed in his nutrient-turbulence mandala [...diatoms like high turbulence and high nutrients; cocos like low turbulence and low nutrients; dinos like low turbulence and either high or low nutrients].

These ecological niches correspond remarkably well to the distributions of the two groups in the ocean. Diatom relative abundance is positively correlated with nitrogen (and phosphorus) concentrations and negatively correlated with the stability of the water column. In contrast, coccolithophorid abundance is greater at low nitrate and phosphate and high water column stability and irradiance. Consequently, the abundances of the two groups are significantly negatively correlated. ...

All algal groups appear to preferentially take up ammonium over nitrate, likely because nitrate but not ammonium has to be reduced before assimilation and thus may require more energy to be assimilated. However, as our analysis indicates, the relative preference for ammonium over nitrate is greater in green algae, compared to diatoms and other taxonomic groups of marine eukaryotic phytoplankton. This may reflect the effect of the oceanic redox conditions at the time of origin of respective groups: green algae appeared around 1.5 billion years ago in mid-Proterozoic, when suboxic conditions could have caused the reduced form of N (i.e. ammonium) to be prevalent. In agreement with this reasoning, cyanobacteria, the earliest [oxygenic] photoautotrophs, evolved under anoxic conditions, also have a strong preference for ammonium over nitrate. Diatoms appeared much later, c. 150 million years ago, when the oceans were highly oxidized and consequently are better adapted at utilizing nitrate. Therefore, modern strategies of nutrient utilization by major taxonomic groups appear to be consistent with the conditions at the time of their origin and⁄or diversification and suggest conservatism in trait values over groups' evolutionary histories.
Closed captioned for the Science impaired, that means the nutrient requirements of different kinds of algae were shaped by the availability of nutrients in the environments in which they first evolved and have largely been preserved since that time.


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Originally Posted by Toward a stoichiometric framework for evolutionary biology
Changes in the relative abundances of elements appear to have been one of the major determinants of macroevolutionary patterns. For example, Quigg et al. (2003) show that micronutrient stoichiometry of extant marine phytoplankton taxa reflects the composition of their symbiotic plastids.
For phyto in general, the expanded Redfield ratio according to a 2008 review is...

C 124
N 16
P 1
S 1.3
K 1.7
Mg 0.56
Ca 0.5
Fe 0.0075
Zn 0.0008
Cu 0.00038
Cd 0.00021
Co 0.00019


A paper from 2010 gives an average of 29 species of phyto and includes manganese...

C 132
N 18
P 1
S 0.99
Fe 0.018
Mn 0.0028
Zn 0.00134
Cu 0.0005
Cd 0.00011
Co 0.00011

Other researchers compared the requirements for the trace elements Fe, Mn, Zn, Cu, Co, and Cd in what I'm guessing were eight common laboratory strains of coccolithophores, diatoms, and dinos -- the three dominant primary producers in the modern oceans -- and found that the dinos had relatively high quotas for all six metals. The diatoms, interestingly, had very low requirements for all six of these micronutrients (though some planktonic diatoms are known to have high requirements for Fe, possibly because they host cyanobacterial endosymbionts) while the cocos had high quotas for Mn, Co, and Cd, but low requirements for iron, zinc, and copper.

Dinos' high requirements for trace elements would explain and confirm these and a number of similar observations over the life of this thread...


Quote:
06/24/2013, 01:55 PM #1
DNA
Water changes
Dinoflagellates love water changes and not doing them will for sure make the dinos suffer.
Quote:
08/29/2013, 04:24 PM #19
Squidmotron
5) I agree that water changes -- if anything -- make it worse. They seem to die off more the longer between the water changes. I read a few articles that they like and depend on selenium and iron. Maybe that affects it.
6) Obvious, but do not dose trace elements.
Quote:
11/19/2013, 10:08 AM #99
bazeball05
stop doing water changes (Dino's are fueled by trace elements)
Quote:
10/11/2014, 03:26 PM #342
cal_stir
I to am in the midst of a battle with ostreopsis, about six weeks now, I to am convinced that water changes feed it
As for other primary producers, diazotrophic cyano hearts iron because those species need Fe to make nitrogenase, the enzyme they need to fix nitrogen. Green algaes need iron, zinc, and copper; red algaes have higher requirements for Mn, Co, and Cd and lower quotas than greens for Fe, Zn, and Cu.

Coralline is a red algae, incidentally, and when I looked into its nutrient requirements, I found that the reason hobbyists haven't had any luck pinning down what nutrient levels coralline grows best at is that it grows pretty well at any nutrient level from oligotrophic conditions on a healthy reef to eutrophic conditions on a dying reef. In all likelihood, the reason coralline's epiphytic bacterial community is coral-friendly is that the algae adapted to derive nutrients from the decomposition of coral mucus and its payload of detritus, which explains how it can grow when there's no measurable N or P in the water, but at the same time coralline didn't lose the ability to take in mineralized nutrients from the water -- whatever it can get, it'll use (...there are actually many different species of coralline adapted to different microenvironments, but funny science fact: even scientists who study coralline can't tell them apart without genetic analyses, so I'm sticking with the hobbyist convention of speaking about coralline in the singular).

The bad news for coralline is that it's pretty much flat, which means it can easily be outcompeted for light, if nothing else, by any algae capable of vertical growth. Coralline frequently sheds its surface layer to prevent biofouling and death by overgrowth, but basically coralline's secret weapon is that nothing wants to eat it.

Reef grazers have a clear order of preference in their diets: they like to eat young, nontoxic macroalgae most of all, and then they'll go for the turfs, and nothing really likes to eat coralline. It's chalky and not very nutritious. Basically, coralline is dominant on healthy reefs because in the wild, coralline is nuisance algae.

It's a funny ol' world, innit?

Grazers selecting for a variety of algae that they don't like to eat, or can't eat because it's toxic or too large to fit in their mouths, is a common phenomenon both in the wild and in aquariums. So the good news is that exactly this sort of selection pressure explains the success of coralline, but the bad news is that we lack several keystone grazers in our systems, so this effect may yet prove to be the Achilles' heel of the dirty method.


Quote:
Originally Posted by Adrnalnrsh
I added an urchin when I added my new fish a few weeks ago and it's almost destroyed everything any algae I've had on my rocks and back wall.
Quote:
Originally Posted by karimwassef
I'll share a personal ally - urchins. The cheapest ones you can find. Get a bunch.
Urchins are one of those keystone grazers, though not all species are herbivores. The other big ones I'm aware of are surgeonfish, which we call tangs, and parrotfish. Interestingly, though, the biggest algae eater among reef fish is the humble damsel. The others are grazers, but damselfish are farmers -- they're highly territorial and scrupulous about clearing away algae they don't like so as to leave only their preferred food, filamentous turf algae, which they fertilize with their feces. Turns out damsels nom through way more algal biomass than the wandering grazers by growing their own food.

This is the basic, no-frills model of how top-down (grazing) and bottom-up (nutrient) pressures influence the algae population on reefs. If you go looking for exceptions in the scientific literature, you'll find them, but they're the results of real-world complexities, not failures of the underlying model.

Code:
               decreasing ecological resilience  ---->
    d
    e              HIGH GRAZING    |   LOW GRAZING
    c                ACTIVITY      |     ACTIVITY
    r          |-------------------|------------------|
    e          |                   |                  |
    a          |  massive corals   |   low-growing    |  
 |  s  LOW     |                   |                  |
 |  i  NUTRIENT|  and corallines   |    algae and     |
 |  n  LEVELS  |                   |                  |
 |  g          |  (healthy reef)   |      turfs       |
 |             |                   |                  |
\|/ r  --------|-------------------|------------------|
 V  e          |                   |                  |
    s          |                   |      large       |
    i  ELEVATED|     coralline     |                  |
    l  NUTRIENT|                   |     frondose     |
    i  LEVELS  |       algae       |                  |
    e          |                   |    macroalgae    |
    n          |                   |                  |
    c          |-------------------|------------------|
    e
Shifts in either nutrient or grazing levels can buy you a little slack in the other. That is, lowering nutrient levels can compensate for a decrease in herbivory -- which is basically how we run our little artificial reefs. Conversely, an increase in grazing pressure can compensate for additional algae growth triggered by a rise in nutrients -- indeed, many natural reefs have nutrient levels above the tipping point that should trigger overgrowth by algae, but grazers are holding the algae in check and maintaining the health of these reefs. This tipping point, where a reef ecosystem dominated by mixotrophic corals begins to transition to one dominated by autotrophic primary producers, occurs at vanishingly low nutrient levels.


Quote:
Originally Posted by Health of Coral Reefs: Measuring Benthic Indicator Groups and Calculating Tipping Points
Low-nutrient tipping points, where increasing nutrients reach hypothetically critical levels that begin to reduce recoverability from phase shifts (i.e., 0.040 ppm NO3 and 0.007 ppm PO4), have been broadly corroborated for sustaining macroalgal overgrowth of both coral reefs and seagrass beds. As examples, low-nutrient tipping points also have been correlated for macroalgal overgrowth of coral-reef communities at Kaneohe Bay in Hawaii, fringing reefs of Barbados, inshore reefs within the Great Barrier Reef lagoon, and the reefs of the Houtman Abrolhos Islands, Western Australia. ... In our experience, if modern analytical instruments can detect measurable nutrient levels, so can growth-limited macroalgae.
Since cal_stir mentioned he's dosing nannochloris, which is in a sense artificially creating a phase shift from mixotrophic primary production to autotrophy before rising nutrient levels do it for you, and since he said this...


Quote:
Originally Posted by cal_stir
The diverse micro fauna/plankton was the key but the phytoplankton was the nail in the coffin IMO.
...I went poking around and found that nannochloris in NSW has a very diverse population of bacteria associated with it, but surprisingly, no gamma-proteobacteria were found. The microbiome of nannochloris is probably hostile to the bacteria associated with dinos, which routinely consort with gamma-pros. And as I noted earlier, the decomposition of green algae seems to be associated with flavobacteria and thus may help tip the benthic bacterial community away from dino-friendly Bacteroidetes.

CONTINUED...


34cygni is offline   Reply With Quote
Old 01/04/2016, 09:19 AM   #2516
34cygni
Registered Member
 
Join Date: Mar 2013
Posts: 59
Thinking about that led me to wonder if green phyto might be uniquely hostile towards dinos, as dinoflagellates horned in on a cozy duopoly: green algae and cyano basically ran the oceans for about a billion-and-a-quarter years before dinos evolved. Green algae outcompetes cyano for P at high N levels; cyano outcompetes green algae for N at high P levels. This was so effective at scouring nutrients out of NSW that dinos didn't even try to buck the system, but instead went with a radical, outside-the-box solution: heterotrophy. And because dinos were the first of the three main primary producers of the modern oceans to evolve, there was nothing to distract green algae from looking for ways to beat them down. That might explain this...


Quote:
12/10/2015, 01:12 AM #2319
DNA
I've seen this green stuff on the image above punch a hole in my dino mat in a single day and then disappear the following day.
Cocos were the second of the modern triumvirate to evolve...


Quote:
04/12/2015, 04:06 AM #941
DNA
I'd like to share something with you guys that I think is important.

First I'd like to introduce the Coccolithophores. (Emiliania Huxley)
They are about 5 micron and 5 times smaller than e.g. an Ostreopsis dinflagellate.
I noticed a bloom out of the coast here in Iceland at the same time I was jet again looking for a reason for my constant low calcium level. ...

A friend and myself simply can't get calcium levels to the SPS standard and they hover under 400 or lower if something happens to Ca production. ...

After my last water change the water column had a haze to it for a few days and I think that is possibly Coccolithophores and other calcareous algae.

They have a very short live span and use up a lot of calcium. Their armor falls of and slowly falls to the ocean floor, meanwhile they reflect light so well their blooms can be seen from space.
I can imagine they produce an organic mass that is like a dead fish in the tank at all times. Is this what fuels dinoflagellates?
Quote:
04/12/2015, 06:56 AM #945
DNA
Here is Newbie Aquarists shot from yesterday.

Dinos, Cyano and Calcareous algae all going at the same time.
A 600 gallon tank makes the haze more visible.
His shots from last year are this way as well.
Cocos like high light levels and are adapted to compete effectively in very low nutrient environments -- their low requirements for Fe, Zn, and Cu keep them from being in direct competition with green algae for those micronutrients, which have low solubility in oxygenated NSW. In the wild, cocos dislike turbulence because they don't want to be churned down to lower depths where the light is dimmer, but they probably don't mind it so much in our tanks because there is no deep water and high flow conditions should help keep them suspended in the water column.

Like dinos, cocos are descended from predators, and there is evidence of mixotrophy in cocos, including consumption of dissolved organic carbon. Not all cocos make coccoliths -- some are "naked" and others, including Emiliania huxleyi, go through stages in which they lack a shell. This may facilitate heterotrophic feeding, which cocos apparently can't do when they're armored, though it can also result from cocos radically altering their biochemistry as blooms collapse to escape rapidly spreading pathogenic viruses.

E. huxleyi is the most common coco in the wild and thus of considerable ecological significance, and it is easily cultured and thus common in marine biology labs, as well, but it's unusual in some ways, such as its small size. As predation in aquatic environments is in large part a function of what any given predator can fit into its mouth, E. hux might be dino chow, and I have come across mention of E. hux blooms being surrounded by dinos and co-occuring with dinos... But to my enormous vexation, I don't have any hard evidence regarding the feeding behavior of O. ovata or O. lenticularis, which is externally very similar and often co-occurs with ovata in the wild. Micrographs of O. ovata (and also O. lenticularis) show that it lacks a classic physiological adaptation dinos use for opening up a large gap in their armor to ingest food and instead goes in the other direction, with a small opening between their armor plates. The other two ways dinos feed are with a pallium, which is a pseudopod or a sort of external stomach dinos use to enshroud and externally digest their prey, and a peduncle, which is a feeding tube dinos jab into their prey to suck out their insides. Peduncles are generally associated with heterotrophic dinos, but there are mixotrophic species with peduncles (though none of them are known to prey on large animals like fish as heterotrophic dinos do). Pallium feeders can take prey larger than the dinos themselves and can grow very quickly as a result. Either approach could be effective on cocos, but if I were a betting man, I'd put my money on O. ovata being a pallium feeder -- though I'd also lay a side bet that ostis have both a peduncle and a pallium, just because that seems like the option of maximum evilness.

Regardless of whether or not dinos eat cocos, their co-occurrence would make sense, as both are adapted to thrive in low nutrient environments but wouldn't be in competition for the same ecological niche, as cocos can efficiently absorb nutrients from the water column, which it turns out dinos suck at. One computer model of marine primary production predicted over and over that, given the measured abilities of dinos to absorb nutrients, other primary producers should outcompete them and rapidly drive dinoflagellates into extinction -- no amount of tweaking the model, such as by reducing dinos' appeal to grazers, could save them. But the model didn't include mixotrophy, suggesting that dinos are profoundly dependent on heterotrophic feeding to get the nutrients they need for phototrophic growth.


Quote:
Originally Posted by The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level
Marine dinoflagellates have significantly lower maximum carbon-specific nutrient uptake rates than diatoms, and significantly higher half-saturation constants for nitrate uptake and relatively low maximum growth rates (although some dinoflagellates are capable of rapid growth), thus being poor competitors for nitrate. It is likely that such "dirty tricks" as the ability to feed heterotrophically and migrate in the water column allows dinoflagellates to persist, despite the relatively non-competitive parameters for nitrogen uptake and growth.

Quote:
12/31/2014, 05:14 PM #604
Montireef
Dinoflagellates are so delicate and easy to kill...
In this battle, the fundamental problem we face as reefers is that dinos and corals essentially have the same business model. They're both mixotrophs and thus thrive in oligotrophic conditions. The difference seems to be organic carbon... My interpretation of the evidence is that corals prefer a low N, low P, low C environment, while dinos are into a low N, low P, high C environment. This might be further broken down to specify that corals prefer low-ish levels of labile DOC and recalcitrant organic carbon, but high levels of particulate organic carbon (pods and other tasty morsels the corals can capture and eat), while dinos prefer high levels of labile DOC (which they make), high levels of recalcitrant organic carbon (which they need for their bacteria farms), and high levels of particulate organic carbon (which in this case would be the bacteria and other organisms of the dinoflagellate holobiont, stuff the dinos can eat or kill with their toxins and feed to their bacteria, and I guess also the dinos themselves).

I would go so far as to speculate that the difference between a healthy reef dominated by corals (or a broken reef dominated by algae) and one dominated by benthic dinos could come down to a phase shift driven by copiotrophy... As noted earlier, eutrophy tends to favor flavobacteria from among the Bacteroidetes, possibly because they're geared to consume the remains of green algae. But ostis are partnered with different bacteria that need different conditions -- not the decaying remains of algae, but an environment enriched in the degraded, recalcitrant remains of animal proteins. Or as we hobbyists would put it, detritus.

It's tempting to connect this to the Mesozoic Marine Revolution, an extended arms race between predators and prey that recent research shows began in the early Triassic, after the oceans recovered from the devastating end Permian mass extinction that wiped out >96% of known marine species and >70% of terrestrial species 252 million years ago. The MMR doomed the surviving benthic fauna of the Paleozoic, which was characterized by relatively dense populations of sessile, armored creatures, as creatures able to crack them open evolved after the end Permian extinction, eventually driving the survivors underground or forcing them to evolve mobility. The first dino cysts appear in the fossil record 228 million years ago, and here are a couple more fun science facts: the ancestors of symbiodinium dinos were among the earliest lineages to emerge, and corals experienced a burst of speciation in the Triassic that followed the evolution of dinos. Good bet at least some of those early dinos were mixotrophic, and the team-up with corals happened pretty quickly (...most likely, some corals already had photosynthetic endosymbiotes -- either cyano or algae -- that were poorly suited to the oligotrophic reef environment, so they would have been happy to switch over to them thar newfangled dinoflagellates). Certainly, dinos show up just as the first waves of New & Improved predators were consuming mass quantities of the immobile Paleozoic benthic fauna and pooping out their remains, and judging by where their fossilized cysts were found, dinos were on Triassic reefs during a time when the reef sands would plausibly have been enriched in old, degraded, recalcitrant animal proteins... That would explain their high quotas for trace metals.

Though on the other hand, so would evolving in a Canfield ocean following a mass extinction, as widespread euxinia would raise the availability of trace nutrients with low solubility in oxygenated seawater (most notably iron, but also zinc and copper) and a Canfield ocean is dominated by bacteria and thus would seem to be the ideal environment for a marine eukaryote to evolve that specializes in eating bacteria and stealing their DNA. But the cyano/green algae duopoly held up through a billion-plus years' worth of euxinic episodes without dinos popping up... What changed? If primary producers preserve in their nutritional habits evidence of the ecological circumstances in which they first evolved, then it's reasonable to suppose that a primary producer adapted to thrive not in eutrophic but copiotrophic conditions evolved during a period characterized by copiotrophy, so as I said, it's hard to resist connecting the emergence of dinos to the Mesozoic Marine Revolution.

But either scenario would posit an incomplete food web that eases top-down grazing pressure on primary producers, allowing the drawdown of macronutrients until N and P are zeroed out, and reduces the efficiency of the CUC, resulting in the increased availability of organic C pumping up the bacteria population. Or looked at another way: the conditions that seem to open the door to a dino bloom in our fish tanks. And once toxic dinoflagellates break out into a bloom, dino-friendly bacteria that thrive in copiotrophic conditions help them kill stuff, which of course makes conditions even more copiotrophic...

Just as coral-friendly bacteria reinforce conditions amenable to coral and algae-friendly bacteria help algae take over reefs, dino-friendly bacteria want to remake the ecosystem to suit dinos. Quiet_Ivy's tank and others may be pointing us at O. ovata's endgame: a collapsed "hypercopiotrophic" food web dominated by dinos and their bacteria farms, recreating the landscape of death that the first dinos evolved to exploit.

It seems that benthic dinos and corals have diametrically opposed philosophies about how to make the most of mixotrophy in oligotrophic reef environments. Dinos are selfish and want it all, while corals are into enlightened self-interest. Rather than take a bigger slice of the pie, corals make the pie bigger.

Or so it looks to me, at any rate, so I took my cue from corals and wrote up this massive wall of text. I'm no scientist, nor do I have any education in microbiology -- for that matter, the last biology class I took was freshman year of high school -- meaning that's about as far as I can take this on my own. Time to get some more minds in on this to look for what I overlooked, to identify connections to what we see in our tanks, and to try to make the pie bigger.

In closing, gaze not into the dino bloom, for the dinos gaze also into you!


--

References

The Coral Probiotic Hypothesis
https://www.researchgate.net/profile...2d9b000000.pdf

Bacteria Associated with Toxic Clonal Cultures of the Dinoflagellate Ostreopsis lenticularis
https://www.researchgate.net/profile...8c1361fe17.pdf

Ecology of marine Bacteroidetes: a comparative genomics approach
https://www.researchgate.net/profile...ba13000000.pdf

Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum
http://femsec.oxfordjournals.org/con...3/345.full.pdf

The effect of quorum-sensing blockers on the formation of marine microbial communities and larval attachment
https://www.researchgate.net/profile...c75a000000.pdf

Ostreopsis cf. ovata (Dinophyta) bloom in an equatorial island of the Atlantic Ocean
https://www.researchgate.net/profile...698be33058.pdf

Regulation of microbial populations by coral surface mucus and mucus-associated bacteria
https://www.researchgate.net/profile...e80b000000.pdf

Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica
http://onlinelibrary.wiley.com/doi/1...9.01490.x/full

Bacteria Associated with Toxic Clonal Cultures of the Dinoflagellate Ostreopsis lenticularis
https://www.researchgate.net/profile...8c1361fe17.pdf

Production of Antibacterial Compounds and Biofilm Formation by Roseobacter Species Are Influenced by Culture Conditions
http://aem.asm.org/content/73/2/442.full

Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides
https://www.researchgate.net/profile...e6a6000000.pdf

Microbial community composition of black band disease on the coral host Siderastrea siderea from three regions of the wider Caribbean
https://www.researchgate.net/profile...d5a6000000.pdf

Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea
https://www.researchgate.net/profile...5d63000000.pdf

Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico
http://aslo.org/lo/toc/vol_49/issue_2/0597.pdf

Algicidial Bacteria from fish culture areas in Bolinao, Pangasinan, Northern Philippines
http://www.journals.uplb.edu.ph/inde...wnload/922/846

Organic matter release by Red Sea coral reef organisms - potential effects on microbial activity and in situ O2 availability
https://www.researchgate.net/profile...fd262781e3.pdf

Induction of Larval Settlement in the Reef Coral Porites astreoides by a Cultivated Marine Roseobacter Strain
http://www.biolbull.org/content/228/2/98.full.pdf

Unseen players shape benthic competition on coral reefs
https://www.researchgate.net/profile...b61f000000.pdf

Advanced Aquarist feature article Total Organic Carbon (TOC) and the Reef Aquarium: an Initial Survey, Part I
http://www.advancedaquarist.com/2008/8/aafeature3

Influence of coral and algal exudates on microbially mediated reef metabolism
http://www.ncbi.nlm.nih.gov/pmc/arti...erj-01-108.pdf

abstract of Microbial photosynthesis in coral reef sediments (Heron Reef, Australia)
http://adsabs.harvard.edu/abs/2008ECSS...76..876W

Sponge waste that fuels marine oligotrophic food webs: a re-assessment of its origin and nature
http://onlinelibrary.wiley.com/doi/1...aec.12256/full

Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)
http://broker.edina.ac.uk/294215/1/PMC3934968.pdf

Endoscopic exploration of Red Sea coral reefs reveals dense populations of cavity-dwelling sponges
see page 17 of Feeding ecology of coral reef sponges
https://www.deutsche-digitale-biblio...YIY/full/1.pdf

The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level
https://www.researchgate.net/profile...6ee2000000.pdf

Toward a stoichiometric framework for evolutionary biology
http://preston.kbs.msu.edu/reprints/...0al%202005.pdf

Health of Coral Reefs: Measuring Benthic Indicator Groups and Calculating Tipping Points
http://archive.rubicon-foundation.or...pdf?sequence=1


--


Recommended reading

Black reefs: iron-induced phase shifts on coral reefs
https://www.researchgate.net/profile...6444000000.pdf

Cataloguing Diseases and Pests in Captive Corals
http://scholarcommons.usf.edu/cgi/vi...ve%20Corals%22

Communities of coral reef cavities in Jordan, Gulf of Aqaba
see page 40 of Feeding ecology of coral reef sponges
https://www.deutsche-digitale-biblio...YIY/full/1.pdf

Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases
http://royalsocietypublishing.org/co...22328.full.pdf

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
http://www.nature.com/ismej/journal/...mej201539a.pdf

Coral Disease, Environmental Drivers, and the Balance Between Coral and Microbial Associates
http://researchonline.jcu.edu.au/270...et_al_2007.pdf

Coral mucus-associated bacterial communities from natural and aquarium environments
http://onlinelibrary.wiley.com/doi/1...7.00921.x/full

Coral Reef Bacterial Communities
https://www.researchgate.net/profile...6595000000.pdf

Herbivory, Nutrients, Stochastic Events, and Relative Dominances of Benthic Indicator Groups on Coral Reefs: A Review and Recommendations
http://www.littlersworks.net/reprints/Littler2009c.pdf

How Microbial Community Composition Regulates Coral Disease Development
http://data.nodc.noaa.gov/coris/libr...al_disease.pdf

Mass Mortality of Porites Corals on Northern Persian Gulf Reefs due to Sediment-Microbial Interactions
https://www.researchgate.net/profile...63d4000000.pdf

Master recyclers: features and functions of bacteria associated with phytoplankton blooms
https://www.researchgate.net/profile...6cbf760d7d.pdf

Nutritional ecology of nominally herbivorous fishes on coral reefs
http://researchonline.jcu.edu.au/683...et_al_2005.pdf

The Role of Microorganisms in Coral Health, Disease, and Evolution
https://www.researchgate.net/profile...1872000000.pdf

Viruses of reef-building scleractinian corals
https://www.researchgate.net/profile...0c82000000.pdf

What we can learn from sushi: a review on seaweed–bacterial associations
https://www.researchgate.net/profile...9c8c000000.pdf

CONTINUED...


34cygni is offline   Reply With Quote
Old 01/04/2016, 09:23 AM   #2517
34cygni
Registered Member
 
Join Date: Mar 2013
Posts: 59
And some more for the hardcore...

Algae as an important environment for bacteria - phylogenetic relationships among new bacterial species isolated from algae
https://www.researchgate.net/profile...a0a076bb89.pdf

Aquaculture application and ecophysiology of marine bacteria from the Roseobacter clade
http://orbit.dtu.dk/fedora/objects/o...3f094d/content

Beyond carbon and nitrogen: how the microbial energy economy couples elemental cycles in diverse ecosystems
https://www.researchgate.net/profile...163d000000.pdf

The boring microflora in modern coral reef ecosystems: a review of its roles
https://www.researchgate.net/profile...f841000000.pdf

Chemotaxis by natural populations of coral reef bacteria
http://stockerlab.ethz.ch/wp-content..._ISME_2015.pdf

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur
http://citeseerx.ist.psu.edu/viewdoc...=rep1&type=pdf

Coral Mucus: The Properties of Its Constituent Mucins
https://www.researchgate.net/profile...bdb9016865.pdf

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts
https://www.researchgate.net/profile...0ddf000000.pdf

Degradation and mineralization of coral mucus in reef environments
https://www.researchgate.net/profile...dae8000000.pdf

Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem
https://www.researchgate.net/profile...e7ee000000.pdf

Diverse communities of active Bacteria and Archaea along oxygen gradients in coral reef sediments
http://www.soest.hawaii.edu/GG/FACUL.../rusch2008.pdf

Diversity and Abundance of the Bacterial Community of the Red Macroalga Porphyraumbilicalis: Did Bacterial Farmers Produce Macroalgae?
http://www.ncbi.nlm.nih.gov/pmc/arti...ne.0058269.pdf

The driving forces of porewater and groundwater flow in permeable coastal sediments: A review
https://www.researchgate.net/profile...8a7491b336.pdf

Evidence for a persistent microbial seed bank throughout the global ocean
https://www.researchgate.net/profile...036e000000.pdf

The genomic basis of trophic strategy in marine bacteria
http://www.pnas.org/content/106/37/15527.full.pdf

Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways
https://www.researchgate.net/profile...968f000000.pdf

Interactions between herbivorous fish guilds and their influence on algal succession on a coastal coral reef
http://reefresilience.org/pdf/Ceccarelli_etal_2011.pdf

Microbial Structuring of Marine Ecosystems
https://www.researchgate.net/profile...a78d000000.pdf

Mucus trap in coral reefs: formation and temporal evolution of particle aggregates caused by coral mucus
https://www.researchgate.net/profile...cc29000000.pdf

The nature and taxonomic composition of coral symbiomes as drivers of performance limits in scleractinian corals
https://www.researchgate.net/profile...c2dc000000.pdf

New directions in coral reef microbial ecology
https://www.researchgate.net/profile...bee98824fd.pdf

Roseobacticides: Small Molecule Modulators of an Algal-Bacterial Symbiosis
http://pubs.acs.org/doi/pdf/10.1021/ja207172s

The second skin: ecological role of epibiotic biofilms on marine organisms
https://www.researchgate.net/profile...20bc000000.pdf

Sinkhole-like structures as bioproductivity hotspots in the Abrolhos Bank
https://www.researchgate.net/profile...6245000000.pdf

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom
https://www.researchgate.net/profile...1c6a000000.pdf

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis
https://www.researchgate.net/profile...28ad000000.pdf

Viriobenthos in freshwater and marine sediments: a review
https://www.researchgate.net/profile...8b7a000000.pdf

Viruses manipulate the marine environment
https://www.researchgate.net/profile...6410000000.pdf


--

Shout out to all the scientists who posted PDFs of their work on researchgate.net and other open access, non-paywall sites where I could read them after Google Scholar found them for me -- THANK YOU!!!

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Old 01/04/2016, 09:42 AM   #2518
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Thank you, 34cygni, for typing all that out. The biggest thing I got out of your posts is that "Thinking about that led me to wonder if green phyto might be uniquely hostile towards dinos, as dinoflagellates horned in on a cozy duopoly: green algae and cyano basically ran the oceans for about a billion-and-a-quarter years before dinos evolved. Green algae outcompetes cyano for P at high N levels; cyano outcompetes green algae for N at high P levels. This was so effective at scouring nutrients out of NSW that dinos didn't even try to buck the system, but instead went with a radical, outside-the-box solution: heterotrophy. And because dinos were the first of the three main primary producers of the modern oceans to evolve, there was nothing to distract green algae from looking for ways to beat them down."

It seems that the "magic bullet" might actually be just dosing live phyto, in particular, nannochloris? As we've never actually seen any evidence that copepods predate on dinos, we've just assumed dosing phyto promotes zooplankton which predate on dino.


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Old 01/04/2016, 10:20 AM   #2519
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I read it all and gathered the same.


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Old 01/04/2016, 11:24 AM   #2520
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Dinoflagellates.

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Originally Posted by PorkchopExpress View Post

It seems that the "magic bullet" might actually be just dosing live phyto, in particular, nannochloris? As we've never actually seen any evidence that copepods predate on dinos, we've just assumed dosing phyto promotes zooplankton which predate on dino.

I did that along with a few other things. Day #4 with no trace of Dino's under the microscope


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I read it all and gathered the same.

I read it all twice and I agree


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Old 01/04/2016, 12:00 PM   #2521
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I did that along with a few other things. Day #4 with no trace of Dino's under the microscope





I read it all twice and I agree
Pretty interesting, Did you notice any growth of other types of algae?


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Old 01/04/2016, 02:04 PM   #2522
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Pretty interesting, Did you notice any growth of other types of algae?
Not yet. Hoping to see some type of green algae soon. Remembering PaulB's comments about how some green/hair algae is a sign of a healthy tank.

Might be a coincident but clearing my DT of algae was definitely a prelude to dinos.


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Old 01/04/2016, 05:53 PM   #2523
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Originally Posted by seamonster124 View Post

Might be a coincident but clearing my DT of algae was definitely a prelude to dinos.
Don't think its a coincidence. Immediately after I got rid of a pretty significant hair algae problem in my DT, dinos showed up for the first time and exploded quickly.

I posted in this thread back before Christmas, and started a 3 day black out as my first step in getting rid of these dinos. At the same time, I added a couple lbs of LR from my LFS, some pods, quit doing water changes, and began dosing phytoplankton. Christmas morning, I ended the blackout, and the tank looked amazing. Almost no dinos to be seen, but there was still a little bit remaining. Over the next few days the dinos slowly started to regain ground, but I kept doing what I was doing. Continued to add phyto and pods from a couple different sources. Not once have I ever actually siphoned dinos out, but I have been considering it.

But, as I said, the dinos started to regain ground and I kept sticking with my plan. Over the past 2 days, I have actually noticed the dinos thinning out and receeding a little bit. I'm hoping this continues.


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Old 01/04/2016, 06:16 PM   #2524
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Removing algae without reducing nutrient input will leave room for other organisms to grow, so I'm not all that surprised that in some cases dinoflagellates bloom.


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Old 01/04/2016, 08:28 PM   #2525
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It's a great story but a number of links are based on some pretty wild assumptions. I don't know where to take it except to a marine microbiologist to support or refute the interesting connections here.

The question is - what experiment can we run to see if this is the right link? The next question is - what do we need to do more of to support the coral-friendly bacteria if they are the heroes we've been waiting for?

Carbon dosing is used by a lot of reef keepers but only a few develop dinos. Why don't they all develop dino plagues if those bacteria are dino allies? Is it a function of their skimming efficiency? The more mucus that can be extracted from the water, the better?

I skimmed very heavily and used UV and it worked - with the addition of phyto and pods. Why? Was my UV killing the bacteria floating with the dinos vs. the bacteria living in the coral mucus at night? Was my skimming pulling it out?

lots of interesting ideas and questions. we need some empirical detective work to prove/disprove the assumptions.


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