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01/03/2016, 10:09 PM
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#2501 | |
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Registered Member
Join Date: Sep 2014
Location: Chicago
Posts: 105
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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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01/03/2016, 10:16 PM
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#2502 | |
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Registered Member
Join Date: Sep 2014
Location: Chicago
Posts: 105
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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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01/03/2016, 10:20 PM
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#2503 | |
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Join Date: Aug 2014
Posts: 557
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01/03/2016, 10:23 PM
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#2504 | |
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Registered Member
Join Date: Sep 2014
Location: Chicago
Posts: 105
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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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01/03/2016, 10:32 PM
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#2505 |
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Registered Member
Join Date: May 2004
Location: Dallas, TX
Posts: 11,033
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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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Failure isn't an option It's a requirement. 660g 380inwall+280smp/surge S/L/Soft/Maxima/RBTA/Clown/Chromis/Anthias/Tang/Mandarin/Jawfish/Goby/Wrasse/D'back. DIY 12' Skimmer ActuatedSurge ConcreteScape |
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01/03/2016, 10:33 PM
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#2506 | |
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Registered Member
Join Date: May 2004
Location: Dallas, TX
Posts: 11,033
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__________________
Failure isn't an option It's a requirement. 660g 380inwall+280smp/surge S/L/Soft/Maxima/RBTA/Clown/Chromis/Anthias/Tang/Mandarin/Jawfish/Goby/Wrasse/D'back. DIY 12' Skimmer ActuatedSurge ConcreteScape |
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01/04/2016, 07:56 AM
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Registered Member
Join Date: Mar 2013
Posts: 59
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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:
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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:
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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:
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:
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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01/04/2016, 08:12 AM
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#2508 | |
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Registered Member
Join Date: Mar 2013
Posts: 59
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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:
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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01/04/2016, 08:31 AM
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#2509 | |||||
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Registered Member
Join Date: Mar 2013
Posts: 59
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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:
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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:
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:
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:
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01/04/2016, 08:45 AM
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#2510 | ||||||||||
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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:
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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:
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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:
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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:
So I went looking for them... Quote:
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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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01/04/2016, 09:01 AM
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#2511 | |||
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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...
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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:
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:
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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01/04/2016, 09:36 AM
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#2512 | |||||||
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Join Date: Mar 2013
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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.
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As noted, however, cytophaga in the wild has been associated with decaying phyto blooms and sick macro. And some species are considered algicidal... Quote:
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:
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:
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:
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01/04/2016, 09:37 AM
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#2513 |
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Location: United States
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Can You maybe paste that on a blog and post a link on the forum?
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01/04/2016, 09:46 AM
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#2514 | |||||
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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. Quote:
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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:
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01/04/2016, 10:06 AM
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#2515 | ||||||||||||
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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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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... Quote:
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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:
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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:
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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 |
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V e | | |
s | | large |
i ELEVATED| coralline | |
l NUTRIENT| | frondose |
i LEVELS | algae | |
e | | macroalgae |
n | | |
c |-------------------|------------------|
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01/04/2016, 10:19 AM
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#2516 | |||||
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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...
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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:
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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... |
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01/04/2016, 10:23 AM
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#2517 |
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Registered Member
Join Date: Mar 2013
Posts: 59
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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!!! FIN |
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01/04/2016, 10:42 AM
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#2518 |
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Location: Wrigleyville
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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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01/04/2016, 11:20 AM
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#2519 |
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I read it all and gathered the same.
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01/04/2016, 12:24 PM
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#2520 | ||
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Join Date: Jun 2015
Location: United States
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Dinoflagellates.
Quote:
I did that along with a few other things. Day #4 with no trace of Dino's under the microscope Quote:
I read it all twice and I agree
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01/04/2016, 01:00 PM
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#2521 | |
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Quote:
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01/04/2016, 03:04 PM
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#2522 | |
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Location: United States
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Quote:
Might be a coincident but clearing my DT of algae was definitely a prelude to dinos.
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01/04/2016, 06:53 PM
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#2523 | |
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Location: Westchester, NY
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Quote:
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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--Brian-- |
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01/04/2016, 07:16 PM
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#2524 |
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RC Mod
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Location: Mountain View, CA, USA
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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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01/04/2016, 09:28 PM
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#2525 |
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Join Date: May 2004
Location: Dallas, TX
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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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Failure isn't an option It's a requirement. 660g 380inwall+280smp/surge S/L/Soft/Maxima/RBTA/Clown/Chromis/Anthias/Tang/Mandarin/Jawfish/Goby/Wrasse/D'back. DIY 12' Skimmer ActuatedSurge ConcreteScape |
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