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

Originally Posted by Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico
Members of the alpha-proteobacteria dominated DMSP assimilation, accounting for 3540% of bacteria assimilating DMSP. Cytophaga-like bacteria and gamma-proteobacteria each accounted for 1530% of DMSP-assimilating cells. The alpha-proteobacteria accounted for a greater fraction of the DMSP-assimilating community than expected based on their overall abundance, whereas Cytophaga-like bacteria were typically underrepresented in the DMSP-assimilating community. Members of the Roseobacter clade assimilated more DMSP on a per-cell basis than any other group, but they did not account for most of the DMSP assimilation, nor were they always present even when DMSP turnover was high. These results indicate that the biogeochemical flux of dissolved DMSP is mediated by a large and diverse group of heterotrophic bacteria. ...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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