Biology
Disciplinary Groups: Biology
Moderator: Pete Girguis; Co-moderator: Costa Vetriani
Participants (list your name here):
• Tim Shank
• Breea Govenar
• Stefan Sievert
• Costa Vetriani
• Liz Podowski
• anna-louise reysenbach
• gilbert flores
• kristen myers
Discussion topics (list ideas and suggestions here):
Microbial interactions with hydrothermal fluids:
Fluid chemistry – water/rock interactions
Fluid flux – circulation – petrology
Fluid temperature - circulation
Substrate availability and type
Availability of redox couples for energy conservation
Role of trace elements - microbial metabolism
Nature and extent of subseafloor biosphere
Microbial interactions with macrofauna:
Endosymbiotic and episymbiotic associations
Detoxification – enzymatic – efflux pumps - exopolysaccharide
Role of biofilms – primary and secondary colonizers
Biofilms and larval recruitment
Trophic structure, interactions
Macrofauna – microbe – fluid interactions:
Larval dispersal
Substrate availability and type
Sessile vs. mobile
Symbiotic or free feeding
Symbionts – vertical vs. horizontal transmission
Physiological adaptations – temperature, chemistry
Metal homeostasis - detoxification – metallothioneins
Competition over space and time
Comparison among the three ISS
What we know vs. what we do not know
Identification of datasets ready for integration
Summary of Discussion
Define key processes to focus on (across disciplines)
Rates of microbial primary productivity
• Some existing (empirical) data
• More empirical data may be necessary for better models
• E.g. fluid flux as it relates to nutrient delivery
• E.g. constraints on trace elements (enzyme function, toxicity)
• However, with existing data (chem, temp, lab microbio), models can provide insight / constraints
How microbial activity influences microbial and metazoan ecology
• Alteration of fluid chemistry (e.g. detoxification)
• Conditioning of substrates (e.g. larval settlement)
• Influence on both microbial and metazoan community succession
Define key processes to focus on (continued):
• Where does most of the biomass production occur?
• Subseafloor vs. the seafloor vs. the water column
• We know a bit about production at the seafloor, but little about subsurface productivity
• Some plume work, but not well linked to subsurface processes
• How do each of these pools influence geochemistry, macrofaunal community?
A key approach to addressing (some of) these questions
Simplify the system, by focusing on model microbes as proxies
• Keystone “Species” as proxies
• Studying better constrained systems
• EPR Post eruption basalt communities
Incorporate the existing carbon and nitrogen isotope data
• Metazoans, microbes
Comparison among the three ISS
Simplified models, “compare apples to apples”
Identification of datasets ready for integration
• Open for discussion
Is biological sampling adequate?
• Issues of scale are problematic and need to be considered
Notes from R2K meeting, integration and synthesis, St Louis MO Oct 2009
Biology interdisciplinary working group
Costa Vetriani and Pete Girguis, co-moderators - Transcript kindly provided by Pete Girguis
This is a transcript of our conversation, showing the comments made by the participants. We have demarcated points in the conversation where the topic changed. We have also included a summary description of each topic (in parentheses at the beginning of each section) to make it easier to browse these notes.
(Comparing microbial ecology to macrofaunal ecology)
Tim Shank: can you compare the ecology of microbial communities form different sites? Can you do this? Is it even possible?
AL Reysenbach: Yes, but there are issues with sampling, analyses. There’s no standard protocol which makes comparisions difficult. You can currently generate lists of “who’s there”, via phylogenetic techniques.
Jim Holden: There are software available that enable such comparisons, analogous to what you see in macrofaunal ecology.
Tim: So, can you make maps of distributions of organisms, like with animals.
Costa: Yes, but it depends on the level of resolution of the map, that is you may not be able to do species, but you can do major guilds.
Pete: You can, but there are problems with these analyses since there are many bugs about which we know very little, and who may be facultative, and there processes are largely unknown.
Tim: Do you know much about their function? How far along do you think we are?
Costa: We know something about function, but it’s pretty limited.
Jim Holden: We are lacking rates and constraints on processes in situ. We know some key pathways quite well, but allying these pathways to rates and proceses? It’s tough.
Chuck: You are asking two separate questions though, namely can you study the ecology of microbes in the way you do for animals, vs. do you understand their physiology.
AL Reysenbach: It would be nice to identify some innovative questions that maybe the macro folks have, that maybe we can see if the micro folks can do something similar.
Tim Shank: Well, a question might be whether the distribution of the macrofauna is controlled by the microbes? What is the functional role of microbes in controlling the distribution of animals, including:
- as a food source
- via the alteration of fluid chemistry by microbes, that governs the ecology and life history of animals
Costa: This is a KEY QUESTION.
Chuck and Tim: also, what’s the production of the free living bacteria? What are the rates of primary productivity by free living bacteria? THIS IS A KEY LINK! That is what fuels the ecosystem.
Pete: that’s true. So do we know enough about the density and distribution of microbes to place such a rate measurement in context? In other words, if we measure rates of processes, can we ally those rates to particular bugs?
Costa: Maybe for some.
Stephan: The problem is that vent primary production occurs at a variety of conditions. Such studies are relatively easy in the water column. At vents, on surfaces, this is more challenging. What are representative conditions at vents? What is productivity at 4 C? 100 C?
Chuck: Given the variables, is this best suited for modeling? You may not be able to empirically measure all of these things, and this is where models are very powerful…hey can give you insights into processes that are difficult to constrain empirically.
Jim: FYI, we collected high temp fluids and diffuse fluids from the same structure, and normalized to silicate, to get a handle on fluxes. This will help constrain (empirically) some of these relationships. However, we know you need a Z component to get flux, but at least this begins to constrain the degree to which MICROBES alter fluids.
Chuck Fisher: In the beginning of vent research, they used to say that the bulk of the primary production is chemautotrophic sulfide-based carbon fixation. Does this hold up? Can we say that this is the majority of productivity?
Stephan: I don’t think so. There are things like hydrogen oxidation, methanogenesis, etc that are not sulfide based.
Pete: I think this is true for diffuse flow as the energetics are very good…
Chuck Fisher: That’s true, but can we use a model constrain the relative contribution of DIFFERENT functional guilds?
AL Reysenbach: You can use what you know about these different functional groups to theoretically predict the contribution of each of these.
Stephan: Everett’s done this to some degree…
Everett: Sulfide is dominant, because the amount of energy from this process(es) is higher at the oxic-anoxic interface. At higher temps, there is no oxygen, and this may not hold true.
AL Reysenbach: That’s what Chuck was getting at….you can incorporate gradients, endproducts, interactions between different microbial groups…you could in theory figure that out, determining what kind of production is most favored at the different conditions.
Breea: So what are the limiting factors for microbes at vents? When it comes to trying to box that in, what limits productivity? When it comes to vents, you have inorganic carbon that available but it’s a function of pH, etc. So, which env. Factors are really constraining ?
(How do we model primary productivity?)
Christof: The question I have as a modeler, is that we need to establish kinetic models to deal with these issues. You need to parameterize these models. Do you have the data to actually parameterize the model? Namely, do these data exist?
Costa: so one goal of this meeting is to identify gaps in experimental data to “feed” the model.
Pete: Let’s talk about what we know and what we don’t know. Lets talk about this for a while.
Costa: Fluid flux. We need to know fluid flux.
Pete: I don’t think we know fluid flux.
Chuck: it’s been somewhat measured in diffuse flow and focused flow. There are some data that can be used. I don’t think we have no idea.
Pete: Are we to suggest to NSF that we need to measure fluid flux in the field still?
“Many people”: yes.
Everett: Well, just constrain fluid flux, as geochemists do. If we don’t have flux for each system, then we simply extrapolate it from a plot showing maximum and minimum rates.
Chuck: Flux is only important -to a degree- if a nutrient is limited by fluid flux, then its important. If not, then it’s not important to productivity until the flow is so high (or hot, etc) it perturbs biology.
Jim: This is still important in terms of mass balance, right?
Chuck: True, but that’s a different question.
Everett: However, if you know the composition and flux, then you can constrain chemical flux.
Breea: That’s why I think fluid flux is important, because like the plankton paradox it could constrain productivity with trace nutrients.
AL Reysenbach: Also biological interactions (syntrophy) and microbial competition are important.
Costa: Is the role of trace elements important in affecting microbial activity? Is this important?
EVERETT: The answer is yes, it’s yes! This is really important for productivity. You need trace elements for enzymes to function, etc.
Peter: Trace metals can also be toxic.
NSF program manager: How much work as been done on laboratory isolates? Do we have rates of production from lab work?
ALR: Good question, Jim does a fair bit of looking at rates, but it’s very limited number of studies. Many of them you can’t grow in the lab.
NSF PM: Yes, but have you taken your lab measurements and applied those data to the field?
Stephan: Yes, lab systems are very informative, but in the lab what’s important by thermodynamic models you can find out how efficiently microbes convert energy to biomass, and that’s useful to understand the fundamentals of microbial physiology, but to some extent you can use this to put some constraints. This could be important in constraining the efficiency of these processes for models.
Jim Holden: What you measure in the lab and in the field is going to be hugely different, but these are constraints.
(The question of scale)
Comment: The question is one of scale. There are disconnects in terms of the scale…what’s appropriate the microbial scale may not be so appropriate at the geochemical scale. The question of scale is a BIG ONE.
Liz Podowski: If you were to map microbes, what scale would you map at?
ALR: Many different scales. Think of them as patterns.
Chuck: What scale do you need to understand production? mm? microns?
Liz: There are two different scales, right? Vertical and horizontal?
Breea: Yes. So, given that, do we have a representative sample for chimney vs. diffuse flow? From top to bottom of a sulfide?
Tim Shank: But the scales are a function of sampling at time. You grab rocks, you slurp…does biological sampling as it stands capture processes at different scales? Probably not.
ALR: There are two studies in microbial ecology (Jennifer Hughes)…they looked at scale and its impact on microbes and its not clear that we know what we are doing. So, taking a chimney we don’t really know what’s going on and at what scale…it’s a problem, a huge problem.
Costa: going back to the mapping, we can say that we have looked at enough biofilms on basalt or colonizers that we can make some inferences about the communities found at 25-40 C (with a certain sulfide concentration), can we make predictions? I think we can. A chimney may be a little bit tougher, as it has to do with petrology, diffusion and advection, etc. In sum, I think we have some data we can work with.
Pete: I think Costa is correct, we have some systems that are reasonably well constrained, so how can we work wit these systems to think about the relationship between microbes and macrofauna?
Erin: At Lau, for example, we see that the symbioses are distributed based on the availability of sulfide. At Mariner, the iron and manganese scrubs out the sulfide, so it’s not available for the symbioses. There is a clear linkage between microbial activity (maybe lack of activity) and macrofaunal distribution (no symbionts there, BUT THERE ARE other grazers)
Breea: Do microbiologists understand the trophic structure and how that might influence the macrofauna?
Dan Fornari: Whether the microbial sampling is sufficient, given the somewhat disparate approaches in sampling, also at different scales? Is this going to be a problem? Do we need to do more wet bench work to address this issue?
AL Reysenbach: We do not see changes at the bulk level in diversity, but we see changes in the “branches and bushes” of a phylogenetic tree. This may not be necessary to capture in a model.
Costa: Going back to the EPR, we have been sampling over time during the past three to four years, and we’ve been looking at fluids over time, sulfides over time….so we can process the entire time series. We have those samples, though some financial support to analyze these might be in order.
Dan: One of the points that has been brought to my attention is that many of you have collected data for the primary proposal ideas and you have these samples sitting around….and there’s opportunities to revisit these samples to look at more integrative questions USING these samples in hand. The question is …is this a supplement (providing a little bit of money to START new lab analyses, or should it be a new proposal).
NSF PM: Many proposals came in asking for money for analyses, but there’s NO $$ for actual integration and synthesis. It’s frustrating to see this, requests for support that do not directly address integration and synthesis.
(Can we produce a model that captures these relationships?)
Pete: Back to the subject, can we predict macrofaunal secondary productivity based on a set of geochemical conditions?
Chuck: Let’s look at this from a modeling perspective….we have the data in hand to do much of what we want to do using models, right?
Breea: That’s true, but there are some complexities that might warrant more in depth investigations. For example, the grazers might be a better proxy for understanding carbon cycling by the microbes.
Chuck: True, but bear in mind that 90-95% of the biomass is symbiont containing species.
Breea: Yeah, but the work at the EPR shows that when these primary producers die that heterotrophs colonize them, and these may reflect the composition of the microbes.
Pete: Do you all agree with Chuck, are the data there?
Chuck: In addition, are the data there for microbes?
Stephan: Another overarching question is WHERE does most of the biomass production occur, in the subseafloor vs. the surface vs. the water column? We know quite a bit about production AT the seafloor, but little about production in the subsurface.
Chuck: We have not well constrained the productivity subsurface.
Stephan: I would challenge that we don’t know if the bulk of the biomass is below or above the surface. This is still open.
Costa: It’s a big question…and Stephan is right. Snowblowers look like there’s LOTS of productivity subsurface.
ALR: Based on qPCR, you could quantify the standing stock of primary producers and better understand the linkage between microbes and macrofauna. This is a good start, maybe does not tell you flux but does tell you standing stock.
Costa: Can we simplify the model by focusing on a number of key species as proxies for the system? This makes it more tractable for modeling.
Everett: From the outside perspective, that seems very wise. The advent of high throughput phylogenies build “haystacks” which doesn’t always help the effort to understand the system as a whole, if you are interested in understanding energy and material flow through the system. Simplifying is good.
Chuck: How can we simplify? Start with grazers…they are constrained to areas below 50 C. That limits you to zones that are cohabitated by microbes and macrofauna. This is a good place to study “mantle to microbes” (paraphrased).
Everett: As long as you know that they are eating what was produced in situ.
Chuck: true, but we can rule out photosynthesis or surface productivity influencing these communities. That’s been well covered. No input.
Costa: you can produce bugs at higher temperatures that dust the surface, for example so they cannot be totally ignored.
Jim Holden: Also, alvinellids are a GREAT source of hyperthermophilic heterotrophs, so this is an example of how deep subsurface bugs might feed macrofauna.
Pete: True, but because they are hyperthermophilic does not mean they “came from” and “grew in” the subsurface.
Chuck: Also, there are animals that are symbiotic with methanotrophs, and if there are heterotrophs that eat methanotrophs, then this might be cool. This couples methane to productivity. It’s not all just sulfide-dependent carbon fixation.
(CLOSING THOUGHTS)
Chuck: It seems like one thing we are centering in on is that we are trying to get at the microbial link….what is the microbial biomass that’s important? It is diverse? Are they heterotrophs? Methanotrophs? Chemaoutotrophs? Can the microbiologists constrain these in terms of biomass, activity. What about their stable isotopes (like sulfur)? These can tell you a lot about the source of sulfur in these systems.
AL Reysenbach: Tracers are good idea, because microbes are facultative so that with tracers you may distinguish between heterotrophy and autotrophy. Also I like the idea of FOCUSING on keystone groups to reduce complexity, using them as proxies for the community productivity, to better constrain these phenomenon. You CAN THEN DO CROSS COMPARISIONS between these groups at different sites.
Chuck: you’re going to find out that the same functional groups are important in all sites:
Pete: You might be able to use these “common” groups as an index among the different ISSs, to tell you about what differs or is similar between these sites.
Stephan: carbon isotopes are of course useful as well.
Chuck: Note that there’s LOTS of good 13C and 15N exist for the major macrofauna, that can be tied into integration and synthesis.
Tim: So…Can you map microbes in space or in time? I heard that you really can’t compare…but now I heard that maybe we can.
Breea: So, what are integration products? We haven’t had a good review of macrofauna and microbes at vents in a LONG LONG time… Is that attractive to people or not? Do we want to have a product come out of these discussions?
Stephan: Someone should do this and bring the microbiologists from the different ISS together to talk.
Costa/Stephan/Pete: Perhaps we can have a microbiology-macrofaunal workshop to A) identify “data ready for integration” from all ISS , B) come up with some “Standard” data from each ISS For comparison (e.g. diversity assessments), C) and produce a review of microbiology at vents.