Microbial community analysis with an eye toward synthesis

Anthony Yannarell

Key Participants: Patrick Schloss, Fred Rainey, James T. Hollibaugh, John Hobbie

ABSTRACT:

This workshop was organized around the theme of microbial community ecology, as practiced at the various LTER sites. The workshop goals were to get people to start examining how microbial studies are currently being conducted and to facilitate dialogue about future approaches to microbial ecology that could encourage synthesis both within the field and between other sub-disciplines of ecology. Four speakers were invited to give short talks dealing with several different approaches to microbial ecology. Following the talks, the participants organized themselves into smaller groups, which convened to talk about the key synthetic questions in microbial ecology and the methods that could be appropriately applied to answering those questions. The final twenty minutes of the session were reserved for summaries from each group and for general discussion.

There were about 30 workshop participants in attendance.

SESSION SUMMARY: SPEAKERS

Anthony Yannarell briefly introduced the theme of the session and outlined the session structure.

Patrick Schloss gave a talk calling for increased collaborative efforts and for a concerted attempt to link microbial community composition (i.e. the microbial “black box”) to macro-ecological research. He outlined several of the major difficulties facing microbial community studies, including: the difficulty of defining operational taxonomic units; the difficulty of defining meaningful differences, on both a taxonomic and community level; and the problem of accumulating enough microbial sequences to complete an adequate community census.

Fred Rainey talked about logical methods of isolating bacterial strains and obtaining cultures of environmentally relevant species. He proposed that a careful consideration of the environment, based upon the sorts of data that LTER sites are particularly good at collecting, can help researchers identify likely targets for isolation. As an example of this, he presented information about his research group’s isolation from desert soils of several strains of Deinoccus, which had been targeted due to a priori knowledge of increased ultraviolet radiation resistance in some members of that clade. Also in this talk was an implicit call for the use of isolates from different sites to begin to investigate microbial biogeography.

James Hollibaugh spoke about the metagenomics approach to microbial ecology, which involves collecting data about community-wide functional genes from environmental samples. These genes represent the functional potential of the microbial community, and this approach represents an attempt to focus microbial community ecology on function instead of (or in addition to) community composition. Implicit in this approach is the question of how the metagenome of a community relates to species distributions. This talk also introduced the idea of an “LTER microbial SWAT team,” which would be a voluntary group of researchers who agree to utilize common methodology and to seek infrastructure assistance to address a common set of questions through cross-site research.

John Hobbie’s talk echoed some of the themes from earlier talks, including a call for cross-site research and work addressing both microbial biogeography and microbial processes. John expressed the idea that research in these areas would help move microbial ecology from a description-oriented discipline to a more synthetic one. In particular, he expressed the desire for more studies investigating microbial processes and their controls. Are process controls the same as those that control community composition? Is there a common set of controls of microbial processes among different sites, or are the controls site-specific?

SESSION SUMMARY: BREAK-OUT GROUPS

Following the talks, Anthony Yannarell asked the workshop participants to organize themselves into smaller discussion groups, and he charged the groups to discuss 1) the key synthetic questions in microbial ecology, and 2) some methods and approaches particularly suitable for addressing those questions. The participants organized themselves into three groups. Below are some of the highlights of their discussions, as presented by representatives of the groups when the session reconvened.

One group discussed the idea that cross-site synthetic questions can emerge from a consideration of both the similarities and differences between sites. As an example, the group pointed out that at many sites primary productivity is dominated by grasses, but at some sites these grasses are constantly submerged in water (e.g. wetlands, lake littoral zones), in some sites they are occasionally submerged (e.g. intertidal marshes), and in some sites they are never submerged (i.e. prairie). How do these features influence the composition and activity of microbes, and can generalizations emerge from their consideration?

One group talked about ideas of how evolution and change can influence microbial processes. Not only are communities changing their structure over time, but the organisms involved are also evolving. What is the pace of these two aspects of change? What patterns could be revealed through a cross-site study of evolutionary histories?

One group called for the development of a list of “quick and dirty” measurements that could be performed at many different sites to facilitate synthetic comparisons and questions. This discussion recalls the idea of the SWAT team suggested in one of the opening talks.

One group discussed issues of scale. It was pointed out that a gram of soil contains microbial populations on the order of magnitude of the global human population. What are the effects of very large-scale phenomena (e.g. global climate change) on these small-scale systems?

From discussions occurring in several different groups, two major ideas were suggested for potential synthetic work:

1) Microbial biogeography and dispersal vectors. Several groups discussed the idea of investigating microbes present in the air at a variety of LTER sites. This allows for questions related to microbial biogeography (global distributions vs. centers of endemism; island biogeography theory) and for a comparison of the importance of biological and abiotic vectors.

2) Common microbial processes: decomposition. All of the groups discussed the idea of looking at a common microbial process at different sites. It was proposed that decomposition is a good target process. Do all microbes have the ability to degrade common metabolites, or is decomposition necessarily the result of many different actors? Is decomposition rate controlled by a series of microbes, or are there a few dominant or rate-limiting species that control the process? It was suggested that the use of radioactive or istopic labels could be used to study the decomposition of recalcitrant compounds at a variety of sites.

These two research areas, along with the SWAT team idea discussed above, represent the most tangible intellectual products of this session. Each one is a potential kernel around which a collaborative, cross-site proposal can be written.

CONCLUDING REMARKS:

More than a third of the workshop participants, representing 9 different LTER sites, submitted their email addresses to receive news and updates from this session. They have each received a copy of this document. It is hoped that the ideas discussed above will continue to generate sufficient interest to spark one or more research proposals centered on the ideas discussed at this session.

Finally, as a workshop organizer, I recommend that the LTER office encourage this type of structure for future workshops at All Scientist Meetings. Several people have reported that they felt that they got the most out of sessions that included speakers and both small group and larger group discussions. The short talks are generally informative and interesting and help to provide a common ground for discussion. This is important, and it can happen even if the speakers do not directly address the larger goal of the session. For example, even though some of the speakers at our session did not directly tackle the idea of synthesis, the talks, by addressing approaches to microbial ecology, all provided a framework that allowed session participants to think about and evaluate current and proposed strategies for conducting microbial studies. This frame of mind contributed naturally to a discussion about synthetic questions and strategies. Furthermore, by providing both small (i.e. breakout groups) and large (i.e. questions following the talks and the concluding session-wide discussion) fora for discussion, sessions take advantage of two different but important dynamics: small groups tend to be hotbeds of idea generation, creativity, and brainstorming; large groups tend to be more conservative, evaluative, and critical. Both of these dynamics are important for the generation of “good” ideas.