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Project Progress

Projects continue to revolve around the development and use of ribosomal ribonucleic acid (rRNA) based molecular methods to survey and study the microbial constituents of ecosystems in extreme environments without the requirement for cultivation of the organisms. This cultivation-independent approach to ecosystems analysis is essential because most microbes, >99%, cannot be cultured using standard techniques. With the molecular methods, rRNA genes are cloned directly from environmental DNA, and then sequenced to gain a phylogenetic snapshot of the organisms represented by the cloned genes. Some properties of organisms can be inferred from the phylogenetic results, and the sequences can be used to design hybridization probes to visualize organisms and their interactions in the environment. NAI sponsored studies include:

• Antarctic and Colorado endolithic communities. Primary productivity in rocks occurs through the action of endolithic microbial communities (photosynthesis-driven communities in the outer few cm of any rock surface exposed to light). These communities so far have received only limited study, and only with classic microscopy and culture techniques. Ongoing rRNA gene analyses of two selected communities from Antarctica (Collaboration with Imre Friedman) and four rock types from Colorado have revealed many novel kinds of organisms, some closely related to described organisms but others very different. Although previously considered dominated by cyanobacteria, an abundance of chloroplast sequences has been detected. The nature of the eucaryal component expected is not yet known. Remarkably, an abundance of representatives of the Thermus/Deinococcus division of Bacteria has been detected that were previously unknown, but are related to the “radiation resistant” deinococci. These new organisms also may predictably be similarly robust; the “radiation resistant” property of the deinococci is now thought to be protection against dessication/oxidative damage.
• Yellowstone high-temperature settings: This laboratory has for many years studied thermophilic ecosystems at Yellowstone and elsewhere. Current activities continue to explore the makeup of properties of communities driven by hydrogen-metabolism, probably the dominant form of primary productivity in high-temperature settings anywhere. Immediate goals include the detailed mapping of recently recognized, (probably) hydrogen-supported stromatolite-like structures in Yellowstone’s Obsidian Pool.
• Anaerobic environmental eucaryotes. We have continued an rRNA-based survey of eucaryal phylotypes in anaerobic settings, for instance, anaerobic marine and freshwater sediments. Recent results have identified a wealth of novel eucaryotic microbial diversity, including eight (!) novel kingdom-level clades, some among the most deeply divergent of eucaryal rRNA sequences. Current efforts focus on hypersaline ecosystems, mainly Guerrero Negro.
• We have begun extensive analysis of the microbial composition of Guerrero Negro hypersaline mats, in concert with geochemical and other biological studies of the NAI Ecogenomics group. Particularly noteworthy at this stage is the finding, based on rRNA gene abundance, that so-called Green Nonsulfur Bacteria, not cyanoacteria, are the dominant species. This poses many hypotheses and new questions.
  

Overall, we are making excellent progress and this work is conspicuous.