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Project Progress

Projects revolve around the development and use of ribosomal RNA (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 rather than classic methods because most microbes, >99%, are not 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. Studies relevant to NAI include:

1. Antarctic endolithic communities (collaboration with Imre Friedmann, U. FL). Most primary productivity in Antarctica is due to endolithic microbial communities, photosynthesis-driven communities in the outer few cm of any rock surface exposed to light. These communities so far have only received limited study, only with classic microscopy and culture techniques. Ongoing rRNA gene analysis of two selected communities has 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 toward dessication/oxidative damage.

2. Yellowstone high-temperature settings (some collaboration with Sherry Cady, U. Portland). The 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 settingsanywhere. A novel, field hydrogen detector will be used during this year to survey hydrogen fluxes in selected Yellowstone hot springs. An array-based culture system has been devised that allows the study in culture of particular organisms (“phylotypes”) in mixed-community enrichment cultures. Fluorescence in situ hybridization, with probes based on rRNA gene sequences, is used to detect specific phylotypes in complex enrichment cultures.

3. Anaerobic environmental eucaryotes. We have been conducting 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 seven (!) novel kingdom-level clades, some among the most deeply divergent of eucaryal rRNA sequences. Attempts to learn more about those organisms represented by the sequences are underway.

4. Application for NAI augmentation support for a study of hypersaline microbial communities has been made.

The PI participates in numerous astrobiology-related public and institutional activities, for instance service on the new Space Studies Board committee, Committee on the Origin and Evolution of Life; and organizing (with others) the recent SSB/NRC workshop report, “Size Limits of Very Small Microorganisms.”