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Project Progress

Molecular analysis of microbial ecosystems in extreme environments (dm)

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%,can not 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. Studies relevant to NAI 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, with classic microscopy and culture techniques. Ongoing rRNA gene analyses of two selected communities from Antarctica and two in 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 toward dessication/oxidative damage.

- Yellowstone high-temperature settings: 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 settings anywhere.

- 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.

- Studies of hypersaline microbial mats in concert with other NAI representatives began with an expedition to Guerrero Negro.