Diversity and Evolution of MicroOrganisms.

Woese's seminal work funded through NASA's original Exobiology program unveiled a Universal Tree of Life that included three primary lines of descent; the Archaea, Bacteria and Eukarya. The MBL Astrobiology team continues to use and develop new molecular methodologies that can more efficiently describe microbial evolution, microbial diversity and how these organisms function in extreme environments. This information will expand our definition of habitable conditions and may suggest new targets for developing life detection capabilities. We now seek greater resolution in studies of microbial population structures as well as information about their association with specific metabolic functions. For example, we have explored the phylogenetic and functional diversity of sulfate-reducing bacteria in the sediments of Guaymas Basin (Gulf of California). In this hydrothermal vent site, thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material. These hydrocarbons are a significant carbon source to the vent microbial communities, which includes diverse sulfate reducing bacteria.

Microorganisms and their reactions (sulfate reduction, methanogenesis, methane oxidation, sulfide oxidation) in the methane and sulfur cyles in the Guaymas Basin hydrothermal vents.

Using conserved primers, we polymerase chain reaction (PCR) amplified dissimilatory sulfate reductase genes, the key gene for sulfate reduction (dsrAB), and 16S ribosomal ribonucleic acid (rRNA) genes from the upper 4 cm of Guaymas sediment. Figure 3 is a phylogenetic analysis of the nearly full length dsr sequences. In this analysis the dsrAB sequences revealed a major clade that branched with dsr sequences of the genus Desulfobacter, acetate oxidizers of the family Desulfobacteriaceae within the delta Proteobacteria, and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Two other clones showed similarity to dsr genes of gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the toluene degrader Desulfobacula toluolica, while one was related to Desulforhabdus amnigena and Thermodesulforhabdus norvegica.

Phylogenetic tree based on the translated amino acid sequences of PCR-amplified dsr AB genes from sulfate reducing prokaryotes.

The two-pronged approach of using 16S rRNA and dsr clone library sequencing has resulted in a more detailed picture of the sulfate-reducing bacterial community at Guaymasthan each of these approaches alone. At Guaymas, the 16S rRNA and the dsrAB datasets indicate the significance of members of the Desulfobacteriaceae, most likely the genus Desulfobacterium, in the Guaymas sediment. The dsrAB dataset also demonstrated the presence of uncultured and unknown major clades of sulfate reducing prokaryotes in the Guaymas sediments that could not be identified by 16S rRNA sequencing.

We also seek to establish linkages between patterns of gene expression that underlie metabolic activity and the formation of biogeochemical gradients. To meet this objective, we must obtain information about global gene expression patterns and detailed information about microbial population structures. We have constructed a custom microarray to examine how the cyanobacterium Microcoleus chthonoplastes responds to changes in environmental conditions. The array contains 1090 unique sequences and it has provided information about changing gene expression patterns in response to diel cycling and salinity changes of Microcoleus cultures. High and low salt shocks induced quite distinct expression signatures; genes involved in metabolism, signal transduction, transportation of compounds across membranes, and other cellular processes appear to change their expression levels in response to this environmental stimulus. With knowledge about coordinate gene expression patterns associated with changing metabolic patterns, we will be able to faithfully model fluxes in microbial ecosystems and identify biomarkers for detecting and monitoring biological activity.