The genus Shewanella has been studied since 1931 with regard t o a variety of topics of relevance t o both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used t o impart an additional layer of information. Molecular characterizations employing smallsubunit 16s rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specif ic PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition t o the ten described Shewanella species, two new species, Shewanella oneidensis and ' Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator , composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

A culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold mines was performed by performing a PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with a sequencing analysis of archaeal rDNA clone libraries. The water samples used represented various environments, including deep fissure water, mine service water, and water from an overlying dolomite aquifer. T-RFLP analysis revealed that the ribotype distribution of archaea varied with the source of water. The archaeal communities in the deep gold mine environments exhibited great phylogenetic diversity; the majority of the members were most closely related to uncultivated species. Some archaeal rDNA clones obtained from mine service water and dolomite aquifer water samples were most closely related to environmental rDNA clones from surface soil (soil clones) and marine environments (marine group I [MGI]). Other clones exhibited intermediate phylogenetic affiliation between soil clones and MGI in the Crenarchaeota. Fissure water samples, derived from active or dormant geothermal environments, yielded archaeal sequences that exhibited novel phylogeny, including a novel lineage of Euryarchaeota. These results suggest that deep South African gold mines harbor novel archaeal communities distinct from those observed in other environments. Based on the phylogenetic analysis of archaeal strains and rDNA clones, including the newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain Archaea are reevaluated.Recent molecular phylogenetic analyses based on small-subunit (SSU) rRNA gene (rDNA) sequencing have revealed that the phylogenetic diversity of Archaea in naturally occurring microbial communities is much greater than previously assumed on the basis of the results obtained with standard cultivation and isolation methods (3,6,14,15,20,24,43,45). Initially, a small collection of isolates was referred to as archaebacteria, and now this varied assemblage is known to be both ubiquitous and cosmopolitan. Molecular phylogenetic approaches have revealed that environmental archaeal populations are both diverse and complex, often consisting of uncultivated and unidentified members. Because pure-culture phenotypic characterizations of many environmental Archaea are currently not possible, the physiological features and ecological significance of archaeal communities remain difficult to assess. The phylogenetic structure derived from archaeal rDNA clones from a given habitat, however, frequently corresponds to measurable environmental constraints (8, 42). When phylogenetic features intrinsic to archaeal communities are related to the environment, they may provide important insights into the physiological functions and ecological roles of the communities.The gold mines of South Africa are the deepest accessible excavations in the world and provide a unique opportunity for direct exploration of the deep s...

Geochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes . These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates.

[1] H 2 is probably the most important substrate for terrestrial subsurface lithoautotrophic microbial communities. Abiotic H 2 generation is an essential component of subsurface ecosystems truly independent of surface photosynthesis. Here we report that H 2 concentrations in fracture water collected from deep siliclastic and volcanic rock units in the Witwatersrand Basin, South Africa, ranged up to two molar, a value far greater than observed in shallow aquifers or marine sediments. The high H 2 concentrations are consistent with that predicted by radiolytic dissociation of H 2 O during radioactive decay of U, Th, and K in the host rock and the observed He concentrations. None of the other known H 2 -generating mechanisms can account for such high H 2 abundance either because of the positive free energy imposed by the high H 2 concentration or pH or because of the absence of required mineral phases. The radiolytic H 2 is consumed by methanogens and abiotic hydrocarbon synthesis. Our calculations indicate that radiolytic H 2 production is a ubiquitous and virtually limitless source of energy for deep crustal chemolithoautotrophic ecosystems.

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