The Distribution of Microbial Taxa in the Subsurface Water of the Kalahari Shield, South Africa

Gihring, Thomas M.; Moser, Duane P.; Lin, Li; Davidson, Marilyn J.; Onstott, Tullis C.; Morgan, Leah E.; Milleson, Mary; Kieft, Thomas L.; Trimarco, E.; Balkwill, David L.; Dollhopf, Michael E.

doi:10.1080/01490450600875696

Cited by 112 publications

(112 citation statements)

References 41 publications

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“…South Africa gold mine euryarchaeotic group 1 was detected at 200-1000 m and at 1300-1500 m. At 1900 and 2300 m, over 99% of the sequences were classified to Methanobacteriaceae family, causing a reduction in community evenness, diversity and richness (Supplementary Table S4). The prevalence of Proteobacteria, Firmicutes and methanogenic archaea in Outokumpu was consistent with the detection of these taxa in geographically distant continental crustal areas (Gihring et al, 2006;Sahl et al, 2008).…”

Section: Resultssupporting

confidence: 81%

“…Previous studies using 16S rRNA gene cloning have reported up to 42 bacterial OTUs in continental crystalline rocks (Gihring et al, 2006;Sahl et al, 2008;Onstott et al, 2009), whereas analysis of rarefied pyrotag data obtained from Outokumpu in this study inferred 48-110 bacterial OTUs per sample (Supplementary Table S4). Archaeal OTU richness also greatly exceeded expectations based on earlier studies, with up to 112 OTUs detected in samples recovered above 1500 m (Takai et al, 2001;Sahl et al, 2008).…”

Section: Resultscontrasting

confidence: 49%

“…Yet, studies conducted in mines and deep drill holes have documented that microbial life extends several kilometers into the Earth's crystalline crust with diverse microbial communities detected in a variety of continental areas (Havemann et al, 1999;Zhang et al, 2005;Gihring et al, 2006;Sahl et al, 2008;Onstott et al, 2009;Itävaara et al, 2011a;Nyyssö nen et al, 2012). Culture-based studies under laboratory conditions show that these microbial communities include both autotrophic and heterotrophic members with variable modes of metabolism including sulfate and iron reduction, methanogenesis and acetogenesis (Haveman et al, 1999;Haveman and Pedersen, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

et al. 2013

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Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere.

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Section: Resultssupporting

confidence: 81%

Section: Resultscontrasting

confidence: 49%

Section: Introductionmentioning

confidence: 99%

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Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

et al. 2013

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“…The geochemistry of the Driefontein Au Mine borehole water was consistent with groundwater from the karstic, sulfidic, Transvaal dolomite aquifer 13 . The Tau Tona Au Mine borehole water was consistent with other highly saline fracture water from >3 km depth and distinct from the mining water and acid mine drainage water in this mining district 13,15 . The 16S rRNA gene clone libraries were comprised of sulfate reducing Firmicutes and δ Proteobacteria, heterotrophic Proteobacteria (fermenters and/or methanotrophs), Nitrospira and chemolithotrophic Proteobacteria that have been previously detected in the fracture water of these mines 15 (Supplementary Tables and Discussion).…”

supporting

confidence: 57%

Nematoda from the terrestrial deep subsurface of South Africa

Borgonie

García-Moyano

Litthauer

et al. 2011

Nature

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210

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Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single cell organisms, extending >3 km into the Earth's crust and comprising a significant fraction of the global biosphere 1,2,3,4 . The constraints of temperature, energy, O 2 and space seemed to preclude the possibility of more complex multi-cellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9-3.6 km deep fracture water encountered in the deep mines of South Africa, but have not been detected in the mining water. These subsurface nematodes, including a new species Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. 14 C data indicate that the fracture water in which the nematodes reside is 3-12 kyr old paleometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits and that they may control the microbial population density by grazing upon fracture surface biofilm patches. Our results expand the known Metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multi-cellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other worlds in our solar system. . Halicephalobus mephisto

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“…The subsurface residence time of the bulk fracture water of MP104 was on the order of tens of Ma and the Δ 2 H H2-H2O geothermometry suggested that the fracture water originated from a depth of 4.2 kmbls (Lin et al, 2006b). Other fracture water sites, ranging in depth from 0.6 to 3.2 kmbls and distributed over 300 km across the Basin, were found to contain assemblages of bacteria primarily consisting of Proteobacteria, Firmicutes, and, occasionally, a minor portion of Euryarchaeota based on the analyses of 16S rRNA genes (Takai et al, 2001;Baker et al, 2003;Moser et al, 2003;Onstott et al, 2003;Kieft et al, 2005;Gihring et al, 2006;Lin et al, 2006a;Silver et al, 2010;Davidson et al, 2011;Magnabosco et al, 2014). The surprisingly low to no observed archaeal 16S rRNA genes, the low TOC and DOC concentrations, and the low porosity (0.5% matrix, 0.01% fracture) of the Witwatersrand Basin sites distinguishes them from the more prominent archaeal communities often reported to inhabit the shallower, higher TOC bearing, higher porosity (50-90%) sub-seafloor sediments (Biddle et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

et al. 2015

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Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H 2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)-by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.

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The Distribution of Microbial Taxa in the Subsurface Water of the Kalahari Shield, South Africa

Cited by 112 publications

References 41 publications

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

Nematoda from the terrestrial deep subsurface of South Africa

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

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