Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates

Nevin, Kelly P.; Holmes, Dawn E.; Woodard, Trevor L.; Hinlein, Erich S.; Ostendorf, David W.; Lovley, Derek R.

doi:10.1099/ijs.0.63417-0

Cited by 169 publications

(128 citation statements)

References 58 publications

(48 reference statements)

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“…We also propose that the Geobacter taxon carries out ferric iron reduction using H 2 as its energy source (Nevin et al, 2005). Further, that the relative of Sulfuricurvum kujiense oxidizes sulfide, elemental sulfur (S 0 ) and thiosulfate (S 2 O 3 ) at low oxygen concentrations (Kodama and Watanabe, 2004).…”

Section: Discussionmentioning

confidence: 99%

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

et al. 2012

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Subglacial lakes beneath the Vatnajö kull ice cap in Iceland host endemic communities of microorganisms adapted to cold, dark and nutrient-poor waters, but the mechanisms by which these microbes disseminate under the ice and colonize these lakes are unknown. We present new data on this subglacial microbiome generated from samples of two subglacial lakes, a subglacial flood and a lake that was formerly subglacial but now partly exposed to the atmosphere. These data include parallel 16S rRNA gene amplicon libraries constructed using novel primers that span the v3-v5 and v4-v6 hypervariable regions. Archaea were not detected in either subglacial lake, and the communities are dominated by only five bacterial taxa. Our paired libraries are highly concordant for the most abundant taxa, but estimates of diversity (abundance-based coverage estimator) in the v4-v6 libraries are 3-8 times higher than in corresponding v3-v5 libraries. The dominant taxa are closely related to cultivated anaerobes and microaerobes, and may occupy unique metabolic niches in a chemoautolithotrophic ecosystem. The populations of the major taxa in the subglacial lakes are indistinguishable (499% sequence identity), despite separation by 6 km and an ice divide; one taxon is ubiquitous in our Vatnajö kull samples. We propose that the glacial bed is connected through an aquifer in the underlying permeable basalt, and these subglacial lakes are colonized from a deeper, subterranean microbiome.

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Section: Discussionmentioning

confidence: 99%

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

et al. 2012

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“…Fe(III) reduction is an important terminal electron-accepting process in portions of the aquifer (Lovley et al, 1989;Lovley, 1995;Anderson et al, 1998;Rooney-Varga et al, 1999;Holmes et al, 2005;Nevin et al, 2005). Sediments were collected from the Fe(III) reduction zone of the contaminant plume in 2004 with split spoon sample cores and transported immediately to the laboratory as previously described .…”

Section: Methodsmentioning

confidence: 99%

“…In sediments collected in 2004 from the previously described (Lovley et al, 1989;Lovley, 1995;Anderson et al, 1998;Rooney-Varga et al, 1999;Holmes et al, 2004bHolmes et al, , 2005Nevin et al, 2005) petroleum-contaminated aquifer in which Geobacter Serial dilutions were made in medium containing acetate (10 mM) provided as the electron donor, and poorly crystalline Fe(III)-oxide (100 mM) provided as the electron acceptor. A standard three-tube MPN chart was consulted to estimate cell numbers (95% confidence interval).…”

Section: Geobacter Metallireducens (L07834)mentioning

confidence: 99%

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

et al. 2007

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There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

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“…Contrary to the often-repeated statement that the most environmentally relevant microorganisms cannot be studied in pure culture, it has become increasingly apparent that pure cultures of some of the most environmentally relevant organisms can be recovered (Chisholm et al, 1992;Button et al, 1993;Rappe et al, 2002;Konneke et al, 2005;Nevin et al, 2005;Giovannoni and Stingl, 2007;Shelobolina et al, 2008;Holmes et al, 2008a). When these organisms are available in pure culture, it is possible to combine genome sequence information with physiological, transcriptomic and proteomic studies.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

et al. 2008

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To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.

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Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates

Cited by 169 publications

References 58 publications

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

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