Hitherto Unknown [Fe-Fe]-Hydrogenase Gene Diversity in Anaerobes and Anoxic Enrichments from a Moderately Acidic Fen

Schmidt, Oliver; Drake, Harold L.; Horn, Marcus A.

doi:10.1128/aem.02895-09

Cited by 54 publications

(61 citation statements)

References 38 publications

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“…Only few non-target sequences occurred and were excluded from further analyses; 95±7% of sequences generated from amplicons obtained with a certain structural gene-specific (that is, narG, nirK, nirS or nosZ) primer set were related to publicly available target genes of that primer set. Such amplification specificity is above or in the range of values obtained for other structural gene marker analyses (for example, average of 87±11% for narG, dsrAB, [FeFe]-hydrogenase and dioxygenase genes; Philippot et al, 2002;Loy et al, 2004;Iwai et al, 2010;Schmidt et al, 2010).…”

Section: Denitrifiers In Cryoturbated and Unturbated Peat K Palmer Et Almentioning

confidence: 97%

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

2011

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Cryoturbated peat circles (that is, bare surface soil mixed by frost action; pH 3-4) in the Russian discontinuous permafrost tundra are nitrate-rich 'hotspots' of nitrous oxide (N 2 O) emissions in arctic ecosystems, whereas adjacent unturbated peat areas are not. N 2 O was produced and subsequently consumed at pH 4 in unsupplemented anoxic microcosms with cryoturbated but not in those with unturbated peat soil. Nitrate, nitrite and acetylene stimulated net N 2 O production of both soils in anoxic microcosms, indicating denitrification as the source of N 2 O. Up to 500 and 10 lM nitrate stimulated denitrification in cryoturbated and unturbated peat soils, respectively. Apparent maximal reaction velocities of nitrite-dependent denitrification were 28 and 18 nmol N 2 O g DW À1 h À1 , for cryoturbated and unturbated peat soils, respectively. Barcoded amplicon pyrosequencing of narG, nirK/nirS and nosZ (encoding nitrate, nitrite and N 2 O reductases, respectively) yielded E49 000 quality-filtered sequences with an average sequence length of 444 bp. Up to 19 species-level operational taxonomic units were detected per soil and gene, many of which were distantly related to cultured denitrifiers or environmental sequences. Denitrification-associated gene diversity in cryoturbated and in unturbated peat soils differed. Quantitative PCR (inhibition-corrected per DNA extract) revealed higher copy numbers of narG in cryoturbated than in unturbated peat soil. Copy numbers of nirS were up to 1000 Â higher than those of nirK in both soils, and nirS nirK À1 copy number ratios in cryoturbated and unturbated peat soils differed. The collective data indicate that the contrasting N 2 O emission patterns of cryoturbated and unturbated peat soils are associated with contrasting denitrifier communities.

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Section: Denitrifiers In Cryoturbated and Unturbated Peat K Palmer Et Almentioning

confidence: 97%

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

2011

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“…Molecular hydrogen is an important metabolic intermediary in wetlands, sewage sludge, serpentinized rocks and the intestinal track of insects and animals (Schmidt et al, 2010;Ballor and Leadbetter, 2011;Brazelton et al, 2012). It is possible a similar hydrogen exchange may link fermentation and respiratory metabolisms in aquifer communities, given the extensive evidence for fermentation-based metabolism identified in these genomes.…”

Section: Metabolic Interdependencies In An Aquifer Microbial Communitmentioning

confidence: 99%

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

et al. 2014

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Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.

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“…Hydrogenases are also important in the fermentative metabolism of C. thermocellum (29), and three relevant sets of genes are present (Fe-only hydrogenase genes [Cthe_0342, Cthe_0430, and Cthe_3003], Ni-dependent hydrogenase genes [Cthe_0355 and Cthe_3020 to Cthe_3024], and the NiFeS cofactor assembly system [Cthe_3013 to Cthe_3018]). Among these, the Fe-only hydrogenase gene Cthe_0342 was expressed above the 5th percentile under all conditions, while Cthe_0430 changed from the 29th percentile to the 2nd percentile as the growth rate on cellulose increased.…”

Section: Genes Encoding Transportersmentioning

confidence: 99%

Global Gene Expression Patterns in Clostridium thermocellum as Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose

Riederer

Takasuka

Makino³

et al. 2011

Appl Environ Microbiol

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A microarray study of chemostat growth on insoluble cellulose or soluble cellobiose has provided substantial new information on Clostridium thermocellum gene expression. This is the first comprehensive examination of gene expression in C. thermocellum under defined growth conditions. Expression was detected from 2,846 of 3,189 genes, and regression analysis revealed 348 genes whose changes in expression patterns were growth rate and/or substrate dependent. Successfully modeled genes included those for scaffoldin and cellulosomal enzymes, intracellular metabolic enzymes, transcriptional regulators, sigma factors, signal transducers, transporters, and hypothetical proteins. Unique genes encoding glycolytic pathway and ethanol fermentation enzymes expressed at high levels simultaneously with previously established maximal ethanol production were also identified. Ranking of normalized expression intensities revealed significant changes in transcriptional levels of these genes. The pattern of expression of transcriptional regulators, sigma factors, and signal transducers indicates that response to growth rate is the dominant global mechanism used for control of gene expression in C. thermocellum.

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Hitherto Unknown [Fe-Fe]-Hydrogenase Gene Diversity in Anaerobes and Anoxic Enrichments from a Moderately Acidic Fen

Cited by 54 publications

References 38 publications

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Global Gene Expression Patterns in Clostridium thermocellum as Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose

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