Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas

Takai, Ken; Suzuki, Motoo; Nakagawa, Satoshi; Miyazaki, Masaru; Suzuki, Yohey; Inagaki, Fumio; Horikoshi, Koki

doi:10.1099/ijs.0.64255-0

Cited by 229 publications

(212 citation statements)

References 42 publications

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“…In addition, anaerobic denitrification is suggested to be a common process in the studied lakes as indicated by the presence of Sulfurimonas and the oversaturation of N 2 in the suboxic hypolimnia . Sulfurimonas isolates represent sulphur-oxidizing chemolithoautotrophs (for example, Inagaki et al, 2003;Takai et al, 2006) that can perform autotrophic denitrification. This chemolithotrophic process couples denitrification with the oxidation of reduced inorganic sulphur compounds and members of the genus Sulfurimonas have been identified as the main denitrifiers in chemoclines of the Baltic Sea (Glaubitz et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

et al. 2012

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Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.

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Section: Discussionmentioning

confidence: 99%

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

et al. 2012

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“…The nirK clones in Clusters I-IV and the nirS clones in Clusters I and II were obtained from all environmental samples examined, that is, cropland, rice paddy, forest soils and lake sediment (Figures 2 and 3) (Supplementary Table S3). The nirS clones in Cluster III, which contained the entire nirS sequence from deep-sea sediments in hydrothermal fields (Takai et al, 2006), were not obtained from these environmental samples.…”

Section: Diversity Of Nirk and Nirs Genes In Various Environmentsmentioning

confidence: 99%

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

et al. 2015

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Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2-6 times more abundant than those revealed with the conventional primers. RNA-and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.

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“…However, the isolation and characterization of a number of novel bacteria and archaea from deep-sea hydrothermal vents revealed that most of them can use nitrate in addition to sulfur as their terminal electron acceptor. During growth, these microorganisms reduce nitrate to dinitrogen (Takai et al, 2004;Nakagawa et al, 2005;Takai et al, 2006) or ammonium (Blochl et al, 1997;Vetriani et al, 2004;Voordeckers et al, 2008;Perez-Rodriguez et al, 2010, 2012. In most cases, nitrate reduction is coupled to the oxidation of molecular hydrogen (and less frequently of formate or thiosulfate), and these organisms have a shorter doubling time when nitrate, rather than sulfur, is supplemented as the terminal electron acceptor (Vetriani et al, 2004;Voordeckers et al, 2005;Perez-Rodriguez et al, 2010, 2012.…”

Section: Introductionmentioning

confidence: 99%

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

et al. 2014

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Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.

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Cited by 229 publications

References 42 publications

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

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