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Joel E Kostka - One of the best experts on this subject based on the ideXlab platform.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Denitrifying Bacteria isolated from terrestrial subsurface sediments exposed to mixed waste contamination
    Applied and Environmental Microbiology, 2010
    Co-Authors: Stefan J Green, Om Prakash, Thomas M Gihring, Denise M Akob, Puja Jasrotia, Philip M Jardine, David B Watson, Steven D Brown, Anthony V Palumbo, Joel E Kostka
    Abstract:

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of Denitrifying Bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (AlphaproteoBacteria), Rhodanobacter (GammaproteoBacteria), Intrasporangium (ActinoBacteria), and Bacillus (Firmicutes). Isolates from the phylum ProteoBacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that Bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of Denitrifying Bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

Stefan J Green - One of the best experts on this subject based on the ideXlab platform.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Denitrifying Bacteria from the genus rhodanobacter dominate Bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site
    Applied and Environmental Microbiology, 2012
    Co-Authors: Stefan J Green, Om Prakash, Puja Jasrotia, David B Watson, James M Tiedje, Will A Overholt, Erick Cardenas, Daniela Hubbard, Christopher W Schadt, Scott C Brooks
    Abstract:

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that Denitrifying Bacteria from the genus Rhodanobacter (class GammaproteoBacteria) dominate at low pH. The relative abundance of Bacteria from this genus was positively correlated with lower-pH conditions, and these Bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter Bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of Bacterial community structure in this contaminated subsurface environment.

  • Denitrifying Bacteria isolated from terrestrial subsurface sediments exposed to mixed waste contamination
    Applied and Environmental Microbiology, 2010
    Co-Authors: Stefan J Green, Om Prakash, Thomas M Gihring, Denise M Akob, Puja Jasrotia, Philip M Jardine, David B Watson, Steven D Brown, Anthony V Palumbo, Joel E Kostka
    Abstract:

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of Denitrifying Bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (AlphaproteoBacteria), Rhodanobacter (GammaproteoBacteria), Intrasporangium (ActinoBacteria), and Bacillus (Firmicutes). Isolates from the phylum ProteoBacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that Bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of Denitrifying Bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

Om Prakash - One of the best experts on this subject based on the ideXlab platform.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Isolation and physiological characterization of psychrophilic Denitrifying Bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway)
    Environmental Microbiology, 2013
    Co-Authors: Andy Canion, Linda L. Jahnke, Stefan J Green, Marcel M. M. Kuypers, Om Prakash, Joel E Kostka
    Abstract:

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic Denitrifying Bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)10(sup 6) cells of psychrophilic nitrate-respiring Bacteria g(sup 1) of sediment. Fifteen strains within the ProteoBacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (GammaproteoBacteria), Arcobacter (EpsilonproteoBacteria) and Herminiimonas (BetaproteoBacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic Denitrifying Bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  • Denitrifying Bacteria from the genus rhodanobacter dominate Bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site
    Applied and Environmental Microbiology, 2012
    Co-Authors: Stefan J Green, Om Prakash, Puja Jasrotia, David B Watson, James M Tiedje, Will A Overholt, Erick Cardenas, Daniela Hubbard, Christopher W Schadt, Scott C Brooks
    Abstract:

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that Denitrifying Bacteria from the genus Rhodanobacter (class GammaproteoBacteria) dominate at low pH. The relative abundance of Bacteria from this genus was positively correlated with lower-pH conditions, and these Bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter Bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of Bacterial community structure in this contaminated subsurface environment.

  • Denitrifying Bacteria isolated from terrestrial subsurface sediments exposed to mixed waste contamination
    Applied and Environmental Microbiology, 2010
    Co-Authors: Stefan J Green, Om Prakash, Thomas M Gihring, Denise M Akob, Puja Jasrotia, Philip M Jardine, David B Watson, Steven D Brown, Anthony V Palumbo, Joel E Kostka
    Abstract:

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of Denitrifying Bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (AlphaproteoBacteria), Rhodanobacter (GammaproteoBacteria), Intrasporangium (ActinoBacteria), and Bacillus (Firmicutes). Isolates from the phylum ProteoBacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that Bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of Denitrifying Bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

James M Tiedje - One of the best experts on this subject based on the ideXlab platform.

  • Denitrifying Bacteria from the genus rhodanobacter dominate Bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site
    Applied and Environmental Microbiology, 2012
    Co-Authors: Stefan J Green, Om Prakash, Puja Jasrotia, David B Watson, James M Tiedje, Will A Overholt, Erick Cardenas, Daniela Hubbard, Christopher W Schadt, Scott C Brooks
    Abstract:

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that Denitrifying Bacteria from the genus Rhodanobacter (class GammaproteoBacteria) dominate at low pH. The relative abundance of Bacteria from this genus was positively correlated with lower-pH conditions, and these Bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter Bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of Bacterial community structure in this contaminated subsurface environment.

  • nitrite reductase genes nirk and nirs as functional markers to investigate diversity of Denitrifying Bacteria in pacific northwest marine sediment communities
    Applied and Environmental Microbiology, 2000
    Co-Authors: Gesche Ake, Jizhong Zhou, Alla H Devol, James M Tiedje
    Abstract:

    Genetic heterogeneity of Denitrifying Bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK and nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for Denitrifying Bacteria. nirS sequences could be amplified from samples of both sampling sites, whereas nirK sequences were detected only in samples from the Washington margin. To assess the underlying nir gene structure, PCR products of both genes were cloned and screened by restriction fragment length polymorphism (RFLP). Rarefraction analysis revealed a high level of diversity especially for nirS clones from Puget Sound and a slightly lower level of diversity for nirK and nirS clones from the Washington margin. One group dominated within nirK clones, but no dominance and only a few redundant clones were seen between sediment samples for nirS clones in both habitats. Hybridization and sequencing confirmed that all but one of the 228 putative nirS clones were nirS with levels of nucleotide identities as low as 45.3%. Phylogenetic analysis grouped nirS clones into three distinct subclusters within the nirS gene tree which corresponded to the two habitats from which they were obtained. These sequences had little relationship to any strain with known nirS sequences or to isolates (mostly close relatives of Pseudomonas stutzeri) from the Washington margin sediment samples. nirK clones were more closely related to each other than were the nirS clones, with 78.6% and higher nucleotide identities; clones showing only weak hybridization signals were not related to known nirK sequences. All nirK clones were also grouped into a distinct cluster which could not be placed with any strain with known nirK sequences. These findings show a very high diversity of nir sequences within small samples and that these novel nir clusters, some very divergent from known sequences, are not known in cultivated denitrifiers.

Yuhei Inamori - One of the best experts on this subject based on the ideXlab platform.