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Robert A Sanford - One of the best experts on this subject based on the ideXlab platform.

  • mass dependent selenium isotopic fractionation during microbial reduction of seleno oxyanions by phylogenetically diverse bacteria
    Geochimica et Cosmochimica Acta, 2020
    Co-Authors: Kathrin Schilling, Celine Pallud, Thomas Martin Johnson, Robert A Sanford, Christoph Wanner, Anirban Basu, Paul R.d. Mason
    Abstract:

    Abstract Selenium (Se) isotope fractionation has been widely used for constraining redox conditions and microbial processes in both modern and ancient environments, but our knowledge of the controls on fractionation during microbial reduction of Se-oxyanions is based on a limited number of studies. Here we complement and expand the currently available pure culture data for Se isotope fractionation by investigating for the first time six phylogenetically diverse, mesophilic, and non-respiring bacterial strains that reduce Se-oxyanions to elemental Se [Se(0)]. Experiments were performed with either selenate [Se(VI)] or selenite [Se(IV)] at lower, more environmentally-relevant Se (9–47 μM) and carbon (500 μM) concentrations than previously investigated. Enterobacter cloacae SLD1a-1, Desulfitobacterium chlororespirans Co23 and Desulfitobacterium sp. Viet-1 were incubated with Se(VI) and Se(IV). Geobacter sulfurreducens PCA, Anaeromyxobacter Dehalogenans FRC-W and Shewanella sp. (NR) were examined for their ability reducing Se(IV) to Se(0). Our data confirm that microbial reduction of both Se-oxyanions is accompanied by large kinetic isotopic fractionation (reported as 82/76e = 1000×(82/76α-1) in ‰). Under our experimental conditions, microbial reduction of Se(VI) shows consistently greater isotope fractionation (e = −9.2‰ to −11.8‰) than reduction of Se(IV) (e = −6.2 to −7.8‰) confirming the difference in metabolic pathways for the reduction of the two Se-oxyanions. For Se(VI), an inverse relationship between normalized cell specific reduction rate (cSRR) and Se isotope fractionation suggests that the kinetic isotope effect for Se(VI) reduction is governed by an enzymatically-specific pathway related to the bacterial strain-specific physiology. In contrast, the lack of correlation between normalized cSRR and isotope fractionation for Se(IV) reduction indicates a non-enzyme specific pathway which is dominantly extracellular. Our study highlights the importance to understand microbially-mediated Se isotope fractionation depending on Se species, and cell-specific reduction rates before Se isotope ratios can become a fully applicable tool to interpret Se isotopic changes in modern and ancient environments.

  • denitrification by Anaeromyxobacter Dehalogenans a common soil bacterium lacking the nitrite reductase genes nirs and nirk
    Applied and Environmental Microbiology, 2017
    Co-Authors: Jenny R Onley, Robert A Sanford, Samiha Ahsan, Frank E Löffler
    Abstract:

    ABSTRACT The versatile soil bacterium Anaeromyxobacter Dehalogenans lacks the hallmark denitrification genes nirS and nirK (encoding NO2−→NO reductases) and couples growth to NO3− reduction to NH4+ (respiratory ammonification) and to N2O reduction to N2. A. Dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2− to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3− or NO2− to Fe(III)-grown axenic cultures of A. Dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3− to N2 in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology of A. Dehalogenans. The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lacking nirS or nirK but with Fe(III) reduction potential and genes for NO3− and N2O reduction are not rare, indicating that NO3− reduction to N2 through linked biotic-abiotic reactions is not limited to A. Dehalogenans. Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3− reducers, denitrification independent of NO-forming NO2− reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux. IMPORTANCE Current attempts to gauge N loss from soils rely on the quantitative measurement of nirK and nirS genes and/or transcripts. In the presence of iron, the common soil bacterium Anaeromyxobacter Dehalogenans is capable of denitrification and the production of N2 without the key denitrification genes nirK and nirS. Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.

  • uranium isotopic fractionation factors during u vi reduction by bacterial isolates
    Geochimica et Cosmochimica Acta, 2014
    Co-Authors: Anirban Basu, Thomas Martin Johnson, Craig Campbell Lundstrom, Robert A Sanford, Frank E Löffler
    Abstract:

    We experimentally determined the magnitude of uranium isotopic fractionation induced by U(VI) reduction by metal reducing bacterial isolates. Our results indicate that microbial U(VI) reduction induces isotopic fractionation; heavier isotopes (i.e., 238 U) partition into the solid U(IV) products. The magnitudes of isotopic fractionation (expressed as e = 1000& � (a� 1)) for 238 U/ 235 U were 0.68& ± 0.05& and 0.99& ± 0.12& for Geobacter sulfurreducens strain PCA and strain IFRC-N, respectively. The e values for Anaeromyxobacter Dehalogenans strain FRC-W, strain FRC-R5, a novel Shewanella isolate, and Desulfitobacterium sp. strain Viet1 were 0.72& ± 0.15&, 0.99& ± 0.12&, 0.96& ± 0.16& and 0.86& ± 0.06&, respectively. Our results show that the maximum e values of � 1.0& were obtained with low biomass (� 10 7 cells/mL) and low electron donor concentrations (� 500 lM). These results provide an initial assessment of 238 U/ 235 U shifts induced by microbiallymediated U(VI) reduction, which is needed as 238 U/ 235 U data are increasingly applied as redox indicators in various

  • The Mosaic Genome of Anaeromyxobacter Dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
    2013
    Co-Authors: Sara H Thomas, Robert A Sanford, Adrian K Arakaki, Jeffrey Skolnick, John R Kirby, Ryan D. Wagner, Lawrence J, Frank E Löffler
    Abstract:

    Anaeromyxobacter Dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. Dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. Analysis of the 5.01 Mb strain 2CP-C genome substantiated that this organism is a myxobacterium but shares genotypic traits with the anaerobic majority of the delta-Proteobacteria (i.e., the Desulfuromonadales). Reflective of its respiratory versatility, strain 2CP-C possesses 68 genes coding for putative c-type cytochromes, including one gene with 40 heme binding motifs. Consistent with its relatedness to the myxobacteria, surface motility was observed in strain 2CP-C and multiple types of motility genes are present, including 28 genes for gliding, adventurous (A-) motility and 17 genes for type IV pilus-based motility (i.e., social (S-) motility) that all have homologs in Myxococcus xanthus. Although A. Dehalogenans shares many metabolic traits with the anaerobic majority of the delta-Proteobacteria, strain 2CP-C grows under microaerophilic conditions and possesses detoxification systems for reactive oxygen species. Accordingly, two gene clusters coding for NADH dehydrogenase subunits and two cytochrome oxidase gene clusters in strain 2CP-C are similar to those in M. xanthus. Remarkably, strain 2CP-C possesses a third NADH dehydrogenase gene cluster and a cytochrome cbb 3 oxidase gene cluster, apparently acquired through ancient horizonta

  • unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils
    Proceedings of the National Academy of Sciences of the United States of America, 2012
    Co-Authors: Robert A Sanford, Sara H Thomas, Darlene D Wagner, Joanne C Cheesanford, Claribel Cruzgarcia, Gina P Rodriguez, Arturo Massoldeya, K K Krishnani, Kirsti M Ritalahti
    Abstract:

    Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over the past century with drastic consequences, including increased atmospheric nitrous oxide (N2O) concentrations. N2O is a potent greenhouse gas and contributor to ozone layer destruction, and its release from fixed N is almost entirely controlled by microbial activities. Mitigation of N2O emissions to the atmosphere has been attributed exclusively to denitrifiers possessing NosZ, the enzyme system catalyzing N2O to N2 reduction. We demonstrate that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers. nos clusters with atypical nosZ occur in Bacteria and Archaea that denitrify (44% of genomes), do not possess other denitrification genes (56%), or perform dissimilatory nitrate reduction to ammonium (DNRA; (31%). Experiments with the DNRA soil bacterium Anaeromyxobacter Dehalogenans demonstrated that the atypical NosZ is an effective N2O reductase, and PCR-based surveys suggested that atypical nosZ are abundant in terrestrial environments. Bioinformatic analyses revealed that atypical nos clusters possess distinctive regulatory and functional components (e.g., Sec vs. Tat secretion pathway in typical nos), and that previous nosZ-targeted PCR primers do not capture the atypical nosZ diversity. Collectively, our results suggest that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N2O consumption. Apparently, a large, previously unrecognized group of environmental nosZ has not been accounted for, and characterizing their contributions to N2O consumption will advance understanding of the ecological controls on N2O emissions and lead to refined greenhouse gas flux models.

Frank E Löffler - One of the best experts on this subject based on the ideXlab platform.

  • denitrification by Anaeromyxobacter Dehalogenans a common soil bacterium lacking the nitrite reductase genes nirs and nirk
    Applied and Environmental Microbiology, 2017
    Co-Authors: Jenny R Onley, Robert A Sanford, Samiha Ahsan, Frank E Löffler
    Abstract:

    ABSTRACT The versatile soil bacterium Anaeromyxobacter Dehalogenans lacks the hallmark denitrification genes nirS and nirK (encoding NO2−→NO reductases) and couples growth to NO3− reduction to NH4+ (respiratory ammonification) and to N2O reduction to N2. A. Dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2− to form N2O (i.e., chemodenitrification). Following the addition of 100 μmol of NO3− or NO2− to Fe(III)-grown axenic cultures of A. Dehalogenans, 54 (±7) μmol and 113 (±2) μmol N2O-N, respectively, were produced and subsequently consumed. The conversion of NO3− to N2 in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology of A. Dehalogenans. The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lacking nirS or nirK but with Fe(III) reduction potential and genes for NO3− and N2O reduction are not rare, indicating that NO3− reduction to N2 through linked biotic-abiotic reactions is not limited to A. Dehalogenans. Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO3− reducers, denitrification independent of NO-forming NO2− reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N2O flux. IMPORTANCE Current attempts to gauge N loss from soils rely on the quantitative measurement of nirK and nirS genes and/or transcripts. In the presence of iron, the common soil bacterium Anaeromyxobacter Dehalogenans is capable of denitrification and the production of N2 without the key denitrification genes nirK and nirS. Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.

  • uranium isotopic fractionation factors during u vi reduction by bacterial isolates
    Geochimica et Cosmochimica Acta, 2014
    Co-Authors: Anirban Basu, Thomas Martin Johnson, Craig Campbell Lundstrom, Robert A Sanford, Frank E Löffler
    Abstract:

    We experimentally determined the magnitude of uranium isotopic fractionation induced by U(VI) reduction by metal reducing bacterial isolates. Our results indicate that microbial U(VI) reduction induces isotopic fractionation; heavier isotopes (i.e., 238 U) partition into the solid U(IV) products. The magnitudes of isotopic fractionation (expressed as e = 1000& � (a� 1)) for 238 U/ 235 U were 0.68& ± 0.05& and 0.99& ± 0.12& for Geobacter sulfurreducens strain PCA and strain IFRC-N, respectively. The e values for Anaeromyxobacter Dehalogenans strain FRC-W, strain FRC-R5, a novel Shewanella isolate, and Desulfitobacterium sp. strain Viet1 were 0.72& ± 0.15&, 0.99& ± 0.12&, 0.96& ± 0.16& and 0.86& ± 0.06&, respectively. Our results show that the maximum e values of � 1.0& were obtained with low biomass (� 10 7 cells/mL) and low electron donor concentrations (� 500 lM). These results provide an initial assessment of 238 U/ 235 U shifts induced by microbiallymediated U(VI) reduction, which is needed as 238 U/ 235 U data are increasingly applied as redox indicators in various

  • The Mosaic Genome of Anaeromyxobacter Dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
    2013
    Co-Authors: Sara H Thomas, Robert A Sanford, Adrian K Arakaki, Jeffrey Skolnick, John R Kirby, Ryan D. Wagner, Lawrence J, Frank E Löffler
    Abstract:

    Anaeromyxobacter Dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. Dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. Analysis of the 5.01 Mb strain 2CP-C genome substantiated that this organism is a myxobacterium but shares genotypic traits with the anaerobic majority of the delta-Proteobacteria (i.e., the Desulfuromonadales). Reflective of its respiratory versatility, strain 2CP-C possesses 68 genes coding for putative c-type cytochromes, including one gene with 40 heme binding motifs. Consistent with its relatedness to the myxobacteria, surface motility was observed in strain 2CP-C and multiple types of motility genes are present, including 28 genes for gliding, adventurous (A-) motility and 17 genes for type IV pilus-based motility (i.e., social (S-) motility) that all have homologs in Myxococcus xanthus. Although A. Dehalogenans shares many metabolic traits with the anaerobic majority of the delta-Proteobacteria, strain 2CP-C grows under microaerophilic conditions and possesses detoxification systems for reactive oxygen species. Accordingly, two gene clusters coding for NADH dehydrogenase subunits and two cytochrome oxidase gene clusters in strain 2CP-C are similar to those in M. xanthus. Remarkably, strain 2CP-C possesses a third NADH dehydrogenase gene cluster and a cytochrome cbb 3 oxidase gene cluster, apparently acquired through ancient horizonta

  • comparative c type cytochrome expression analysis in shewanella oneidensis strain mr 1 and Anaeromyxobacter Dehalogenans strain 2cp c grown with soluble and insoluble oxidized metal electron acceptors
    Biochemical Society Transactions, 2012
    Co-Authors: Frank E Löffler, Silke Nissen, Xiaoxin Liu, Karuna Chourey, Robert L Hettich, Darlene D Wagner, Susan M Pfiffner
    Abstract:

    The genomes of Shewanella oneidensis strain MR-1 and Anaeromyxobacter Dehalogenans strain 2CP-C encode 40 and 69 putative c-type cytochrome genes respectively. Deletion mutant and biochemical studies have assigned specific functions to a few c-type cytochromes involved in electron transfer to oxidized metals in S. oneidensis strain MR-1. Although promising, the genetic approach is limited to gene deletions that produce a distinct phenotype and to an organism for which a genetic system is available. To investigate and compare c-type cytochrome expression in S. oneidensis strain MR-1 and Anaeromyxobacter Dehalogenans strain 2CP-C more comprehensively, proteomic measurements were used to characterize lysates of cells grown with soluble Fe(III) (as ferric citrate) and insoluble Mn(IV) (as MnO2) as electron acceptors. Strain MR-1 expressed 19 and 20, and strain 2CP-C expressed 27 and 25, c-type cytochromes when grown with Fe(III) and Mn(IV) respectively. The majority of c-type cytochromes (77% for strain MR-1 and 63% for strain 2CP-C) were expressed under both growth conditions; however, the analysis also revealed unique c-type cytochromes that were specifically expressed in cells grown with soluble Fe(III) or insoluble Mn(IV). Proteomic characterization proved to be a promising approach for determining the c-type cytochrome complement expressed under different growth conditions, and will help to elucidate the specific functions of more c-type cytochromes that are the basis for Shewanella and Anaeromyxobacter respiratory versatility.

  • unique ecophysiology among u vi reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter Dehalogenans strain 2cp c
    Applied and Environmental Microbiology, 2010
    Co-Authors: Sara H Thomas, Robert A Sanford, Benjamin K Amos, Mary Beth Leigh, Erick Cardenas, Frank E Löffler
    Abstract:

    Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter Dehalogenans cells increased approximately 5-fold from 2.2 10 7 8.6 10 6 to 1.0 10 8 2.2 10 7 cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. Dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3 10 4 1.1 10 4 cells per liter) than sediment-associated cells, suggesting that A. Dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. Dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [ (0.09 pO2) 0.051; R 2 0.923] was observed between the instantaneous specific growth rate and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. Dehalogenans from other known U(VI)reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

Sara H Thomas - One of the best experts on this subject based on the ideXlab platform.

  • The Mosaic Genome of Anaeromyxobacter Dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria
    2013
    Co-Authors: Sara H Thomas, Robert A Sanford, Adrian K Arakaki, Jeffrey Skolnick, John R Kirby, Ryan D. Wagner, Lawrence J, Frank E Löffler
    Abstract:

    Anaeromyxobacter Dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. Dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. Analysis of the 5.01 Mb strain 2CP-C genome substantiated that this organism is a myxobacterium but shares genotypic traits with the anaerobic majority of the delta-Proteobacteria (i.e., the Desulfuromonadales). Reflective of its respiratory versatility, strain 2CP-C possesses 68 genes coding for putative c-type cytochromes, including one gene with 40 heme binding motifs. Consistent with its relatedness to the myxobacteria, surface motility was observed in strain 2CP-C and multiple types of motility genes are present, including 28 genes for gliding, adventurous (A-) motility and 17 genes for type IV pilus-based motility (i.e., social (S-) motility) that all have homologs in Myxococcus xanthus. Although A. Dehalogenans shares many metabolic traits with the anaerobic majority of the delta-Proteobacteria, strain 2CP-C grows under microaerophilic conditions and possesses detoxification systems for reactive oxygen species. Accordingly, two gene clusters coding for NADH dehydrogenase subunits and two cytochrome oxidase gene clusters in strain 2CP-C are similar to those in M. xanthus. Remarkably, strain 2CP-C possesses a third NADH dehydrogenase gene cluster and a cytochrome cbb 3 oxidase gene cluster, apparently acquired through ancient horizonta

  • unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils
    Proceedings of the National Academy of Sciences of the United States of America, 2012
    Co-Authors: Robert A Sanford, Sara H Thomas, Darlene D Wagner, Joanne C Cheesanford, Claribel Cruzgarcia, Gina P Rodriguez, Arturo Massoldeya, K K Krishnani, Kirsti M Ritalahti
    Abstract:

    Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over the past century with drastic consequences, including increased atmospheric nitrous oxide (N2O) concentrations. N2O is a potent greenhouse gas and contributor to ozone layer destruction, and its release from fixed N is almost entirely controlled by microbial activities. Mitigation of N2O emissions to the atmosphere has been attributed exclusively to denitrifiers possessing NosZ, the enzyme system catalyzing N2O to N2 reduction. We demonstrate that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers. nos clusters with atypical nosZ occur in Bacteria and Archaea that denitrify (44% of genomes), do not possess other denitrification genes (56%), or perform dissimilatory nitrate reduction to ammonium (DNRA; (31%). Experiments with the DNRA soil bacterium Anaeromyxobacter Dehalogenans demonstrated that the atypical NosZ is an effective N2O reductase, and PCR-based surveys suggested that atypical nosZ are abundant in terrestrial environments. Bioinformatic analyses revealed that atypical nos clusters possess distinctive regulatory and functional components (e.g., Sec vs. Tat secretion pathway in typical nos), and that previous nosZ-targeted PCR primers do not capture the atypical nosZ diversity. Collectively, our results suggest that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N2O consumption. Apparently, a large, previously unrecognized group of environmental nosZ has not been accounted for, and characterizing their contributions to N2O consumption will advance understanding of the ecological controls on N2O emissions and lead to refined greenhouse gas flux models.

  • unique ecophysiology among u vi reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter Dehalogenans strain 2cp c
    Applied and Environmental Microbiology, 2010
    Co-Authors: Sara H Thomas, Robert A Sanford, Benjamin K Amos, Mary Beth Leigh, Erick Cardenas, Frank E Löffler
    Abstract:

    Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter Dehalogenans cells increased approximately 5-fold from 2.2 10 7 8.6 10 6 to 1.0 10 8 2.2 10 7 cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. Dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3 10 4 1.1 10 4 cells per liter) than sediment-associated cells, suggesting that A. Dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. Dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [ (0.09 pO2) 0.051; R 2 0.923] was observed between the instantaneous specific growth rate and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. Dehalogenans from other known U(VI)reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

  • diversity and distribution of Anaeromyxobacter strains in a uranium contaminated subsurface environment with a nonuniform groundwater flow
    Applied and Environmental Microbiology, 2009
    Co-Authors: Sara H Thomas, Robert A Sanford, Elizabeth Padillacrespo, Phillip M Jardine, Frank E Löffler
    Abstract:

    ABSTRACT Versaphilic Anaeromyxobacter Dehalogenans strains implicated in hexavalent uranium reduction and immobilization are present in the fractured saprolite subsurface environment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge (IFC) site near Oak Ridge, TN. To provide insight into the in situ distribution of Anaeromyxobacter strains in this system with a nonuniform groundwater flow, 16S rRNA gene-targeted primers and linear hybridization (TaqMan) probes were designed for Oak Ridge IFC Anaeromyxobacter isolates FRC-D1 and FRC-W, along with an Anaeromyxobacter genus-targeted probe and primer set. Multiplex quantitative real-time PCR (mqPCR) was applied to samples collected from Oak Ridge IFC site areas 1 and 3, which are not connected by the primary groundwater flow paths; however, transport between them through cross-plane fractures is hypothesized. Strain FRC-W accounted for more than 10% of the total quantifiable Anaeromyxobacter community in area 1 soils, while strain FRC-D1 was not detected. In FeOOH-amended enrichment cultures derived from area 1 site materials, strain FRC-D1 accounted for 30 to 90% of the total Anaeromyxobacter community, demonstrating that this strain was present in situ in area 1. The area 3 total Anaeromyxobacter abundance exceeded that of area 1 by 3 to 5 orders of magnitude, but neither strain FRC-W- nor FRC-D1-like sequences were quantifiable in any of the 33 area 3 groundwater or sediment samples tested. The Anaeromyxobacter community in area 3 increased from

  • diversity and distribution of Anaeromyxobacter strains in a uranium contaminated subsurface environment with a nonuniform groundwater flow
    Applied and Environmental Microbiology, 2009
    Co-Authors: Sara H Thomas, Robert A Sanford, Elizabeth Padillacrespo, Phillip M Jardine, Frank E Löffler
    Abstract:

    Molecular analyses enable specific detection of target organisms, providing insight into microbial biogeography and the factors controlling microbial community structure and function over temporal and spatial scales (reviewed in references 16, 31, and 37). Spatial isolation in disconnected environments has been demonstrated for plant rhizospheres (36), saturated soils versus unsaturated soils (47, 55), and undisturbed (pristine) top soils (8, 10). One unresolved issue of biogeography involves the spatial distribution of distinct populations (of a given species) in physically connected environments, such as heterogeneous subsurface media with nonuniform flow characteristics (e.g., fractured saprolite). A complex matrix of aged bedrock makes up the uranium-contaminated subsurface environment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge (IFC) site, near Oak Ridge, TN (formerly known as the Field Research Center [FRC]). Connectivity and transport between two distinct Oak Ridge IFC study areas (a near-source contaminant plume in area 3 and a farther-source plume in area 1) have been hypothesized based on evidence of flow through fractured bedding planes that extend from the vicinity of area 3 (near the S-3 waste disposal ponds) to area 1 (35). Whether microbes are transported between these two subsurface areas is unclear, but the implications are important for understanding spatially variable biogeochemical processes that control contaminant fate and migration at the site (35). Anaeromyxobacter Dehalogenans populations are relevant to bioremediation at the Oak Ridge IFC site due to their capacity to metabolically reduce soluble U(VI) to sparingly soluble, immobile U(IV) (30, 41, 50). More than a dozen different Anaeromyxobacter 16S rRNA gene sequences have been identified in contaminated site materials derived from the Oak Ridge IFC site (7, 32, 33). Distinct A. Dehalogenans strains were isolated from IFC site materials from area 1 (GenBank accession numbers {"type":"entrez-nucleotide-range","attrs":{"text":"FJ190048 to FJ190062","start_term":"FJ190048","end_term":"FJ190062","start_term_id":"206598459","end_term_id":"206598473"}}FJ190048 to FJ190062 [16S rRNA gene sequences]). Laboratory characterization of A. Dehalogenans strains that are very closely related (>99.9% 16S rRNA gene similarity) demonstrated metabolic variability in terms of growth rates as well as substrates (18, 40, 46). This is consistent with observations from other studies that have demonstrated that exploring diversity at the subspecies level is crucial for understanding microbial interactions and processes (9, 10, 14, 23, 24, 38). Tools that capture the distribution and abundance of A. Dehalogenans strains in spatially and temporally heterogeneous subsurface environments are desirable to comprehensively describe biogeochemical processes controlling contaminant migration. Quantitative real-time PCR (qPCR) approaches using TaqMan probe detection chemistry offer high specificity (i.e., distinguish sequences that differ by only 1 or 2 bp) and allow the quantification of multiple targets in a single reaction mix (2, 29). The multiplex qPCR (mqPCR) technique reduces material consumption, labor, and the probability for experimental errors and has been applied successfully for discrimination of pathogenic bacteria, including Listeria monocytogenes strains (25) and Brucella isolates (42), as well as for simultaneous identification of four bioterrorism agents (48). Despite successful applications in the medical and biodefense fields, mqPCR approaches have had limited application to monitoring bioremediation processes. To demonstrate that strain-specific resolution of Anaeromyxobacter strains is feasible and provides relevant information about microbial distribution, we designed and applied an mqPCR approach to characterize and monitor the Anaeromyxobacter community at the Oak Ridge IFC site across areas 1 and 3. The results from this study provide new information about microbial, and hence functional, heterogeneity in a uranium-contaminated, saturated subsurface environment with nonuniform flow.

Anirban Basu - One of the best experts on this subject based on the ideXlab platform.

  • mass dependent selenium isotopic fractionation during microbial reduction of seleno oxyanions by phylogenetically diverse bacteria
    Geochimica et Cosmochimica Acta, 2020
    Co-Authors: Kathrin Schilling, Celine Pallud, Thomas Martin Johnson, Robert A Sanford, Christoph Wanner, Anirban Basu, Paul R.d. Mason
    Abstract:

    Abstract Selenium (Se) isotope fractionation has been widely used for constraining redox conditions and microbial processes in both modern and ancient environments, but our knowledge of the controls on fractionation during microbial reduction of Se-oxyanions is based on a limited number of studies. Here we complement and expand the currently available pure culture data for Se isotope fractionation by investigating for the first time six phylogenetically diverse, mesophilic, and non-respiring bacterial strains that reduce Se-oxyanions to elemental Se [Se(0)]. Experiments were performed with either selenate [Se(VI)] or selenite [Se(IV)] at lower, more environmentally-relevant Se (9–47 μM) and carbon (500 μM) concentrations than previously investigated. Enterobacter cloacae SLD1a-1, Desulfitobacterium chlororespirans Co23 and Desulfitobacterium sp. Viet-1 were incubated with Se(VI) and Se(IV). Geobacter sulfurreducens PCA, Anaeromyxobacter Dehalogenans FRC-W and Shewanella sp. (NR) were examined for their ability reducing Se(IV) to Se(0). Our data confirm that microbial reduction of both Se-oxyanions is accompanied by large kinetic isotopic fractionation (reported as 82/76e = 1000×(82/76α-1) in ‰). Under our experimental conditions, microbial reduction of Se(VI) shows consistently greater isotope fractionation (e = −9.2‰ to −11.8‰) than reduction of Se(IV) (e = −6.2 to −7.8‰) confirming the difference in metabolic pathways for the reduction of the two Se-oxyanions. For Se(VI), an inverse relationship between normalized cell specific reduction rate (cSRR) and Se isotope fractionation suggests that the kinetic isotope effect for Se(VI) reduction is governed by an enzymatically-specific pathway related to the bacterial strain-specific physiology. In contrast, the lack of correlation between normalized cSRR and isotope fractionation for Se(IV) reduction indicates a non-enzyme specific pathway which is dominantly extracellular. Our study highlights the importance to understand microbially-mediated Se isotope fractionation depending on Se species, and cell-specific reduction rates before Se isotope ratios can become a fully applicable tool to interpret Se isotopic changes in modern and ancient environments.

  • uranium isotopic fractionation factors during u vi reduction by bacterial isolates
    Geochimica et Cosmochimica Acta, 2014
    Co-Authors: Anirban Basu, Thomas Martin Johnson, Craig Campbell Lundstrom, Robert A Sanford, Frank E Löffler
    Abstract:

    We experimentally determined the magnitude of uranium isotopic fractionation induced by U(VI) reduction by metal reducing bacterial isolates. Our results indicate that microbial U(VI) reduction induces isotopic fractionation; heavier isotopes (i.e., 238 U) partition into the solid U(IV) products. The magnitudes of isotopic fractionation (expressed as e = 1000& � (a� 1)) for 238 U/ 235 U were 0.68& ± 0.05& and 0.99& ± 0.12& for Geobacter sulfurreducens strain PCA and strain IFRC-N, respectively. The e values for Anaeromyxobacter Dehalogenans strain FRC-W, strain FRC-R5, a novel Shewanella isolate, and Desulfitobacterium sp. strain Viet1 were 0.72& ± 0.15&, 0.99& ± 0.12&, 0.96& ± 0.16& and 0.86& ± 0.06&, respectively. Our results show that the maximum e values of � 1.0& were obtained with low biomass (� 10 7 cells/mL) and low electron donor concentrations (� 500 lM). These results provide an initial assessment of 238 U/ 235 U shifts induced by microbiallymediated U(VI) reduction, which is needed as 238 U/ 235 U data are increasingly applied as redox indicators in various

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  • comprehensive proteome profiling of the fe iii reducing myxobacterium Anaeromyxobacter Dehalogenans 2cp c during growth with fumarate and ferric citrate
    Proteomics, 2010
    Co-Authors: Tzuchiao Chao, Jorn Kalinowski, Julius O Nyalwidhe, Nicole Hansmeier
    Abstract:

    Anaeromyxobacter Dehalogenans is a microaerophilic member of the delta-proteobacteria which is able to utilize a wide range of electron acceptors, including halogenated phenols, U(VI), Fe(III), nitrate, nitrite, oxygen and fumarate. To date, the knowledge regarding general metabolic activities of this ecologically relevant bacterium is limited. Here, we present a first systematic 2-D reference map of the soluble A. Dehalogenans proteome in order to provide a sound basis for further proteomic studies as well as to gain first global insights into the metabolic activities of this bacterium. Using a combination of 2-DE and MALDI-TOF-MS, a total of 720 proteins spots were identified, representing 559 unique protein species. Using the proteome data, altogether 50 metabolic pathways were found to be expressed during growth with fumarate as primary electron acceptor. An analysis of the pathways revealed an extensive display of enzymes involved in the catabolism and anabolism of a variety of amino acids, including the unexpected fermentation of lysine to butyrate. Moreover, using the reference gel as basis, a semi-quantitative analysis of protein expression changes of A. Dehalogenans during growth with ferric citrate as electron acceptor was conducted. The adaptation to Fe(III) reducing conditions involved the expression changes of a total of 239 proteins. The results suggest that the adaptation to Fe(III) reductive conditions involves an increase in metabolic flux through the tricarboxylic acid cycle, which is fueled by an increased catabolism of amino acids.