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  • Bacteria  (2)
  • Phylogenomics  (2)
  • Anaerobic chemolithoautotrophic metabolism  (1)
  • 1
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    Gradients in dimethylsulfide, dimethylsulfoniopropionate, dimethylsulfoxide, and bacteria near the sea surface (2011)
    Inter-Research
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    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2005. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 295 (2005): 33-42, doi:10.3354/meps295033.
    Description: Gradients of dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), dimethylsulfoxide (DMSO), and bacterial numbers and diversity from the surface microlayer to 500 cm depth were assessed in coastal waters surrounding the Martha’s Vineyard Coastal Observatory, Massachusetts, USA. Microlayer samples were collected with a surface skimmer: a partially submerged, rotating glass cylinder (‘drum’) that allows the collection of a thin layer of water by adherence to the drum. A depletion of DMS towards the water surface (10 cm) was found at all sampling days, with largest gradients during rough sea surface conditions. The steep gradients show that gas fluxes and transfer velocities, based on the concentration disequilibrium between the water and the atmosphere, need to be based on near surface gas concentration values. Elevated DMSP, DMSO concentrations and bacterial numbers were found at the sea surface during calm conditions. Although degassing and photo-oxidation on the skimmer will bias the microlayer data, the results indicate stratification of DMSP, DMSO and bacteria during periods of smooth sea surface conditions.
    Description: We also thank the postdoctoral scholar program at the Woods Hole Oceanographic Institution, with funding provided by the J. Seward Johnson Fund.
    Keywords: Marine sulfur ; Bacteria ; Depth profiles ; Microlayer sampling ; Coastal waters ; DMS ; DMSP ; DMSO
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Epsilonbacterota ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Kinetics of H2–O2–H2O redox equilibria and formation of metastable H2O2 under low temperature hydrothermal conditions (2011)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 75 (2011): 1594-1607, doi:10.1016/j.gca.2010.12.020.
    Description: Hydrothermal experiments were conducted to evaluate the kinetics of H2(aq) oxidation in the homogeneous H2-O2-H2O system at conditions reflecting subsurface/near-seafloor hydrothermal environments (55-250 oC and 242-497 bar). The kinetics of the water-forming reaction that controls the fundamental equilibrium between dissolved H2(aq) and O2(aq), are expected to impose significant constraints on the redox gradients that develop when mixing occurs between oxygenated seawater and high- temperature anoxic vent fluid at near-seafloor conditions. Experimental data indicate that, indeed, the kinetics of H2(aq)-O2(aq) equilibrium become slower with decreasing temperature, allowing excess H2(aq) to remain in solution. Sluggish reaction rates of H2(aq) oxidation suggest that active microbial populations in near-seafloor and subsurface environments could potentially utilize both H2(aq) and O2(aq), even at temperatures lower than 40 oC due to H2(aq) persistence in the seawater/vent fluid mixtures. For these H2-O2 disequilibrium conditions, redox gradients along the seawater/hydrothermal fluid mixing interface are not sharp and microbially-mediated H2(aq) oxidation coupled with a lack of other electron acceptors (e.g. nitrate) could provide an important energy source available at low-temperature diffuse flow vent sites. More importantly, when H2(aq)-O2(aq) disequilibrium conditions apply, formation of metastable hydrogen peroxide is observed. The yield of H2O2(aq) synthesis appears to be enhanced under conditions of elevated H2(aq)/O2(aq) molar ratios that correspond to abundant H2(aq) concentrations. Formation of metastable H2O2 is expected to affect the distribution of dissolved organic carbon (DOC) owing to the existence of an additional strong oxidizing agent. Oxidation of magnetite and/or Fe++ by hydrogen peroxide could also induce formation of metastable hydroxyl radicals (•OH) through Fenton-type reactions, further broadening the implications of hydrogen peroxide in hydrothermal environments.
    Description: This research was conducted with partial support from the NSF OCE-0752221 and the Geophysical Laboratory Postdoctoral Fellowship. We would also like to acknowledge contributions by the W.M. Keck Foundation and Shell towards supporting the hydrothermal lab at the Geophysical Lab. SMS acknowledges support from NSF OCE-0452333 and the Alfried-Krupp Wissenschaftskolleg Greifswald (Germany), while WES acknowledges support from NSF grants OCE-0549457 and OCE- 0813861.
    Keywords: Knallgas reaction ; H2 oxidation ; Metastable hydrogen peroxide ; Anaerobic chemolithoautotrophic metabolism ; Fenton reaction ; Hydrothermal systems
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 4
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    Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2017)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Ancestral absence of electron transport chains in Patescibacteria and DPANN (2020)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.
    Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
    Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.
    Keywords: Bacteria ; Archaea ; evolution ; genomics fermentation ; respiration ; oxidoreductases
    Repository Name: Woods Hole Open Access Server
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