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  • Articles  (5)
  • Epsilonproteobacteria  (4)
  • COARE gas flux parameterization
  • Frontiers Media  (5)
  • American Chemical Society
  • American Institute of Physics (AIP)
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  • Articles  (5)
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  • Frontiers Media  (5)
  • American Chemical Society
  • American Institute of Physics (AIP)
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  • 1
    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
    Type: Article
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  • 2
    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
    Type: Article
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 901, doi:10.3389/fmicb.2015.00901.
    Description: Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
    Description: This work was partly supported by grants from the US National Science Foundation to SS (OCE-0452333, 1136727), to TS (OCE-0117117, 0525907, 0961186, 1043064, 0327261, 1131620), to WS and KD (1434798), as well as a grant by the WHOI Deep Ocean Exploration Institute to SB, TS, and SS.
    Keywords: Hydrothermal vents ; Colonization ; Species sorting ; Settlement ; Volcanic eruption ; 16S rRNA ; Epsilonproteobacteria ; Disturbance
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 153, doi:10.3389/fmicb.2013
    Description: Microbial processes within the subseafloor can be examined during the ephemeral and uncommonly observed phenomena known as snowblower venting. Snowblowers are characterized by the large quantity of white floc that is expelled from the seafloor following mid-ocean ridge eruptions. During these eruptions, rapidly cooling lava entrains seawater and hydrothermal fluids enriched in geochemical reactants, creating a natural bioreactor that supports a subseafloor microbial “bloom.” Previous studies hypothesized that the eruption-associated floc was made by sulfide-oxidizing bacteria; however, the microbes involved were never identified. Here we present the first molecular analysis combined with microscopy of microbial communities in snowblower vents from samples collected shortly after the 2011 eruption at Axial Seamount, an active volcano on the Juan de Fuca Ridge. We obtained fluid samples and white flocculent material from active snowblower vents as well as orange flocculent material found on top of newly formed lava flows. Both flocculent types revealed diverse cell types and particulates when examined by phase contrast and scanning electron microscopy (SEM). Distinct archaeal and bacterial communities were detected in each sample type through Illumina tag sequencing of 16S rRNA genes and through sequencing of the sulfide oxidation gene, soxB. In fluids and white floc, the dominant bacteria were sulfur-oxidizing Epsilonproteobacteria and the dominant archaea were thermophilic Methanococcales. In contrast, the dominant organisms in the orange floc were Gammaproteobacteria and Thaumarchaeota Marine Group I. In all samples, bacteria greatly outnumbered archaea. The presence of anaerobic methanogens and microaerobic Epsilonproteobacteria in snowblower communities provides evidence that these blooms are seeded by subseafloor microbes, rather than from microbes in bottom seawater. These eruptive events thus provide a unique opportunity to observe subseafloor microbial communities. - See more at: http://journal.frontiersin.org/Journal/10.3389/fmicb.2013.00153/abstract#sthash.bg9RZMA7.dpuf
    Description: This work was supported by a National Science Foundation Grant OCE-0929167 (to Julie A. Huber), a NASA Astrobiology Postdoctoral Fellowship (to Nancy H. Akerman), and a Center for Dark Energy Biosphere Investigations Postdoctoral Fellowship (to Julie L. Meyer).
    Keywords: Hydrothermal vents ; Epsilonproteobacteria ; Snowblowers ; Eruption ; Subseafloor
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2023-02-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fairall, C. W. W., Yang, M., Brumer, S. E. E., Blomquist, B. W. W., Edson, J. B. B., Zappa, C. J. J., Bariteau, L., Pezoa, S., Bell, T. G. G., & Saltzman, E. S. S. Air-Sea trace gas fluxes: direct and indirect measurements. Frontiers in Marine Science, 9, (2022): 826606, https://doi.org/10.3389/fmars.2022.826606.
    Description: The past decade has seen significant technological advance in the observation of trace gas fluxes over the open ocean, most notably CO2, but also an impressive list of other gases. Here we will emphasize flux observations from the air-side of the interface including both turbulent covariance (direct) and surface-layer similarity-based (indirect) bulk transfer velocity methods. Most applications of direct covariance observations have been from ships but recently work has intensified on buoy-based implementation. The principal use of direct methods is to quantify empirical coefficients in bulk estimates of the gas transfer velocity. Advances in direct measurements and some recent field programs that capture a considerable range of conditions with wind speeds exceeding 20 ms-1 are discussed. We use coincident direct flux measurements of CO2 and dimethylsulfide (DMS) to infer the scaling of interfacial viscous and bubble-mediated (whitecap driven) gas transfer mechanisms. This analysis suggests modest chemical enhancement of CO2 flux at low wind speed. We include some updates to the theoretical structure of bulk parameterizations (including chemical enhancement) as framed in the COAREG gas transfer algorithm.
    Description: This work, and the contributions of MY and TB, is supported by the UK Natural Environment Research Council’s ORCHESTRA (Grant No. NE/N018095/1) and PICCOLO (Grant No. NE/P021409/1) projects, and by the European Space Agency’s AMT4OceanSatFlux project (Grant No. 4000125730/18/NL/FF/gp). CF and BB are funded by the National Oceanic and Atmospheric Administration’s Global Ocean Monitoring and Observing program (http://data.crossref.org/fundingdata/funder/10.13039/100018302). CZ was funded by the National Science Foundation (CJZ: OCE-2049579, Grants OCE-1537890 and OCE-1923935). Funding for HiWinGS was provided by the US National Science Foundation grant AGS-1036062. The Knorr-11 and SOAP campaigns were supported by the NSF Atmospheric Chemistry Program (Grant No. ATM-0426314, AGS-08568, -0851472, -0851407 and -1143709).
    Keywords: Gas transfer velocity ; Chemical enhancement ; Bubble mediated transfer ; COARE gas flux parameterization ; Dimethylsufide (DMS) ; Cardon dioxide (CO2) ; Bulk algorithm ; Direct observation
    Repository Name: Woods Hole Open Access Server
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