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Title: Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin

Abstract

Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 – 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13 T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13 T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C 15:0, C 15:0, C 16:0 and C 14:0.more » The percentage of the straight-chain fatty acid C 15:0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13 T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13 T = DSM 100382 T = ATCC TSD-12 T).« less

Authors:
 [1];  [2];  [3];  [4];  [4];  [5];  [6];  [6];  [7];  [6];  [6]
  1. Desert Research Inst., Las Vegas, NV (United States); Southern Illinois Univ., Carbondale, IL (United States)
  2. Madison Area Technical College, Madison, WI (United States)
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  4. Univ. of Oklahoma, Norman, OK (United States)
  5. Princeton Univ., Princeton, NJ (United States)
  6. Desert Research Inst., Las Vegas, NV (United States)
  7. Univ. of Toronto, ON (Canada)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1568019
Report Number(s):
LLNL-JRNL-784018
Journal ID: ISSN 1664-302X; 977592
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 10; Journal Issue: na; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
Biological and medical sciences; 16S rRNA; subsurface; deep biosphere; Firmicutes; aquifer; borehole; Death Valley

Citation Formats

Hamilton-Brehm, Scott D., Stewart, Laura E., Zavarin, Mavrik, Caldwell, Matt, Lawson, Paul A., Onstott, Tullis C., Grzymski, Joseph, Neveux, Iva, Lollar, Barbara Sherwood, Russell, Charles E., and Moser, Duane P. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin. United States: N. p., 2019. Web. doi:10.3389/fmicb.2019.02224.
Hamilton-Brehm, Scott D., Stewart, Laura E., Zavarin, Mavrik, Caldwell, Matt, Lawson, Paul A., Onstott, Tullis C., Grzymski, Joseph, Neveux, Iva, Lollar, Barbara Sherwood, Russell, Charles E., & Moser, Duane P. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin. United States. doi:10.3389/fmicb.2019.02224.
Hamilton-Brehm, Scott D., Stewart, Laura E., Zavarin, Mavrik, Caldwell, Matt, Lawson, Paul A., Onstott, Tullis C., Grzymski, Joseph, Neveux, Iva, Lollar, Barbara Sherwood, Russell, Charles E., and Moser, Duane P. Fri . "Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin". United States. doi:10.3389/fmicb.2019.02224. https://www.osti.gov/servlets/purl/1568019.
@article{osti_1568019,
title = {Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin},
author = {Hamilton-Brehm, Scott D. and Stewart, Laura E. and Zavarin, Mavrik and Caldwell, Matt and Lawson, Paul A. and Onstott, Tullis C. and Grzymski, Joseph and Neveux, Iva and Lollar, Barbara Sherwood and Russell, Charles E. and Moser, Duane P.},
abstractNote = {Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 – 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15:0, C15:0, C16:0 and C14:0. The percentage of the straight-chain fatty acid C15:0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).},
doi = {10.3389/fmicb.2019.02224},
journal = {Frontiers in Microbiology},
number = na,
volume = 10,
place = {United States},
year = {2019},
month = {9}
}

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