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Title: The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

Abstract

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as anmore » endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [4];  [5];  [5];  [6];  [7];  [8];  [8];  [8];  [1]
  1. Harvard Univ., Cambridge, MA (United States). Dept. of Organismic and Evolutionary Biology
  2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
  3. Polar Research Inst. of China, Shanghai (China). SOA Key Lab. for Polar Science
  4. TNO, Zeist (The Netherlands). Microbiology & Systems Biology Group
  5. Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology
  6. Indiana Univ., Bloomington, IN (United States). Dept. of Biology
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Univ. of California, Davis, CA (United States). Genome Center
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1407257
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Symbiosis; Chemosynthesis; Sulfur oxidation; Respiratory flexibility; H+/Na+ -membrane cycles; Calvin cycle; Pyrophosphate-dependent phosphofructokinase; Heterotrophy; Motility; Mobile genetic elements

Citation Formats

Dmytrenko, Oleg, Russell, Shelbi L., Loo, Wesley T., Fontanez, Kristina M., Liao, Li, Roeselers, Guus, Sharma, Raghav, Stewart, Frank J., Newton, Irene LG, Woyke, Tanja, Wu, Dongying, Lang, Jenna, Eisen, Jonathan A., and Cavanaugh, Colleen M. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. United States: N. p., 2014. Web. doi:10.1186/1471-2164-15-924.
Dmytrenko, Oleg, Russell, Shelbi L., Loo, Wesley T., Fontanez, Kristina M., Liao, Li, Roeselers, Guus, Sharma, Raghav, Stewart, Frank J., Newton, Irene LG, Woyke, Tanja, Wu, Dongying, Lang, Jenna, Eisen, Jonathan A., & Cavanaugh, Colleen M. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. United States. doi:10.1186/1471-2164-15-924.
Dmytrenko, Oleg, Russell, Shelbi L., Loo, Wesley T., Fontanez, Kristina M., Liao, Li, Roeselers, Guus, Sharma, Raghav, Stewart, Frank J., Newton, Irene LG, Woyke, Tanja, Wu, Dongying, Lang, Jenna, Eisen, Jonathan A., and Cavanaugh, Colleen M. Thu . "The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis". United States. doi:10.1186/1471-2164-15-924. https://www.osti.gov/servlets/purl/1407257.
@article{osti_1407257,
title = {The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis},
author = {Dmytrenko, Oleg and Russell, Shelbi L. and Loo, Wesley T. and Fontanez, Kristina M. and Liao, Li and Roeselers, Guus and Sharma, Raghav and Stewart, Frank J. and Newton, Irene LG and Woyke, Tanja and Wu, Dongying and Lang, Jenna and Eisen, Jonathan A. and Cavanaugh, Colleen M.},
abstractNote = {Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.},
doi = {10.1186/1471-2164-15-924},
journal = {BMC Genomics},
number = 1,
volume = 15,
place = {United States},
year = {Thu Oct 23 00:00:00 EDT 2014},
month = {Thu Oct 23 00:00:00 EDT 2014}
}

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