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

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.

doi:10.1186/1471-2164-15-924

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

Journal Article · Thu Oct 23 00:00:00 EDT 2014 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-15-924· OSTI ID:1407257

Dmytrenko, Oleg ^[1]; Russell, Shelbi L. ^[1]; Loo, Wesley T. ^[1]; Fontanez, Kristina M. ^[2]; Liao, Li ^[3]; Roeselers, Guus ^[4]; Sharma, Raghav ^[5]; Stewart, Frank J. ^[5]; Newton, Irene LG ^[6]; Woyke, Tanja ^[7]; Wu, Dongying ^[8]; Lang, Jenna ^[8]; Eisen, Jonathan A. ^[8]; Cavanaugh, Colleen M. ^[1]

Harvard Univ., Cambridge, MA (United States). Dept. of Organismic and Evolutionary Biology
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
Polar Research Inst. of China, Shanghai (China). SOA Key Lab. for Polar Science
TNO, Zeist (The Netherlands). Microbiology & Systems Biology Group
Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology
Indiana Univ., Bloomington, IN (United States). Dept. of Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of California, Davis, CA (United States). Genome Center

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1407257

Journal Information:: BMC Genomics, Vol. 15, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 20 works

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Genomes of ubiquitous marine and hypersaline Hydrogenovibrio , Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments : Hydrogenovibrio, Thiomicrorhabdus, Thiomicrospira Scott, Kathleen M.; Williams, John; Porter, Cody M. B. Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14090	journal	April 2018
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Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi McCuaig, Bonita; Peña-Castillo, Lourdes; Dufour, Suzanne C. Animal Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/s42523-020-00025-9	journal	March 2020
The role of microbial motility and chemotaxis in symbiosis Raina, Jean-Baptiste; Fernandez, Vicente; Lambert, Bennett Nature Reviews Microbiology, Vol. 17, Issue 5 https://doi.org/10.1038/s41579-019-0182-9	journal	March 2019
Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont Ikuta, Tetsuro; Igawa, Kanae; Tame, Akihiro Royal Society Open Science, Vol. 3, Issue 5 https://doi.org/10.1098/rsos.160130	journal	May 2016
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59 BASIC BIOLOGICAL SCIENCES
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Heterotrophy
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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

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