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Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific.

Price MT, Fullerton H, Moyer CL - Front Microbiol (2015)

Bottom Line: The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus.In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus.The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Western Washington University Bellingham, WA, USA.

ABSTRACT
Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

No MeSH data available.


Location of vents within the two main regions sampled. The Juan de Fuca Ridge and associated vent segments with the Gorda Ridge to the south, and the East Pacific Rise. Sample sites within these two regions are at comparable distances from one another and provide nested sampling within regions. Image reproduced from the GEBCO world map 2014, www.gebco.net.
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Figure 1: Location of vents within the two main regions sampled. The Juan de Fuca Ridge and associated vent segments with the Gorda Ridge to the south, and the East Pacific Rise. Sample sites within these two regions are at comparable distances from one another and provide nested sampling within regions. Image reproduced from the GEBCO world map 2014, www.gebco.net.

Mentions: Sample material was collected from hydrothermal vent sites during research cruises between the years of 1988–2008. Study sites and sampling are as previously described (Holden et al., 2001; Summit and Baross, 2001; Huber et al., 2006; Davis and Moyer, 2008). Both submersible and remotely operated vehicles (ROV's) were used to collect a diversity of sample material that included plume samples, hot fluids, diffuse fluids, chimney walls, sulfide muds, and Alvinellid polychaete tissue samples. Sample material was used to inoculate liquid media for the enrichment of Thermococcales. Media formulations and methods are as previously described (Holden et al., 2001). Isolates in this culture collection were previously characterized through analysis of the SSU rRNA for genus level associations (Holden et al., 2001; Summit and Baross, 2001; Huber et al., 2006). The collection of 90 Thermococcus isolates contains representatives from the Juan de Fuca Ridge (JdF), Gorda Ridge, East Pacific Rise (EPR), Mid Atlantic Ridge (MAR), Mariana Arc and Loihi Seamount (Table 1). Sample sites within the JdF and EPR are at similar spatial distances providing nested sampling within these two regions (Figure 1). Distances among vents within regions range from ~65 to ~450 km, with distances between the main study sites, the JdF and EPR, up to ~7000 km. Thermococcus isolates and type strains from other regions, as well as Pyrococcus type strains, were included for comparison. Table S1 lists Thermococcus type strains included in AFLP and MLST analysis. Cultures of the type strains Thermococcus kodakarensis (JCM 12380) and Thermococcus onnurines (JCM 13517) were acquired through the Riken BioResource Center (Ibaraki, Japan) and were cultured in the same manner as other isolates in the collection. Genomic DNA for the type strains Thermococcus barophilus and Thermococcus peptonophilus were acquired from the American Type Culture Collection (Manassas, VA).


Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific.

Price MT, Fullerton H, Moyer CL - Front Microbiol (2015)

Location of vents within the two main regions sampled. The Juan de Fuca Ridge and associated vent segments with the Gorda Ridge to the south, and the East Pacific Rise. Sample sites within these two regions are at comparable distances from one another and provide nested sampling within regions. Image reproduced from the GEBCO world map 2014, www.gebco.net.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585236&req=5

Figure 1: Location of vents within the two main regions sampled. The Juan de Fuca Ridge and associated vent segments with the Gorda Ridge to the south, and the East Pacific Rise. Sample sites within these two regions are at comparable distances from one another and provide nested sampling within regions. Image reproduced from the GEBCO world map 2014, www.gebco.net.
Mentions: Sample material was collected from hydrothermal vent sites during research cruises between the years of 1988–2008. Study sites and sampling are as previously described (Holden et al., 2001; Summit and Baross, 2001; Huber et al., 2006; Davis and Moyer, 2008). Both submersible and remotely operated vehicles (ROV's) were used to collect a diversity of sample material that included plume samples, hot fluids, diffuse fluids, chimney walls, sulfide muds, and Alvinellid polychaete tissue samples. Sample material was used to inoculate liquid media for the enrichment of Thermococcales. Media formulations and methods are as previously described (Holden et al., 2001). Isolates in this culture collection were previously characterized through analysis of the SSU rRNA for genus level associations (Holden et al., 2001; Summit and Baross, 2001; Huber et al., 2006). The collection of 90 Thermococcus isolates contains representatives from the Juan de Fuca Ridge (JdF), Gorda Ridge, East Pacific Rise (EPR), Mid Atlantic Ridge (MAR), Mariana Arc and Loihi Seamount (Table 1). Sample sites within the JdF and EPR are at similar spatial distances providing nested sampling within these two regions (Figure 1). Distances among vents within regions range from ~65 to ~450 km, with distances between the main study sites, the JdF and EPR, up to ~7000 km. Thermococcus isolates and type strains from other regions, as well as Pyrococcus type strains, were included for comparison. Table S1 lists Thermococcus type strains included in AFLP and MLST analysis. Cultures of the type strains Thermococcus kodakarensis (JCM 12380) and Thermococcus onnurines (JCM 13517) were acquired through the Riken BioResource Center (Ibaraki, Japan) and were cultured in the same manner as other isolates in the collection. Genomic DNA for the type strains Thermococcus barophilus and Thermococcus peptonophilus were acquired from the American Type Culture Collection (Manassas, VA).

Bottom Line: The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus.In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus.The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Western Washington University Bellingham, WA, USA.

ABSTRACT
Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

No MeSH data available.