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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.


Maximum likelihood phylogenetic tree of the concatenated amino acid and SSU rRNA sequences constructed using RAxML with a mixed/partitioned model and per gene optimization of branch lengths with 100 bootstraps. Bootstrap values of 20 and above are reported. The Crenarchaeota Staphylothermus marinus was used as an outgroup. Genomes containing carbon monoxide dehydrogenase genes are labeled CODH.
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Figure 2: Maximum likelihood phylogenetic tree of the concatenated amino acid and SSU rRNA sequences constructed using RAxML with a mixed/partitioned model and per gene optimization of branch lengths with 100 bootstraps. Bootstrap values of 20 and above are reported. The Crenarchaeota Staphylothermus marinus was used as an outgroup. Genomes containing carbon monoxide dehydrogenase genes are labeled CODH.

Mentions: The ML phylogeny of concatenated MLST loci differentiated isolates into clades that are in general agreement with isolate groupings through AFLP cluster analysis (Figure 2 and Figure S2). Isolates from the JdF and EPR are differentiated into lineages that are phylogenetically related across these two regions (Figure 2). The regional divergence among phylogenetically related isolates is most apparent in the paraphyly observed between Clades VII and VIII. A general pattern of isolates differentiated by region was observed with individual clades made up of isolates from that same region. Regional groupings were most apparent in the isolates associated with the JDF and EPR; however, regional groupings were also observed in the two isolates from the Mariana Arc, the type strains T. peptonophilus and T. kodakaraenis both from Japan, and the type strains T. sp. 4557 and T. sp. AM4 isolated from the EPR (which both group with lineages also from the EPR). Exceptions to regional groupings are seen in Clades I and X, a pattern also observed through AFLP cluster analysis. Clade I contains isolates from the JdF Ridge, Loihi Seamount, and the type strain T. barophilus from the Mid Atlantic Ridge (MAR). Clade X contains isolates from the Gorda Ridge, an isolate from the CoAxial Segment (of the JdF), and the type strain T. onnurines from the PACMANUS Basin, with all of these isolates sharing 99% sequence identity. Pyrococcus type strains along with Clade I, the type strain T. sibiricus and isolate MV5 are placed in a basal position in the phylogenetic tree, ancestral to Clades II through X. The type strain P. yayanosii has the shortest distance, from these basal groups, to Thermococcus isolates in Clades II through X. The ancestral relationship between Pyrococcus type strains and Thermococcus isolates in the ML phylogeny of concatenated MLST loci remains unresolved.


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

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

Maximum likelihood phylogenetic tree of the concatenated amino acid and SSU rRNA sequences constructed using RAxML with a mixed/partitioned model and per gene optimization of branch lengths with 100 bootstraps. Bootstrap values of 20 and above are reported. The Crenarchaeota Staphylothermus marinus was used as an outgroup. Genomes containing carbon monoxide dehydrogenase genes are labeled CODH.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Maximum likelihood phylogenetic tree of the concatenated amino acid and SSU rRNA sequences constructed using RAxML with a mixed/partitioned model and per gene optimization of branch lengths with 100 bootstraps. Bootstrap values of 20 and above are reported. The Crenarchaeota Staphylothermus marinus was used as an outgroup. Genomes containing carbon monoxide dehydrogenase genes are labeled CODH.
Mentions: The ML phylogeny of concatenated MLST loci differentiated isolates into clades that are in general agreement with isolate groupings through AFLP cluster analysis (Figure 2 and Figure S2). Isolates from the JdF and EPR are differentiated into lineages that are phylogenetically related across these two regions (Figure 2). The regional divergence among phylogenetically related isolates is most apparent in the paraphyly observed between Clades VII and VIII. A general pattern of isolates differentiated by region was observed with individual clades made up of isolates from that same region. Regional groupings were most apparent in the isolates associated with the JDF and EPR; however, regional groupings were also observed in the two isolates from the Mariana Arc, the type strains T. peptonophilus and T. kodakaraenis both from Japan, and the type strains T. sp. 4557 and T. sp. AM4 isolated from the EPR (which both group with lineages also from the EPR). Exceptions to regional groupings are seen in Clades I and X, a pattern also observed through AFLP cluster analysis. Clade I contains isolates from the JdF Ridge, Loihi Seamount, and the type strain T. barophilus from the Mid Atlantic Ridge (MAR). Clade X contains isolates from the Gorda Ridge, an isolate from the CoAxial Segment (of the JdF), and the type strain T. onnurines from the PACMANUS Basin, with all of these isolates sharing 99% sequence identity. Pyrococcus type strains along with Clade I, the type strain T. sibiricus and isolate MV5 are placed in a basal position in the phylogenetic tree, ancestral to Clades II through X. The type strain P. yayanosii has the shortest distance, from these basal groups, to Thermococcus isolates in Clades II through X. The ancestral relationship between Pyrococcus type strains and Thermococcus isolates in the ML phylogeny of concatenated MLST loci remains unresolved.

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.