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Metagenomic comparison of two Thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments.

Brazelton WJ, Baross JA - PLoS ONE (2010)

Bottom Line: Comparative genomic analyses also revealed substantial genomic changes that must have occurred since the divergence of the two lineages, including large genomic rearrangements, gene fusion events, a prophage insertion, and transposase activity.Our results show significant genomic similarity between Thiomicrospira organisms inhabiting different kinds of hydrothermal systems in different oceans, suggesting that these organisms are widespread and highly adaptable.These data also indicate genomic processes potentially associated with the adaptation of these lineages into strikingly different habitats.

View Article: PubMed Central - PubMed

Affiliation: School of Oceanography and Center for Astrobiology and Early Evolution, University of Washington, Seattle, Washington, United States of America. braz@uw.edu

ABSTRACT

Background: The most widespread bacteria in oxic zones of carbonate chimneys at the serpentinite-hosted Lost City hydrothermal field, Mid-Atlantic Ridge, belong to the Thiomicrospira group of sulfur-oxidizing chemolithoautotrophs. It is unclear why Thiomicrospira-like organisms thrive in these chimneys considering that Lost City hydrothermal fluids are notably lacking in hydrogen sulfide and carbon dioxide.

Methodology/principal findings: Here we describe metagenomic sequences obtained from a Lost City carbonate chimney that are highly similar to the genome of Thiomicrospira crunogena XCL-2, an isolate from a basalt-hosted hydrothermal vent in the Pacific Ocean. Even though T. crunogena and Lost City Thiomicrospira inhabit different types of hydrothermal systems in different oceans, their genomic contents are highly similar. For example, sequences encoding the sulfur oxidation and carbon fixation pathways (including a carbon concentration mechanism) of T. crunogena are also present in the Lost City metagenome. Comparative genomic analyses also revealed substantial genomic changes that must have occurred since the divergence of the two lineages, including large genomic rearrangements, gene fusion events, a prophage insertion, and transposase activity.

Conclusions/significance: Our results show significant genomic similarity between Thiomicrospira organisms inhabiting different kinds of hydrothermal systems in different oceans, suggesting that these organisms are widespread and highly adaptable. These data also indicate genomic processes potentially associated with the adaptation of these lineages into strikingly different habitats.

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Most metagenomic reads from a Lost City carbonate chimney have moderate sequence similarity with Thiomicrospira crunogena XCL-2.Shotgun reads with >500 bp BLASTN alignments with the T. crunogena genome are binned according to the nucleotide sequence similarity (x-axis) of the BLASTN alignments. The y-axis represents the T. crunogena coverage for the reads in each bin where coverage corresponds to the ratio of the total number of aligned base pairs in each bin to the total number of base pairs in the T. crunogena genome, as in Figure 2 of [31].
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pone-0013530-g001: Most metagenomic reads from a Lost City carbonate chimney have moderate sequence similarity with Thiomicrospira crunogena XCL-2.Shotgun reads with >500 bp BLASTN alignments with the T. crunogena genome are binned according to the nucleotide sequence similarity (x-axis) of the BLASTN alignments. The y-axis represents the T. crunogena coverage for the reads in each bin where coverage corresponds to the ratio of the total number of aligned base pairs in each bin to the total number of base pairs in the T. crunogena genome, as in Figure 2 of [31].

Mentions: As previously reported [17], we obtained 35 Mb of metagenomic sequence from 46 361 shotgun reads of two pUC18 libraries constructed by the DOE Joint Genome Institute with DNA extracted from ∼1 kg of a single Lost City carbonate chimney sample. A large proportion of the total shotgun reads (14.6%) had BLASTN alignments >500 bp with the Thiomicrospira crunogena XCL-2 genome [12]. Most of these reads exhibited 67–71% nucleotide similarity with T. crunogena, and very few reads contained sequences with >84% similarity (Figure 1). These data indicate that the Lost City metagenomic dataset is dominated by a population that is genotypically uniform and contains moderate sequence similarity with T. crunogena.


Metagenomic comparison of two Thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments.

Brazelton WJ, Baross JA - PLoS ONE (2010)

Most metagenomic reads from a Lost City carbonate chimney have moderate sequence similarity with Thiomicrospira crunogena XCL-2.Shotgun reads with >500 bp BLASTN alignments with the T. crunogena genome are binned according to the nucleotide sequence similarity (x-axis) of the BLASTN alignments. The y-axis represents the T. crunogena coverage for the reads in each bin where coverage corresponds to the ratio of the total number of aligned base pairs in each bin to the total number of base pairs in the T. crunogena genome, as in Figure 2 of [31].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2958825&req=5

pone-0013530-g001: Most metagenomic reads from a Lost City carbonate chimney have moderate sequence similarity with Thiomicrospira crunogena XCL-2.Shotgun reads with >500 bp BLASTN alignments with the T. crunogena genome are binned according to the nucleotide sequence similarity (x-axis) of the BLASTN alignments. The y-axis represents the T. crunogena coverage for the reads in each bin where coverage corresponds to the ratio of the total number of aligned base pairs in each bin to the total number of base pairs in the T. crunogena genome, as in Figure 2 of [31].
Mentions: As previously reported [17], we obtained 35 Mb of metagenomic sequence from 46 361 shotgun reads of two pUC18 libraries constructed by the DOE Joint Genome Institute with DNA extracted from ∼1 kg of a single Lost City carbonate chimney sample. A large proportion of the total shotgun reads (14.6%) had BLASTN alignments >500 bp with the Thiomicrospira crunogena XCL-2 genome [12]. Most of these reads exhibited 67–71% nucleotide similarity with T. crunogena, and very few reads contained sequences with >84% similarity (Figure 1). These data indicate that the Lost City metagenomic dataset is dominated by a population that is genotypically uniform and contains moderate sequence similarity with T. crunogena.

Bottom Line: Comparative genomic analyses also revealed substantial genomic changes that must have occurred since the divergence of the two lineages, including large genomic rearrangements, gene fusion events, a prophage insertion, and transposase activity.Our results show significant genomic similarity between Thiomicrospira organisms inhabiting different kinds of hydrothermal systems in different oceans, suggesting that these organisms are widespread and highly adaptable.These data also indicate genomic processes potentially associated with the adaptation of these lineages into strikingly different habitats.

View Article: PubMed Central - PubMed

Affiliation: School of Oceanography and Center for Astrobiology and Early Evolution, University of Washington, Seattle, Washington, United States of America. braz@uw.edu

ABSTRACT

Background: The most widespread bacteria in oxic zones of carbonate chimneys at the serpentinite-hosted Lost City hydrothermal field, Mid-Atlantic Ridge, belong to the Thiomicrospira group of sulfur-oxidizing chemolithoautotrophs. It is unclear why Thiomicrospira-like organisms thrive in these chimneys considering that Lost City hydrothermal fluids are notably lacking in hydrogen sulfide and carbon dioxide.

Methodology/principal findings: Here we describe metagenomic sequences obtained from a Lost City carbonate chimney that are highly similar to the genome of Thiomicrospira crunogena XCL-2, an isolate from a basalt-hosted hydrothermal vent in the Pacific Ocean. Even though T. crunogena and Lost City Thiomicrospira inhabit different types of hydrothermal systems in different oceans, their genomic contents are highly similar. For example, sequences encoding the sulfur oxidation and carbon fixation pathways (including a carbon concentration mechanism) of T. crunogena are also present in the Lost City metagenome. Comparative genomic analyses also revealed substantial genomic changes that must have occurred since the divergence of the two lineages, including large genomic rearrangements, gene fusion events, a prophage insertion, and transposase activity.

Conclusions/significance: Our results show significant genomic similarity between Thiomicrospira organisms inhabiting different kinds of hydrothermal systems in different oceans, suggesting that these organisms are widespread and highly adaptable. These data also indicate genomic processes potentially associated with the adaptation of these lineages into strikingly different habitats.

Show MeSH