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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.

Show MeSH
The Lost City Thiomicrospira population is represented by the largest metagenomic contigs.(A) All contigs larger than 10 kb have tblastn hits with at least one T. crunogena protein with an E value better than 10−50. These large contigs are present at 5–8x sequencing coverage. (B) Large contigs with T. crunogena-related sequences are ∼38%GC; the T. crunogena genome is 43%GC.
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pone-0013530-g002: The Lost City Thiomicrospira population is represented by the largest metagenomic contigs.(A) All contigs larger than 10 kb have tblastn hits with at least one T. crunogena protein with an E value better than 10−50. These large contigs are present at 5–8x sequencing coverage. (B) Large contigs with T. crunogena-related sequences are ∼38%GC; the T. crunogena genome is 43%GC.

Mentions: 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].


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

Brazelton WJ, Baross JA - PLoS ONE (2010)

The Lost City Thiomicrospira population is represented by the largest metagenomic contigs.(A) All contigs larger than 10 kb have tblastn hits with at least one T. crunogena protein with an E value better than 10−50. These large contigs are present at 5–8x sequencing coverage. (B) Large contigs with T. crunogena-related sequences are ∼38%GC; the T. crunogena genome is 43%GC.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0013530-g002: The Lost City Thiomicrospira population is represented by the largest metagenomic contigs.(A) All contigs larger than 10 kb have tblastn hits with at least one T. crunogena protein with an E value better than 10−50. These large contigs are present at 5–8x sequencing coverage. (B) Large contigs with T. crunogena-related sequences are ∼38%GC; the T. crunogena genome is 43%GC.
Mentions: 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].

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