The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs View Full Text


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Article Info

DATE

2012-06-14

AUTHORS

Ryan A Lesniewski, Sunit Jain, Karthik Anantharaman, Patrick D Schloss, Gregory J Dick

ABSTRACT

Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3–4 times) and microbially mediated manganese oxidation rates (15–125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10–20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California. More... »

PAGES

2257-2268

References to SciGraph publications

  • 2011-02-20. Metal flux from hydrothermal vents increased by organic complexation in NATURE GEOSCIENCE
  • 1986-04. Microorganisms in deep-sea hydrothermal plumes in NATURE
  • 2008-11-26. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic in NATURE
  • 2011-11-17. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-11-14. Carbon release by off-axis magmatism in a young sedimented spreading centre in NATURE GEOSCIENCE
  • 1986-07. Bacterial scavenging of Mn and Fe in a mid- to far-field hydrothermal particle plume in NATURE
  • 2012-06-14. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-03-14. Hydrothermal contribution to the oceanic dissolved iron inventory in NATURE GEOSCIENCE
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2010-12-09. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2004-08-24. Molecular Analysis of Deep-Sea Hydrothermal Vent Aerobic Methanotrophs by Targeting Genes of 16S rRNA and Particulate Methane Monooxygenase in MARINE BIOTECHNOLOGY
  • 2004-10-14. Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay in MICROBIAL ECOLOGY
  • 2008-09-19. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes in BMC BIOINFORMATICS
  • 2008-12-10. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs in NATURE
  • 2009-05. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column in NATURE
  • 2008-05-08. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 1984-05. Bacterial chemolithotrophy in the ocean is associated with sinking particles in NATURE
  • 2010-02-11. Distributions of putative aerobic methanotrophs in diverse pelagic marine environments in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2001-01. Archaeal dominance in the mesopelagic zone of the Pacific Ocean in NATURE
  • 2009-02-08. Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume in NATURE GEOSCIENCE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2012.63

    DOI

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22695860


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    45 schema:description Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3–4 times) and microbially mediated manganese oxidation rates (15–125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10–20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.
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