Abstract
Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.
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Acknowledgements
This work was supported by the China Ocean Mineral Resources R&D Association (COMRA DYXM115-05), the National Natural Science Foundation of China (40625016), the State High-Tech Development Project (2006AA09Z433, 2007AA091904 and 2008AA092603), project 2007DFA30840 of International S&T Cooperation Program from the Ministry of Science and Technology of China, key project of the Commission of Science and Technology of Guangdong Province and Guangzhou City and project of Sun Yet-sen University Science Foundation. SMS was supported by National Science Foundation grant OCE-0452333 and a fellowship awarded by the Alfried Krupp Wissenschaftskolleg Greifswald, Germany. We thank Huaiyang Zhou (Tongji University, Shanghai, China), Maurice A. Tivey (Woods Hole Oceanographic Institution, Woods Hole, MA, USA), Marvin D Lilley (University of Washington, Seattle, WA, USA), Deborah Kelly (University of Washington, Seattle, WA, USA), Kang Ding (University of Minnesota, Minneapolis, MN, USA) and all of the crew members from R/V Atlantis/DSV Alvin for their efforts and help in sample collection.
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Xie, W., Wang, F., Guo, L. et al. Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries. ISME J 5, 414–426 (2011). https://doi.org/10.1038/ismej.2010.144
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DOI: https://doi.org/10.1038/ismej.2010.144
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