Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

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.

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

“…Recent technological advances in DNA sequencing and single-cell study are opening up new and exciting pathways for studying microbial life in the dark ocean. The recent revolution in next-generation sequencing technology enables an improved understanding of the rare biosphere in nature (63,233,505) and allows comparisons of metagenomic data from geographically and geochemically distinct dark ocean habitats to determine differences in metabolic and life strategy potential (45,619). As sequencing costs decrease, the possibility of generating nearly complete genomes of uncultivated species from environmental samples is on the horizon, which may reveal new metabolic pathways in dark ocean habitats.…”

Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean

“…The database contained marine GSOs 'Candidatus Vesicomyosocius okutanii HA', 'Candidatus Ruthia magnifica Cm', the SUP05 metagenome (Walsh et al, 2009) and SCGC AAA001-B15 (Arctic96BD-19 draft genome); the methylotrophs Methylobacter tundripaludum SV96 and Methylomicrobium alcaliphilum; ironoxidizing bacteria Gallionella capsiferriformans ES-2 and Sideroxydans lithotrophicus ES-1; abundant lineages in seawater 'Candidatus Pelagibacter ubique HTCC1062' and 'Candidatus Pelagibacter ubique HTCC1002'; ammonia-oxidizing archaea Nitrosopumilus maritimus SCM1, an uncultured marine group II (Iverson et al, 2012); an incomplete hydrothermal vent metagenome (Xie et al, 2011); and common contaminants. SEQUEST (version UW2011.01.1) was used to correlate observed tandem mass spectra to peptide sequence via theoretical tandem mass spectra from the composite database described above (Eng et al, 1994(Eng et al, , 2008.…”

A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity

“…Approaches that are currently used for gathering information on environmental RubisCO gene clusters rely on sequence searches (for example, Xie et al, 2011). In some cases this has been advanced to subsequently determine the recombinant RubisCO activity in a surrogate host after having identified the RubisCO gene through sequence similarity first (Witte et al, 2010).…”