Jelly-like Microbial Mats over Subsurface Fields of Gas Hydrates at the St. Petersburg Methane Seep (Central Baikal)

<div><p>Jelly-like microbial mat samples were collected from benthic surfaces at the St. Petersburg methane seep located in Central Baikal. The concentrations of certain ions, specifically chloride, bromide, sulphate, acetate, iron, calcium, and magnesium, were 2–40 times higher in the microbial mats than those in the pore and bottom water. A large number of diatom valves, cyanobacteria, and filamentous, rod-shaped and coccal microorganisms were found in the samples of bacterial mats using light, epifluorescence and scanning microscopy.Comparative analysis of a 16S rRNA gene fragment demonstrated the presence of bacteria and archaea belonging to the following classes and phyla: Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Verrucomicrobia, Cytophaga-Flavobacteria-Bacteroidetes, Cyanobacteria, and Euryarchaeota. The chemical composition and phylogenetic structure of the microbial community showed that the life activity of the mat occurs due to methane and its derivatives involved. Values of δ¹³C for the microbial mats varied from −73.6‰ to −65.8‰ and for animals from −68.9‰ to −36.6‰. Functional genes of the sequential methane oxidation (<i>pmoA</i> and <i>mxaF</i>) and different species of methanotrophic bacteria inhabiting cold ecosystems were recorded in the total DNA. Like in other psychroactive communities, the destruction of organic substances forming formed as a result of methanotrophy, terminates at the stage of acetate formation in the microbial mats of Lake Baikal (1,400 m depth). Its further transformation is limited by hydrogen content and carried out in the subsurface layers of sediments.</p></div

Diversity of <i>Archaea</i> in Bottom Sediments of the Discharge Areas With Oil- and Gas-Bearing Fluids in Lake Baikal

<p>Using massively parallel sequencing (the Roche 454 platform) we have studied the diversity of archaeal 16S rRNA gene sequences in oxic and anoxic sediments at six sites in Lake Baikal with oil- and gas-bearing fluids discharge. Archaeal communities appeared to be represented mainly by five phyla: <i>Euryarchaeota, Crenarchaeota, Thaumarchaeota, Bathyarchaeota</i> (miscellaneous Crenarchaeotic group), and <i>Woesearchaeota</i> (deep sea hydrothermal vent group 6). Among them we detected sequences of methanogens of the orders <i>Methanomicrobiales, Methanosarsinales, Methanococcales</i>, as well as representatives of the following uncultured archaeal lineages: Group C3, Marine Benthic Group D, and Terrestrial Miscellaneous Group. We have also identified sequences of ammonia-oxidizing archaea of the phyla <i>Crenarchaeota</i> and <i>Thaumarchaeota</i>. Phylogenetic analysis showed the presence ANME-2d-related sequences. However, the analysis of <i>mcr</i>A genes libraries has not revealed typical representatives of ANME groups. Comparison of amplicon libraries 16S rRNA gene fragments from different samples proved the widespread presence of previously detected Baikal archaeal lineages, which are members of the phylum <i>Crenarchaeota</i> and <i>Thaumarchaeota</i> (formerly Group C3 of <i>Crenarchaeota</i>).</p

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.</p