Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor

Peer reviewedPostprin

Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-IMRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-IMRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-IMRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens

Sulfur-assisted urea synthesis from carbon monoxide and ammonia in water

Efficient conversion of carbon monoxide into urea in an aqueous ammonia solution was demonstrated through coupling with the elemental sulfur reduction to polysulfides. Polysulfides control the overall reaction rate while suppressing the accumulation of a by-product, hydrogen sulfide. These functions follow basic kinetic and thermodynamic theories, enabling prediction-based reaction control. This operational merit, together with the superiority of water as a green solvent, suggests that our demonstrated urea synthesis is a promising option for sulfur utilization beneficial for agricultural production

In situ measurement of liquid and gas CO₂ with high purity at deep-sea hydrothermal vents in the Mariana Arc using Raman spectroscopy

Supercritical and liquid CO2 (sc-/liq-CO2) emitted from deep-sea hydrothermal vents create a unique dry environment distinct from seawater and hydrothermal fluids, whose physicochemical characteristics could play an important role in the ocean biogeochemical cycles of the present Earth and even in the prebiotic chemical evolution of the early Earth. While previous studies attempted to sample and analyze sc-/liq-CO2 in several hydrothermal fields, the sampling and analysis without seawater contamination have been unsuccessful. In this study, we developed the method and apparatus for sampling and analyzing CO2 in different phases in which in situ Raman measurements can be directly performed and applied them to the CO2 emissions in two hydrothermal vent fields in the Mariana Arc. The in situ Raman spectra taken at both fields indicate that the high purity of CO2 emissions without seawater contamination was successfully sampled and measured. In the North-West Eifuku seamount, the collected hydrothermal fluid was monitored from the seafloor (approximately 1600  m) to the surface. The phase transitions of CO2─hydrate, liquid, and gas─were successfully observed in the Raman spectra. At the Daikoku seamount, the in situ Raman spectra taken at the seafloor (approximately 400 m) identified that the CO2 emission consisted of the gas phase. The in situ Raman measurement also revealed that gas H2S was abundant in the emissions at both the fields. This study demonstrates the ability of the Raman spectroscopic technique to monitor the phase transition of hydrothermal CO2 emissions and the chemical composition in different phases of CO2 in the oceans in real time

Viruses, Vesicles, and other Biological Nanoparticles: The Sub-cellular Biosphere of a Deeply Buried 2km-Deep, 20-Million-Year-Old Coalbed Community

Horizontal gene transfer is an important driver of adaptation and evolution in microorganisms. Transducing biological nanoparticles such as viral particles are believed to be key facilitators of horizontal gene transfer. In deep subseafloor sediments, energy can be highly limiting, supporting only extremely slow metabolisms. In such low-energy, isolated environments where communities may subsist for millions of years, the mechanisms of subsurface microbial adaptation and evolution remain a mystery. Virus particles have been found everywhere that life has been found, including deep subsurface environments. Although microorganisms are abundant and active in the Earth's subsurface, the role of viruses in shaping and influencing these slow-growing communities is only recently starting to be explored. Here, we analyzed the deeply buried microbial community from a lignite coalbed layer 2km below the seafloor offshore Shimokita, Japan (IODP Expedition 337) that had been buried for 20 million years. We harvested cells (>0.2µm) and biological nanoparticles (<0.2µm) from a bioreactor enrichment seeded by lignite core samples. We sequenced DNA from the cells and nanoparticles and subsequently analyzed the metagenomes. Within the nanoparticle metagenome, numerous complete novel virus genomes were reconstructed. Comparison of the virus genomes to the prokaryotic MAGs (metagenome assembled genomes) revealed that many of the virus genomes had been integrated prophage within bacterial genomes, suggesting the potential for virus-host interactions to occur in the deep subseafloor. Additionally, lysogeny may be an important survival mechanism for viruses in deeply buried, low-energy environments. Host genes were found to be packaged by viral particles, demonstrating the potential for specialized and general transduction by viruses. Not only viral particles, but there was also evidence that membrane vesicles and gene transfer agents may participate in transduction in this deep subsurface community. Horizontal gene transfer mediated by biological nanoparticles may be an important mechanism of adaptation for deep subsurface microbial communities and may provide insight into possible evolutionary processes shaping microbial communities in the deep subsurface. These results may also shed some light onto the nature of viral infection in the subsurface, potentially revealing insights about the long-term persistence of life under extreme energy limitation and how viruses may survive this over geological timescales