Biology subjects

Takamiya, H.

Publications and source records attributed to Takamiya, H..

2 recordsLinked to original sources

bioRxiv2023

Genome-resolved meta-omics unveils rock-hosted lifestyle of enigmatic DPANN archaea

Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats remains controversial. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock fractures, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be isolated from their hosts attached to rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we show the dominance of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea, in a deep-sea hydrothermal vent chimney. Metagenomic analysis of the rock sample revealed a symbiotic lifestyle of the chimney Pacearchaeota, based on the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids. Genome-resolved metaproteomic analysis clarified the co-occurrence of bacteria actively fixing carbon and nitrogen and thermophilic archaea in the rock habitat. Pacearchaeota has ecological advantages in colonizing the chimney rock interior, because the availability of nutrients and space is limited by silica deposition from hydrothermal fluids. We propose that the diversification of rock-hosted DPANN archaea could be profoundly influenced by coexisting microbes and minerals.

microbiology↗

bioRxiv2021

Ultra-small cells and DPANN genome unveiled inside an extinct vent chimney

Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. In contrast to actively venting chimneys, the nature of microbial life in extinct chimneys without fluid venting remains largely unknown. Here, the occurrence of ultra-small cells in silica-filled grain boundaries inside an extinct chimney is demonstrated by high-resolution bio-signature mapping. The ultra-small cells are associated with extracellularly precipitated Cu2O nanocrystals. Single-gene analysis shows that the chimney interior is dominated by a member of Pacearchaeota known as a major phylum of DPANN. Genome-resolved metagenomic analysis reveals that the chimney Pacearchaeota member is equipped with a nearly full set of genes for fermentation-based energy generation from nucleic acids, in contrast to previously characterized Pacearchaeota members lacking many genes for nucleic acid fermentation. We infer that the ultra-small cells associated with silica and extracellular Cu2O nanocrystals in the grain boundaries are Pacearchaeota, on the basis of the experimentally demonstrated capability of silica to concentrate nucleic acids from seawater and the presence of Cu-exporting genes in a reconstructed Pacearchaeota genome. Given the existence of ~3-billion-year-old submarine hydrothermally deposited silica, proliferation of microbial life using silica-bound nucleic acids might be relevant to the primitive vent biosphere.

microbiology↗