Targeted isolation based on metagenome-assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere

Most microorganisms from deep terrestrial subsurface remain yet uncultured. Recent achievements in recovery of metagenome-assembled genomes (MAG) provide clues for improving cultivation via metabolic reconstructions and other genomic characteristics. Here we report the isolation in pure culture of a thermophilic spirochete with the use of MAGs binned from metagenomes of the deep (>2 km) aquifers broached by two artesian boreholes in Western Siberia. The organism constitutes a minor share in the aquifer microbial community and could not be cultivated by traditional techniques. The obtained two pure culture isolates along with three bacteria identified by MAGs represent a novel family-level lineage in the orderBrevinematales. Based on genomic and phenotypic characteristics the novel spirochete is proposed to be classified asLonginema margulisiaegen. nov., sp. nov. within a novel family,Longinemaceaefam. nov. Both cultivated strains, NS(T)and N5R, are anaerobic hemoorganoheterotrophes growing by fermentation of starch and a few sugars. They can form recalcitrant round bodies under unfavourable growth conditions, which survive up to 15 min at 95 degrees C and can revert to the original helical cells. We suggest that the round bodies may facilitate global distribution of this lineage, detected from molecular signaturesand colonization of subsurface environments.

Automated summary

This study reports the isolation and cultivation of a thermophilic spirochete from deep groundwater, with genomic and phenotypic characteristics suggesting a novel taxonomic classification. The isolated strains, identified as anaerobic hemoorganoheterotrophs, exhibit unique growth features such as forming recalcitrant round bodies under unfavorable conditions. These round bodies may aid in the global distribution and colonization of this lineage in subsurface environments.