Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Area of Science:

• Microbiology
• Genomics
• Biotechnology

Background:

• Traditional microbial functional assignment relies on cultivation or known biomarkers.
• Function-driven single-cell genomics offers a new paradigm for identifying microbes by their in situ functions.
• Uncultivated microbes represent a vast, unexplored source of novel biological functions.

Purpose of the Study:

• To develop and validate a function-driven single-cell screen for identifying cellulose-degrading microorganisms.
• To characterize novel microbial taxa involved in cellulose degradation from a geothermal environment.
• To link microbial taxonomy directly to in situ function for uncultivated species.

Main Methods:

• Developed a function-driven single-cell screen using fluorescently labeled cellulose particles.
• Employed fluorescence-activated cell sorting (FACS) to isolate single microbe-bound particles.
• Utilized whole genome amplification, shotgun sequencing, phylogenetic placement, and gene expression analysis.

Main Results:

• Successfully identified and characterized novel cellulose-degrading microbes from the Great Boiling Spring (GBS) Geothermal Field.
• Discovered divergent cellulases in a candidate phylum, Goldbacteria, from the rare biosphere.
• Proposed a new species, Candidatus 'Cellulosimonas argentiregionis', with novel cellulolytic activity.

Conclusions:

• The function-driven single-cell approach is effective for discovering uncultivated microbes with specific functions.
• This methodology expands the identification of cellulose degraders beyond known taxa.
• The approach holds potential for broad application in linking microbial taxonomy to diverse in situ functions across various substrates.