Assembling the marine metagenome, one cell at a time

Area of Science:

• Microbiology
• Genomics
• Marine Biology

Background:

• Cultivating microorganisms and reconstructing genomes from complex microbial communities is challenging.
• Marine bacterioplankton are numerically significant but often uncultured, limiting genomic study.

Purpose of the Study:

• To obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms using single cell sequencing.
• To analyze the metabolic potential, ecological significance, and biogeography of these uncultured taxa.

Main Methods:

• Single cell sequencing utilizing fluorescence-activated cell sorting and multiple displacement amplification.
• Shotgun sequencing, genome finishing, and rigorous quality control for contaminant removal.
• Metagenomic recruitment using Global Ocean Sampling (GOS) data and metabolic reconstruction.

Main Results:

• High-quality genome assemblies (1.9 Mbp and 1.5 Mbp) were generated for two marine flavobacteria with high recovery rates (91% and 78%).
• Single cell genomes recruited strongly to GOS metagenomic data, confirming numerical significance and revealing biogeographic patterns linked to ocean currents.
• Metabolic reconstruction indicated diverse energy sources, and comparative analysis revealed small genome sizes and adaptations to narrow ecological niches in uncultured flavobacteria.

Conclusions:

• Single cell DNA sequencing is a powerful method for generating reference genomes of uncultured taxa from complex microbial communities.
• The study provides insights into the genomic content, metabolic adaptations, and biogeography of abundant, yet previously uncultured, marine bacterioplankton.
• Genomic features of these uncultured flavobacteria may explain their abundance and resistance to cultivation.