Genomic Analysis of Deeply-Branching Bacteria and Archaea from IODP Leg 347: Baltic Sea Paleoenvironment

Abstract:

Among the diverse inhabitants of the marine subsurface are “deeply-branching” bacteria and archaea, whose recent evolutionary ancestors have eluded isolation and characterization by traditional culture-based methods. By using single-cell genomics, we were able to target members of common deeply-branching mircorganisms found in a sediment core acquired during IODP Leg 347. Cells were separated from sediment layers (37 and 84 meters below the seafloor) deposited at site 60, hole B, near Anholt Island tens to hundreds of thousands of years ago. Ten single amplified genomes from 4 bacterial and 1 archaeal lineages were chosen from the 60 successfully sorted cells. The lineages include: Desulfobacterium sp., OPB41, OP8, NT-B2, Marine Group II archaea. Two lineages have not been genomically sampled before, while all 5 are frequently found in a variety of marine sediment habitats. The genome assemblies range in completeness from 45 – 85% and contain a number of phylogenetically relevant genes that has helped to anchor their position in the tree of life. The metabolic strategies, including putative sulfate reduction and carbon degradation pathways, employed by these cells have allowed them to survive in an environment with diminishing sources of labile carbon substrates.