title: Microbial community assembly and evolution in subseafloor sediment.
abstract: Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Piotr
authors.initials: P
authors.lastname: Starnawski
authors.affiliation: Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bataillon
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden.
authors.forename: Thijs J G
authors.initials: TJ
authors.lastname: Ettema
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Lara M
authors.initials: LM
authors.lastname: Jochum
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Lars
authors.initials: L
authors.lastname: Schreiber
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Xihan
authors.initials: X
authors.lastname: Chen
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Lever
authors.affiliation: Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
authors.forename: Martin F
authors.initials: MF
authors.lastname: Polz
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
authors.forename: Bo B
authors.initials: BB
authors.lastname: Jørgensen
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; andreas.schramm@bios.au.dk kasperuk@bios.au.dk.|Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schramm
authors.affiliation: Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; andreas.schramm@bios.au.dk kasperuk@bios.au.dk.
authors.forename: Kasper U
authors.initials: KU
authors.lastname: Kjeldsen
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D005075:Biological Evolution; D018533:Biomass; D014644:Genetic Variation; D019015:Geologic Sediments / Q000382:microbiology*; D056186:Metagenomics / Q000379:methods; D064307:Microbiota; D009154:Mutation
keywords: bacteria; evolution; marine sediment; metagenomics; single-cell genomics