title: Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat.
abstract: Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Hanke
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Emmo
authors.initials: E
authors.lastname: Hamann
authors.affiliation: UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Ritin
authors.initials: R
authors.lastname: Sharma
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Jeanine S
authors.initials: JS
authors.lastname: Geelhoed
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Theresa
authors.initials: T
authors.lastname: Hargesheimer
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Beate
authors.initials: B
authors.lastname: Kraft
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Meyer
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Lenk
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany.
authors.forename: Harald
authors.initials: H
authors.lastname: Osmers
authors.affiliation: Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands.
authors.forename: Rong
authors.initials: R
authors.lastname: Wu
authors.affiliation: Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands.
authors.forename: Kofi
authors.initials: K
authors.lastname: Makinwa
authors.affiliation: UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.affiliation: Department of Earth and Planetary Science, Department of Environmental Science, Policy, and Management, University of California Berkeley, CA, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany.
authors.forename: Halina E
authors.initials: HE
authors.lastname: Tegetmeyer
authors.affiliation: Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada.
authors.forename: Marc
authors.initials: M
authors.lastname: Strous
keywords: Maritimibacter; Roseobacter; chemostat; continuous culture; enrichment; stop codon