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

Journal Article · Wed Jan 01 00:00:00 EST 2014 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2014.00231· OSTI ID:1149760

Hanke, Anna ^[1]; Hamann, Emmo ^[1]; Sharma, Ritin ^[2]; Geelhoed, Jeanine ^[1]; Hargesheimer, Theresa ^[1]; Kraft, Beate ^[1]; Meyer, Volker ^[1]; Lenk, Sabine ^[1]; Osmers, Harald ^[1]; Wu, Rong ^[3]; Makinwa, Kofi ^[3]; Banfield, Jillian F. ^[4]; Tegetmeyer, Halina ^[1]; Strouss, Marc ^[5]

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1. Max Planck Institute for Marine Microbiology
2. ORNL
3. Delft University of Technology, Delft, Netherlands
4. University of California, Berkeley
5. University of Calgary, ALberta, Canada

Sandy coastal sediments are global hot spots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective pore water flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfuroxidizing Gammaproteobacteria and members of the enigmaticBD1-5/ SN-2 candidatephylumwereabundantinsitu (>10% and 2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sedimentin a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescenceinsituhybridization showed that this simplified community contained both a potential sulfuroxidizing Gamma proteobacteria (at 24 2% abundance) and a member of the BD1-5 / SN-2candidatephylum (at 7 6%abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gamma proteobacterium grew partially auto trophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2candidatephylum enabled, for the first time, direct microscopic observation by fluorescent insitu hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: Work for Others (WFO)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 1149760
• Journal Information: Frontiers in Microbiology, Vol. 5, Issue 231
• Country of Publication: United States
• Language: English