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.

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla

“…Consistent with previous metagenomic reconstruction of BD1‐5 genomes, the CG Bin 11 BD1‐5 is predicted to use an alternative genetic code (Wrighton et al ., ), in which the UGA stop codon is translated as glycine, as predicted for related CP SR1 bacteria (Campbell et al ., ; Kantor et al ., ). This coding was recently confirmed by proteomic analysis (Hanke et al ., ). Notably, the incidence of the UGA codon in the CG BD1‐5 genotype is low (0.74%), relative to the incidence in other similarly alternatively coded BD1‐5 and SR1 genomes (0.81–4.72%) (Wrighton et al ., ; Kantor et al ., ) (Table ).…”

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

“…Halomonas sp. HL-93 was isolated, its genomic DNA was extracted, and its 16S rRNA gene was sequenced and analyzed in the same manner as previously described (16); sequencing was performed by Functional Biosciences (Madison, WI). Isolate genomes were sequenced and assembled by the JGI under CSP 701 using the Pacific Biosciences (PacBio) sequencing technology (19).…”

“…Microdiversity further hampers genome assembly and segregation, as current assembly, coverage, and composition analysis techniques are insufficient for distinguishing many closely related genomes. To date, only one community, composed of only five members, has been comprehensively sequenced and reconstructed (16).…”

Methane oxidation and methylotroph population dynamics in groundwater mesocosms

“…Thus, in both field and mesocosm studies, a period of famine appeared to stimulate growth of these bacteria. Gracilibacteria is part of the Candidate Phyla Radiation (CPR) (Brown et al, 2015;Hug et al, 2016), comprised uncultured bacteria, ubiquitous in groundwater, and having "incomplete" central metabolism (Wrighton et al, 2012;Hanke et al, 2014;Dudek et al, 2017). Although their metabolic repertoire is very sparse, the genomes of some Gracilibacteria have been shown to encode several proteins of the serine pathway for formaldehyde assimilation and amino acid biosynthesis (Hanke et al, 2014) including serine hydroxymethyltransferase, formate-tetrahydrofolate ligase, and bifunctional protein FolD.…”