Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments

Abstract

To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.

Microbial metal‐sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

“…Contradicting the initial attribution of Thiogranum to Ectothiorhodospiraceae (Mori et al, ), the phylogenetic tree reconstructions of basal Gammaproteobacteria based on 16S rRNA genes and concatenated marker genes in this work affiliated it robustly as a sister branch to the Woeseiaceae/JTB255 clade (Du et al, ; Dyksma et al, ; Mußmann et al, ). Although the name giving isolate, Woeseia oceanii , is a heterotroph (Du et al, ), genomic bins attributed to Woeseiaceae in this and other studies exhibit a chemolithoautotrophic potential (Baker et al, ; Dyksma et al, ; Mußmann et al, ). Confirming this prediction, we detected proteins indicating that Woeseiaceae are the main carbon fixers in aerobic inactive chimney communities sampled in this study.…”

“…We also managed to obtain the first genomic information for the recently isolated genus Thiogranum (Mori et al, 2015). Contradicting the initial attribution of Thiogranum to Ectothiorhodospiraceae (Mori et al, 2015), the phylogenetic tree reconstructions of basal Gammaproteobacteria based on 16S rRNA genes and concatenated marker genes in this work affiliated it robustly as a sister branch to the Woeseiaceae/JTB255 clade (Du et al, 2016;Dyksma et al, 2016;Mußmann et al, 2017). Although the name giving isolate, Woeseia oceanii, is a heterotroph (Du et al, 2016), genomic bins attributed to Woeseiaceae in this and other studies exhibit a chemolithoautotrophic potential (Baker et al, 2015;Dyksma et al, 2016;Mußmann et al, 2017).…”

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

“…Other abundant bacterial groups putatively involved in respiration of oxidized S and N compounds included members of Xanthomonadales and Desulfobacterales . These organisms appear to be ubiquitous in sediments of the Bothnian Sea and other brackish sediments (Leloup et al ; Ruff et al ; Dyksma et al ; Mußmann et al ; Rasigraf et al ). Xanthomonadales were shown to be the major players in sedimentary dark CO 2 fixation while being involved in sulfide oxidation (Dyksma et al ).…”

Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments

“…() or at the Microbial Single Cell Genomics facility at SciLifeLab in Uppsala, Sweden (https://www.scilifelab.se/facilities/single-cell) as described by Mußmann et al . ().…”