Genome-resolved transcriptomics reveals novel organohalide-respiring bacteria from Aarhus Bay sediments

Abstract

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from PCE-respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 high quality bins with over 75 % completeness and less than 5 % contamination. Sixteen bins harbored RDase genes, and were affiliated taxonomically to the class of Bacilli, and phyla of Bacteroidota, Synergistota, and Spirochaetota, that have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically closely related to the genus Vulcanibacillus, contained an unprecedented 97 RDase genes. Of these, 84 RDase genes of bin.26 were transcribed during PCE dechlorination in addition to RDase genes from members of Synergistales (bin.15 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested the RDase genes were likely under the regulation of transcriptional regulators not previously associated with OHR, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to provide evidence towards the diversity, activity and regulation of reductive dehalogenases.