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Abstract
Pristine marine environments have been reported to contain microorganisms capable of organohalide respiration (OHR). In addition, over 5000 natural halogenated compounds were discovered recently in marine sediments, indicating the importance of the marine environment to local and global halogen cycles. We therefore started the exploration of marine sediments from Aarhus Bay for their OHR potential. To this end, sediments were incubated with a variety of halogenated compounds, followed by eco-physiological characterization of potential organohalide respiring bacteria (OHRB) through enrichment, dilution-to-extinction, phylogenomic and transcriptomic analyses.
Chapter 1gave an overview of the current knowledge of OHR, including a summary of diversity and distribution of reductive dehalogenases (RDase), RDase-containing gene clusters, and RDase-based electron transfer chains.
Chapter 2 verified the OHR potential of marine sediments of Aarhus Bay for chlorinated, brominated and iodinated compounds. The obtained tetrachloroethene (PCE) dechlorinating enrichment was found to be composed of bacteria distinct from the well-documented OHRB. Moreover, a switch in organohalides from PCE to 2,6-dibromophenol (2,6-DBP) significantly affected microbial composition. Of interest, we found that the reductive deiodination of 2,4,6- triiodophenol (2,4,6-TIP) increased the relative abundance of Lokiarchaeota belonging to Asgardarchaeota,which are seen as the origin of eukaryotes.
Chapter 3 introduced metagenomic and -transcriptomic analyses to pinpoint the dehalogenators responsible for PCE dechlorination under both sulfate-free and sulfate-amended conditions. Metagenome-assembled genomes (MAGs) bearing RDase genes were found to belong to phyla not previously associated with OHR, including Bacteroidota, Synergistota, and Spirochaetota. Furthermore, a MAG classified into Vulcanibacillus(CH3_bin.26) carried an unprecedent number of 97 RDase genes, 84 of which were found to be expressed during PCE dechlorination. Noticeably, many transcriptional regulators were found encoded in the vicinity of RDase genes, such as extra-cytoplasmic factor (ECF-σ), SigW, and co-expressed with the adjacent RDase genes indicating the involvement of diverse regulatory systems in OHR.
Chapter 4 reported the isolation of a consortium that is capable of reductive debromination of 2,6-DBP to phenol. Thereinto, bins (MAGs) belonging to Desulfoplanes (CH4_bin.3) and Marinifilaceae (CH4_bin.4) were shown to contain respiratory RDase genes, the expression of which was induced in the presence of 2,6-DBP. Interestingly, the pangenomic analysis revealed most of the Marinifilum representatives are potential OHRB. Moreover, CH4_bin.5 belonging to Desulforhopaluswas found predominant with a relative abundance of up to 29%. This bin contained a gene coding for a thiolytic, non-respiratory reductive dehalogenase, TPh-RDase, which was also highly-induced upon addition of 2,6-DBP. This constitutes the first report of a thiolytic RDase being active in an anaerobic microorganism. Further, CH4_bin.5 was predicted to encode a complete de novo vitamin B12 (B12) biosynthesis pathway, which was likely functioning as the B12 supplier for reductive dehalogenation of CH4_bin.3 and CH4_bin.4 in the consortium. This suggests that this isolated consortium executed reductive dehalogenation in a syntrophic manner.
