Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Abstract

<jats:title>Abstract</jats:title><jats:p>Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. The lack of CF removal in the abiotic control cultures without artificial electron donors indicated that the observed CF removal is a biotic process. Metabolite analysis with <jats:sup>13</jats:sup>C labelled CF in the sediment-free enrichment cultures (pH 8.5, salinity 5%) revealed that increasing the vitamin B<jats:sub>12</jats:sub> concentration from 0.04 to 4 μM enhanced CF removal, reduced DCM formation, and increased <jats:sup>13</jats:sup>CO<jats:sub>2</jats:sub> production, which is likely a product of CF oxidation. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected by quantitative PCR nor metagenomic analysis. Rather, members of the order <jats:italic>Clostridiales</jats:italic>, known to co-metabolically transform CF to DCM and CO<jats:sub>2</jats:sub>, were detected in the enrichment cultures. Genome-resolved metagenome analysis indicated that their genomes encode enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis that are known to be involved in co-metabolic CF transformation.</jats:p><jats:sec><jats:title>Importance</jats:title><jats:p>More than 90% of the global CF emission to the atmosphere originates from natural sources, including saline environments such as salt lake sediments. However, knowledge about the microbial metabolism of CF in such extreme environments is lacking. Here we showed CF transformation potential in a hypersaline lake that was reported as a natural source of CF production. Application of interdisciplinary approaches of microbial cultivation, stable isotope labelling, and metagenomics aided in defining potential chloroform transformation pathways. This study indicates that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere, and expands our knowledge of halogen cycling in extreme hypersaline environments.</jats:p></jats:sec>

Chlorine cycling and the fate of Cl in terrestrial environments

“…organohalide respiration; there is a wide literature regarding dehalogenation processes in terms of biochemistry of specific compounds (Dolfing 2000;Fetzner 1998;Olivas et al 2002;Pries et al 1994;Smidt and de Vos 2004;van Pee and Unversucht 2003). There are also studies that show netuptake of chloromethane without evidence of organohalide respiration (Peng et al 2020), and a cometabolic dechlorination has been suggested (Atashgahi et al 2018;Peng et al 2020). However, rates and regulation of dechlorination of bulk Cl org in nature are still rarely quantified although the limited available information suggests rates are high (Montelius et al 2016).…”

2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

“…The transformation of 2,4-D in our microcosms could likely be due to co-metabolism. Co-metabolic reductive dechlorination mediated by vitamin B12 has been demonstrated for other chlorinated compounds such as chloroform, tetrachloromethane, tetrachloroethene, among others (Gantzer and Wackett 1991 , Workman et al 1997 , Smidt and de Vos 2004 , Guereiro-Barajas and Field 2005 ; Becker and Freedman 2014, Peng et al 2020 ). The genus Clostridium was one of the most dominant groups among all microcosms (Fig.…”

“…5 ), and Clostridium that has been identified before as one of the main genera involved in cometabolic transformation of 2,4-D (Yang et al 2018 ). Furthermore, members of the genus Clostridium are also known for their potential for co-metabolic transformation of chlorinated compounds using enzymes involved in the Wood-Ljungdahl pathway (WLP) (Peng et al 2020 ). Unfortunately, we did not monitor cobalamin, but as mentioned before, we observed 2,4-D transformation, and no enrichment of OHRB.…”

“…Members of the genera Dehalobacter and Desulfitobacterium can respire, or are associated, with the reduction of 2,4-D and its intermediates 2,4-DCP, 4-CP and 2-CP (Wang et al 2014 ; Li et al 2013 ; Madsen and Licht et al 1992 ; Thibodeau et al 2004 ). Although co-metabolic reductive dechlorination of chlorinated aromatics was previously reported to be rare (Holliger et al 2004 ), however recent research has also reported co-metabolic degradation of chlorinated compounds (Becker and Freedman 2014, Peng et al 2020 ). Dehalococcoides mccartyi strain CBDB1 has been shown to co-metabolically dechlorinate 2,4-DCP to 4-CP (Adrian et al 2007 ).…”