Ecophysiology and environmental distribution of organohalide-respiring bacteria

Abstract

Organohalide-respiring bacteria (OHRB) are able to breathe natural and anthropogenically produced organohalides persistent in a broad range of oxygen-depleted environments. Therefore, these microorganisms are of high interest for organohalide-contaminated site bioremediation and natural halogen and carbon cycle. Nevertheless, to assess and adjust in situ bioremediation strategies and to enhance current understanding about the role of OHRB in natural habitats, thorough understanding of their ecophysiology and interaction with surrounding biotic and abiotic forces is necessary. To this end, this thesis focused on exploring ecophysiology and environmental distribution of OHRB in pristine and contaminated sites and unraveling their interactions with the co-existing microbial guilds in the community and geochemical parameters by application of a suite of physiological, molecular and geochemical analyses. Based on a comprehensive overview of currently known organohalide-respiring isolates and their environmental distribution, the presence of yet unknown OHRB in extreme environments was proposed as the known organohalide-respiring isolates survive/thrive at a moderate range of pH and salinity in laboratory culture. Therefore, the OHRB were surveyed in alkaline and hypersaline sediments collected from Lake Strawbridge, Western Australia, that was known to emit organohalides. As a result, for the first time, the dechlorination of chloroform and perchloroethene (PCE) to dichloromethane and trichloroethene, respectively， was documented from an alkaline hypersaline pristine environment. Corrinoids are essential cofactors for the activity of reductive dehalogenase enzymes. Ironically, some OHRB are reported to be corrinoid auxotrophs. Using transcriptional analysis and shotgun proteomics, here we show corrinoid auxotrophy in Dehalobacter restrictus PER-K23T. This detrimental deficiency seems to be compensated by up-regulation of relevant cobalamin salvaging and transport pathways to ensure sufficient corrinoid supply under partial corrinoid starvation. Hence, such OHRB incapable of de novo corrinoid synthesis will be dependent on non-dechlorinating community members to fulfill their nutritional needs indicating paramount importance of syntrophic interactions in supporting robust growth and activity of OHRB. Bacterial community analysis of chlorinated benzene dechlorinating consortia derived from contaminated harbour sludge suggested members of the Bacteroidetes phylum and Clostridiales order as well as sulfate-reducing Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to OHRB i.e. D. mccartyi and Dehalobacter. However, despite well-controlled lab condition, syntrophic interactions could be influenced by geochemical parameters under field settings. Accordingly, analysis of geochemical and microbial determinants of OHR at a site biostimulated by glycerol injection further verified supportive role of fermenters and sulfate reducers under highly reduced condition following biostimulation. However, towards the end of field experiment, reducing condition faded and sulfate increased concurrent with the appearance of Epsilonproteobacteria and Deferribacteres as putative oxidizers of reduced sulfur compounds. The latter guilds might serve as detoxifiers of sulfide and thereby stimulate D. mccartyi, but could also be inhibitory as successors of the more important syntrophic fermenting and sulfate reducing bacteria. In conclusion, this thesis expands our understanding of ecophysiology and environmental distribution of OHRB, addressing their presence in pristine environments as well as providing further evidence for their dependencies on other microbial community members in order to meet their nutritional requirements. Hence, research described here strengthens the scientific foundation for evaluating and optimizing strategies for the bioremediation of organohalide-contaminated sites and expands the natural niche of OHRB to extreme pristine environments.