Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater

Common herbicides such as metolachlor (MET), and their transformation products, are frequently detected in groundwater worldwide. Little is known about the response of groundwater bacterial communities to herbicide exposure, and its potential use for ecotoxicological assessment. The response of bacterial communities exposed to different levels of MET from the Ariège alluvial aquifer (Southwest of France) was investigated in situ and in laboratory experiments. Variations in both chemistry and bacterial communities were observed in groundwater, but T-RFLP analysis did not allow to uncover a pesticide-specific effect on endogenous bacterial communities. To circumvent issues of hydrogeochemical and seasonal variations in situ, groundwater samples from two monitoring wells of the Ariège aquifer with contrasting records of pesticide contamination were exposed to different levels of MET in laboratory experiments. The standard Microtox® acute toxicity assay did not indicate toxic effects of MET, even at 5 mg L-1 (i.e., 1000-fold higher than in contaminated groundwater). Analysis of MET transformation products and compound-specific isotope analysis (CSIA) in laboratory experiments demonstrated MET biodegradation but did not correlate with MET exposure. High-throughput sequencing analysis (Illumina MiSeq) of bacterial communities based on amplicons of the 16S rRNA gene revealed that bacterial community differed mainly by groundwater origin rather than by its response to MET exposure. OTUs correlating with MET addition ranged between 0.4 to 3.6% of the total. Predictive analysis of bacterial functions impacted by pesticides using PICRUSt suggested only minor changes in bacterial functions with increasing MET exposure. Taken together, results highlight MET biodegradation in groundwater, and the potential use of bacterial communities as sensitive indicators of herbicide contamination in aquifers. Although detected effects of MET on groundwater bacterial communities were modest, this study illustrates the potential of integrating DNA- and isotopic analysis-based approaches to improve ecotoxicological assessment of pesticide-contaminated aquifers. GRAPHICAL ABSTRACTAn integrative approach was develop to investigate in situ and in laboratory experiments the response of bacterial communities exposed to different levels of MET from the Ariége alluvial aquifer (Southwest of France).

Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium

Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C₁ growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.