A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology

Abstract

Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the alpha-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.

Changing concentrations of CO, CH 4 , C 5 H 8 , CH 3 Br, CH 3 I, and dimethyl sulfide during the Southern Ocean Iron Enrichment Experiments

“…Methyl halides are known to be produced in seawater by marine microorganisms (32)(33)(34)(35). Some methyl halides are known to be chemically removed from seawater by nucleophilic attack (36), hydrolysis (37), and bacteria (38)(39)(40). The observed decrease in CH 3 I was negatively correlated with CO 2 uptake and O 2 ( Table 1).…”

Bacterial Populations Active in Metabolism of C 1 Compounds in the Sediment of Lake Washington, a Freshwater Lake

“…A wide range of C 1 compounds are consumed by methylotrophs in the environment, including methane, methanol, methylated amines, methylated glycines, halomethanes, and methylated sulfur species (1,21,24,31,44). Traditional microbial techniques such as enrichment and isolation on defined culture media have revealed that methylotrophic bacteria occur in a variety of environments, such as freshwater, marine, and terrestrial habitats, including habitats characterized by extreme conditions of temperature, salinity, or pH (8,26,44).…”

“…As many methylotrophic bacteria are difficult to isolate, cultivation-independent molecular tools have been developed to characterize natural methylotrophic populations. These tools included oligonucleotide probes and PCR primer sets targeting genes conserved among methylotrophic bacteria, such as 16S RNA genes, or genes encoding specific methylotrophic enzymes, such as particulate and soluble methane monooxygenases, methanol dehydrogenase, corrinoid-linked methyltransferase, or methanesulfonic acid monooxygenase (3,15,21,30,31). However, none of these probes or primers aimed at detection of C 1 -oxidizing populations in a broader sense, encompassing their actual diversity.…”

Chloromethane-Dependent Expression of the cmu Gene Cluster of Hyphomicrobium chloromethanicum

“…strain IMB-1 (41) were shown to be able to oxidize tropospheric concentrations of CH 3 Br (12 pptv), indicating that these and other methyl halide utilizers are responsible for the biological oxidation of tropospheric CH 3 Br and possibly CH 3 Cl in various terrestrial and marine environments (15). This also indicated that ambient concentrations of CH 3 Br and possibly CH 3 Cl were adequate for the induction of methyl halide utilization pathway(s).All four CH 3 Cl-utilizing soil isolates were found to possess the gene cmuA along with other CH 3 Cl-specific genes within their cmu (chloromethane utilization) gene clusters (6,31,32,50,54). The cmuA gene encodes methyltransferase I (CmuA), which catalyzes the initial dehalogenation step of the CH 3 Cl degradation pathway (Fig.…”

“…All four CH 3 Cl-utilizing soil isolates were found to possess the gene cmuA along with other CH 3 Cl-specific genes within their cmu (chloromethane utilization) gene clusters (6,31,32,50,54). The cmuA gene encodes methyltransferase I (CmuA), which catalyzes the initial dehalogenation step of the CH 3 Cl degradation pathway (Fig.…”