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Methylmercury is a potent neurotoxin produced in natural environments from inorganic mercury by anaerobic bacteria. However, until now the genes and proteins involved have remained unidentified. Here, we report a two-gene cluster, hgcA and hgcB, required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In either bacterium, deletion of hgcA, hgcB, or both genes abolishes mercury methylation. The genes encode a putative corrinoid protein, HgcA, and a 2[4Fe-4S] ferredoxin, HgcB, consistent with roles as a methyl carrier and an electron donor required for corrinoid cofactor reduction, respectively. Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in nonmethylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.

A global metagenome assessment reveals a low risk of methylmercury production in humans and a high potential in Arctic permafrost.

We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.

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Temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium Shewanella oneidensis MR-1 to an acute chromate shock. The complex dynamics of cellular processes demand the integration of methodologies that describe biological systems at the levels of regulation, gene and protein expression, and metabolite production. Genomic microarray analysis of the transcriptome dynamics of midexponential phase cells subjected to 1 mm potassium chromate (K(2)CrO(4)) at exposure time intervals of 5, 30, 60, and 90 min revealed 910 genes that were differentially expressed at one or more time points. Strongly induced genes included those encoding components of a TonB1 iron transport system (tonB1-exbB1-exbD1), hemin ATP-binding cassette transporters (hmuTUV), TonB-dependent receptors as well as sulfate transporters (cysP, cysW-2, and cysA-2), and enzymes involved in assimilative sulfur metabolism (cysC, cysN, cysD, cysH, cysI, and cysJ). Transcript levels for genes with annotated functions in DNA repair (lexA, recX, recA, recN, dinP, and umuD), cellular detoxification (so1756, so3585, and so3586), and two-component signal transduction systems (so2426) were also significantly up-regulated (p < 0.05) in Cr(VI)-exposed cells relative to untreated cells. By contrast, genes with functions linked to energy metabolism, particularly electron transport (e.g. so0902-03-04, mtrA, omcA, and omcB), showed dramatic temporal alterations in expression with the majority exhibiting repression. Differential proteomics based on multidimensional HPLC-MS/MS was used to complement the transcriptome data, resulting in comparable induction and repression patterns for a subset of corresponding proteins. In total, expression of 2,370 proteins were confidently verified with 624 (26%) of these annotated as hypothetical or conserved hypothetical proteins. The initial response of S. oneidensis to chromate shock appears to require a combination of different regulatory networks that involve genes with annotated functions in oxidative stress protection, detoxification, protein stress protection, iron and sulfur acquisition, and SOS-controlled DNA repair mechanisms.

The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.The symbiosis between legumes and the root nodule bacteria collectively known as rhizobia is of critical agronomic and environmental importance, accounting for the majority of the nitrogen fixed through biological processes. Rhizobia are phylogenetically diverse, falling into five genera of ␣-proteobacteria (Rhizobium, Bradyrhizobium, Sinorhizobium, Azorhizobium, and Mesorhizobium) (64, 70) and at least two genera of ␤-proteobacteria (Burkholderia and Ralstonia) (35). It is thought that the rhizobial lineages diverged well before the evolution of legumes and that the genes required for the formation of the symbiosis were subsequently acquired by lateral transfer from undefined sources (8,33). Reflecting the accessory nature of the traits, several species of rhizobia contain the genes required for nodulation and nitrogen fixation on large plasmids that can be cured under laboratory conditions without affecting the survival of the bacteria (31). Exceptions in which the symbiosis genes are encoded on the chromosome include Bradyrhizobium species, in which the symbiosis genes are clustered but not known to be mobile (18), and at least one strain of Mesorhizobium loti, strain ICMP3153, in which the genes are located on a mobile symbiosis island (57).M. loti is the microsymbiont of several Lotus species, including Lotus corniculatus and L. japonicus. The symbiosis island of M. loti strain ICMP3153 was discovered through its ability to transfe...