Tamar Barkay

Bacterial mercury resistance from atoms to ecosystems

Bacterial resistance to inorganic and organic mercury compounds (HgR) is one of the most widely observed phenotypes in eubacteria. Loci conferring HgR in Gram-positive or Gram-negative bacteria typically have at minimum a mercuric reductase enzyme (MerA) that reduces reactive ionic Hg(II) to volatile, relatively inert, monoatomic Hg(0) vapor and a membrane-bound protein (MerT) for uptake of Hg(II) arranged in an operon under control of MerR, a novel metal-responsive regulator. Many HgR loci encode an additional enzyme, MerB, that degrades organomercurials by protonolysis, and one or more additional proteins apparently involved in transport. Genes conferring HgR occur on chromosomes, plasmids, and transposons and their operon arrangements can be quite diverse, frequently involving duplications of the above noted structural genes, several of which are modular themselves. How this very mobile and plastic suite of proteins protects host cells from this pervasive toxic metal, what roles it has in the biogeochemical cycling of Hg, and how it has been employed in ameliorating environmental contamination are the subjects of this review.

The extraction and purification of microbial DNA from sediments

Abstract A new method for the isolation of intracellular and extacellular DNA from a range of sediment types has been developed. This method is based upon the direct lysis of cells in the sediment, extraction of released DNA from the sediments and its subsequent purification by CsCL-EtBr gradient centrifugation and/or hydroxyapatite chromatography. Yields of 26 μg intracellular DNA and 1 μg extracellular DNA have been obtained per gram of sediment.

Microbial Transformations of Mercury: Potentials, Challenges, and Achievements in Controlling Mercury Toxicity in the Environment

Publisher Summary This chapter reviews achievements in mercury microbiology research during the past 35 years and identifies areas in which more information is needed to complete our understanding of how microbes in the diverse ecological niches that exist on earth interact with mercury. Mercury is a potent toxic substance, the toxicity of which is elicited at very low concentrations. Although all chemical forms of mercury are toxic, public health concerns are focused on methylmercury (MeHg). The major routes of human exposure to this toxic element are through the consumption of contaminated fish, where mercury is mostly present in its methylated form. This is the result of the bioaccumulation and biomagnification of MeHg in the aquatic food chain. MeHg is a neurotoxin that causes pathologies ranging from mild numbness of the extremities to blindness, loss of balance, and death. Because MeHg is more toxic than other forms of mercury, and mercury is mostly deposited in the environment in its ionic form, the biogeochemical cycling of mercury in the environment plays a key role in modulating mercury toxicity. Furthermore, microbial transformations play critical roles in the mercury geochemical cycle, and understanding the mechanisms of these transformations is essential for controlling mercury transport and accumulation in the biosphere.

Metal and radionuclide bioremediation: issues, considerations and potentials

Recent demonstrations of the removal and immobilization of inorganic contaminants by microbial transformations, sorption and mineralization show the potential of both natural and engineered microbes as bioremedial tools. Demonstrations of microbe-mediated mineral formation in biofilms implicate this mode of microbial life in geological evolution and remediation of inorganic contaminants.

Application of a mer-lux biosensor for estimating bioavailable mercury in soil

Abstract A previously described bioassay using a mer-lux gene fusion for detection of bioavailable mercury was applied for the estimation of the bioavailable fraction of mercury in soil. The bioavailable fraction is defined here as being part of the water leachable fraction. Due to masking of light emission of soil particles leachates had to be cleaned prior to assays. Filtration of leachates through nitro-cellulose filters using pressure resulted in an underestimation of bioavailable mercury. Gravity filtration and centrifugation showed elevated (as compared with untreated leachate) and very similar responses. The utility of the mer-lux biosensor assay was tested by relating measurements of bioavailable and total mercury to the response of the soil microbial community to mercury exposure. Two different soil types (an agricultural and a beech forest soil) were spiked with 2.5 μg Hg(II) g−1 in microcosms and the frequency of mercury resistant heterotrophs and changes in community diversity, defined as the number of different 16S rDNA bands observed in DGGE gels, were monitored. In the agricultural soil the initial concentration of bioavailable mercury was estimated to be 40 ng g−1. This concentration did not change during the first 3 d and coincided with increased degrees of resistance and a decrease in diversity. The concentration of bioavailable mercury decreased subsequently rapidly and remained just above the detection level (0.2 ng g−1) for the remainder of the experiment. As a possible consequence of the decreased selection pressure of mercury, the resistance and diversity gradually returned to pre-exposure amounts. In the beech forest soil the concentration of bioavailable mercury was found to be about 20 ng g−1 throughout the experiment. This concentration did not at any time result in changes in resistance or diversity. This study showed that the bioassay using the mer-lux biosensor is a useful and sensitive tool for estimation of bioavailable mercury in soil.

Horizontal gene transfer: perspectives at a crossroads of scientific disciplines.

Horizontal gene transfer (HGT) has a crucial role in microbial evolution, in shaping the structure and function of microbial communities and in controlling a myriad of environmental and public-health problems. Here, Barth F. Smets and Tamar Barkay assess the importance of HGT and place the selection of articles in this Focus issue in context.

Mercury Adaptation among Bacteria from a Deep-Sea Hydrothermal Vent

ABSTRACT Since deep-sea hydrothermal vent fluids are enriched with toxic metals, it was hypothesized that (i) the biota in the vicinity of a vent is adapted to life in the presence of toxic metals and (ii) metal toxicity is modulated by the steep physical-chemical gradients that occur when anoxic, hot fluids are mixed with cold oxygenated seawater. We collected bacterial biomass at different distances from a diffuse flow vent at 9°N on the East Pacific Rise and tested these hypotheses by examining the effect of mercuric mercury [Hg(II)] on vent bacteria. Four of six moderate thermophiles, most of which were vent isolates belonging to the genus Alcanivorax, and six of eight mesophiles from the vent plume were resistant to >10 μM Hg(II) and reduced it to elemental mercury [Hg(0)]. However, four psychrophiles that were isolated from a nearby inactive sulfide structure were Hg(II) sensitive. A neighbor-joining tree constructed from the deduced amino acids of a PCR-amplified fragment of merA, the gene encoding the mercuric reductase (MR), showed that sequences obtained from the vent moderate thermophiles formed a unique cluster (bootstrap value, 100) in the MR phylogenetic tree, which expanded the known diversity of this locus. The temperature optimum for Hg(II) reduction by resting cells and MR activity in crude cell extracts of a vent moderate thermophile corresponded to its optimal growth temperature, 45°C. However, the optimal temperature for activity of the MR encoded by transposon Tn501 was found to be 55 to 65°C, suggesting that, in spite of its original isolation from a mesophile, this MR is a thermophilic enzyme that may represent a relic of early evolution in high-temperature environments. Results showing that there is enrichment of Hg(II) resistance among vent bacteria suggest that these bacteria have an ecological role in mercury detoxification in the vent environment and, together with the thermophilicity of MR, point to geothermal environments as a likely niche for the evolution of bacterial mercury resistance.

Contribution of coexisting sulfate and iron reducing bacteria to methylmercury production in freshwater river sediments

We investigated microbial methylmercury (CH(3)Hg) production in sediments from the South River (SR), VA, an ecosystem contaminated with industrial mercury (Hg). Potential Hg methylation rates in samples collected at nine sites were low in late spring and significantly higher in late summer. Demethylation of (14)CH(3)Hg was dominated by (14)CH(4) production in spring, but switched to producing mostly (14)CO(2) in the summer. Fine-grained sediments originating from the erosion of river banks had the highest CH(3)Hg concentrations and were potential hot spots for both methylation and demethylation activities. Sequencing of 16S rRNA genes of cDNA recovered from sediment RNA extracts indicated that at least three groups of sulfate-reducing bacteria (SRB) and one group of iron-reducing bacteria (IRB), potential Hg methylators, were active in SR sediments. SRB were confirmed as a methylating guild by amendment experiments showing significant sulfate stimulation and molybdate inhibition of methylation in SR sediments. The addition of low levels of amorphous iron(III) oxyhydroxide significantly stimulated methylation rates, suggesting a role for IRB in CH(3)Hg synthesis. Overall, our studies suggest that coexisting SRB and IRB populations in river sediments contribute to Hg methylation, possibly by temporally and spatially separated processes.

Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems

Proteorhodopsins (PRs) are light-driven proton pumps that have been found in a variety of marine environments. The goal of this study was to search for PR presence in different freshwater and brackish environments and to explore the diversity of non-marine PR protein. Here, we show that PRs exist in distinctly different aquatic environments, ranging from clear water lakes to peat lakes and in the Baltic Sea. Some of the PRs observed in this study formed unique clades that were not previously observed in marine environments, whereas others were similar to PRs found in non-marine samples of the Global Ocean Sampling (GOS) expedition. Furthermore, the similarity of several PRs isolated from lakes in different parts of the world suggests that these genes are dispersed globally and that they may encode unique functional capabilities enabling successful competition in a wide range of freshwater environments. Phylogenomic analysis of genes found on these GOS scaffolds suggests that some of the freshwater PRs are found in freshwater Flavobacteria and freshwater SAR11-like bacteria.

Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils.

ABSTRACT Aerobic heterotrophs were isolated from subsurface soil samples obtained from the U.S. Department of Energys (DOE) Field Research Center (FRC) located at Oak Ridge, Tenn. The FRC represents a unique, extreme environment consisting of highly acidic soils with cooccurring heavy metals, radionuclides, and high nitrate concentrations. Four hundred isolates obtained from contaminated soil were assayed for heavy metal resistance, and a smaller subset was assayed for tolerance to uranium. The vast majority of the isolates were gram-positive bacteria and belonged to the high-G+C- and low-G+C-content genera Arthrobacter and Bacillus, respectively. Genomic DNA from a randomly chosen subset of 50 Pb-resistant (Pbr) isolates was amplified with PCR primers specific for PIB-type ATPases (i.e., pbrA/cadA/zntA). A total of 10 pbrA/cadA/zntA loci exhibited evidence of acquisition by horizontal gene transfer. A remarkable dissemination of the horizontally acquired PIB-type ATPases was supported by unusual DNA base compositions and phylogenetic incongruence. Numerous Pbr PIB-type ATPase-positive FRC isolates belonging to the genus Arthrobacter tolerated toxic concentrations of soluble U(VI) (UO22+) at pH 4. These unrelated, yet synergistic, physiological traits observed in Arthrobacter isolates residing in the contaminated FRC subsurface may contribute to the survival of the organisms in such an extreme environment. This study is, to the best of our knowledge, the first study to report broad horizontal transfer of PIB-type ATPases in contaminated subsurface soils and is among the first studies to report uranium tolerance of aerobic heterotrophs obtained from the acidic subsurface at the DOE FRC.