Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps.
ABSTRACT: The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.
Project description:Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the "core" microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired "core" microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired "core" bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.
Project description:Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
Project description:Mercury is a neurotoxin, with certain organic forms of the element being particularly harmful to humans. The Minamata Convention was adopted to reduce the intentional use and emission of mercury. Because mercury is an element, it cannot be decomposed. Mercury-containing products and mercury used for various processes will eventually enter the waste stream, and landfill sites will become a mercury sink. While landfill sites can be a source of mercury pollution, the behavior of mercury in solid waste within a landfill site is still not fully understood. The purpose of this study was to determine the depth profile of mercury, the levels of methyl mercury (MeHg), and the factors controlling methylation in an old landfill site that received waste for over 30 years. Three sampling cores were selected, and boring sampling was conducted to a maximum depth of 18 m, which reached the bottom layer of the landfill. Total mercury (THg) and MeHg were measured in the samples to determine the characteristics of mercury at different depths. Bacterial species were identified by 16S rRNA amplification and sequencing, because the methylation process is promoted by a series of genes. It was found that the THg concentration was 19?975 ng/g, with a geometric mean of 298 ng/g, which was slightly less than the 400 ng/g concentration recorded 30 years previously. In some samples, MeHg accounted for up to 15?20% of THg, which is far greater than the general level in soils and sediments, although the source of MeHg was unclear. The genetic data indicated that hgcA was present mostly in the upper and lower layers of the three cores, merA was almost as much as hgcA, while the level of merB was hundreds of times less than those of the other two genes. A significant correlation was found between THg and MeHg, as well as between MeHg and MeHg/THg. In addition, a negative correlation was found between THg and merA. The coexistence of the three genes indicated that both methylation and demethylation processes could occur, but the lack of merB was a barrier for demethylation.
Project description:BACKGROUND:Maternal blood total mercury (THg) is a biomarker for prenatal methylmercury (MeHg) exposure. Few studies have quantified both blood THg and MeHg during pregnancy, and few studies have reported longitudinal trends. OBJECTIVES:We analyzed blood THg and MeHg in a cohort of pregnant mothers in Charleston, South Carolina (n?=?83), and investigated whether blood THg or MeHg changed between early and late gestation. METHODS:THg and MeHg were analyzed in blood samples from early (12?±?1.7 weeks) and late (35?±?2.2 weeks) gestation. RESULTS:Blood %MeHg (of THg) averaged 63% (range: 10-114%) and 61% (range: 12-117%) during early and late gestation, respectively. In unadjusted analyses, blood MeHg decreased from early to late pregnancy (paired t-test, p?=?0.04), while THg did not change (paired t-test, p?=?0.34). When blood MeHg was normalized by the hematocrit, this decrease was no longer statistically significant (paired t-test, p?=?0.09). CONCLUSIONS:In unadjusted analyses, blood MeHg, but not THg, decreased significantly between early and late gestation; this decrease was due in part to hemodilution. Percent MeHg (of THg) varied by up to one order of magnitude. Results highlight the importance of Hg speciation in maternal blood samples to assess prenatal MeHg exposure.
Project description:Despite the public health and toxicologic interest in methyl mercury (MeHg) and ethyl mercury (EHg), these mercury species have been technically difficult to measure in large population studies.Using NHANES 2011-2012 data, we calculated reference ranges and examined demographic factors associated with specific mercury species concentrations and the ratio of MeHg to THg. We conducted several multiple regression analyses to examine factors associated with MeHg concentrations and also with the ratio of MeHg to THg.Asians had the highest geometric mean concentrations for MeHg, 1.58 µg/L (95% CI 1.29, 1.93) and THg, 1.86 µg/L (1.58, 2.19), followed by non-Hispanic blacks with MeHg, 0.52 µg/L (0.39, 0.68) and THg, 0.68 µg/L (0.54, 0.85). Greater education attainment in adults and male sex were associated with higher MeHg and THg concentrations. Race/ethnicity, age, and sex were significant predictors of MeHg concentrations, which increased with age and were highest in Asians in all age categories, followed by non-Hispanic blacks. Mexican Americans had the lowest adjusted MeHg concentrations. The ratio of MeHg to THg was highest in Asians, varied by racial/ethnic group, and increased with age in a non-linear fashion. The amount of increase in the MeHg to THg ratio with age depended on the initial ratio, with a greater increase as age increased. Of the overall population, 3.05% (95% CI 1.77, 4.87) had MeHg concentrations >5.8 µg/L (a value that corresponds to the U.S. EPA reference dose). The prevalence was highest in Asians at 15.85% (95% CI 11.85, 20.56), increased with age, reaching a maximum of 9.26% (3.03, 20.42) at ages 60-69 years. Females 16-44 years old had a 1.76% (0.82-3.28) prevalence of MeHg concentrations >5.8 µg/L.Asians, males, older individuals, and adults with greater educational attainment had higher MeHg concentrations. The ratio of MeHg to THg varied with racial/ethnic group, increased with age, and was nonlinear. U.S. population reference values for MeHg and the ratio of MeHg to THg can assist in more precise assessment of public health risk from MeHg consumed in seafood.
Project description:Fur is a common biomarker of environmental mercury (Hg) exposure. Further, there are well-established relationships between total mercury (THg) in fur and organs. However, these models assumed that THg is uniformly distributed across the fur in a pelt. In this study, we assess the distribution of THg and methylmercury (MeHg) across the pelts of four river otters (Lontra canadensis). THg concentrations were measured in the topcoat (n = 95) and undercoat fur (n = 95). MeHg was measured in a subset of these samples (n = 10). Patterns of THg and MeHg were explored using cluster analyses and ANOVAs. Significant differences existed between THg in topcoat and undercoat and between anatomical region (head/body/tail/legs) and fur regions (dorsal/ventral/furline). The cluster analysis showed significant THg clusters in undercoat fur and to a lesser extent topcoat fur. Further, the error rate for predicting internal THg is lowest in the forebody region of the topcoat, thus, making this the optimal region to sample for biomonitoring. Fur samples taken outside of this region could result in prediction error as high as 140% when estimating internal organ THg. The ratio of MeHg in THg in topcoat fur was measured at 95.7 ± 3.4% indicating THg concentrations can be used to assess MeHg exposure.
Project description:Houttuynia cordata Thunb. (HCT) is a common vegetable native to southwest China, and grown for consumption. The results suggested that THg contents in all parts and MeHg in underground parts of HCT in Hg mining areas were much higher than those in non-Hg mining areas. The highest THg and MeHg content of HCT were found in the roots, followed by the other tissues in the sequence: roots?>?leaves?>?rhizomes?>?aboveground stems (THg), and roots?>?rhizomes?>?aboveground stems?>?leaves (MeHg). The average THg bioaccumulation factor (BCF) of HCT root in the Hg mining area and in non-Hg mining areas could reach 1.02?±?0.71 and 0.99?±?0.71 respectively, indicating that HCT is a Hg accumulator. And the THg and MeHg contents in all tissues of HCT, including the leaves, were significantly correlated with THg and MeHg content in the soil. Additionally, preferred dietary habits of HCT consumption could directly affect the Hg exposure risk. Consuming the aboveground parts (CAP) of HCT potentially poses a high THg exposure risk and consuming the underground parts (CUP) may lead to a relatively high MeHg exposure risk. Only consuming the rhizomes (OCR) of the underground parts could significantly reduce the exposure risk of THg and to some extent of MeHg. In summary, HCT should not be cultivated near the Hg contaminated sites, such as Hg tailings, as it is associated with a greater risk of Hg exposure and high root Hg levels, and the roots should be removed before consumption to reduce the Hg risk.
Project description:As top predators in the Pearl River Estuary (PRE) of China, Indo-Pacific humpback dolphins (Sousa chinensis) are bioindicators for examining regional trends of environmental contaminants in the PRE. We examined samples from stranded S. chinensis in the PRE, collected since 2004, to study the distribution and fate of total mercury (THg), methylmercury (MeHg) and selenium (Se) in the major tissues, in individuals at different ages and their prey fishes from the PRE. This study also investigated the potential protective effects of Se against the toxicities of accumulated THg. Dolphin livers contained the highest concentrations of THg (32.34±58.98 µg g(-1) dw) and Se (15.16±3.66 µg g(-1) dw), which were significantly different from those found in kidneys and muscles, whereas the highest residue of MeHg (1.02±1.11 µg g(-1) dw) was found in dolphin muscles. Concentrations of both THg and MeHg in the liver, kidney and muscle of dolphins showed a significantly positive correlation with age. The biomagnification factors (BMFs) of inorganic mercury (Hginorg) in dolphin livers (350×) and MeHg in muscles (18.7×) through the prey fishes were the highest among all three dolphin tissues, whereas the BMFs of Se were much lower in all dolphin tissues. The lower proportion of MeHg in THg and higher Se/THg ratios in tissues were demonstrated. Our studies suggested that S. chinensis might have the potential to detoxify Hg via the demethylation of MeHg and the formation of tiemannite (HgSe) in the liver and kidney. The lower threshold of hepatic THg concentrations for the equimolar accumulation of Se and Hg in S. chinensis suggests that this species has a greater sensitivity to THg concentrations than is found in striped dolphins and Dall's porpoises.
Project description:Exposure to microbial pathogens is the primary concern of sanitary sewer overflows; however, sewage spills may also be a significant source of toxic metals, including methylmercury (MeHg). Between November 2015 and January 2017, after Hurricane Joaquin, surface water samples were collected routinely from three creeks in Columbia, SC. Routine sampling coincided with six sewage spills. Total mercury (THg) and MeHg (unfiltered and filtered) and 32 other metals (filtered) were measured. Compared with surface water samples, THg (unfiltered and filtered), MeHg (unfiltered), and 19 other metals were significantly higher in sewage spills (all log-transformed) (two-tailed test, < 0.05 for all, = 38-42). Toxic weighting factors were applied to 18 metals, including THg and MeHg, in samples collected directly from sewage spills ( = 3-4) and a wastewater outfall ( = 5). On average, sewage was 18.2 and 12.0 times more toxic for THg and MeHg, respectively, and 1.75 times more toxic for all 18 metals, compared to treated effluent from the wastewater outfall. Results suggest sewage spills were a source of inorganic Hg, MeHg, and other metals to the receiving waters and may potentially contribute to water quality impairments.
Project description:In Berlin, New Hampshire, USA, the Androscoggin River flows adjacent to a former chlor-alkali facility that is a US Environmental Protection Agency Superfund site and source of mercury (Hg) to the river. The present study was conducted to determine the fate and bioaccumulation of methylmercury (MeHg) to lower trophic-level taxa in the river. Surface sediment directly adjacent to the source showed significantly elevated MeHg (10-40× increase, mean?±?standard deviation [SD]: 20.1?±?24.8 ng g(-1) dry wt) and total mercury (THg; 10-30× increase, mean?±?SD: 2045?±?2669 ng g(-1) dry wt) compared with all other reaches, with sediment THg and MeHg from downstream reaches elevated (3-7× on average) relative to the reference (THg mean?±?SD: 33.5?±?9.33 ng g(-1) dry wt; MeHg mean?±?SD: 0.52?±?0.21?ng g(-1) dry wt). Water column THg concentrations adjacent to the point source for both particulate (0.23?ng L(-1)) and dissolved (0.76?ng L(-1)) fractions were 5-fold higher than at the reference sites, and 2-fold to 5-fold higher than downstream. Methylmercury production potential of periphyton material was highest (2-9?ng g(-1) d(-1) dry wt) adjacent to the Superfund site; other reaches were close to or below reporting limits (0. 1?ng g(-1) d(-1) dry wt). Total Hg and MeHg bioaccumulation in fauna was variable across sites and taxa, with no clear spatial patterns downstream of the contamination source. Crayfish, mayflies, and shiners showed a weak positive relationship with porewater MeHg concentration.