Clostridia initiate heavy metal bioremoval in mixed sulfidogenic cultures

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Impact of current anthropogenic activities on Blesbokspruit wetland microbiome and functions

Till present, natural wetlands have been continuously subjected to intensive pollution stress in recent years, mainly because of the rapidly growing industrialization and urbanization that are associated with a myriad of anthropogenic activities and land use practices. These man-made sources of pollution change the chemical properties of the natural wetlands, which in turn alter their microbial ecological biodiversity and functions. For the first time, the impact of the current anthropogenic activities and land use practices on the Blesbokspruit wetland chemical status and their consequential effect on the microbial structure and functions were investigated. Sites of high pollution intensity were identified using geographic information systems mapping (GISMapping) and the wetland microbiome and functional profile were studied through the use of high throughput shotgun metagenomics sequencing analysis. The predominant phyla that stemmed along the Blesbokspruit wetland were found to be Proteobacteria which was more dominant in water (93 %) than in the sediments (89 %), followed by firmicutes which was more abundant in sediments (9 %) than in water (6 %), and Bacteroidetes were relatively low in abundance within both the sediments (2 %) and the overlying water (1 %). The genera Klebsiella (70.4 %-28.2 %), Citrobacter (52.0 %-30.6 %), Escherichia (51.0 %-8.4 %), and Lynsinibacillus (9.3 %-1.5 %) were observed in most water and sediment samples. Within the six polluted sites, Site 2 was found to be the most highly polluted site in the Blesbokspruit wetland with very high COD (900 mg/L), TOC (11.60 mg/L), NO3- (39.74 mg/L), NO2- (12.64 mg/L), PO43 (4.14 mg/L), Fl- (143.88 mg/L), Cl- (145.95 mg/L) concentrations recorded in the water and high levels of TOC (0.37 mg/L), TC (6.92 %), TN (1.82 %), TS (0.53 %) in sediments. The microbial community structure and functions were found to be strongly influenced by the high organic content from the intense agricultural activities and sewage spillages and heavy metals from the mining activities nearby.

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.

Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments

Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.

Treatment and remediation of metal-contaminated water and groundwater in mining areas by biological sulfidogenic processes: A review

Heavy metal pollution in the mining areas leads to serious environmental problems. The biological sulfidogenic process (BSP) mediated by sulfidogenic bacteria has been considered an attractive technology for the treatment and remediation of metal-contaminated water and groundwater. Notwithstanding, BSP driven by different sulfidogenic bacteria could affect the efficiency and cost-effectiveness of the treatment performance in practical applications, such as the microbial intolerance of pH and metal ions, the formation of toxic byproducts, and the consumption of organic electron donors. Sulfur-reducing bacteria (S⁰RB)-driven BSP has been demonstrated to be a promising alternative to the commonly used sulfate-reducing bacteria (SRB)-driven BSP for treating metal-contaminated wastewater and groundwater, due to the cost-saving in chemical addition, the high efficiency in sulfide production and metal removal efficiency. Although the S⁰RB-driven BSP has been developed and applied for decades, the present review works mainly focus on the developments in SRB-driven BSP for the treatment and remediation of metal-contaminated wastewater and groundwater. Accordingly, a comprehensive review for metal-contaminated wastewater treatment and groundwater remediation should be provided with the incorporation of the SRB- and S⁰RB-driven BSP. To identify the bottlenecks and to improve BSP performance, this paper reviews sulfidogenic bacteria presenting in metal-contaminated water and groundwater; highlight the critical factors for the metabolism of sulfidogenic bacteria during BSP; the ecological roles of sulfidogenic bacteria and the mechanisms of metal removal by sulfidogenic bacteria; and the application of the present sulfidogenic systems and their drawbacks. Accordingly, the research knowledge gaps, current process limitations, and future prospects were provided for improving the performance of BSP in the treatment and remediation of metal-contaminated wastewater and groundwater in mining areas.

Comparison of composting factors, heavy metal immobilization, and microbial activity after biochar or lime application in straw-manure composting

Composting is an efficient way of disposing agricultural solid wastes as well as passivating heavy metals (HMs). Herein, equivalent (3%) biochar (BC) or lime (LM) were applied in rice straw and swine manure composting, with no additives applied as control group (CK). The results indicated that both the additives increased NO₃^--N content, organic matter degradation, humus formation, and HM immobilization in composting, and the overall improvement of lime was more significant. In addition, the additives optimized the bacterial community of compost, especially for thermophilic and mature phase. Lime stimulated the growth of Bacillus, Peptostreptococcus, Clostridium, Turicibacter, Clostridiaceae and Pseudomonas, which functioned well in HM passivation via biosorption, bioleaching, or promoting HM-humus formation by secreting hydrolases. Lime (3%) as additive is recommended in swine manure composting to promote composting maturity and reduce HM risk. The study present theoretical guidance in improving composting products quality for civil and industrial composting.

Integrated network analysis reveals that exogenous cadmium-tolerant endophytic bacteria inhibit cadmium uptake in rice

Most previous studies have focused on the diversity and species richness of microbial communities, however, understanding the interactions between species and detecting key functional members of the community can help us better understand how microorganisms perform their functions. In this study, the response of the rice plant microbial community to the inoculation of cadmium-resistant endophytic bacterium R5 (Stenotrophomonas) was investigated for the first time using a microbial phylogenetic molecular ecological network. The results showed that inoculation of R5 changed the topological characteristics of the microbial network in rice plants, with the resulting network displaying stronger complexity and interaction in roots and aboveground parts, indicating that inoculation of R5 provided favorable conditions for microbial interactions. In addition, these interactions may be related to the absorption and transportation of cadmium by rice. Under the exogenous addition of R5, the network interactions of the rice plant microbial community were more inclined to cooperation. Both in the roots and aboveground parts of rice, the plant Cd content showed a decrease as the complexity and connectivity of the network increased, suggesting that complex microbial networks may be more beneficial to rice than simple microbial networks because as they were more adaptive and resistant to unfavorable environments. After inoculation with the R5 strain, the negative interaction with Cd content in rice plants increased significantly, and there might be more synergy between the microbial community and plants to jointly inhibit the absorption and transportation of Cd.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia - a solution toward acid mine drainage treatment in cold regions

Failure of sulfate-reducing bacteria (SRB)-mediated treatment of acid mine drainage (AMD) in cold regions due to inhibition of bacteria by acidic pH and low temperature can be overcome by enriching psychrophilic and acidophilic microbial consortia from local metal-rich sediments. In this study, we enriched microbial consortia from Arctic mine sediments at varying pH (3-7) and temperatures (15-37 °C) under anaerobic conditions with repeated sub-culturing in three successive stages, and analyzed the microbial community using 16S rRNA gene sequencing. The enriched SRB genera resulted in high sulfate reduction (85-88%), and significant metal removal (49-99.9%) during the initial stages (stage 1 and 2). Subsequently, sub-culturing the inoculum at pH 3-4.5 resulted in lower sulfate reduction (9-34%) due to the inhibition of SRB by accumulated acetic acid (0.3-9 mM). The microbial metabolic interactions for successful sulfate and metal removal involved initial glycerol co-fermentation to acetic acid at acidic pH (by Desulfosporosinus, Desulfotomaculum, Desulfurospora, and fermentative bacteria including Cellulomonas and Anaerovorax), followed by acetic acid oxidation to CO₂ and H₂ (by Desulfitobacterium) at neutral pH, and subsequent H₂ utilization (by Desulfosporosinus). The results, including the structural and functional properties of enriched microbial consortia, can inform the development of effective biological treatment strategies for AMD in cold regions.

Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes

Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.

Efficient removal of heavy metals by synergistic actions of microorganisms and waste molasses

In this study, two bacteria strains (Enterobacter sp. SL and Acinetobacter sp. SL-1) and waste molasses (carbon source) were used to remove Zn(II), Cd(II), Cr(VI), and Cr(Total) in the liquid solution (87 mg·L). The results showed the removal efficiencies of Cr(Total) and Cr(VI) could reach over 98.00% after reaction, and the removal efficiencies of Zn(II) and Cd(II) were all about 90.00% by the synergistic actions of microorganisms and waste molasses. In this process, waste molasses provides nutrients for microorganisms and has the characteristics and capability of Cr, Zn, and Cd. Microorganisms mainly use biological adsorption (36.95% and 45.69%) and metabolism (24.37% and 17.05% by producing humic-acid and fulvic-acid like substances) to remove Zn(II) and Cd(II), while waste molasses could to remove Cr(Total) (81.24%) and Cr(VI) (75.90%). This study has potential application value for the treatment of wastewater containing high concentrations of heavy metals.

Characterization and application of an anaerobic, iron and sulfate reducing bacterial culture in enhanced bioremediation of acid mine drainage impacted soil

Development of an appropriate bioremediation strategy for acid mine drainage (AMD) impacted environment is imperative for sustainable mining but remained critically challenged due to the paucity of knowledge on desired microbiological factors and their nutrient requirements. The present study was conducted to utilize the potential of an anaerobic, acid-tolerant, Fe³⁺ and SO₄^2- reducing microbial consortium for in situ remediation of highly acidic (pH 3.21), SO₄^2- rich (6285 mg/L) mine drainage impacted soil (AIS). A microbial consortium enriched from AMD system and composed of Clostridiales and Bacillales members was characterized and tested for in situ application through microcosms. A combination of bioaugmentation (enriched consortium) and biostimulation (cellulose) allowed 97% reduction in dissolved sulfate and rise in pH up to 7.5. 16S rRNA gene-based amplicon sequencing confirmed that although the bioaugmented community could survive in AIS, availability of carbon source was necessary for superior iron- and sulfate- reduction. Quantitative PCR of dsrB gene confirmed the role of carbon source in boosting the SO₄^2- reduction activities of sulfate reducers. This study demonstrated that native AIS harbored limited catabolic activities required for the remediation but addition of catabolically active microbial populations along with necessary carbon and energy source facilitate the bioremediation of AIS.

Mixotrophic acidophiles increase cadmium soluble fraction and phytoextraction efficiency from cadmium contaminated soils

A profound concern in developing microbially-assisted phytoextraction is that introduced microbes not only remove heavy metals from contaminated soils but also enhance metal uptake into plant tissues from the treated soils. Cadmium (Cd) removal efficiencies were compared after leaching with deionized water (CK), acidified basal salts medium (acid control), cell-free spent medium (spent bioleaching) and mixotrophic acidophiles (two-step bioleaching). Two-step bioleaching using the mixotrophic acidophiles removed 34% of total Cd and 87% of available Cd, significantly more than CK (3% and 4%), acid control (12% and 51%) and spent bioleaching (26% and 75%). Pot experiments of water spinach growing in four treated soils were conducted to evaluate the Cd uptake performance in plants. Notably, the mixotrophic acidophiles increased Cd concentration in plant tissues by 78% compared to the CK group. More interestingly, the mixotrophic acidophiles were not colonized in soils but caused the compositional increase of indigenous microbes such as the genera of Alicyclobacillus, Clostridium sensu strict and Streptacidiphilus. Meanwhile, two-step bioleaching had little effects on soil structure and physicochemical properties determined by the spectroscopy characteristics analysis. These results implied that the mixotrophic acidophiles facilitated the development of microbially-assisted phytoextraction technology.

Anaerobic Bioreduction of Jarosites and Biofilm Formation by a Natural Microbial Consortium

Jarosite occurs naturally in acid sulphate soils and is a common feature of streams impacted by acid mine drainage (AMD). Biological reduction of iron-sulphate minerals, such as jarosite, has the potential to contribute to the natural attenuation of acid mine drainage sites. The reduction of different jarosites (including minerals containing precious and toxic metals) by a natural bacterial/microbial consortium was examined in this study. Jarosites was used as a sole terminal electron acceptor via the reductive dissolution of Fe(III) minerals. The production of Fe(II) and the presence of sulphate-reducing bacteria in the consortium lead to the precipitation of metal sulphides immobilizing toxic heavy metals. Microbial attachment and biofilm formation of minerals have a great impact on the production and transformation of minerals and can influence the mobility of metals. After the adaptation to different jarosites, a unique specie was found: Desulfosporosinus orientis. Desulfosporosinus species are sulphate-reducing bacteria and can be found in sulphate-rich heavy metal-polluted environments, such as acid mine/rock drainage sites, being responsible for the sulphides formation. D. orientis is an obligate anaerobic microorganism and is able to reduce Fe(III) D. orientis is an obligate anaerobic microorganism and is able to reduce Fe(III). Confocal laser scanning microscopy and fluorescent lectin-binding analyses (FLBA) were used to study the arrangement and composition of the exopolysaccharides/glycoconjugates in biofilms indicating the presence of mannose, glucose, and N-acetylglucosamine residues. This study provides insights to understand the processes leading to the mobility or retention of metals in mine waste and industrial landfill environments.

Impact of copper on the diazotroph abundance and community composition during swine manure composting

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg^-1) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs.

Realizing high-rate sulfur reduction under sulfate-rich conditions in a biological sulfide production system to treat metal-laden wastewater deficient in organic matter

Biological sulfur reduction can theoretically produce sufficient sulfide to effectively remove and recover heavy metals in the treatment of organics-deficient sulfate-rich metal-laden wastewater such as acid mine drainage and metallurgic wastewater, using 75% less organics than biological sulfate reduction. However, it is still unknown whether sulfur reduction can indeed compete with sulfate reduction, particularly under high-strength sulfate conditions. The aim of this study was to investigate the long-term feasibility of biological sulfur reduction under high sulfate conditions in a lab-scale sulfur-reducing biological sulfide production (BSP) system with sublimed sulfur added. In the 169-day trial, an average sulfide production rate (SPR) as high as 47 ± 9 mg S/L-h was achieved in the absence of sulfate, and the average SPR under sulfate-rich conditions was similar (53 ± 10 mg S/L-h) when 1300 mg S/L sulfate were fed with the influent. Interestingly, sulfate was barely reduced even at such a high strength and contributed to only 1.5% of total sulfide production. Desulfomicrobium was identified as the predominant sulfidogenic bacterium in the bioreactor. Batch tests further revealed that this sulfidogenic bacteria used elemental sulfur as the electron acceptor instead of the highly bioavailable sulfate, during which polysulfide acted as an intermediate, leading to an even higher bioavailability of sulfur than sulfate. The pathway of sulfur to sulfide conversion via polysulfide in the presence of both sulfur and sulfate was discussed. Collectively, when conditions favor polysulfide formation, sulfur reduction can be a promising and attractive technology to realize a high-rate and low-cost BSP process for treating sulfate-rich metal-laden wastewater.

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.

Syntrophic association and performance of Clostridium, Desulfovibrio, Aeromonas and Tetrathiobacter as anodic biocatalysts for bioelectricity generation in dual chamber microbial fuel cell

Anode chamber of a dual chamber microbial fuel cell (MFC) having raw landfill leachate was inoculated with consortium of sulphate-reducing bacteria (SRB) and sulphide-oxidizing bacteria (SOB) to study the phylogenetic architecture, function and mutualism of anolyte community developed in the reactor. Enriched microbial community was analysed with the help of Illumina MiSeq and indicated the dominance of Firmicutes (41.4%), Clostridia (36.4%) and Clostridium (12.9%) at phylum, class and genus level, respectively. Clostridium was associated with fermentation as well as transfer of electrons to the electrode mediated by ferredoxin. Desulfovibrio (6.7%), Aeromonas (6.6%) and Tetrathiobacter (9.8%) were SRB-SOB associated with direct electron transfer to the electrode. Community analysis disclosed a syntrophic association among novel Firmicutes and Proteobacteria species for bioelectricity generation and degradation of organic matter. Complete removal of chemical oxygen demand was observed from landfill leachate within 3 days of inoculation. Lower oxidative slope and polarization resistance revealed from Tafel analysis backed the feasibility of electron transfer from microbes to anodic electrode and thus development of efficient anode-respiring community. Following enrichment and stabilization of the anodic community, maximum power density achieved was 9.15 W/m³ and volumetric current density was 16.17 A/m³. Simultaneous feeding with SRB-SOB and landfill leachate led to the enrichment of a novel, mutually interdependent microbial community capable of synchronized bioremediation of effluents rich in carbon, sulphate, nitrate and aromatic compounds.

Enantiomer signature and carbon isotope evidence for the migration and transformation of DDTs in arable soils across China

Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ¹³C of o,p’-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p’-DDT and p,p’-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use.

Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria

The 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level.

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction

Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for >3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. In this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase long-term in response to this slowly degrading, complex substrate. To test these hypotheses, groundwater microbial communities were monitored after HRC amendment for >1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO3-, Cr(VI), Fe(II) and SO4(2-). Our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer toward long-term Cr(VI) reduction.

Effect of historical residual hexachlorocyclohexanes and dichlorodiphenyltrichloroethane on bacterial communities in sediment core collected from an estuary in northeastern China by next-generation sequencing

In this study, we evaluate the influence of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethane (DDT) on bacterial communities of sediment core from an estuary formed during the period of 1960-2011. Canonical correspondence analysis showed that o,p'-DDT, o,p'-DDD (mitotane), and depth had important influences on bacterial community distributions (p<0.05). Furthermore, our results found variance explained by all variables was 82.9%, while that by o,p'-DDD was 24.4%, and that of o,p'-DDT was 9.8%, indicating that o,p'-DDD had a greater influence on sediment-dwelling bacteria than o,p'-DDT. Also, bacterial diversity was affected and the Shannon index was significantly negatively correlated with total HCHs (r=-0.579, p<0.05) and total DDTs (r=-0.607, p<0.01), respectively. Furthermore, our results showed that Flavobacteria and Clostridia content can be considered an indicator of pollution of HCHs and DDTs in sediment core samples.