Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage

Comparison of microbial communities in unleached and leached ionic rare earth mines

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

Coal Mining Activities Driving the Changes in Microbial Community and Hydrochemical Characteristics of Underground Mine Water

Coal mining can cause groundwater pollution, and microorganism may reflect/affect its hydrochemical characteristics, yet little is known about the microorganism's distribution characteristics and its influence on the formation and evolution of mine water quality in underground coal mines. Here, we investigated the hydrochemical characteristics and microbial communities of six typical zones in a typical North China coalfield. The results showed that hydrochemical compositions and microbial communities of the water samples displayed apparent zone-specific patterns. The microbial community diversity of the six zones followed the order of surface waters > coal roadways > water sumps ≈ rock roadways ≈ goafs > groundwater aquifers. The microbial communities corresponded to the redox sensitive indices' levels. Coal roadways and goafs were the critical zones of groundwater pollution prevention and control. During tunneling in the panel, pyrite was oxidized by sulfur-oxidizing bacteria leading to SO₄^2- increase. With the closure of the panel and formation of the goaf, SO₄^2- increased rapidly for a short period. However, with the time since goaf closure, sulfate-reducing bacteria (e.g., c_Thermodesulfovibrionia, Desulfobacterium_catecholicum, etc.) proportion increased significantly, leading to SO₄^2- concentration's decrease by 42% over 12 years, indicating the long-term closed goafs had a certain self-purification ability. These findings would benefit mine water pollution prevention and control by district.

Ammonia level influences the assembly of dissimilatory nitrate reduction to ammonia bacterial community in soils under different heavy metal remediation treatments

Heavy metal remediation treatments might influence functional microbial community assembly. Dissimilatory nitrate reduction to ammonia (DNRA) contributes to the nitrogen retention processes in soil ecosystems. We assumed that remediation might reduce heavy metal toxicity and increase some available nutrients for the DNRA microbes, thus balancing the deterministic and stochastic process for DNRA community assembly. Here, we investigated the process of DNRA bacterial community assembly under different heavy metal remediation treatments (including control, biochar, limestone, rice straw, rice straw + limestone, and biochar + limestone) in an Alfisol soil. The abundance of DNRA bacteria diverged across treatments. The α-diversity of the DNRA bacterial community was correlated with pH, available phosphorus (AP), ammonium (NH₄⁺), and extractable Fe (EFe). Metal Cd and Fe significantly affected the abundance of the nrfA gene. The β-diversity was associated with pH, NH₄⁺, and EFe. Deterministic processes dominantly drove the assembly processes of the DNRA bacterial community. NH₄⁺ level played an essential role in the assembly processes than the other soil physicochemical properties and metal availability. High, moderate, and low levels of NH₄⁺ could advocate stochastic process plus selection, heterogeneous selection to stochastic process, and heterogeneous selection, respectively. Network analysis highlighted a predominant role of NH₄⁺ in regulating DNRA bacterial community assembly. However, the relative abundance of modules and some keystone species also were influenced by pH and EFe, respectively. Therefore, the DNRA bacterial community assembly under different heavy metal remediation treatments in this study was dominantly driven by nitrogen availability. pH, phosphorus, and metal availability were auxiliary regulators on DNRA bacterial community.

Indigenous microbial populations of abandoned mining sites and their role in natural attenuation

Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.

Comparison of planktonic bacterial communities indoor and outdoor of aquaculture greenhouses

AIMS

Greenhouses are widely used in agriculture systems to shield crops from unfavourable weather to achieve a year-round food supply. In recent years, aquaculture ponds have been placed in greenhouses in many regions. The impacts of the greenhouses on planktonic bacterial communities should be uncovered.

METHODS AND RESULTS

In this study, two polyolefin film greenhouses accommodating aquaculture ponds were established and planktonic bacterial communities were compared from samples taken in aquaculture ponds inside and outside the greenhouses, using Illumina 16S rRNA sequencing.

CONCLUSIONS

The results showed there were significant variations in bacterial community structure between indoor and outdoor samples. Obvious differences were also found between two greenhouses, whereas the differences in indoor samples were weaker than outdoor samples. Significantly higher temperature (in summer), pH and permanganate index were found in the outdoor pond samples. Results of redundancy analysis showed that Proteobacteria and Bacteroidota were positively related to the dissolved oxygen, total nitrogen and total phosphorus, and Actinobacteriota were positively related to pH, temperature and permanganate index, whereas Cyanobacteria were positively related to the salinity, conductivity, total dissolved solids and ammonia nitrogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study revealed that greenhouses significantly influenced planktonic bacterial communities in aquaculture ponds. This study is expected to provide a scientific basis for aquaculture in greenhouses.

Biodegradation of 2-ethylhexyl-4-methoxycinnamate in river sediments and its impact on microbial communities

Numerous studies have evaluated the toxicity and endocrine disrupting properties of organic UV filters for aquatic organisms, but little is known about their biodegradation in river sediments and their impact on microorganisms. We have set up the sterile and microbiological systems in the laboratory, adding 2-ethylhexyl-4-methoxycinnamate (EHMC), one of organic UV filters included in the list of high yield chemicals, at concentrations of 2, 20 and 200 μg/L, and characterized the microbial community composition and diversity in sediments. Monitoring of EHMC degradation within 30 days revealed that the half-life in the microbial system (3.49 days) was much shorter than that in the sterile system (7.55 days). Two potential degradation products, 4-mercaptobenzoic acid and 3-methoxyphenol were identified in the microbial system. Furthermore, high-throughput 16s and 18s rRNA gene sequencing showed that Proteobacteria dominated the sediment bacterial assemblages followed by Chloroflexi, Acidobacteria, Bacteroidetes and Nitrospirae; Eukaryota_uncultured fungus dominated the sediment fungal assemblages. Correlation analysis demonstrated that two bacterium genera (Anaerolineaceae_uncultured and Burkholderiaceae_uncultured) were significantly correlated with the biodegradation of EHMC. These results illustrate the biodegradability of EHMC in river sediments and its potential impact on microbial communities, which can provide useful information for eliminating the pollution of organic UV filters in natural river systems and assessing their potential ecological risks.

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe

A field pilot-scale passive treatment system was developed for in-situ bioremediation of acid mine drainage (AMD). The microbial community and its variation were analyzed. The data proved that 93.7% of total soluble Fe and 99% of soluble Fe(II) could be removed by the system. Principal coordinates analysis (PCoA) showed that a low pH and an elevated Fe concentration within the system created a unique microbial community that was dominated by acidophilic iron-oxidizing bacteria and iron-reducing bacteria. Canonical correlation analysis (CCA) indicated that the pH, iron content and total sulfur jointly determined the composition of the microbial communities. Species of Ferrovum, Delftia, Acinetobacter, Metallibacterium, Acidibacter and Acidiphilium were highly enriched, which promoted the removal of iron. Furthermore, the results revealed important data for the biogeochemical coupling of microbial communities and environmental parameters. These findings are beneficial for further application of in-situ field bioreactors to remediate AMD.

Bioavailable metal(loid)s and physicochemical features co-mediating microbial communities at combined metal(loid) pollution sites

Heavy metal contamination poses considerable threats to various ecosystems, yet little is known about the assembly and adaptation of microbial communities at sites with combined heavy metal(loid) pollution. Here, we examined metal(loid) pollutants and bacterial communities in three zones (Zones Ⅰ, Ⅱ, and Ⅲ) of an abandoned sewage reservoir with different usage years. The contamination level of multiple metal(loid)s was higher in Zone Ⅰ than in the other zones, and arsenic (As), zinc (Zn), selenium (Se), copper (Cu), tin (Sn), molybdenum (Mo), antimony (Sb), cadmium (Cd), lead (Pb), thallium (Tl), and nickel (Ni) were the major contaminants (pollution load index > 1). Bioavailable forms of titanium (Ti), chromium (Cr), Sn, and cobalt (Co) played essential roles in shaping the microbial structure, and physicochemical properties, especially organic matter (OM) and pH, also mediated the microbial diversity and composition in the metal(loid) contaminated zones. Metal-microbe interactions and heatmap analysis revealed that the bioavailability of metal(loid)s promoted the niche partitioning of microbial species. Metal-resistant species were abundant in Zone Ⅰ that had the highest metal-contaminated level, whereas metal-sensitive species prevailed in Zone Ⅲ that had the lowest pollution level. The bioavailable metal(loid)s rather than physicochemical and spatial variables explained a larger portion of the variance in the microbial community, and the homogeneous selection was the dominant ecological process driving the assembly of the microbial community. Overall, our study highlighted the importance of metal(loid) bioavailability in shaping microbial structure, future bioremediation, and environmental management of metal(loid) contaminated sites.

Microbial insights into the biogeochemical features of thallium occurrence: A case study from polluted river sediments

Thallium (Tl) is a trace element with extreme toxicity. Widespread Tl pollution in riverine systems, mainly due to escalating mining and smelting activities of Tl-bearing sulfide minerals, has attracted increasing attention. Insights into the function of the microbial communities with advanced characterization tools are critical for understanding the biogeochemical cycle of Tl. Herein, microbial communities and their adaptive evolution strategies in river sediments from a representative Tl-bearing pyrite mine area in southern China were profiled via 16S rRNA gene sequence analysis and shotgun metagenomic analysis. In total, 64 phyla and 778 genera of microorganisms were observed in the studied sediments. The results showed that pH, Tl, Pb, Zn and total organic carbon (TOC) had a significant influence on microbial community structure. Some important reductive microorganisms (such as Erysipelothrix, Geobacter, desulfatiferula, desulfatihabadium and fusibacter) were involved in the biogeochemical cycle of Tl. The ruv, rec, ars and other resistance genes enhanced the tolerance of microorganisms to Tl. The study suggested that relevant C, N and S cycle genes were the main metabolic paths of microorganisms surviving in the high Tl-polluted environment. The findings were critical for establishment, operation and regulation in the microbial treatment of Tl containing or related wastewater.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

Impact of acid mine drainage chemistry and microbiology on the development of efficient Fe removal activities

Coal mine derived acid mine drainage (AMD) is formed when oxygenated water infiltrates mine voids and oxidizes FeS phases, generating acidic fluid rich in heavy metals, polluting thousands of miles of streams. Existing remediation options are cost-prohibitive and difficult to sustain. In some cases, AMD flows over previously pristine soil in thin sheets over terrestrial surface, enhancing AMD aeration and Fe(II) oxidizing activities, leading to oxidative Fe(II) precipitation from AMD, without any human intervention. Since robust Fe(II) biooxidation occurs in the mixture of intruding AMD and pristine soil, understanding the effects of chemically variant AMD can be exploited for effective Fe(II) removal. We hypothesized that chemistry and microbiology of AMD intruding pristine soil on surface would influence the development of Fe(II) oxidizing capabilities. Therefore, to investigate the response of pristine soil to the addition of AMD varying in chemical and microbial characteristics, we mixed soil with a near-neutral and moderately acidic AMD, in separate incubations. Incubations with near-neutral AMD developed microbial Fe(II) oxidation activities after 10 days. However, Fe(II) oxidation in moderately acidic AMD incubations was mostly abiotic. 16S rRNA gene sequences and metabolic functional prediction (Tax4Fun) analysis of near-neutral AMD and soil mixture indicated development of taxonomically different communities capable of activities similar to microorganisms in a mine void. In conclusion, results indicate that AMD chemistry and microbiology affects development of Fe(II) biooxidation. Therefore, understanding of the effect of AMD chemistry on the development of FeOB activities in soil can be exploited to design site-specific and sustainable solutions.

The dynamic development of bacterial community following long-term weathering of bauxite residue

Bauxite residue is the industrial waste generated from alumina production and commonly deposited in impoundments. These sites are bare of vegetation due to the extreme high salinity and alkalinity, as well as lack of nutrients. However, long term weathering processes could improve residue properties to support the plant establishment. Here we investigate the development of bacterial communities and the geochemical drivers in bauxite residue, using Illumina high-throughput sequencing technology. Long term weathering reduced the pH in bauxite residue and increased its nutrients content. The bacterial community also significantly developed during long term weathering processes. Taxonomic analysis revealed that natural weathering processes encouraged the populations of Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes, whereas reducing the populations of Firmicutes and Actinobacteria. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was the dominant factors affecting microbial structure. The results have demonstrated that natural weathering processes improved the soil development on the abandoned bauxite residue disposal areas, which also increased our understanding of the correlation between microbial variation and residue properties during natural weathering processes in Bauxite residue disposal areas.

Ecological influences of the migration of micro resin particles from crushed waste printed circuit boards on the dumping soil

About 0.8 million tons of resin particles, which were generated from the recovery of waste printed circuit boards, were dumped on soil at Qingyuan city of China. Resin particles not only belong to micro plastic but also contain brominated flame retardants and heavy metals. There is little information about soil pollution caused by the dumped resin particles. This study found resin particles would transfer from soil surface into soil at least 10 mm downward for six months. Average content of bromine in soil within 10 cm exceeded 2500 mg/kg. The highest content of Pb, Zn, and Cu was 3450, 1143 and 1450 mg/kg, which were approximately 6.9, 2.3 and 3.6 times as much as Grade Ⅲ soil standard of China. Micro plastic, brominated flame retardants, and heavy metals made significant effects on soil bacterial community. Bacterial diversity was destroyed and the number of resistant bacteria increased obviously such as Acinetobacter, Pseudomonas and Paracoccus. This paper presented the ecological destroy of soil when the resin particles were deposited on soil surface. It also suggested the government to urgently manage the resin particles produced in the recovery of waste printed circuit boards.

A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems

Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.

Changes in microbial communities of a passive coal mine drainage bioremediation system

Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%–43%), Bacteroidetes (12%–37%), Firmicutes (3%–11%), and Verrucomicrobia (6%–11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis

This study surveyed physicochemical properties and bacterial community structure of water and sediments from an acid mine drainage (AMD) dam in South Africa. High-throughput sequence analysis revealed low diversity bacterial communities affiliated within 8 dominant phyla; Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Proteobacteria, Saccharibacteria, and ca. TM6_(Dependentiae). Acidiphilium spp. which are common AMD inhabitants but rarely occur as dominant taxa, were the most abundant in both AMD water and sediments. Other groups making up the community are less common AMD inhabitants; Acidibacillus, Acidibacter, Acidobacterium, Acidothermus, Legionella, Metallibacterium, Mycobacterium, as well as elusive taxa (Saccharibacteria, ca. TM6_(Dependentiae) and ca. JG37-AG-4). Although most of the taxa are shared between sediment and water communities, alpha diversity indices indicate a higher species richness in the sediments. From canonical correspondence analysis, DOC, Mn, Cu, Cr, Al, Fe, Ca were identified as important determinants of community structure in water, compared to DOC, Ca, Cu, Fe, Zn, Mg, K, Mn, Al, sulfates, and nitrates in sediments. Predictive functional profiling recovered genes associated with bacterial growth and those related to survival and adaptation to the harsh environmental conditions. Overall, the study reports on a distinct AMD bacterial community and highlights sediments as microhabitats with higher species richness than water.

The Influence on Contaminant Bioavailability and Microbial Abundance of Lake Hongze by the South-to-North Water Diversion Project

The world famous South-to-North Water Transfer Project was built to alleviate serious water shortages in northern China. Considering that lake Hongze is an important freshwater lake in this region, analyzing the influence of water diversion on typical contaminant bioavailability and microbial abundance could aid in achieving a good overall understanding of hydrodynamic variation. Accordingly, in situ high-resolution measurements of diffusive gradients in thin films (DGT) and next-generation high-throughput sequencing were combined in order to survey Lake Hongze and determine the relationship between environmental factors and microbial communities. The DGT method effectively obtained more than the 85% of bioavailable concentrations of the corresponding contaminants; the results showed that labile P, S, Fe, As, and Hg concentrations were higher in areas influenced by water transfer. Moreover, the relative abundance and alpha diversity of the sampling sites distributed in the water transfer area differed significantly from other sites. The pH, conductivity, and labile Mn, As, and P were shown to be the primary environmental factors affecting the abundance and diversity of microbes. With the exception of bioturbation-affected sites controlled by labile Mn and pH, sites distributed in the water diversion area were most affected by As and conductivity, with little spatial discrepancy. Furthermore, site 2, with higher bioturbation abundance, and site 10, with stronger hydrodynamics, had low alpha diversity compared to the other sites. Consequently, the bioavailability of typical contaminants such as P, S, As, Hg, Fe, Mg, Cd, Pb, and Mn, as well as the diversity and abundance of microbial in the sites influenced by the water diversion, were significantly different to the other sites. Thus, the impacts of the South-to-North Water Transfer Project on participant lakes were non-negligible overall in the investigation.

The effects of phytoremediation on soil bacterial communities in an abandoned mine site of rare earth elements

Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria, Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils.

Response of microbial communities and interactions to thallium in contaminated sediments near a pyrite mining area

Thallium (Tl) is a well-recognized hazardous heavy metal with very high toxicity. It is usually concentrated in sulfide minerals, such as pyrite (FeS₂), sphalerite (ZnS), chalcopyrite (CuS) and galena (PbS). Here, this study was carried out to investigate the indigenous microbial communities via 16S rRNA gene sequence analysis in typical surface sediments with various levels of Tl pollution (1.8-16.1 mg/kg) due to acid mine drainage from an active Tl-containing pyrite mining site in South China. It was found with more than 50 phyla from the domain Bacteria and 1 phyla from the domain Archaea. Sequences assigned to the genera Ferroplasma, Leptospirillum, Ferrovum, Metallibacterium, Acidithiobacillus, and Sulfuriferula manifested high relative abundances in all sequencing libraries from the relatively high Tl contamination. Canonical correspondence analysis further uncovered that the overall microbial community in this area was dominantly structured by the geochemical fractionation of Tl and geochemical parameters such as pH and Eh. Spearman's rank correlation analysis indicated a strong positive correlation between acidophilic Fe-metabolizing species and Tl_total, Tl_oxi, and Tl_res. The findings clarify potential roles of such phylotypes in the biogeochemical cycling of Tl, which may facilitate the development of in-situ bioremediation technology for Tl-contaminated sediments.

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments

Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O₂ gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O₂ into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O₂ was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O₂ in shallow portions of the sediments influenced Fe metabolism in deeper, O₂-free sediments. Total potential (E_H + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O₂ on Fe metabolism past where it penetrates into the sediments. This work shows that O₂ availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O₂ can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O₂.

Comparison of greenhouse and open field cultivations across China: Soil characteristics, contamination and microbial diversity

A national scale survey was conducted to determine an array of inorganic and organic contaminants in agricultural soils from two cultivation modes (greenhouse vs. open field) in 20 provinces across China. The investigated contaminants include organochlorine pesticides (OCPs), phthalate esters (PAEs), polycyclic aromatic hydrocarbons (PAHs), lead (Pb), zinc (Zn), copper (Cu) and cadmium (Cd). The large amounts of agrochemicals used and special cultivation mode in greenhouse caused substantial soil pollution and deterioration of soil quality. Mean concentrations of both OCPs and PAEs in greenhouse soil were approximately 100% higher than those in open field. The pH values were 6.85 ± 1.04 and 7.34 ± 0.84 for greenhouse and open field, respectively (p > 0.05). The soil microbial community was predicted to be affected by pollution in greenhouse through the PICRUSt analysis of 16s rRNA sequences. The 12 variables including various chemicals and soil properties together explained 15% of the observed variation in the community composition. In the studied variables, PAEs and lead were the primary factors affecting microbial diversity in greenhouse soils, while pH had the greatest impact on the microbial community in open field soils. These findings enhanced our understanding of the environmental impact and contamination management of greenhouses worldwide.

Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.

Phthalate esters and organochlorine pesticides in agricultural soils and vegetables from fast-growing regions: a case study from eastern China

The present study investigated phthalate esters (PAEs) and organochlorine pesticides (OCPs) in agricultural soils and vegetables from eastern China. The concentrations of PAEs ranged from 109 to 5560 ng/g in soils and 60.1 to 2390 ng/g in cabbages, with average concentrations of 946 and 601 ng/g, respectively. The concentrations of OCPs ranged from <0.1 to 662 ng/g in soils and <0.1 to 42.8 ng/g in cabbages, with average concentrations of 134 and 11.6 ng/g, respectively. OCPs were mainly in the 0-30 cm surface soil layers, while PAEs could infiltrate in deep soil profiles to 70-80 cm layer. Potential source analysis traced the occurrence of OCPs to both historical application and current usage, whereas building materials and agricultural plastic film were possible input sources of PAEs in the ambient environment. OCPs showed no apparent effect on soil microbial communities, whereas significant negative relationship was observed between PAEs and fungi in soils (R = -0.54, p < 0.01). Human health risk assessment data revealed marginal noncarcinogenic risks and low carcinogenic risks in these soils. Notably, PAEs posed a comparable or higher risk level compared with that of OCPs. This study suggests the need for better regulation on pollution control and management of PAE-elevated sites to protect soil quality and food safety.

Bacterial community profile of contaminated soils in a typical antimony mining site

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb_DGT, As_DGT, potential ecological risk index (RI), TC, TN), among which pH, Sb_DGT, and As_DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

Mining activity for rare earth elements (REEs) has caused serious environmental pollution, particularly for soil ecosystems. However, the effects of REEs on soil microbiota are still poorly understood. In this study, soils were collected from abandoned sites of a REEs mine, and the structure, diversity, and co-occurrence patterns of soil microbiota were evaluated by Illumina high-throughput sequencing targeting 16S rRNA genes. Although microbiota developed significantly along with the natural restoration, the microbial structure on the site abandoned for 10 years still significantly differed from that on the unmined site. Potential plant growth promoting bacteria (PGPB) were identified by comparing 16S sequences against a self-constructed PGPB database via BLAST, and it was found that siderophore-producing and phosphorus-solubilizing bacteria were more abundant in the studied soils than in reference soils. Canonical correspondence analysis indicated that species richness of plant community was the prime factor affecting microbial structure, followed by limiting nutrients (total carbon and total nitrogen) and REEs content. Further co-occurring network analysis revealed nonrandom assembly patterns of microbiota in the studied soils. These results increase our understanding of microbial variation and assembly pattern during natural restoration in REE contaminated soils.

Polychlorinated biphenyls in agricultural soils from the Yangtze River Delta of China: Regional contamination characteristics, combined ecological effects and human health risks

The current contamination status of polychlorinated biphenyls (PCBs) was studied in the agricultural soils of the Yangtze River Delta (YRD), one of the largest economic zones in China. The concentrations of PCBs ranged from <0.1 to 130 ng/g dry weight. Higher concentrations of PCBs were observed in the 0-30 cm surface layers relative to the subsurface soils. A distinct spatial distribution was observed with a declining concentration gradient from the northwest to the southeast of the region. The composition of PCBs in the soils was consistent with the Chinese commercial PCB mixtures, but different from the compositions in global background soil. Local sources including large-scale use and disposal of PCB-containing products were the main potential sources to soil. The ecological effects and human health risks associated with combined persistent organic pollutants, including PCBs, organochlorine pesticides (OCPs), phthalate esters (PAEs) and polybrominated diphenyl ethers (PBDEs), were further estimated. The four toxic organic compounds and seven physicochemical parameters together could only explain 12.7% of the variation in microbial community composition, suggesting the soil ecosystem function was not strongly influenced by the combined pollution at low concentrations. However, the potential health risks to residents via multiple pathways were notably higher for PCBs than other chemicals. The potential risks were mainly derived from PCB-126, 81, and 169.

Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity

The recent recognition of the environmental prevalence of perchlorate and its discovery on Mars, Earth's moon, and in meteorites, in addition to its novel application to controlling oil reservoir sulfidogenesis, has resulted in a renewed interest in this exotic ion and its associated microbiology. However, while plentiful data exists on freshwater perchlorate respiring organisms, information on their halophilic counterparts and microbial communities is scarce. Here, we investigated the temporal evolving structure of perchlorate respiring communities under a range of NaCl concentrations (1, 3, 5, 7, and 10 % wt/vol) using marine sediment amended with acetate and perchlorate. In general, perchlorate consumption rates were inversely proportional to NaCl concentration with the most rapid rate observed at 1 % NaCl. At 10 % NaCl, no perchlorate removal was observed. Transcriptional analysis of the 16S rRNA gene indicated that salinity impacted microbial community structure and the most active members were in families Rhodocyclaceae (1 and 3 % NaCl), Pseudomonadaceae (1 NaCl), Campylobacteraceae (1, 5, and 7 % NaCl), Sedimenticolaceae (3 % NaCl), Desulfuromonadaceae (5 and 7 % NaCl), Pelobacteraceae (5 % NaCl), Helicobacteraceae (5 and 7 % NaCl), and V1B07b93 (7 %). Novel isolates of genera Sedimenticola, Marinobacter, Denitromonas, Azoarcus, and Pseudomonas were obtained and their perchlorate respiring capacity confirmed. Although the obligate anaerobic, sulfur-reducing Desulfuromonadaceae species were dominant at 5 and 7 % NaCl, their enrichment may result from biological sulfur cycling, ensuing from the innate ability of DPRB to oxidize sulfide. Additionally, our results demonstrated enrichment of an archaeon of phylum Parvarchaeota at 5 % NaCl. To date, this phylum has only been described in metagenomic experiments of acid mine drainage and is unexpected in a marine community. These studies identify the intrinsic capacity of marine systems to respire perchlorate and significantly expand the known diversity of organisms capable of this novel metabolism.

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients

Located in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO4 (2-) (>6 g/liter). AMD contamination gradually decreases throughout downstream rivers and reservoirs, creating an AMD pollution gradient which has led to a suite of biogeochemical processes along the watershed. In this study, sediment samples were collected along the AMD pollution sites for geochemical and microbial community analyses. High-throughput sequencing found various bacteria associated with microbial Fe and S cycling within the watershed and AMD-impacted creek. A large proportion of Fe- and S-metabolizing bacteria were detected in this watershed. The dominant Fe- and S-metabolizing bacteria were identified as microorganisms belonging to the genera Metallibacterium, Aciditerrimonas, Halomonas, Shewanella, Ferrovum, Alicyclobacillus, and Syntrophobacter. Among them, Halomonas, Aciditerrimonas, Metallibacterium, and Shewanella have previously only rarely been detected in AMD-contaminated environments. In addition, the microbial community structures changed along the watershed with different magnitudes of AMD pollution. Moreover, the canonical correspondence analysis suggested that temperature, pH, total Fe, sulfate, and redox potentials (Eh) were significant factors that structured the microbial community compositions along the Aha watershed.