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

Study on the new slow-release carbon source biochemistry and its improvement of SRB on the acid mine drainage treatment

The content of sulfate and heavy metals in acidic mine drainage (AMD) exceeds the standard severely, and the acidity is extremely high, causing serious harm to the environment. SRB can efficiently remove sulfates through its own metabolism. The treatment of AMD by SRB faces problems such as carbon source scarcity and heavy metal ion toxicity to SRB. In this study, corn cob and polycaprolactone were embedded to prepare a novel slow-release carbon source (PSCL), which simultaneously achieves carbon source supply and metal ion removal. Through adsorption isotherms, kinetics, thermodynamics studies, and various characterization analyses, it is known that PSCL removes Cu2+ and Zn2+ through ion exchange, physical and chemical adsorption, electrostatic attraction, and surface complexation. PSCL carbon release experiments and characterization results confirm that its surface carbon distribution is dense, the molecular weight of DOM in the leachate is small, the degree of humification is low, and it has a porous structure, making it a good carbon release material and biological attachment. The experimental results of PSCL enhanced SRB treatment of AMD showed that the removal rates of SO42-, Cu2+ and Zn2+ could be increased to 97.48%, 98.11% and 90.42%, respectively, with a effluent pH of 7.05, effectively improving the water quality of AMD. This study provides new materials and methods to address the limitations of SRB in treating actual AMD.

Gradient of acid mine drainage regulates microbial community assembly and the diversity of species associated with native plants

Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an AMD impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.

Microbial mediated remediation of heavy metals toxicity: mechanisms and future prospects

Heavy metal pollution has become a serious concern across the globe due to their persistent nature, higher toxicity, and recalcitrance. These toxic metals threaten the stability of the environment and the health of all living beings. Heavy metals also enter the human food chain by eating contaminated foods and cause toxic effects on human health. Thus, remediation of HMs polluted soils is mandatory and it needs to be addressed at higher priority. The use of microbes is considered as a promising approach to combat the adverse impacts of HMs. Microbes aided in the restoration of deteriorated environments to their natural condition, with long-term environmental effects. Microbial remediation prevents the leaching and mobilization of HMs and they also make the extraction of HMs simple. Therefore, in this context recent technological advancement allowed to use of bioremediation as an imperative approach to remediate polluted soils. Microbes use different mechanisms including bio-sorption, bioaccumulation, bioleaching, bio-transformation, bio-volatilization and bio-mineralization to mitigate toxic the effects of HMs. Thus, keeping in the view toxic HMs here in this review explores the role of bacteria, fungi and algae in bioremediation of polluted soils. This review also discusses the various approaches that can be used to improve the efficiency of microbes to remediate HMs polluted soils. It also highlights different research gaps that must be solved in future study programs to improve bioremediation efficency.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Bioremediation of acid mine drainage using sulfate-reducing wetland bioreactor: Filling substrates influence, sulfide oxidation and microbial community

Two sulfate-reducing wetland bioreactors (SRB-1 filled with lignocellulosic wastes and SRB-2 with river sand) were applied for synthetic acid mine drainage treatment with bio-waste fermentation liquid as electron donor, and the influence of filling substrates on sulfate reduction, sulfur transformation and microbial community was studied. The presence of lignocellulosic wastes (mixture of cow manure, bark, sawdust, peanut shell and straw) in SRB-1 promoted sulfate reduction efficiency (68.9%), sulfate reduction rate (42.1 ± 11 mg S/(L·d)), dissolved sulfide production rate (27.4 ± 7 mg S/(L·d)), and particularly caused high conversion ratio of sulfate reduction into dissolved sulfide (66.4%). In comparison, the relatively low sulfate reduction efficiency (42.9%), sulfate reduction rate (27.0 ± 10 mg S/(L·d)), dissolved sulfide production rate (5.6 ± 3 mg S/(L·d)) and low dissolved sulfide conversion efficiency (21.2%) occurred in SRB-2. Mixed organic substrates including easily assimilated electron donors (in manure) and lignocellulosic matter were effective to promote quick start and long-term microbial sulfate reduction. More than 98% of produced dissolved sulfide was oxidized dominantly by photoautotrophic green sulfur bacteria (genera Chlorobium and Chlorobaculum), of which 64.6% and 54.5% was converted into elemental sulfur for SRB-1 and SRB-2. The oxidation of sulfide into elemental sulfur for potential recovery rather than sulfate is preferred. Diverse sulfate reducing bacteria and sulfide oxidizing bacteria co-existed in the treatment system, which led to a sustainable sulfur transformation. High metal removal efficiency for Fe (99.6%, 92.5%), Cd (99.9%, 99.9%), Zn (99.4%, 98.5%), Cu (94.5%, 94.6%) except for Mn (9.3%, 3.6%) was achieved, and effluent pH increased to 6.5-7.7 and 6.7-7.7 for SRB-1 and SRB-2, respectively. Microbial community was regulated by filling substrates. Synergism between lignocellulosic decomposing bacteria and sulfate reducing bacteria played a vital role in lignocellulosic bioreactor treating AMD, in addition to fermentation liquid serving as effective electron donor.

Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil)

Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.

Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings

Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.

Integrated treatment of suburb diffuse pollution using large-scale multistage constructed wetlands based on novel solid carbon: Nutrients removal and microbial interactions

In this study, an integrated treatment system was proposed and applied in situ, including detention tank, multistage constructed wetlands (CWs) and wastewater treatment plants (WWTPs), preventing nutrients flowing into Dianchi Lake, in which the treatment performance of multistage CWs were evaluated principally. Results skillfully realized the bypass purification of upstream river at dry reasons, as well as the effective management and treatment of the collected diffuse pollution at rainy reasons. The purified water flowing into water bodies could satisfy the Grade III of environmental quality standards for surface water in China with the average effluent concentrations of COD, NH₄⁺-N, TN and TP decreased to 10 (51.2-72.7%), 0.5 (67.2-83.0%), 1.0 (71.2-79.6%) and 0.15 (72.3-89.4%) mg L^-1, respectively. High-throughput sequencing results indicated that the application of poly-3-hydroxybutyrate-cohyroxyvelate-sawdust (PS) blends could enrich norank_f_Anaerolineaceae (7.95%) and Bradyrhizobium (10.2%), which were distinct from the dominant genera of Pleurocapsa (13.0%) in gravel-based CWs. Functional genes and metabolism analysis uncovered that the heterotrophic denitrification was the main pathway of nitrogen removal with the abundance of genes encoding TCA cycle, glycolysis and denitrification process up-regulated. In addition, molecular ecological network (MEN) analysis suggested the denitrification genes were positively correlated with the predominant microbes in PS-based CWs, favorable for denitrifiers to transfer and utilize electron donors during denitrification process. This study proved that the developed PS blends as carbon supplies in CWs and the proposed integrated treatment system are effective methods for watershed management, providing valuable reference to low-pollution wastewater treatment in practical engineering projects.

Insights into remediation effects and bacterial diversity of different remediation measures in rare earth mine soil with SO4 2- and heavy metals

The increased demand for rare earth resources has led to an increase in the development of rare earth mines (REMs). However, the production of high-concentration leaching agents (SO₄ ^2-) and heavy metals as a result of rare earth mining has increased, necessitating the removal of contaminants. Here, a series of experiments with different remediation measures, including control (CK), sulfate-reducing bacteria (SRB) alone (M), chemicals (Ca(OH)₂, 1.5 g/kg) plus SRB (CM-L), chemicals (Ca(OH)₂, 3.0 g/kg) plus SRB (CM-M), and chemicals (Ca(OH)₂, 4.5 g/kg) plus SRB (CM-H), were conducted to investigate the removal effect of SO₄ ^2-, Pb, Zn, and Mn from the REM soil. Then, a high-throughput sequencing technology was applied to explore the response of bacterial community diversity and functions with different remediation measures. The results indicated that CM-M treatment had a more efficient removal effect for SO₄ ^2-, Pb, Zn, and Mn than the others, up to 94.6, 88.3, 98.7, and 91%, respectively. Soil bacterial abundance and diversity were significantly affected by treatments with the inoculation of SRB in comparison with CK. The relative abundance of Desulfobacterota with the ability to transform SO₄ ^2- into S^2- increased significantly in all treatments, except for CK. There was a strong correlation between environmental factors (pH, Eh, SO₄ ^2-, Pb, and Zn) and bacterial community structure. Furthermore, functional prediction analysis revealed that the SRB inoculation treatments significantly increased the abundance of sulfate respiration, sulfite respiration, and nitrogen fixation, while decreasing the abundance of manganese oxidation, dark hydrogen oxidation, and denitrification. This provides good evidence for us to understand the difference in removal efficiency, bacterial community structure, and function by different remediation measures that help select a more efficient and sustainable method to remediate contaminants in the REM soil.

Recent Strategies for Bioremediation of Emerging Pollutants: A Review for a Green and Sustainable Environment

Environmental pollution brought on by xenobiotics and other related recalcitrant compounds have recently been identified as a major risk to both human health and the natural environment. Due to their toxicity and non-biodegradability, a wide range of pollutants, such as heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals are present in the environment. Bioremediation is an effective cleaning technique for removing toxic waste from polluted environments that is gaining popularity. Various microorganisms, including aerobes and anaerobes, are used in bioremediation to treat contaminated sites. Microorganisms play a major role in bioremediation, given that it is a process in which hazardous wastes and pollutants are eliminated, degraded, detoxified, and immobilized. Pollutants are degraded and converted to less toxic forms, which is a primary goal of bioremediation. Ex situ or in situ bioremediation can be used, depending on a variety of factors, such as cost, pollutant types, and concentration. As a result, a suitable bioremediation method has been chosen. This review focuses on the most recent developments in bioremediation techniques, how microorganisms break down different pollutants, and what the future holds for bioremediation in order to reduce the amount of pollution in the world.

Effect of Hydroxyapatite on the Migration of Fe(III) Ions: Kinetic, Equilibrium and Thermodynamic Study

The recycling and regeneration of Fe(III) is the key point for promoting the oxidation reaction of ore to produce acidic mine drainage (AMD). Hydroxyapatite (HAP) has excellent adsorption ability of Fe(III), which has good biocompatibility and is widely distributed in nature. In order to achieve the source treatment of AMD, the migration and transformation of Fe(III) in the presence of HAP were systematically investigated. In this study, the influence of HAP on the migration of Fe(III) was evaluated though the transformation capacity of Fe(III) by HAP. The adsorption transformation kinetic, equilibrium and thermodynamics of Fe(III) using HAP were also systematic investigated. The transformation efficiency of Fe(III) increased with the increasing initial pH value and reached 99.8% at a pH of 5 due to the hydrolysis reaction. The transformation efficiency was also up to 99% at an initial pH of 2 when the reaction temperature increased to 313 K. However, the transformation capability of Fe(III) decreases with reaction temperature. The kinetics of the adsorption of Fe(III) fitted the pseudo second order kinetic model. Experimental results were also analyzed by the Langmuir isotherm equations at room temperatures. R_L separation factor for Langmuir isotherm showed that the migration of Fe(III) is successfully hindered by HAP. Various thermodynamic parameters such as enthalpy (ΔH), Gibbs free energy (ΔG) and entropy (ΔS) changes were computed, which showed that the transport lag of Fe(III) caused by HAP is spontaneous and endothermic.

Metagenomic Analysis of Biochemical Passive Reactors During Acid Mine Drainage Bioremediation Reveals Key Co-selected Metabolic Functions

Acid mine drainage (AMD) is the major pollutant generated by the mining industry, and it is characterized by low pH and high concentration of metals and sulfate. The use of biochemical passive reactors (BPRs) is a promising strategy for its bioremediation. To date, there are various studies describing the taxonomical composition of BPR microbial communities, generally consisting of an assemblage of sulfate-reducing organisms inside Deltaproteobacteria, and a diverse set of anaerobic (ligno)cellulolytic bacteria; however, insights about its functional metagenomic content are still scarce. In previous studies, a laboratory-scale AMD bioremediation using biochemical passive reactors was designed and performed, tracking operation parameters, chemical composition, and changes, together with taxonomic composition of the microbiomes harbored in these systems. In order to reveal the main functional content of these communities, we used shotgun metagenomics analyses to explore genes of higher relative frequencies and their inferred functions during the AMD bioremediation from three BPRs representing the main microbiome compositions detected in the system. Remarkably, genes encoding for two-component regulatory systems and ABC transporters related to metal and inorganic ions, cellulose degradation enzymes, dicarboxylic acid production, and sulfite reduction complex were all detected at increased frequency. Our results evidenced that higher taxonomic diversity of the microbiome was arising together with a functional redundancy of the specific metabolic roles, indicating its co-selection and suggesting that its enrichment on BPRs may be implicated in the cumulative efficiency of these systems.

Industrial Biotechnology Based on Enzymes From Extreme Environments

Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.

Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake

Acid mine drainage (AMD) lakes are typical hydrologic features caused by open pit mining and represent extreme ecosystems and environmental challenges. Little is known about microbial distribution and community assembly in AMD lakes, especially in deep layers. Here, we investigated prokaryotic microbial diversity and community assembly along a depth profile in a stratified AMD lake using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. The water column in the AMD lake exhibited tight geochemical gradients, with more acidic surface water. Coupled with vertical hydrochemical variations, prokaryotic microbial community structure changed significantly, and was accompanied by increased diversity with depth. In the surface water, heterogeneous selection was the most important assembly process, whereas stochastic processes gained importance with depth. Meanwhile, microbial co-occurrences, especially positive interactions, were more frequent in the stressful surface water with reduced network modularity and keystone taxa. The pH was identified as the key driver of microbial diversity and community assembly along the vertical profile based on random forest analysis. Taken together, environmental effects dominated by acid stress drove the community assembly and species coexistence that underpinned the spatial scaling patterns of AMD microbiota in the lake. These findings demonstrate the distinct heterogeneity of local prokaryotic microbial community in AMD lake, and provide new insights into the mechanism to maintain microbial diversity in extreme acidic environments.

Effects of long-term discharge of acid mine drainage from abandoned coal mines on soil microorganisms: microbial community structure, interaction patterns, and metabolic functions

More than twenty abandoned coal mines in the Yudong River Basin of Guizhou Province have discharged acid mine drainage (AMD) for a long time. The revelation of microbial community composition, interaction patterns, and metabolic functions can contribute to a better understanding of such ecosystems, which in its turn can be helpful in the development of strategies aiming at the ecological remediation of AMD pollution. In this study, reference and contaminated soil samples were collected along the AMD flow path for high-throughput sequencing. Results showed that the long-term AMD pollution promoted the evolution of γ-Proteobacteria, and the acidophilic iron-oxidizing bacteria Ferrovum (relative abundance of 15.50%) and iron-reducing bacteria Metallibacterium (9.87%) belonging to this class became the dominant genera. Co-occurrence analysis revealed that the proportion of positive correlations among bacteria increased from 51.02 (reference soil) to 75.16% (contaminated soil), suggesting that acidic pollution promotes the formation of mutualistic interaction networks of microorganisms. Metabolic function prediction (Tax4Fun) revealed that AMD contamination enhanced microbial functions such as translation, repair, and biosynthesis of peptidoglycan and lipopolysaccharide, etc., which may be an adaptive mechanism for microbial survival in extremely acidic environment. In addition, acidic pollution promoted the high expression of nitrogen-fixing genes in soil, and the discovery of autotrophic nitrogen-fixing bacteria such as Ferrovum highlights the possibility of using this taxon for bioremediation of AMD pollution.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

A novel biofilm bioreactor derived from a consortium of acidophilic arsenite-oxidizing bacteria for the cleaning up of arsenite from acid mine drainage

Arsenite (As(III)) was considered to be of great concern in acid mine drainage (AMD). A promising approach for cleaning up of arsenite from AMD is microbial oxidation of As(III) followed by adsorptions. However, there is virtually no research about the acidophilic bioreactor for As(III) oxidation so far. In this study, we formed a new biofilm bioreactor with a consortium of acidophilic As(III) oxidation bacteria. It is totally chemoautotrophic, with no need to add any carbon or other materials during the operations. It works well under pH 3.0-4.0, capable of oxidizing 1.0-20.0 mg/L As(III) in 3.0-4.5 h, respectively. A continuous operation of the bioreactor suggests that it is very stable and sustainable. Functional gene detection indicated that the biofilms possessed a unique diversity of As(III) oxidase genes. Taken together, this acidophilic bioreactor has great potential for industrial applications in the cleaning up of As(III) from AMD solution.

Removal of multiple heavy metals from mining-impacted water by biochar-filled constructed wetlands: Adsorption and biotic removal routes

Granular biochar made from walnut shells was layered into sand-based constructed wetlands (CWs) to treat simulated mining-impacted water (MIW). The results showed that the biochar media exhibited markedly high capacities for metal binding and acidity neutralization, supported notably better plant growth and mitigated metal transfer from the plant roots to the shoots. The addition of organic liquid wastes (domestic sewage and plant straw hydrolysation broth) stimulated biogenic sulfate reduction after 40 d of adaptation to effectively remove multiple heavy metals in the MIW. The microbial community compositions were prominently regulated by organic carbon, with desirable communities dominated by Cellulomonas and Desulfobulbus formed in the CWs for MIW biotreatment. The role of macrophytes in the CWs in MIW treatment was insignificant and was dependent on operation conditions and metal species. A biochar-packed CW system with liquid organic waste supplementation was effective in metal removal and acidity neutralization of MIW.

High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.

The biotransformation of arsenic by spent mushroom compost - An effective bioremediation agent

Spent mushroom compost (SMC) is a lignocellulose-rich waste material commonly used in the passive treatment of heavy metal-contaminated environments. In this study, we investigated the bioremediation potential of SMC against an inorganic form of arsenic, examining the individual abiotic and biotic transformations carried out by SMC. We demonstrated, that key SMC physiological groups of bacteria (denitrifying, cellulolytic, sulfate-reducing, and heterotrophic) are resistant to arsenites and arsenates, while the microbial community in SMC is also able to oxidize As(III) and reduce As(V) in respiratory metabolisms, although the SMC did not contain any As. We showed, that cooperation between arsenate and sulfate-reducing bacteria led to the precipitation of As_xS_y. We also found evidence of the significant role organic acids may play in arsenic complexation, and we demonstrated the occurrence of As-binding proteins in the SMC. Furthermore, we confirmed, that biofilm produced by the microbial community in SMC was able to trap As(V) ions. We postulated, that the above-mentioned transformations are responsible for the sorption efficiency of As(V) (up to 25%) and As(III) (up to 16%), as well as the excellent buffering properties of SMC observed in the sorption experiments.

Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance

A unique terrace with sharp gradient of environmental conditions was selected to study the microbial response and survival strategies to the extreme environments introduced by acid mine drainage (AMD) contamination. A combination of geochemical analyses, metagenomic sequencing, ex-situ microcosm setups, and statistical analyses were used to investigate the environment-microbe interactions. The microbial communities and metabolic potentials along the terrace were studied by focusing on the genes associated with important biogeochemical processes (i.e., C, N, S cycling and metal resistance). Results show that the variations of geochemical parameters substantially shaped the indigenous microbial communities. Sharp environmental gradients also impacted the microbial metabolic potentials, especially for C, N, and S cycling. Although the relative abundances of carbon fixing genes did not significantly vary along the environmental gradients, the taxa for carbon fixation varied significantly in more contaminated fields versus less contaminated fields, indicating the effects of AMD contamination on the autotrophic microbial communities. AMD input also influenced the N cycling, especially for nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). In addition, ex situ experiments were undertaken to evaluate the effects of AMD contamination on nitrogen fixation rates. Random Forest (RF) analysis indicated that nitrate, pH, total N, TOC exhibited positive correlations with the rates of nitrogen fixation while total Fe, Fe(III), and sulfate showed negative effects. Two co-occurrence networks at taxonomic and genomic levels indicated that geochemical parameters such as pH, TOC, total N, total S, and total Fe substantially influenced the innate microbial communities and their metabolic potentials. The current study provides an understanding for microbial response to AMD contamination and lays the foundation for future potential AMD bioremediation.

Biological remediation of acid mine drainage: Review of past trends and current outlook

Formation of acid mine drainage (AMD) is a widespread environmental issue that has not subsided throughout decades of continuing research. Highly acidic and highly concentrated metallic streams are characteristics of such streams. Humans, plants and surrounding ecosystems that are in proximity to AMD producing sites face immediate threats. Remediation options include active and passive biological treatments which are markedly different in many aspects. Sulfate reducing bacteria (SRB) remove sulfate and heavy metals to generate non-toxic streams. Passive systems are inexpensive to operate but entail fundamental drawbacks such as large land requirements and prolonged treatment period. Active bioreactors offer greater operational predictability and quicker treatment time but require higher investment costs and wide scale usage is limited by lack of expertise. Recent advancements include the use of renewable raw materials for AMD clean up purposes, which will likely achieve much greener mitigation solutions.