Phytostabilization is an important way for the remediation of mine tailings, but the associated microbial processes and community succession remain largely unknown. In this study, we investigated the assembly mechanisms maintaining the core and satellite subcommunities diversity during phytostabilizaion of a mercury-rich mine tailings. The contents of total Hg and methylmercury decreased with a concomitant increase of total and available phosphorus content along the successive remediation stages. Microbial community composition, profiled by 16S rRNA gene sequencing, revealed amplicon sequence variants (ASVs) that were separated according to their abundance within either the core community or the satellite community. Community dynamics analysis showed that alpha diversity indices increased for the core community while decreased for the satellite community. Both satellite and core communities were mainly driven by stochastic drift process, and homogeneous selection was relatively higher in shaping the core community organization. The core community included ASVs affiliated to Proteobacteria, Crenarchaeota, Bacteroidota, Verrucomicrobiota, Acidobacteriota, and Myxococcota phyla, which were driven primarily by heterogeneous selection and drift. The satellite community included ASVs affiliated to Acidobacteriota, Ktedonobacteria, Anaerolineae and Verrucomicrobiota phyla, which were mainly influenced by heterogeneous selection. Nineteen taxa and one taxon were identified as keystone taxa for the satellite and core communities respectively. This study provides important insights on the assemble rules within the core and satellite communities, and theoretical guidance for further ecological restoration and management during microbial remediation of metal-mined derelict land.

Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.

Toxic metal(loid)s released into the soil by non-ferrous metal mining and smelting activities pose a serious threat to residents and the surrounding ecosystem. Considering only total metal(loid) concentrations likely overestimates routine (eco)toxicological risk assessment of soil. We hypothesize that considering metal(loid) bioavailability/accessibility will improve the accuracy of risk assessment. To test this hypothesis, four mining areas in Southwest China, including mining and surrounding sites, were studied. Bioavailability was determined considering metal(loid)s leached by a simulated strong acid rain (SSAR) treatment. In the four areas, the mining site showed higher cumulative releases of metal(loid)s under SSAR treatment than the agricultural field located in the surrounding sites. Thus, the bioavailable metal(loid)s contents were continuously being released during SSAR treatment and likely increased the environmental risk. Ecological and health risk assessment of soil, calculated using total metal(loid)s content, was corrected considering bioavailable/accessible metal(loid)s, which was determined by the heavy metal(loid)s forms and in vitro simulated intestinal stages. Although the corrected indices indicated that the risk of metal(loid)s-contaminated soil was reduced, unfavorable ecological and health risks remained in the four areas. Our study provides new perspectives to better predict the risk of bioavailable/accessible metal(loid)s in non-ferrous metal contaminated and surrounding soils.

Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA >4). Acidiferrobacter and Thermoplasmataceae were found to be pH -tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH -sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu - Zn - Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.

Sulfate-reducing bacteria (SRB) are used in the remediation of mine pollution; however, the mechanism of stabilizing multiple heavy metal(loid)s by the SRB consortium under low oxygen conditions needs further study. Indigenous microflora were extracted from non-ferrous metal-contaminated soil co-inoculated with enriched SRB consortium and assembled as the HQ23 consortium. The presence of Desulfovibrio (SRB) in HQ23 was confirmed by 16S rRNA sequencing and qPCR. The effects of culture media, dissolved oxygen (DO), SO42¯, and pH on the HQ23 growth rate, and the SO42¯-reducing activity were examined. Data indicates that the HQ23 sustained SRB function under low DO conditions (3.67 ± 0.1 mg/L), but the SRB activity was inhibited at high DO content (5.75 ± 0.39 mg/L). The HQ23 can grow from pH 5 to pH 9 and can decrease mobile or bioavailable Cr, Cu, and Zn concentrations in contaminated soil samples. FTIR revealed that Cu and Cr adsorbed to similar binding sites on bacteria, likely decreasing bacterial Cu toxicity. Increased abundances of DSV (marker for Desulfovibrio) and nifH (N-fixation) genes were observed, as well as an accumulation of nitrate-N content in soils suggesting that HQ23 stimulates the biological N-fixation in soils. This study strongly supports the future application of SRB for the bioremediation of heavy metal-polluted sites.

The quality of soil containing heavy metals (HMs) around nonferrous metal mining areas is often not favorable for plant growth. Three types of plant growth promoting rhizobacteria (PGPR)-assisted ryegrass were examined here to treat Cd, Pb, and Zn contaminated soil collected from a nonferrous metal smelting facility. The effects of PGPR-assisted plants on soil quality, plant growth, and the migration and transformation of HMs were evaluated. Results showed that inter-root inoculation of PGPR to ryegrass increased soil redox potential, urease, sucrase and acid phosphatase activities, microbial calorimetry, and bioavailable P, Si, and K content. Inoculation with PGPR also increased aboveground parts and root length, P, Si, and K contents, and antioxidant enzyme activities. The most significant effect was that the simultaneous inoculation of all three PGPRs increased the ryegrass extraction (%) of Cd (59.04-79.02), Pb (105.56-157.13), and Zn (27.71-40.79), compared to CK control (without fungi). Correspondingly, the inter-root soil contents (%) of total Cd (39.94-57.52), Pb (37.59-42.17), and Zn (34.05-37.28) were decreased compared to the CK1 control (without fungi and plants), whereas their bioavailability was increased. Results suggest that PGPR can improve soil quality in mining areas, promote plant growth, transform the fraction of HMs in soil, and increase the extraction of Cd, Pb, and Zn by ryegrass. PGPR is a promising microbe-assisted phytoremediation strategy that can promote the re-greening of vegetation in the mining area while remediating HMs pollution.

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Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.

Globally, most high-grade ores have already been exploited. Contemporary mining tends to focus on the extraction of lower-grade ores thereby leaving large stored tailings open to the environment. As a result, current mines have emerged as hotspots for the migration of metal(loid)s and resistance genes, thereby potentially contributing to a looming public health crisis. Therefore, the management and remediation of tailings are the most challenging issues in environmental ecology. Bioremediation, a cost-effective solution for the treatment of multi-element mixed pollution (co-contamination), shows promise for the restoration of mine tailings. This review focuses on the bioremediation technologies developed to untangle the issues of non-ferrous metal mine tailings. These technologies address the environmental risks of multi-element exposure to the ecosystem and human health risks. It provides a review and comparison of current bioremediation technologies used to mineralize metal(loid)s. The role of plant-microorganisms and their mechanisms in the remediation of tailings are also discussed. The importance of "treating waste with wastes" is crucial for advancing bioremediation technologies. This approach underscores the potential for waste materials to contribute to environmental cleanup processes. The concept of a circular economy is pertinent in this context, emphasizing recycling and reuse. There's an immediate need for international collaboration. Collaboration is needed in policy-making, funding, and data accessibility. Sharing data is essential for the growth of bioremediation globally.

Bioremediation is a promising environmental friendly strategy for the treatment of oil drilling waste, which is particularly challenging in arid areas concerned by high petroleum production activities. Microbial consortia adapted to such environmental conditions are required for the implementation of bioaugmentation treatments. Here four metal(loid)s-resistant hydrocarbon-degrading microbial consortia growing at 40 °C were obtained from oil drilling waste maintained in different phyto-management conditions. The microbial consortia exhibited different microbial compositions with the capacity to degrade 15 to 35

The main objective of this work was to formulate a suitable medium for protease production by Streptomyces sp. which was isolated from Ezzemoul saltpans (Algeria). The phenotypic and phylogenetic studies of this strain showed that it represents probably a new species. The fermentation was carried out on two different media, prepared at three pH values. The results showed the presence of an alkaline protease with optimal pH and temperature of 8 and 40°C, respectively. The enzyme was stable up to 90°C, having a residual activity of 79% after 90 min. The enzyme production media were optimized according to statistical methods while using two plans of experience. The first corresponded to the matrices of Plackett and Burman in N=16 experiences and N-1 factors, twelve were real and three errors. The second was the central composite design of Box and Wilson. The analysis of the results allowed the selection of two factors having a significant effect on the production of the enzyme (fructose and malt extract), then defining their optima (7 g/l of fructose and 12 g/l of malt extract). This Study show the high biotechnological potential of this Streptomyces strain for the production of the thermostable alkaline protease.

Non-ferrous mine waste dumps globally generate soil pollution characterized by low pH and high metal(loid)s content. In this study, the steel slag (SS), gypsum (G), and coal gangue (CG) combined with functional bacteria consortium (FB23) were used for immobilizing metal(loid)s in the soil. The result shown that FB23 can effectively decrease As, Pb, and Zn concentrations within 10 d in an aqueous medium experiment. In a 310-day field column experiment, solid waste including SS, G, and CG combined with FB23 decreased As, Cd, Cu, and Pb concentrations in the aqueous phase. Optimized treatment was obtained by combining FB23 with 1% SS, 1% G, and 1.5% CG. Furthermore, the application of solid waste (SS, G, and CG) increased the top 20 functional bacterial consortium (FB23) abundance at the genus level from 1% to 21% over 50 days in the soil waste dump. Moreover, dissolved organic carbon (DOC) and pH were identified as the main factors influencing the reduction in bioavailable As, Cd, Cu, and Pb in the combination remediation. Additionally, the reduction of Fe and sulfur S was crucial for decreasing the mobilization of the metal(loid)s. This study provides valuable insights into the remediation of metal contamination on a larger scale.

Abandoned chemical smelting sites containing toxic substances can seriously threaten and pose a risk to the surrounding ecological environment. Soil samples were collected from different depths (0 to 13 m) and analyzed for metal(loid)s content and fractionation, as well as microbial activities. The potential ecological risk indices for the different soil depths (ordered from high to low) were: 1 m (D-1) > surface (S-0) > 5 m (D-5) > 13 m (D-13) > 9 m (D-9), ranging between 1840.65–13,089.62, and representing extremely high environmental risks, of which Cd (and probably not arsenic) contributed to the highest environmental risk. A modified combined pollution risk index (MCR) combining total content and mobile proportion of metal(loid)s, and relative toxicities, was used to evaluate the degree of contamination and potential environmental risks. For the near-surface samples (S-0 and d-1 layers), the MCR considered that As, Cd, Pb, Sb, and Zn achieved high and alarming degrees of contamination, whereas Fe, Mn, and Ti were negligible or low to moderate pollution degrees. Combined microcalorimetry and enzymatic activity measurements of contaminated soil samples were used to assess the microbial metabolic activity characteristics. Correlation analysis elucidated the relationship between metal(loid)s exchangeable fraction or content and microbial activity characteristics (p < 0.05). The microbial metabolic activity in the d-1 layer was low presumably due to heavy metal stress. Enzyme activity indicators and microcalorimetric growth rate (k) measurements were considered sensitive indicators to reflect the soil microbial activities in abandoned chemical smelting sites.

Many non-ferrous metal mining and smelting activities have caused severe metal(loid) contamination in the local soil environment. The metabolic activity of soil microorganisms in four areas affected by different metallurgical activities (production vs. waste disposal) was characterized using a contamination gradient from the contaminated site to the surrounding soils. Results indicated that the soil microcalorimetric and enzyme activities were correlated with the fractionated metal(loid) properties (p < 0.05). All four areas had high total As, Cd, Pb, Sb, and Zn concentrations, of which mobile As, Cu, Ni, Pb, Sb, and Zn were higher in the contaminated sites than the surrounding sites, reflecting an elevated environmental risk. Three contaminated site areas had lower microbial activities than their surrounding sites suggesting that high metal(loid) concentrations inhibited soil microbial communities. Interestingly, the fourth area (tailing pond) showed an opposite trend (i.e., increased microbial activity in contaminated vs. surrounding areas). The microbial thermodynamic parameters of this contaminated site were higher than its surrounding sites, suggesting that the selected microbial communities can develop a functional resistance to metal(loid)s stress. This study provides a theoretical basis for ecological prevention and control of metal-polluted areas.

Performic acid (PFA), a new generation of disinfectant, has shown outstanding performance for wastewater treatment. However, the effect of PFA on wastewater microbial community changes as well as the differences in comparison to the commonly disinfectants used are poorly documented. We provide an overview of the PFA effect and that of chlorine and UV, two commonly used disinfectants, on microbial community diversity and structure. The study was performed using wastewaters from three municipal wastewater treatment plants (WWTPs) processed by activated sludge, lagoon and reed beds, and biofilter. We focused on disinfection of pathogen microorganisms, identifying sensitive and resistant bacteria to disinfectants that can serve as biomarkers for evaluating the disinfectant performances. As well, we investigated the modifications of microbial functions after treatment by functional predictive analysis. The more efficient E. coli inactivation was obtained with initial concentration of 4 mg/L of PFA with 15 min disinfectant contact time that achieved 95.71-99.99% inactivation efficiency. Although the origin of wastewater was the main factor determining the microbial community diversity and composition, the microbial communities were specific to the disinfectant used. Linear discriminant analysis Effect Size (LEfSe) identified 18 and 10 biomarkers, including pathogenic microorganisms affiliated to Chromobacterium, Flavobacterium, Aeromonas, Enterobacteriaceae, Escherichia_Shigella and Fusobacteriaceae, which were sensitive to PFA, while being resistant to chlorine and/or UV. Consistently, the predicted bacterial functional patterns diverged according to the wastewater origin and the disinfectant used. Pathogen microorganisms were more sensitive to PFA than the other treatments, demonstrating its potential for implementing a safe reuse of wastewater.

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3–28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.