Description and Genomic Characteristics of Diaphorobacter limosus sp. nov., Isolated from a Sewage-Treatment Plant.

A Gram-stain-negative, rod-shaped, non-motile, catalase-positive, denitrifying bacterium, designated strain Y-1T, was isolated from an aeration tank of a sewage treatment plant in China and characterized using polyphasic taxonomic approaches. Strain Y-1T could grow at 10-37 °C (optimum 25 °C), at pH 5.0-10.0 (optimum 7.0) and in the presence of 0-3.0% (w/v) NaCl (optimum 0.5%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain Y-1T was a member of genus Diaphorobacter, and showed the highest sequence similarities with Diaphorobacter oryzae RF3T (97.50%), Diaphorobacter nitroreducens NA10BT (97.38%) and Diaphorobacter aerolatus 8604S-37T (96.56%). In terms of carbon source utilization and enzyme activities, strain Y-1T was significantly different from its similar strains. The major respiratory quinone was Q-8, and the main polar lipid was phosphatidylethanolamine. Comparative genomic analysis of strain Y-1T and other Diaphorobacter species was conducted to explore the mechanisms underlying the differences among these strains. Strain Y-1T encoded 3957 genes, consisting of 3813 protein-coding genes and 144 RNA coding genes, and encoded 652 enzymes with 31 unique enzymes compared with other related species. The DNA G + C content was 69.95 mol%. Strain Y-1T exhibited 41.71% DNA-DNA relatedness and 95% ANIb with the most related type strains.On the basis of the evidence presented from polyphasic analysis, strain Y-1T was suggested as a novel species within the genus Diaphorobacter, for which the name Diaphorobacter limosus sp. nov. is proposed, with the type strain Y-1T (= KCTC 92852T = CCTCC AB 2023032T).

Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust.

Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.

New Insights into the Role of Natural Organic Matter in Fe-Cr Coprecipitation: Importance of Molecular Selectivity.

Coprecipitation of Fe/Cr hydroxides with natural organic matter (NOM) is an important pathway for Cr immobilization. However, the role of NOM in coprecipitation is still controversial due to its molecular heterogeneity and diversity. This study focused on the molecular selectivity of NOM toward Fe/Cr coprecipitates to uncover the fate of Cr via Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS). The results showed that the significant effects of Suwannee River NOM (SRNOM) on Cr immobilization and stability of the Fe/Cr coprecipitates did not merely depend on the adsorption of SRNOM on Fe/Cr hydroxides. FT-ICR-MS spectra suggested that two pathways of molecular selectivity of SRNOM in the coprecipitation affected Cr immobilization. Polycyclic aromatics and polyphenolic compounds in SRNOM preferentially adsorbed on the Fe/Cr hydroxide nanoparticles, which provided extra binding sites and promoted the aggregation. Notably, some specific compounds (i.e., polyphenolic compounds and highly unsaturated phenolic compounds), less unsaturated and more oxygenated than those adsorbed on Fe/Cr hydroxide nanoparticles, were preferentially incorporated into the insoluble Cr-organic complexes in the coprecipitates. Kendrick mass defect analysis revealed that the insoluble Cr-organic complexes contained fewer carbonylated homologous compounds. More importantly, the spatial distribution of insoluble Cr-organic complexes was strongly related to Cr immobilization and stability of the Fe/Cr-NOM coprecipitates. The molecular information of the Fe/Cr-NOM coprecipitates would be beneficial for a better understanding of the transport and fate of Cr and exploration of the related remediation strategy.

The effectiveness of sewage sludge biochar amendment with Boehmeria nivea L. in improving physicochemical properties and rehabilitating microbial communities in mine tailings.

Biochar amendment can be adopted to improve soil substrate, in turn facilitated phytoremediation. However, improvements to the properties of tailings following different feedstocks of biochar amendment in phytoremediation, particularly the impacts on nitrogen cycle and the related nitrogen-fixing microorganisms remain unclear. In this study, a 100-day pot experiment was designed to determine the co-effects of different combinations of woody and non-woody biochar, namely hibiscus cannabinus core biochar (HB), sewage sludge biochar (SB), chicken manure biochar (MB) and two crops (Cassia alata L., Boehmeria nivea L.). It was found that, on the one hand, biochar amendment directly immobilized heavy metal (loid) contamination in the tailings; on the other hand, biochar amendment, particularly non-woody SB, improved soil properties (i.e., the combination of SB with crops increased the total nitrogen content by 4.7-7.5 times). This indirectly improved phytostabilization (i.e., SB increased crop height 1.5-1.8 fold, root length 3.3-3.7 fold, decreased NH4NO3-extractable Pb, Cu, Cd and also increased the relative abundance of nitrogen-fixing bacteria such as Mesorhizobium, Bradyrhizobium, and Rhizobium). Besides this, redundant analysis shown that the carbon, nitrogen sources, and pH provided by the biochar were identified as the key factors associated with the nitrogen-fixing bacteria. Through the comprehensive evaluation of different biochar amendment in phytoremediation, it was found that the non-woody SB got higher comprehensive score (3.1-3.6) in biochar amendment in phytoremediation, especially in Boehmeria nivea L. Thus, the combination of non-woody SB and Boehmeria nivea L. improved microbial function, while the microorganisms in turn promoted crop growth. Our results revealed the prospect of using non-woody SB assisted Boehmeria nivea L. for phytoremediation in multi-metal mine tailings.

The interplay between microalgae and toxic metal(loid)s: mechanisms and implications in AMD phycoremediation coupled with Fe/Mn mineralization.

Acid mine drainage (AMD) is low-pH with high concentration of sulfates and toxic metal(loid)s (e.g. As, Cd, Pb, Cu, Zn), thereby posing a global environmental problem. For decades, microalgae have been used to remediate metal(loid)s in AMD, as they have various adaptive mechanisms for tolerating extreme environmental stress. Their main phycoremediation mechanisms are biosorption, bioaccumulation, coupling with sulfate-reducing bacteria, alkalization, biotransformation, and Fe/Mn mineral formation. This review summarizes how microalgae cope with metal(loid) stress and their specific mechanisms of phycoremediation in AMD. Based on the universal physiological characteristics of microalgae and the properties of their secretions, several Fe/Mn mineralization mechanisms induced by photosynthesis, free radicals, microalgal-bacterial reciprocity, and algal organic matter are proposed. Notably, microalgae can also reduce Fe(III) and inhibit mineralization, which is environmentally unfavorable. Therefore, the comprehensive environmental effects of microalgal co-occurring and cyclical opposing processes must be carefully considered. Using chemical and biological perspectives, this review innovatively proposes several specific processes and mechanisms of Fe/Mn mineralization that are mediated by microalgae, providing a theoretical basis for the geochemistry of metal(loid)s and natural attenuation of pollutants in AMD.

Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm.

BACKGROUND: Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond. RESULTS: We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system. CONCLUSIONS: Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.

Increasing soil Mn abundance promotes the dissolution and oxidation of Cr(III) and increases the accumulation of Cr in rice grains.

Hexavalent chromium (Cr(VI)) is more readily taken up by plants than trivalent chromium (Cr(III)) due to its similar chemical structure to phosphate and sulfate. In paddy soils, Cr(VI) of natural origin are mainly produced from Cr(III) oxidized by O2 and Mn(III/IV) oxides, which are affected by rice radial oxygen loss (ROL) and Mn(II)-oxidizing microorganisms (MOM). However, little is known about the effect of ROL and Mn abundance on rice Cr uptake. Here, we investigated the effects on Cr(VI) generation and the subsequent Cr uptake and accumulation with the involvement of two rice cultivars with distinct ROL capacities by increasing soil Mn abundance. Results showed that Mn(II) addition to the soil led to more Cr(III) being released into the pore water, and the dissolved Cr(III) was oxidized to Cr(VI) by ROL and biogenic Mn(III/IV) oxides. The concentration of Cr(VI) in soil and pore water increased linearly with the addition of Mn(II) doses. Mn(II) addition promoted the root-to-shoot translocation and grain accumulation of Cr derived mainly from newly generated Cr(VI) in the soil. These results emphasize that rice ROL and MOM promote the oxidative dissolution of Cr(III) at a high level of soil Mn, resulting in more Cr accumulation in rice grains and increasing dietary Cr exposure risks.

Mechanism of arsenic immobilization and biotransformation in the biological aqua crust of mine drainage.

Biological aqua crust (BAC), as a novel biological crust with high arsenic (As) immobilization capacity, might be an ideal nature-based solution for As removal in mine drainage. This study examined the As speciation, binding fraction and biotransformation genes in the BACs to find out the underlying mechanism of As immobilization and biotransformation. Results showed that the BACs could immobilize As from mine drainage up to 55.8 g/kg, and their As immobilization concentrations were 1.3-6.9 times higher than that of sediments. Extremely high As immobilization capacity was attributed to the processes of bioadsorption/absorption and biomineralization driven by Cyanobacteria. The high abundance of As(III) oxidation genes (27.0 %) enhanced microbial As(III) oxidation, resulting in >90.0 % of As(V) with low toxicity and mobility in the BACs. The increase in abundances of aioB, arsP, acr3, arsB, arsC and arsI with As was the key process for microbiota in the BACs for resistance to the As toxicity. In conclusion, our findings innovatively confirmed the potential mechanism of As immobilization and biotransformation mediated by the microbiota in the BACs and highlighted the important role of BACs for As remediation in mine drainage.

Mechanism of polycyclic aromatic hydrocarbons degradation in the rhizosphere of Phragmites australis: Organic acid co-metabolism, iron-driven, and microbial response.

Microbial co-metabolism is crucial for the efficient biodegradation of polycyclic aromatic hydrocarbons (PAHs); however, their intrinsic mechanisms remain unclear. To explore the co-metabolic degradation of PAHs, root organic acids (ROAs) (phenolic ROAs: caffeic acid [CA] and ferulic acid [FA]; non-phenolic ROAs: oxalic acid [OA]) were exogenously added as co-metabolic substrates under high (HFe) and low (LFe) iron levels in this study. The results demonstrated that more than 90% of PAHs were eliminated from the rhizosphere of Phragmites australis. OA can promote the enrichment of unrelated degrading bacteria and non-specific dioxygenases. FA with a monohydroxy structure can activate hydroxylase; however, it relies on phytosiderophores released by plants (such as OA) to adapt to stress. Therefore, non-specific co-metabolism occurred in these units. The best performance for PAH removal was observed in the HFe-CA unit because: (a) HFe concentrations enriched the Fe-reducing and denitrifying bacteria and promoted the rate-limiting degradation for PAHs as the enzyme cofactor; (b) CA with a dihydroxyl structure enriched the related degrading bacteria, stimulated specific dioxygenase, and activated Fe to concentrate around the rhizosphere simultaneously to perform the specific co-metabolism. Understanding the co-metabolic degradation of PAHs will help improve the efficacy of rhizosphere-mediated remediation.

Enhanced trichloroethylene biodegradation: The mechanism and influencing factors of combining microorganism and carbon­iron materials.

Trichloroethylene (TCE) is one of the most prevalent contaminants with long-term persistence and a strong carcinogenic risk. Biological dechlorination has gradually become the mainstream method due to its advantages of low treatment cost and high environmental friendliness. However, microorganisms are easily restricted by environmental factors, such as an insufficient energy supply and a slow biological dechlorination process. This study focused on the coupled degradation of TCE with the combination of microorganisms and assistant materials (biochar, nZVI, nZVI modified biochar, HPO3 modified biochar), and set up microorganisms (alone) and materials (alone) as separate controls. Biochar provided nutrients, increased contact with pollutants, and promoted electron transfer to improve TCE degradation, although it did not change the pathway of degradation. The coupled treatment with anaerobic microorganisms (Micro) and 1 g/L unmodified biochar (BC) had the strongest degradation capacity. Compared with microorganisms alone, the addition of biochar resulted in the complete removal of TCE within 4 days. The influence of ambient temperature was mainly related to microbial activity, and 35 °C showed better degradation than 20 °C. Under 20 °C, 1 g/L of nZVI significantly promoted microbial dechlorination. As the dosage increased to 2 g/L and 4 g/L, nZVI showed a strong toxic effect. After 16 days, TCE was completely converted to ethylene by Micro-BC with C3H5O3Na, while 4.40 µmol dichloroethane (DCE) and 1.48 µmol vinyl chloride (VC) remained in the treatment with Micro-BC alone. As an electron acceptor, NaNO3 directly competed with TCE in the reduction process, which decreased the reduction efficiency of TCE. These findings provide a better understanding of the mechanism of the chemical materials coupling microbial dechlorination process and an optimal treatment method for trichloroethylene degradation.

Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China.

Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China.

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Biogeochemical dynamics of nutrients and rare earth elements (REEs) during natural succession from biocrusts to pioneer plants in REE mine tailings in southern China.

The exploitation of ion-adsorption rare earth element (REE) deposits has resulted in large quantities of abandoned mine tailings, which pose significant risks to the surrounding environment. However, the natural evolutional patterns at early successional stages and related biogeochemical dynamics (e.g. nutrient and REE cycling) on such mine tailings remains poorly understood. To this end, a chronosequence of REE mine tailings abandoned for up to 15 years was investigated in a post-mining site in south China. Our results showed that biocrusts were the earliest colonizers on these tailings, reaching a peak of 10% of surface coverage after 10 years of abandonment. Later on, after 15 years, the biocrusts began to be replaced by pioneer plants (e.g. Miscanthus sinensis), suggesting a rather rapid succession. This ecological succession was accompanied by obvious changes in soil nutrients and microbial community structure. Compared to bulk soils, both the biocrusts and rhizospheric soils favored an accumulation of nutrients (e.g. P, S, N, C). Notably, the autotrophic bacteria (e.g. Chloroflexi and Cyanobacteria) with C and N fixation abilities were preferentially enriched in biocrusts, while heterotrophic plant growth promoting bacteria (e.g. Pseudoocardiaceae and Acidobacteriales) were mainly present in the rhizosphere. Moreover, the biocrusts showed a remarkably high concentration of REEs (up to 1820 mg kg-1), while the rhizospheric soils tended to decrease REE concentrations (~400 mg kg-1) in comparison with bulk soils, indicating that the REEs could be redistributed by biological processes. Principal component analysis and mantel tests showed that the concentrations of nutrients and REEs were the most important factors affecting the microbial communities in biocrusts, rhizospheric and bulk soils. In sum, based on the observation of nutrient accumulation and pollutant (i.e. REE) dynamics in the initial successional stages, this work provides a feasible theoretical basis for future restoration practices on REE mine tailings.

Interactions between soil protists and pollutants: An unsolved puzzle.

Soil protists are essential but often overlooked in soils, although they play crucial functional roles in the terrestrial ecosystem. While soil protists have drawn increased attention to their functional role in soils, their interaction with soil pollutants remains unresolved. This review provides a first overview of the current understanding of interactions between soil protists and major pollutants (heavy metals, organic pollutants, nanoparticles, and soil pathogens). We summarize how soil pollutants affect protists and vice versa, showing that we are just beginning to understand their complex interactions. In addition, we identify five research gaps, including hidden diversity, adaptive mechanisms, species interactions, soil bioindicators and environmental applications, and we hope that our review will help promote and build research guidelines for the future. In conclusion, a better understanding of soil pollutant-protist interactions will significantly increase our knowledge of the pollution ecology in the soil and how soil organisms respond and adapt to environmental pollution, which will contribute to the bioremediation and environmental applications of protists in soil.

Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China.

Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs-AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome-resolved metagenomics were performed on microbial community collected from a REEs-AMD contaminated river. The results showed that REEs-AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs-dependent enzyme-encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome-assembled genomes covering 70.4% of identifying indicators. Genome-centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs-AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs-AMD bioremediation.

Removal pathway quantification and co-metabolic mechanism evaluation of alkylphenols from synthetic wastewater by phenolic root exudates in the rhizosphere of Phragmites australis.

Phenolic root exudates (PREs) released from wetland plants are potentially effective for accelerating the biodegradation of alkylphenols, yet the inherent behavior is still unclear. In this study, two representative root exudates (REs), namely p-coumaric acid (PREs) and oxalic acid (non-PREs) were exogenously added as specific and non-specific co-metabolic substrates, respectively, to elucidate the quantification of each removal pathway and degradation mechanism of co-metabolism for alkylphenols (i.e. p-tert-butylphenol (PTBP)) from synthetic wastewater. The results showed that soil adsorption (31-37%), microbial degradation (27-37%), and plant uptake (16-41%) are the main removal pathways of PTBP by PREs in the Phragmites australis rhizosphere. Both REs enriched anaerobic functional community (anaerobic ammonium oxidation bacteria and denitrifying bacteria) and promoted the usage of PTBP as carbon source and/or electron donor. The activity of non-specific enzyme (polyphenol oxidase) was enhanced by RE which owning a significant positive correlation with bacterial abundance, whereas only PREs strengthened the activity of specific enzyme (monophenol oxidase) catalyzing the phenolic ring hydroxylation of PTBP followed by a dehydrogenation route. Moreover, exogenous PREs significantly improved the growth of degrading-related bacteria (Sphingomonas and Gemmatimonas), especially in unplanted soils with high activity of dioxygenase catalyzing the cleavage pathway of PTBP, instead of plant presence.

Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.

Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.

Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review.

Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.

Biological aqua crust mitigates metal(loid) pollution and the underlying immobilization mechanisms.

Biocrust-mediated in situ bioremediation could be an alternative strategy to mitigate metal(loid) pollution in aquatic habitats. To better understand the roles of biocrusts in regulating the fate of metal(loid)s, we examined the morphology, composition and structure of biological aqua crusts (BAC) developed in the mine drainage of a representative Pb/Zn tailing pond, and tested their effectiveness for immobilizing typical metal(loid)s. Unlike terrestrial biocrusts, BAC results from an assembly of compounds produced by the strong microbial activity and mineral compounds present in the aquatic environment. The BAC exhibited a unique flexible, spongy and porous structure with a specific surface area of 12-22 m2 g-1, and was able to effectively concentrate various metal(loid)s (e.g. Cd, 0.26-0.60 g kg-1; Pb, 0.52-0.66 g kg-1; As, 10.4-24.3 g kg-1). The concentrations of metal(loid)s (e.g. Cd and As) in the BAC were even three to seven times higher than those in the source tailings, and more than 98% of immobilized metal(loid)s were present as the highly stable non-EDTA-exchangeable fraction. Adsorption on the well distributed micro-particles of the clay minerals (e.g. kaolinite) and the organic matters (2.0-2.7 wt.%) were found to be the major mechanisms for BAC to bind metal cations, whereas adsorption and coprecipitation on Fe/Mn oxide (e.g. FeOOH), was proposed to be the dominant pathway for accumulating metal(loid)s, especially As. The decrease in aqueous concentrations of the metal(loid)s along the drainage could be attributed in part to the scavenging effects of the BAC. These findings therefore provide new insights into the possible and efficient strategy for metal(loid) removal from water bodies, and highlighted the important role of BAC as a nature-based solution to benefit the bioremediation of mining area.

Factors influencing heavy metal availability and risk assessment of soils at typical metal mines in Eastern China.

China exemplifies the serious and widespread soil heavy metal pollution generated by mining activities. A total of 420 soil samples from 58 metal mines was collected across Eastern China. Total and available heavy metal concentrations, soil physico-chemical properties and geological indices were determined and collected. Risk assessments were applied, and a successive multivariate statistical analysis was carried out to provide insights into the heavy metal contamination characteristics and environmental drivers of heavy metal availability. The results suggested that although the degrees of pollution varied between different mine types, in general they had similar contamination characteristics in different regions. The major pollutants for total concentrations were found to be Cd and As in south and northeast China. The availability of Zn and Cd is relatively higher in south China. Soil physico-chemical properties had major effect on metal availability where soil pH was the most important factor. On a continental scale, soil pH and EC were influenced by the local climate patterns which could further impact on heavy metal availability. Enlightened by this study, future remediation strategies should be focused on steadily increasing soil pH, and building adaptable and sustainable ecological system to maintain low metal availabilities in mine site soils.