Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis

Novel Photoelectron-Assisted Microbial Reduction of Arsenate Driven by Photosensitive Dissolved Organic Matter in Mine Stream Sediments

The microbial reduction of arsenate (As(V)) significantly contributes to arsenic migration in mine stream sediment, primarily driven by heterotrophic microorganisms using dissolved organic matter (DOM) as a carbon source. This study reveals a novel reduction pathway in sediments that photosensitive DOM generates photoelectrons to stimulate diverse nonphototrophic microorganisms to reduce As(V). This microbial photoelectrophic As(V) reduction (PEAsR) was investigated using microcosm incubation, which showed the transfer of photoelectrons from DOM to indigenous sediment microorganisms, thereby leading to a 50% higher microbial reduction rate of As(V). The abundance of two marker genes for As(V) reduction, arrA and arsC, increased substantially, confirming the microbial nature of PEAsR rather than a photoelectrochemical process. Photoelectron ion is unlikely to stimulate photolithoautotrophic growth. Instead, diverse nonphototrophic genera, e.g., Cupriavidus, Sphingopyxis, Mycobacterium, and Bradyrhizobium, spanning 13 orders became enriched by 10-50 folds. Metagenomic binning revealed their genetic potential to mediate the photoelectron-assisted reduction of As(V). These microorganisms contain essential genes involved in respiratory As(V) reduction, detoxification As(V) reduction, dimethyl sulfoxide reductase family, c-type cytochromes, and multiple heavy-metal resistance but lack a complete photosynthesis system. The novel microbial PEAsR pathway offers new insights into the interaction between photoelectron utilization and nonphototrophic As(V)-reducing microorganisms, which may have profound implications for arsenic pollution transportation in mine stream sediment.

Interactive effects of microplastics and cadmium on soil properties, microbial communities and bok choy growth

The simultaneous presence of microplastics (MPs) and cadmium (Cd) in soil environments has raised concerns regarding their potential interactive effects on soil-plant ecosystems. This study explores how polyethylene (PE) at concentrations of 0.5 % (w/w), 1 % (w/w), and 2 % (w/w), and Cd at concentrations of 3 mg kg-1 and 12 mg kg-1, either alone or combined, impact soil physicochemical properties, microbial community structures, and bok choy growth through a 40-day pot experiment. Our findings reveal that the addition of 2 % (w/w) PE significantly increased soil organic carbon (SOC). However, when 2 % PE coexisted with Cd, SOC levels decreased, potentially due to a reduction in enzyme activity (β-1,4-glucosidase). PE increased the proportion of 1-2 mm soil aggregates, while the coexistence of 2 % PE and Cd significantly increased the content of soil aggregates larger than 2 mm. The coexistence of PE and Cd increased available potassium (AK) in the soil by approximately 13 % to 41 %. Regarding bok choy growth, the aboveground biomass under 2 % PE was approximately 210 % of that under 0.5 % PE, possibly because of the enhancement in soil nutrients. The presence of Cd, however, reduced the chlorophyll content of bok choy by approximately 18 % to 34 %. Notably, the coexistence of high PE concentration (2 % w/w) and low Cd concentration (3 mg kg-1) resulted in the highest aboveground biomass among all coexistence treatments. Furthermore, the addition of PE and Cd significantly altered the structure of soil bacterial and fungal communities, with fungi showing a greater response. Bacteria were significantly associated with soil inorganic N content and plant growth. This study provides new insights into the interactions of microplastics and Cd within microbial-soil-plant systems.

A cyclic shift-temperature operation method to train microbial communities of mesophilic anaerobic digestion

Temperature is the critical factor affecting the efficiency and cost of anaerobic digestion (AD). The current work develops a shift-temperature AD (STAD) between 35 °C and 55 °C, intending to optimise microbial community and promote substrate conversion. The experimental results showed that severe inhibition of biogas production occurred when the temperature was firstly increased stepwise from 35 °C to 50 °C, whereas no inhibition was observed at the second warming cycle. When the organic load rate was increased to 6.37 g VS/L/d, the biogas yield of the STAD reached about 400 mL/g VS, nearly double that of the constant-temperature AD (CTAD). STAD promoted the proliferation of Methanosarcina (up to 57.32 %), while severely suppressed hydrogenophilic methanogens. However, when the temperature was shifted to 35 °C, most suppressed species recovered quickly and the excess propionic acid was quickly consumed. Metagenomic analysis showed that STAD also promoted gene enrichment related to pathways metabolism, membrane functions, and methyl-based methanogenesis.

Groundwater chromate removal by autotrophic sulfur disproportionation

Chromate [Cr(VI)] contamination in groundwater is a global environmental challenge. Traditional elemental sulfur-based biotechnologies for Cr(VI) removal depend heavily on the synthesis of dissolved organic carbon to fuel heterotrophic Cr(VI) reduction, a bottleneck in the remediation process. Here we show an alternative approach by leveraging sulfur-disproportionating bacteria (SDB) inherent to groundwater ecosystems, offering a novel and efficient Cr(VI) removal strategy. We implemented SDB within a sulfur-packed bed reactor for treating Cr(VI)-contaminated groundwater, achieving a notable removal rate of 6.19 mg L-1 h-1 under oligotrophic conditions. We identified the chemical reduction of Cr(VI) via sulfide, produced through sulfur disproportionation, as a key mechanism, alongside microbial Cr(VI) reduction within the sulfur-based biosystem. Genome-centric metagenomic analysis revealed a symbiotic relationship among SDB, sulfur-oxidizing, and chromate-reducing bacteria within the reactor, suggesting that Cr(VI) detoxification by these microbial communities enhances the sulfur-disproportionation process. This research highlights the significance of sulfur disproportionation in the cryptic sulfur cycle in Cr(VI)-contaminated groundwater and proposes its practical application in groundwater remediation efforts.

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota

Members of the phylum Acidobacteriota inhabit a wide range of ecosystems including soils. We analyzed the global patterns of distribution and habitat preferences of various Acidobacteriota lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline, and terrestrial non-soil ecosystem) in 248,559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia, and Thermoanaerobaculia were highly ubiquitous and showed clear preference to soil over non-soil habitats, class Polarisedimenticolia showed comparable ubiquity and preference between soil and non-soil habitats, while classes Aminicenantia and Holophagae showed preferences to non-soil habitats. However, while specific preferences were observed, most Acidobacteriota lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the Acidobacteriota. The observed lack of strong habitat specialization and habitat transition driven lineage evolution in the Acidobacteriota suggest ready cross colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of Acidobacteriota as a major component in soil microbiomes post ecosystem disturbance events or during pedogenesis.

Microbiome analysis reveals alteration in water microbial communities due to livestock activities

The Baihe River, a tributary of the Yellow River located in the Ngawa Tibetan and Qiang Autonomous Prefecture in Northern Sichuan, is surrounded by natural resources suitable for animal development. However, the impact of livestock activities water microbiome in this area remains unexplored. This study collected water samples from areas with captive yaks and sheep (NS and YS) and compared them with water samples from Hongyuan Baihe River. Through amplicon sequencing, we investigated the impact of livestock activities on aquatic microorganisms. Diversity analysis, significance analysis, and microbial phenotype prediction indicated a significant decrease in microbial community diversity and function in the NS and YS groups. Pathogenic microorganisms such as Bacteroidales and Thelebolaceae and antibiotic-resistant bacteria genes such as Flavobacteriales and Burkholderiaceae were significantly higher in livestock breeding areas. Additionally, bacteria adapted to acidification, hypoxia, and eutrophication (e.g., Acidobacteria, Flavobacteriales, Deltaproteobacteria, Rhodobacterales) were more abundant in these areas. Our results demonstrate that livestock activities significantly alter the structure and function of microbial communities in surrounding water bodies, deteriorating water quality.

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome

Antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) coexist in organic fertilized agroecosystems based on their correlations in abundance, yet evidence for the genetic linkage of ARG-MRGs co-selected by organic fertilization remains elusive. Here, an analysis of 511 global agricultural soil metagenomes reveals that organic fertilization correlates with a threefold increase in the number of diverse types of ARG-MRG-carrying contigs (AMCCs) in the microbiome (63 types) compared to non-organic fertilized soils (22 types). Metatranscriptomic data indicates increased expression of AMCCs under higher arsenic stress, with co-regulation of the ARG-MRG pairs. Organic fertilization heightens the coexistence of ARG-MRG in genomic elements through impacting soil properties and ARG and MRG abundances. Accordingly, a comprehensive global map was constructed to delineate the distribution of coexistent ARG-MRGs with virulence factors and mobile genes in metagenome-assembled genomes from agricultural lands. The map unveils a heightened relative abundance and potential pathogenicity risks (range of 4-6) for the spread of coexistent ARG-MRGs in Central North America, Eastern Europe, Western Asia, and Northeast China compared to other regions, which acquire a risk range of 1-3. Our findings highlight that organic fertilization co-selects genetically linked ARGs and MRGs in the global soil microbiome, and underscore the need to mitigate the spread of these co-resistant genes to safeguard public health.

Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester

Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.

Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments

Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.

Elucidating the roles of Cr(VI)-Cu(II) Co-pollution in the stress of aniline degradation stress: Insights into metabolic pathways and functional genes

In order to examine the impact of Cu(II)-Cr(VI) co-pollution in printing and dyeing wastewater on the aniline biodegradation system (ABS), loading experiments were conducted on ABS at varying concentrations of Cu(II)-Cr(VI). The synergistic stress imposed by Cu(II)-Cr(VI) accelerated the deterioration of the systems, with only the C2-3 (2 mg/L Cr(VI)-3 mg/L Cu(II)) sustaining stable operation for 42 days. However, its nitrogen removal performance remained significantly impaired, resulting in a total nitrogen (TN) removal rate below 40%. High-throughput sequencing analysis revealed a stronger correlation between Cr(VI) and microbial diversity compared to Cu(II). Metagenomic sequencing results demonstrated that Cu(II) emerged as the dominant factor influencing the distribution of dominant bacteria in C2-3, as well as its contribution to contaminant degradation. The complex co-pollution systems hindered aniline degradation and nitrogen metabolism through the combined bio-toxicity of heavy metals and aniline, thereby disrupting the transport chain within the systems matrix.

Polyamine-producing bacteria inhibit the absorption of Cd by spinach and alter the bacterial community composition of rhizosphere soil

Polyamines (PAs) are small aliphatic nitrogenous bases with strong biological activity that participate in plant stress response signaling and the alleviation of damage from stress. Herein, the effects of the PA-producing bacterium Bacillus megaterium N3 and PAs on the immobilization of Cd and inhibition of Cd absorption by spinach and the underlying mechanisms were studied. A solution test showed that strain N3 secreted spermine and spermidine in the presence of Cd. Both strain N3 and the PAs (spermine+spermidine) immobilized Cd and increased the pH of the solution. Untargeted metabolomics results showed that strain N3 secreted PAs, N1-acetylspermidine, 3-indolepropionic acid, indole-3-acetaldehyde, cysteinyl-gamma-glutamate, and choline, which correlated with plant growth promotion and Cd immobilization. A pot experiment showed that rhizosphere soil inoculation with strain N3 and PAs improved spinach dry weight and reduced spinach Cd absorption compared with the control. These positive effects were likely due to the increase in rhizosphere soil pH and NH4+-N and PA contents, which can be attributed primarily to Cd immobilization. Moreover, inoculation with strain N3 more effectively inhibited the absorption of Cd by spinach than spraying PAs, mainly because strain N3 enabled a better relative abundance of bacteria (Microvirga, Pedobacter, Bacillus, Brevundimonas, Pseudomonas, Serratia, Devosid, and Aminobacter), that have been reported to have the ability to resist heavy metals and produce PAs. Strain N3 regulated the structure of rhizosphere functional bacterial communities and inhibited Cd uptake by spinach. These results provide a theoretical basis for the prevention of heavy metal absorption by vegetables using PA-producing bacteria.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics

Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (Se^IVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative Se^IVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative Se^IVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.

Spatial heterogeneity and source apportionment of soil metal(loid)s in an abandoned lead/zinc smelter

Metal smelting have brought severe metal(loid)s contamination to the soil. Spatial distribution and pollution source analysis for soil metal(loid)s in an abandoned lead/zinc smelter were studied. The results showed that soil was contaminated heavily with metal(loid)s. The mean of lead (Pb), arsenic (As), cadmium (Cd), mercury (Hg) and antimony (Sb) content in topsoil is 9.7, 8.2, 5.0, 2.3, and 1.2 times higher than the risk screening value for soil contamination of development land of China (GB36600-2018), respectively. Cd is mainly enriched in the 0-6 m depth of site soil while As and Pb mainly deposited in the 0-4 m layer. The spatial distribution of soil metal(loid)s is significantly correlated with the pollution source in the different functional areas of smelter. As, Hg, Sb, Pb and copper (Cu) were mainly distributed in pyrometallurgical area, while Cd, thallium (Tl) and zinc (Zn) was mainly existed in both hydrometallurgical area and raw material storage area. Soil metal(loid)s pollution sources in the abandoned smelter are mainly contributed to the anthropogenic sources, accounting for 84.5%. Specifically, Pb, Tl, As, Hg, Sb and Cu mainly from atmospheric deposition (55.9%), Cd and Zn mainly from surface runoff (28.6%), While nickel (Ni) mainly comes from parent material (15.5%). The results clarified the spatial distribution and their sources in different functional areas of the smelter, providing a new thought for the risk prevention and control of metal(loid)s in polluted site soil.

Risk source identification and diffusion trends of metal(loid)s in stream sediments from an abandoned arsenic-containing mine

Stream sediments from mine area are a converging source of water and soil pollution. The risk and development trends of metal(loid)s pollution in sediments from an abandoned arsenic-containing mine were studied using modelling techniques. The results showed that the combined techniques of geographic information system (GIS), random forest (RF), and numerical simulation (NS) could identify risk sources and diffusion trends of metal(loid)s in mine sediments. The median values of As, Cd, Hg, and Sb in sediments were 5.01, 3.02, 5.67, and 3.20 times of the background values of stream sediments in China, respectively. As (14.09%) and Hg (18.64%) pollution in mine stream sediments were severe while As is the main potential risk source with a strong spatial correlation. High-risk blocks were concentrated in the landfill area, with the surrounding pollution shows a decreasing trend of "step-type" pollution. The risk correlation between Hg and As (55.37%) in the landfill area is high. As a case of arsenic, the diffusion capacity of As within 500m is strong and stabilizes at 1 km when driven by the flows of 0.05, 0.5, and 5 m³/s, respectively. With the worst-case scenario flow (86 m³/s), it would take only 147 days for the waters within 3 km to become highly polluted. The high pollution levels in a stream under forecast of different distance intervals (500, 1500, 2000 m) within 6.5 km is arrived at approximate 344, 357, and 384 days, respectively. The study suggested the combined technique of GIS, RF, and NS can serve the risk source identification of contaminated sites and risk forecast of toxic element diffusion in emergency situations.

Contamination vertical distribution and key factors identification of metal(loid)s in site soil from an abandoned Pb/Zn smelter using machine learning

Soil heterogeneity makes the vertical distribution of metal(loid)s in site soil vary considerably and poses a challenge for identifying the key factors of metal(loid)s migration in site soil profiles. In this study, a machine learning (ML) model was developed to study a typical abandoned Pb/Zn smelter using 267 site soils from 46 drilling points. Results showed that a well-trained ML model could be used to identify the key factors in determining the contamination vertical distribution and predict the metal(loid)s contents in subsurface soil. As, Cd, Pb, and Zn were the primary pollutants and their vertical migration depth arrived to 4-6 m. Based on the predictive performance of different ML algorithms, the extreme gradient boosting (XGB) was selected as the best model to produce accurate predictions for the most metal(loid)s content. Contents of As, Cd, Pb, and Zn in the heavily contaminated zones declined with an increase of soil depth. The metal(loid) contents in surface soil of 0-2 m could be readily used to predict the content of Cd, Cr, Hg, and Zn in subsurface soil from 2 m to 10 m. Based on the metal-specific XGB models, sulfur content, functional area, and soil texture were identified as key factors affecting the vertical distribution of As, Cd, Pb, and Zn in site soil. Results suggested the ML method is helpful to manage the potential environmental risks of metal(loid)s in Pb/Zn smelting site.

Characterization of keystone taxa and microbial metabolic potentials in copper tailing soils

Copper mining has caused serious soil contamination and threaten the balance of underground ecosystem. Effects of metal contamination on the soil microbial community assembly and their multifunctionality are still unclear. In this study, the keystone taxa and microbial metabolic potential of soil microorganisms surrounding a typical copper tailing were investigated. Results showed that pH and metal contents of adjacent soil in copper tailing increased, which largely reduced soil microbial communities' diversity. Metal contaminated soils enriched a group of keystone taxa with metal-tolerance such as Bacteroidota (20-54%) and Firmicutes (24-48%), which were distinct from the uncontaminated background soils that dominated by Proteobacteria (19-24%) and Actinobacteria (13-24%). In the contaminated soils, these keystone taxa were identified as Alistipes, Bacteroides, and Faecalibacterium, suggesting their adaptation to the metal-rich environment. Co-occurrence network analysis showed that the microbial community was loosely connected in the metal contaminated soils with a lower number of nodes and links. Co-occurrence networks further revealed that the dynamics of keystone taxa significantly correlated with copper content. Functional gene analysis of soil microorganisms indicated that metal contamination might inhibit important microbial metabolic potentials, such as secondary metabolites biosynthesis, carbon fixation, and nitrogen fixation. Results also found the flexible adaptation strategies of soil microbial communities to metal-rich environments with metal-resistance or bio-transformation, such as efflux (CusB/CusF/CzsB and pcoB/copB) and oxidation (aoxAB). These findings provide insight into the interaction between keystone taxa and soil environment, which is helpful to reveal the microbial metabolic potential and physiological characteristics in tailing contaminated soils.

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.

Characterization of arsenic-metabolizing bacteria in an alkaline soil

Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO₃^-, suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.

Effects of perfluorooctanoic acid (PFOA) on activated sludge microbial community under aerobic and anaerobic conditions

Per- and polyfluoroalkyl substances (PFASs) have received increasing attention due to their widespread presence in diverse environments including wastewater treatment plants (WWTPs) and their potential adverse health effects. Perfluorooctanoic acid (PFOA) is one of the most detected forms of PFASs in WWTPs. However, there is still a paucity of knowledge about the effect of PFASs on microorganisms of the key component of WWTP, activated sludge. In this study, lab-scale microcosm experiments were established to evaluate the influences of PFOA on activated sludge microbes under aerobic and anaerobic conditions. The diversity, structure, and microbe-microbe interaction of microbial community were determined by 16S rRNA gene amplicon sequencing and co-occurrence network analysis. After 90 days of exposure to PFOA, activated sludge microbial richness decreased under both aerobic and anaerobic conditions. Specifically, under aerobic condition, Rhodopseudomonas (mean relative abundance 3.6%), Flavobacterium (2.4%), and Ignavibacterium (6.6%) were enriched in PFOA-spiked activated sludge compared with that in the unspiked sludge (2.6%, 0.1%, and 1.9%, respectively). By contrast, after 90 days of exposure to PFOA, Eubacterium (2.1%), Hyphomicrobium (1.8%), and Methyloversatilis (1.2%) were enriched under anaerobic condition, and more abundant than that in the control sludge (0.4%, 1.5%, and 0.6%, respectively). These genera were the potential PFOA-resistant members. In addition, Azospirillum and Sporomusa were the most connected taxa in PFOA-aerobic and PFOA-anaerobic networks, respectively. Prediction of the functional gene showed that PFOA inhibited some gene expression of sludge microbes, such as transcription, amino acid transport and metabolism, and energy production and conversion. In summary, continued exposure to PFOA induced substantial shifts of the sludge bacterial diversity and composition under both aerobic and anaerobic conditions.

Nitrogen and sulfur fertilizers promote the absorption of lead and cadmium with Salix integra Thunb. by increasing the bioavailability of heavy metals and regulating rhizosphere microbes

Fertilization is an effective agronomic strategy to improve the efficiency of phytoextraction by Salix integra Thunb. However, the specific effects of the simultaneous application of nitrogen (N) and sulfur (S) fertilizers in the rhizosphere remain unclear. We investigated the bioavailability of lead (Pb) and Cadmium (Cd) along with the microbial metabolic functions and community structure in the rhizosphere soil of S. integra after the application of N (0, 100, and 200 kg·ha⁻¹·year⁻¹) and S (0, 100, and 200 kg·ha⁻¹·year⁻¹) fertilizers for 180 days. The simultaneous application of N and S fertilizers significantly enhanced the absorption of Pb and Cd by S. integra, whereas this effect was not observed for the single application of N or S fertilizer. The contents of acid-soluble Pb and Cd in the rhizosphere soil significantly increased after either single or combined fertilize applications. The microbial metabolic activity was enhanced by the N and S fertilizers, whereas the microbial diversity markedly decreased. The metabolic patterns were mainly affected by the concentration of N fertilizer. The dominant fungi and bacteria were similar under each treatment, although the relative abundances of the dominant and special species differed. Compared to the N200S100 and N200S200 treatments, the N100S100 and N100S200 treatments resulted in fewer pathogenic fungi and more rhizosphere growth-promoting bacteria, which promoted phytoremediation by S. integra. Redundancy analysis indicated that the pH and nitrate content were the key factors affecting the structure of the microbial community. Collectively, the results suggest interactive effects between N and S fertilizers on the rhizosphere soil, providing a potential strategy for plant-microbial remediation by S. integra.

Keystone taxa and functional analysis in arsenic and antimony co-contaminated rice terraces

Both arsenic (As) and antimony (Sb) are primary environmental contaminants that often co-exist at contaminated sites. Though the microbial community compositions of As- and Sb-contaminated sites have been previously described, the changes in microbial community interactions and community functions remain elusive. In the current study, several key metabolic processes, such as As/Sb detoxification and carbon fixation, were enriched under heavily contaminated conditions. Furthermore, the identified keystone taxa, which are associated with the families Nitrosomonadaceae, Pedosphaeraceae, Halieaceae, and Latescibacterota, demonstrated positive correlations with As and Sb concentrations, indicating that they may be resistant to As and Sb toxicities. Accordingly, arsenic resistance-related functions, along with several functions such as carbon fixation, were found to be enriched in heavily contaminated sites. The current study elucidated the key microbial populations in As- and Sb-contaminated rice terraces and may provide useful information for remediation purposes.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.

Changes of Microbial Diversity in Rhizosphere of Different Cadmium-Gradients Soil under Irrigation with Reclaimed Water

Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity.

Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities

Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N₂ into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.

Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community

The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.

Occurrence of PFASs and its effect on soil bacteria at a fire-training area using PFOS-restricted aqueous film-forming foams

Fire-training areas (FTAs) are an important source of perfluoroalkyl and polyfluoroalkyl substances (PFASs) pollution. However, the effect of PFASs on soil bacterial communities remains limited. Here, we detected the PFASs in soils ranging from 3.4 to 531.7 μg kg⁻¹ dry weight in seven plots at an FTA where PFOS-restricted aqueous film-forming foams (AFFFs) have been used for 6 years. PFOS was still the dominant homologue despite the restriction by Stockholm Convention, but it was almost three orders of magnitude lower than that in previous studies. PFASs played an important role in shaping the bacterial community, and high levels of PFASs (>100 μg kg⁻¹ dw) reduced the biodiversity and connectivity of soil bacteria. The extreme condition-tolerant bacteria were identified as biomarkers at the FTA. Our study provides valuable insights into the effect of PFOS-restricted AFFFs on soil bacterial communities at the FTA.

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PFOS was still the dominant PFAS despite the restriction by Stockholm Convention

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PFASs played an important role in shaping bacterial community

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High level of PFASs reduced the biodiversity and connectivity of soil bacteria

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The extreme condition-tolerant bacteria were identified as biomarkers at the FTA

Diversity and Metabolic Potentials of As(III)-Oxidizing Bacteria in Activated Sludge

Biological arsenite [As(III)] oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOB) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOB in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOB, while bacteria associated with Hydrogenophaga were identified as aerobic AOB in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOB. Functional genes encoding As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOB in activated sludge and enhance their capacity for As(III) oxidation. IMPORTANCE AOB play an important role in the removal of toxic arsenic from wastewater. Most of the AOB have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities is not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOB community inhabiting the activated sludges. In this study, the putative AOB responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials, including As(III) oxidation, denitrification, carbon fixation, secondary metabolite biosynthesis, and extracellular polymeric substance metabolism, were investigated. This observation provides an understanding of anoxic and/or oxic AOB during the As(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.