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

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.

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.

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

The effect of quorum sensing on cadmium- and lead-containing wastewater treatment using activated sludge: Removal efficiency, enzyme activity, and microbial community

Quorum sensing (QS) is prevalent in activated sludge processes; however, its essential role in the treatment of heavy metal wastewater has rarely been studied. Therefore, in this study, acyl homoserine lactone (AHL)-mediated QS was used to regulate the removal performance, enzyme activity, and microbial community of Cd- and Pb-containing wastewater in a sequencing batch reactor (SBR) over 30 cycles. The results showed that exogenous AHL strengthened the removal of Cd(II) and Pb(II) in their coexistence wastewater during the entire period. The removal of NH4+-N, total phosphorus, and chemical oxygen demand (COD) was also enhanced by the addition of AHL despite the coexistence of Cd(II) and Pb(II). Meanwhile, the protein content of extracellular polymeric substances was elevated and the microbial metabolism and antioxidative response were stimulated by the addition of AHL, which was beneficial for resistance to heavy metal stress and promoted pollutant removal by activated sludge. Microbial sequencing indicated that AHL optimized the microbial community structure, with the abundance of dominant taxa Proteobacteria and Unclassified_f_Enterobacteriaceae increasing by 73.9% and 59.2% maximally, respectively. This study offers valuable insights into the mechanisms underlying Cd(II) and Pb(II) removal as well as microbial community succession under AHL availability in industrial wastewater.

Preparation of bacterial fertilizer from biogas residue after anaerobic co-digestion of kitchen waste and residual sludge

Azotobacter chroococcum and Bacillus subtilis were selected as fermentation strains, and biogas residue after anaerobic digestion of kitchen waste and residual sludge was used as fermentation substrate. A single factor optimization test was used to optimize the solid-state fermentation parameters of biogas residue with the number of viable bacteria and the number of spores as indexes. The results showed that the optimum inoculation conditions involved the following: 55% initial moisture content, 15% initial inoculation amount, 30 ℃, and 1:1 initial inoculation ratio for 13 days. Pot experiment showed that the prepared three kinds of bacterial fertilizers could not only effectively promote the growth of white clover, improve the composition of soil nutrients, but also change the structure of soil bacterial community, which is of great significance to the health of soil ecosystem in white clover.

Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion

Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.

Biological oxidation of As(III) and Sb(III) by a novel bacterium with Sb(III) oxidase rather than As(III) oxidase under anaerobic and aerobic conditions

Sb and As are chemically similar, but the sequences and structures of Sb(III) and As(III) oxidase are totally distinct. It is thus interesting to explore whether Sb(III) oxidase oxidizes As(III), and if so, how microbial oxidations of Sb(III) and As(III) influence one another. Previous investigations have yielded ambiguous or even erroneous conclusions. This study aimed to clarify this issue. Firstly, we prepared a consortium of Sb(III)-oxidizing prokaryotes (SOPs) by enrichment cultivation. Metagenomic analysis reveals that SOPs with the Sb(III) oxidase gene, but lacking the As(III) oxidase gene are predominant in the SOP community. Despite this, SOPs exhibit comparable Sb(III) and As(III)-oxidizing activities in both aerobic and anaerobic conditions, indicating that at the microbial community level, Sb(III) oxidase can oxidize As(III). Secondly, we isolated a representative cultivable SOP, Ralstonia sp. SbOX with Sb(III) oxidase gene but without As(III) oxidase gene. Genomic analysis of SbOX reveals that this SOP strain has a complete Sb(III) oxidase (AnoA) gene, but lacks As(III) oxidase (AioAB or ArxAB) gene. It is interesting to discover that, besides its Sb(III) oxidation activities, SbOX also exhibits significant capabilities in oxidizing As(III) under both aerobic and anaerobic conditions. Moreover, under aerobic conditions and in the presence of both Sb(III) and As(III), SbOX exhibited a preference for oxidizing Sb(III). Only after the near complete oxidation of Sb(III) did SbOX initiate rapid oxidation of As(III). In contrast, under anaerobic conditions and in the presence of both Sb(III) and As(III), Sb(III) oxidation notably inhibited the As(III) oxidation pathway in SbOX, while As(III) exhibited minimal effects on the Sb(III) oxidation. These findings suggest that SOPs can oxidize As(III) under both aerobic and anaerobic conditions, exhibiting a strong preference for Sb(III) over As(III) oxidation in the presence of both. This study unveils a novel mechanism of interaction within the Sb and As biogeochemical cycles.

Bisphenol A affects microbial interactions and metabolic responses in sludge anaerobic digestion

The widespread use of bisphenol A (BPA) has resulted in the emergence of new pollutants in various environments, particularly concentrated in sewage sludge. This study investigated the effects of BPA on sludge anaerobic digestion, focusing specifically on the interaction of microbial communities and their metabolic responses. While the influence of BPA on methane accumulation is not significant, BPA still enhanced the conversion of soluble COD, protein, and polysaccharides. BPA also positively influenced the hydrolysis-acidogenesis process, leading to 17% higher concentrations of volatile fatty acids (VFAs). Lower BPA levels (0.2-0.5 mg/kg dw) led to decreased hydrolysis and acidogenesis gene abundance, indicating metabolic inhibition; conversely, higher concentrations (1-5 mg/kg dw) increased gene abundance, signifying metabolic enhancement. Diverse methane metabolism was observed and exhibited alterations under BPA exposure. The presence of BPA impacted both the diversity and composition of microbial populations. Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi dominated in BPA-treated groups and varied in abundance among different treatments. Changes of specific genera Sedimentibacter, Fervikobacterium, Blvii28, and Coprothermobacter in response to BPA, affecting hydrolysis and acetogenesis. Archaeal diversity declined while the hydrogenotrophic methanogen Methanospirillum thrived under BPA exposure. BPA exposure enabled microorganisms to form structured community interaction networks and boost their metabolic activities during anaerobic digestion. The study also observed the enrichment of BPA biodegradation pathways at high BPA concentrations, which could interact and overlap to ensure efficient BPA degradation. The study provides insights into the digestion performance and interactions of microbial communities to BPA stress and sheds light on the potential effect of BPA during anaerobic digestion.

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.

Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure

Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.

Fabrication, characterization and performance analysis of a two-step arsenic bio-filter column using Delftia spp. BAs29 and fired red mud pellets

Arsenic (As) is considered to be a grave inorganic pollutant, contaminating major aquifers worldwide. In this study, a two-step approach has been designed to combat this toxic metalloid by combining a highly efficient As (III) oxidizing bacteria; Delftia sp. BAs29 and fired red mud pellets to remove the total As from groundwater including both As (III) and As (V) ions. The maximum capacity of As (III) oxidation by Delftia sp. BAs29 was seen to be 95.65% for 500 ml of As contaminated groundwater using an optimized As (III) concentration of 300 ppb and 6.5 g of bacterial cell mass for 7 days. The second step indicated the maximum As (V) adsorption capacity by the stacked red mud pellets to be 97.91% for 500 ml of As contaminated groundwater using the optimized pore size of 106-125 μm for 7 days. The efficiency of As removal increased to 98.76% at a flow rate of 50 ml/h on combining of both the steps. In addition, the morphological properties, chemical composition, and the crystal structure of the As (V) adsorbed red mud pellets were characterized. The techno-economic feasibility of this entire unit was studied using SuperPro 10 software to estimate its optimal demand and potential. Hence, it is believed that scaling up of this two-step bio-filter column can serve as a potent filtration unit to eliminate As, both at the household and industrial level in the near future.

Inoculation of Escherichia coli enriched the key functional bacteria that intensified cadmium accumulation by halophyte Suaeda salsa in saline soils

The enhancement of cadmium (Cd) extraction by plants from contaminated soils associated with phosphate-solubilizing bacteria (PSB) has been widely reported, but the underlying mechanism remains scarcely, especially in Cd-contaminated saline soils. In this study, a green fluorescent protein-labeled PSB, the strain E. coli-10527, was observed to be abundantly colonized in the rhizosphere soils and roots of halophyte Suaeda salsa after inoculation in saline soil pot tests. Cd extraction by plants was significantly promoted. The enhanced Cd phytoextraction by E. coli-10527 was not solely dependent on bacterial efficient colonization, but more significantly, relied on the remodeling of rhizosphere microbiota, as confirmed by soil sterilization test. Taxonomic distribution and co-occurrence network analyses suggested that E. coli-10527 strengthened the interactive effects of keystone taxa in the rhizosphere soils, and enriched the key functional bacteria that involved in plant growth promotion and soil Cd mobilization. Seven enriched rhizospheric taxa (Phyllobacterium, Bacillus, Streptomyces mirabilis, Pseudomonas mirabilis, Rhodospirillale, Clostridium, and Agrobacterium) were obtained from 213 isolated strains, and were verified to produce phytohormone and promote soil Cd mobilization. E. coli-10527 and those enriched taxa could assemble as a simplified synthetic community to strengthen Cd phytoextraction through their synergistic interactions. Therefore, the specific microbiota in rhizosphere soils enriched by the inoculated PSB were also the key to intensifying Cd phytoextraction.

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.

Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO₂ fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).

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.

Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning

Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F₄₂₀H₂ dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.

AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation

Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.

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.

Characterization of Microbial Communities in Wastewater Treatment Plants Containing Heavy Metals Located in Chemical Industrial Zones

Water pollution caused by heavy metals (HMs) poses a serious risk to human health and the environment and can increase the risk of diabetes, cancer, and hypertension in particular. In this study, two full-scale wastewater treatment plants (WWTPs) in industrial zones in southern China were selected to analyze the microbial community structure, diversity, similarity, and differentiation in the anoxic/oxic (AO) and anoxic/oxic membrane bioreactor (AO-MBR) units under the stress of HMs. High-throughput sequencing showed that microbial diversity and abundance were higher in the AO process than in the AO-MBR process. In the two WWTPs, the common dominant phyla were Proteobacteria and Bacteroidetes, while the common dominant genera were Gemmatimonadaceae, Anaerolineaceae, Saprospiraceae, and Terrimonas. Manganese (Mn) and zinc (Zn) positively correlated with Saccharimonadales, Nakamurella, Micrococcales, and Microtrichales, whereas copper (Cu) and iron (Fe) positively correlated with Longilinea and Ferruginibacter. Additionally, the relative abundances of Chloroflexi, Patescibacteria, and Firmicutes differed significantly (p < 0.05) between the two processes. These results may provide comprehensive outlooks on the characterization of microbial communities in WWTPs, which could also help to reduce the potential environmental risks of the effluent from WWTPs located in industrial zones.

Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings

Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and ¹⁵N₂ enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.