Huaqun Yin

Pyrite oxidation generates sulfate and acidity in sulfide-bearing mine soils, but how structural carbon suppresses this process remains unresolved. We combined a 56-day pyrite-amended soil microcosm with geochemical measurements, qPCR, metagenomics, DNA stable isotope probing (DNA-SIP), genome-resolved analysis, and apparent kinetic modeling. Cellulose decreased NaOH-extractable sulfate by 72.71% and HCl-extractable Fe(III) by 55.13% at day 56. DNA-SIP showed that cellulose-derived carbon entered a phylogenetically distributed assimilating guild with genomic potential for oxidative-hydrolytic cellulose deconstruction, Fe(III) reduction, sulfate uptake, and assimilatory sulfate reduction. Enriched metagenome-assembled genomes collocated these C, Fe, and S functions within individual populations, whereas time-series metagenomes showed sustained cellulose-deconstruction and sulfur-assimilation potential without broad enrichment of Fe-reduction genes. Thus, functionally important assimilators could reshape Fe–S cycling without consistently dominating bulk community abundance. Consistent with these genomic and geochemical patterns, the apparent model indicated weaker O2-driven direct oxidation, Fe(II) oxidation/Fe(III) regeneration, and effective reactivity of extractable Fe(III). These results identify a microbial mechanism whereby cellulose utilization redirects C–S–Fe coupling toward more reductive and assimilatory transformations, suppressing pyrite oxidation without detectable mineral-surface coating.

Chalcopyrite is the most abundant copper-bearing sulfide mineral, characterized by a stable crystal structure. Bioleaching of chalcopyrite is inherently slow and further constrained by surface passivation layers during prolonged bioleaching. In this study, bacteriophages released from Acidithiobacillus ferrooxidans were introduced to promote chalcopyrite bioleaching. Mineralogical characterization, microbial profiling, and functional gene analysis were employed to reveal the underlying mechanisms. One day after phage introduction, phage abundance was 9.42 × 10 ⁵ VLPs mL ⁻¹ in the phage-treated group, 150-fold higher than in the control (6.26 × 10 ³ VLPs mL ⁻¹ ). Over a 60-day leaching period, the copper leaching efficiency of the phage-treated group was 31.72%, significantly higher than that of the control (20.43%). Phage introduction alleviated surface passivation, suppressed elemental sulfur (S ⁰ ) and jarosite-type deposition, and increased the apparent product-layer diffusion rate constant 3.60-fold. Bacterial diversity and the relative abundance of heterotrophic bacteria were elevated. The increase in heterotrophic bacteria may alleviate the inhibitory effects of organic matter on autotrophic bioleaching microorganisms. Genes associated with the Sox system, dissimilatory sulfur metabolism, and organic sulfur transformation were significantly enriched in the phage-treated group, consistent with enhanced S ⁰ turnover and reduced surface accumulation. Together, these results indicate that phage introduction enhances chalcopyrite bioleaching by alleviating surface passivation and promoting sulfur turnover through coupled interfacial and microbial regulation. This study provides a novel approach for sustainable intensification of bioleaching of refractory sulfide minerals.

Biological fermentation drying is an eco-friendly method for food waste treatment. It reduces waste mass and volume effectively. Microbial interactions drive drying efficiency. Yet these interactions remain unclear. Here we show that the inoculation of thermophilic strain and enrichment improved drying efficiency by 24.58% to 30.09%. The temperature comprehensive index and crude fat degradation rate in food waste were increased. The total nitrogen content was reduced by inoculation of thermophiles. The bacterial community was primarily composed of Proteobacteria, Bacteroidetes, and Firmicutes, with increased abundances of Proteobacteria, Actinobacteria, and Cyanobacteria. The fungal community included Ascomycota, Basidiomycota, Glomeromycota, and Chytridiomycota. Thermophilic Bacillus inoculation enhanced bacterial diversity, stabilized the fungal network, and influenced the dominant species in the bacterial-fungal cross-domain network at different stages of bio-drying. Environmental factors such as moisture content and conductivity significantly affected the size and complexity of the network. The study highlights the potential benefits of microbial inoculation and underscores the importance of understanding microbial dynamics and environmental factors in this process.

Microbially induced calcium carbonate precipitation (MICP) is recognized as a promising, environmentally sustainable technology with diverse applications in environmental engineering. A bibliometric analysis of 5373 publications indexed in Web of Science from 2005 to 2024 was conducted using CiteSpace and VOSviewer to identify research trends and hotspots in biomineralization and calcium carbonate (CaCO₃) studies. The results showed exponential growth in publications, increasing from 96 in 2004 to 397 in 2024 and spanning 91 interdisciplinary research areas. China, United States of America, and Germany were identified as the leading contributors. Research evolution was categorized into five distinct phases, progressing from initial crystal formation investigations to the current emphasis on underlying microbial mechanisms. Trend analysis revealed four emerging research hotspots: interfaces (0.22), crystal morphology (0.18), amorphous calcium carbonate (0.05), and bacteria (0.02). Mechanisms of MICP across bacteria, fungi, and algae were examined, revealing diverse metabolic pathways, including urea hydrolysis, denitrification, and photosynthesis. These findings suggest a paradigm shift in research toward microbial diversity and the role of extracellular polymeric substances. This shift provides valuable insights for developing sustainable biotechnological applications in environmental remediation.

Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria–phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.

Tobacco bacterial wilt (TBW), caused by Ralstonia solanacearum, significantly impacts tobacco yield and quality, leading to substantial economic losses. This study investigated the effects of the microbial agents JX (Pichia sp. J1 and Klebsiella oxytoca ZS4) on the soil properties, rhizospheric microbial community, tobacco agronomic traits, and TBW incidence through field experiments. Our results revealed that JX effectively suppressed TBW (relative control efficiency reached 85.18%) and promoted plant growth, enhancing agronomic traits by 9.58%-49.12%. The microbial agents JX was also attributed to improving soil properties (e.g., organic matter, total nitrogen, total phosphorus, and total potassium). Results of high-throughput sequencing revealed that JX not only affected the structure and diversity of tobacco rhizospheric bacterial/fungal community but also increased the relative abundances of critical microorganisms (e.g., Mesorhizobium, Pedosphaera, Nocardioides, Massilia, Burkholderia, and Purpureocilliu). Functional predictions showed the relative abundance of the pathways about some key secondary metabolisms (e.g., biosynthesis pathway of nicotinamide, phenylpropanoid, indole alkaloids, penicillin, cephalosporin, and novobiocin) and functional enzymes (e.g., catalase, ferroxidase, and tryptophan synthase) increased, which may also be critical factors in promoting tobacco growth and controlling TBW. These findings underscored the effectiveness of JX in both promoting tobacco growth and inhibiting TBW, supporting its practical application in tobacco cultivation.

Tetrathionate hydrolase (TTH) is a key enzyme for the oxidation of reduced inorganic sulfur compounds (RISCs) with the S₄I pathway, which is distributed in autotrophic or facultative autotrophic sulfur-oxidizing bacteria and archaea. In this study, the enzyme TTH_Mc from the acidothermophilic archaeon Metallosphaera cuprina Ar-4^T, encoded by mcup_1281 and belonging to the pyrroloquinoline quinone (PQQ) family, has been shown to possess tetrathionate hydrolysis activity. The molecular mass of the single subunit of TTH_Mc was determined to be 57 kDa. TTH_Mc is proved to be located in the cytoplasm, periplasmic space, and membrane, and the activity of them accounted for 72.3%, 24.0%, and 3.7% of the total activity. Optimal activity was observed at temperatures above 95 °C and pH 6.0, and the kinetic constants K_m and V_max were 0.35 mmol/L and 86.3 μmol/L, respectively. The presence of 0.01 mol/L Mg²⁺ enhances the activity of TTH_Mc, while 0.01 mol/L Ca²⁺ inhibits its activity. The hydrolysis of tetrathionate (TT) by TTH_Mc results in the production of thiosulfate, pentathionate, and hexathionate. This study represents the first description of TTH in the genus Metallosphaera, providing new theoretical insights into the study of sulfur-oxidizing proteins in acidothermophilic archaea.

Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature ( r = −0.518, P = 0.007) and dissolved oxygen ( r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments. IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.

Tetrathionate hydrolase (TTH) is a key enzyme for oxidation of reduced inorganic sulfur compounds (RISCs) with S4I pathway, which is distributed in autotrophic or facultative auto-trophic sulfur-oxidizing bacteria and archaea. In this study, the enzyme TTHMc from the aci-dothermophilic archaeon Metallosphaera cuprina Ar-4T, encoded by mcup_1281 and belonging to the pyrroloquinoline quinone (PQQ) family, has been shown to possess tetrathionate hydrolysis ac-tivity. The molecular mass of the single subunit of TTHMc was determined to be 57 kDa. TTHMc is proved to locate in the cytoplasm, periplasmic space, and membrane, the activity of them ac-counted for 72.3%, 24.0%, and 3.7% of the total activity. Optimal activity was observed at tem-peratures above 95 °C and pH 6.0, the kinetic constants Km and Vmax were 0.35 mmol/L and 8.63 μmol/L, respectively. The presence of 0.01 mol/L Mg2+ enhances the activity of TTHMc, while 0.01 mol/L Ca2+ inhibits its activity. The hydrolysis of tetrathionate (TT) by TTHMc results in the pro-duction of thiosulfate, pentathionate, and hexathionate. This study represents the first description of TTH in the genus Metallosphaera, providing new theoretical insights into the study of sul-fur-oxidizing proteins in acidothermophilic archaea.

Bioremediation is widely recognized as a promising and efficient approach for the elimination of Cd from contaminated paddy soils. However, the Cd removal efficacy achieved through this method remains unsatisfactory and is accompanied by a marginally higher cost. Cysteine has the potential to improve the bioleaching efficiency of Cd from soils and decrease the use cost since it is green, acidic and has a high Cd affinity. In this study, different combination modes of cysteine and microbial inoculant were designed to analyze their effects on Cd removal and the soil microbial community through the sequence extraction of Cd fraction and high-throughput sequencing. The results demonstrate that the mixture of cysteine and the microbial inoculant was the best mode for increasing the Cd removal efficiency. And a ratio of cysteine to microbial inoculant of 5 mg:2 mL in a 300 mL volume was the most economically efficient matching. The Cd removal rate increased by 7.7–15.1% in comparison with the microbial inoculant treatment. This could be ascribed to the enhanced removal rate of the exchangeable and carbonate-bound Cd, which achieved 94.6% and 96.1%, respectively. After the treatment, the contents of ammonium nitrogen (NH₃–N), total phosphorus (TP), available potassium (AK), and available phosphorus (AP) in the paddy soils were increased. The treatment of combinations of cysteine and microbial inoculant had an impact on the soil microbial diversity. The relative abundances of Alicyclobacillus, Metallibacterium, and Bacillus were increased in the paddy soils. The microbial metabolic functions, such as replication and repair and amino acid metabolism, were also increased after treatment, which benefitted the microbial survival and adaptation to the environment. The removal of Cd was attributed to the solubilizing, complexing, and ion-exchanging effects of the cysteine, the intra- and extracellular adsorption, and the production of organic acids of functional microorganisms. Moreover, cysteine, as a carbon, nitrogen, and sulfur source, promoted the growth and metabolism of microorganisms to achieve the effect of the synergistic promotion of microbial Cd removal. Therefore, this study underscored the potential of cysteine to enhance the bioremediation performance in Cd-contaminated paddy soils, offering valuable theoretical and technical insights for this field.