Biological nitrogen fixation is central to sustainable rice cultivation, yet diazotrophic Paenibacillus species from red paddy soils remain poorly characterized. Here, three novel Paenibacillus strains, sgz500958T, sgz500992T and sgz5001063T, were isolated from red paddy soils in China. Phylogenetic and phylogenomic analyses based on 16S rRNA and whole-genome data revealed that the three strains formed distinct lineages within Paenibacillus, with average nucleotide identity values below 95% relative to their closest reference strains. All strains possessed a complete nif gene cluster and exhibited nitrogenase activity, and strain sgz5001063T maintained high activity at low concentrations (0-3 mM), was inhibited at intermediate concentrations (4-30 mM) and recovered at very high ammonium concentrations (30-300 mM). Utilizing complementary plant growth-promoting traits and co-culture compatibility, two nitrogen-fixing synthetic communities (NFSCs) were assembled. In rice assays, NFSC2 markedly enhanced germination (100%), shoot height (+72.5%) and root growth relative to sgz5001063T alone and NFSC1. The isolates are proposed as Paenibacillus oryziterrae sp. nov. (sgz500958T=MCCC 1K09377T=KCTC 43740T), Paenibacillus paludis sp. nov. (sgz500992T=MCCC 1K09376T=KCTC 43729T) and Paenibacillus diazotrophicus sp. nov. (sgz5001063T=MCCC 1K09391T=KCTC 43741T).

Intercropping tea plants with Ophiopogon japonicus effectively prevents soil erosion and enhances the ecological stability of mountainous tea plantations. However, the underlying ecological facilitation mechanisms remain underexplored. This study investigated the effects of root exudates on rhizosphere soil microbial community structure and tea plant growth under an intercropping system through pot experiments. Results showed that intercropping significantly promoted tea shoot length and plant height. Additionally, rhizosphere microbial diversity increased, with significant changes observed in the microbial community structure. We also analyzed the functional characteristics of the microbiome under different treatments from a microbial functional perspective, such as the enhancement of microbial functions related to glycolysis and cellulose degradation, as well as the enrichment of functional microbes with beneficial genomic traits. Further analysis of root exudate composition under different planting modes revealed that intercropping significantly increased the content of amino acids such as histidine, serine, and leucine in root exudates. KEGG pathway analysis confirmed that metabolic pathways related to amino acid metabolism were significantly enriched, displaying the highest levels of enrichment. These findings highlight the potential of intercropping Ophiopogon japonicus to improve soil ecology and enhance tea plant growth in mountainous plantations.

Protists are pivotal yet understudied in groundwater systems. Linkage of groundwater protists to geogenic high Cr(VI) has remained elusive. Here, we profiled protistan composition, structure, trophic functionality, and Cr(VI)-associated clusters, alongside the interactive effect of Cr(VI) and hydrogeochemical factors. Protistan communities significantly diverged between low (<50 mu g/L) and high Cr(VI) (>50 mu g/L) groundwater. Elevated Cr(VI) favored phototrophs with facultative mixotrophic potential but heterotrophic consumers. Notably, Cr(VI)-tolerant phototrophs with facultative mixotrophic potential were strongly correlated with high dissolved oxygen. Four identified Cr(VI)-associated clusters displayed distinct trophic structures and were linked not only to Cr(VI) but also to the Cr(VI)-associated hydrochemical factors of groundwater depth, total dissolved solids, and dissolved oxygen. Path analysis revealed the effect paths of groundwater depth, total dissolved solids, dissolved oxygen, and Cr(VI) on protistan clusters, suggesting potential divergent, niche-specific responses of cross-trophic clusters to Cr(VI) and covarying hydrochemical factors. Additionally, highly abundant ciliates reflected the bioaccumulation potential for Cr(VI). Our findings highlight groundwater protists as an underexplored microbial group with potential significance in the ecological dynamics of Cr(VI)-contaminated aquifers potentially mediated via their multitrophic interactions.

Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.

Sustainable hygroelectricity generation has emerged as a revolutionary technology capable of harvesting the latent heat from ambient environments and converting it into direct-current electricity. Recently, microbial biofilms have been regarded as promising hydrovoltaic materials for their low-cost, facile fabrication and environmentally friendly nature. However, external moisture dependence and ultra-high internal resistance have greatly limited the output performance of microbial biofilm-based hydrovoltaic electricity generators (BioHEGs). Herein, a core@shell structured biohybrid system (S. o@PPy) was constructed by in situ polymerization of pyrrole monomers on the surface of Shewanella oneidensis (S. o) cells. The presence of polymer-biofilm interfaces resulted in an exceptional performance of hygroelectricity generation originated from the built-in conductivity of hole-doped polypyrrole (PPy), as well the reduced internal resistance and improved water adsorption capacity of S. o biofilms. Hence, the S. o@PPy BioHEG generated a stable short-circuit current of ca. 33.5 μA at the optimal condition, which is significantly higher than all BioHEGs documented hitherto. Moreover, a novel mechanism of asymmetric charge redistribution was confirmed by density function theory (DFT) calculations. These results support a new perspective of hydrovoltaic effects and provide a viable strategy for advancing BioHEGs towards more practical scenarios.

Manganese homeostasis is essential for the environmental adaptability and pathogenic potential of Stenotrophomonas maltophilia, a bacterium that thrives across diverse and fluctuating environments. Here, we characterize the manganese homeostasis network of S. maltophilia strain Sm18, identifying a coordinated system that integrates conserved transporters with previously unrecognized candidate components. Central to this system is an MntR-controlled gene module that includes the canonical Mn²⁺ importer MntH and exporter MntP, together with a TonB-dependent receptor (TBDR) and a periplasmic thioredoxin-fold protein (pTFP), both representing novel protein families with restricted phylogenetic distribution. Transcriptomic analyses under varying Mn²⁺ and Fe²⁺ conditions revealed a tight interplay between these metals, highlighting the ferrophilic nature of S. maltophilia and the differential regulation of module components. Notably, the TBDR-pTFP locus is strongly induced under combined Mn2+ and Fe2+ limitation, suggesting a specialized role in metal acquisition under nutrient-restricted conditions. Functional analyses showed that MntP contributes to protection from Mn toxicity even at sub-inhibitory concentrations, whereas MntH supports growth under oxidative stress and promotes intracellular replication within Acanthamoeba castellanii phagosomes. Together, these findings identify a Mn-responsive module candidate associated with manganese homeostasis and provides new insight into mechanisms that support S. maltophilia adaptation to metal-limited and host-associated environments.

Returning straw to the field is widely recognized for its ability to sustain crop productivity and promote the long-term viability of agricultural ecosystems. However, the impact of prolonged straw return on soil functional microbiomes and their relationship with soil multifunctionality (SMF) remain insufficiently understood. This study is based on an 8-year field experiment comprising four treatments: no straw return (N), rice straw return (R), wheat straw return (W), and combined rice and wheat straw return (RW). All straw incorporation methods increased the wheat yield and SMF. Rice straw increased SMF by 69.7 %, while wheat straw enhanced SMF by 52.1 %, with RW exhibiting the most significant long-term positive effect (74.8 %). This enhancement was primarily attributed to elevated available soil nutrient levels and increased enzymatic activities associated with carbon, nitrogen, and phosphorus cycling. Straw return promoted C, N, and P cycling genes following the trend RW > W > R > N. Random forest analysis identified the composition and abundance of functional microbial communities as key determinants of crop productivity. RW markedly diminished the abundance of plant-associated beneficial bacteria and consumers while promoting fungal pathogens in wheat leaves and reducing their prevalence in rhizosphere soil. Potentially beneficial bacteria exhibited a strong predictive capacity for wheat yield, significant associations with soil functionality, and compensatory effects with soil nutrients in their contributions. Structural equation modeling revealed that straw return was significantly positively correlated with enhanced SMF and C-N-P cycling efficiency, ultimately promoting wheat yield. Consequently, these findings suggest that straw return drives microbial community assembly, enhances nutrient cycling, and fosters improved soil fertility and multifunctionality.

Silicon dioxide nanoparticles (SiO2 NPs) have been shown to alleviate cadmium (Cd) toxicity in plants, but the mechanisms regarding SiO2 NPs-mediated Cd uptake and detoxification on hyperaccumulators are unknown. In this study, physiological and transcriptomic analyses were performed to investigate the impact of SiO2 NPs on the growth and Cd accumulation of the Cd-hyperaccumulator Sedum alfredii. The results showed that SiO2 NPs significantly increased root fresh weight (32.71% to 121.50%) and shoot fresh weight (22.72% to 86.36%). Simultaneously, SiO2 NPs enhanced the Cd uptake and accumulation by S. alfredii (with maximum increases of 232.14%). In the leaves, the Cd content in the phloem of the Si treatment group increased by 1.24 to 1.79-fold, indicating that SiO2 NPs enhanced the transport of Cd to the shoots. Furthermore, SiO2 NPs improved the photosynthetic parameters, with the net photosynthetic rate, transpiration rate and stomatal conductance increasing by 2.86-fold, 1.14-fold, and 1.84-fold of the control, respectively. Furthermore, SiO2 NPs significantly strengthened the antioxidative enzymes activities (SOD, CAT, POD). Transcriptomic analysis revealed that SiO2 NPs enhanced the Cd tolerance and accumulation capacity of S. alfredii by upregulating the expression of genes encoding photosynthesis-related functions (PSI, PSII), antioxidant enzymes, cell wall synthesis functions, heavy metal-responsive transcription factors (WRKY, NAC, bZIP, MYB), and Cd chelation and transport protein functions. Combining physiological and transcriptomic analyses, our findings provide the mechanisms of SiO2 NPs in promoting Cd accumulation and enhancing Cd tolerance in S. alfredii, highlighted the potential of SiO2 NPs to enhance phytoremediation efficiency.

Microbes in mining areas face multifaceted stress from arsenic (As) or antimony (Sb) exposure, yet their distinct adaptations to high levels of arsenite (As(III)) or antimonite (Sb(III)) are not well understood. In this study, we subjected the As(III)-oxidizing bacterium Achromobacter sp. As-55 to laboratory evolution under As(III) or Sb(III) stress, yielding strains capable of oxidizing As(III) under very high levels of As(III)/Sb(III) and displaying increased dual metalloid resistance. Our results showed that Sb(III)-evolved populations achieved hyper-resistance to Sb(III) and antibiotics, a phenotype linked to a significantly higher mutational load (26-254) compared to As(III)-evolved lineages (9-28). Under prolonged exposure to high concentrations of As(III) or Sb(III), the As-55 strain evolved a streamlined and optimized resistance network through adaptive genetic changes. Adaptation to As(III) converged on a single mutation in the acr3 efflux pump across all 12 populations, potentially reflecting a strategy that limits arsenic influx. In contrast, Sb(III) resistance may be associated with extensive genetic alterations. Mutations potentially relieve repression of the arsAB operon, enhancing efflux activity, and remodeling transcriptional networks and energy metabolism, which could contribute to high-level Sb(III) resistance. Crucially, arsO was inactivated by nonsense or frameshift mutations in both As(III)- and Sb(III)-evolved populations. This may reflect an adaptive loss-of-function and suggests a model in which As(III)/Sb(III) evolutionary pressure alters cellular metabolic priorities. Our findings thereby elucidate the mechanistic basis of metalloid-specific adaptation and guide rational genetic modification of strains for environmental bioremediation.

As key components of terrestrial ecosystems, fungi play vital roles in ecological processes and functions, and are associated with innumerable plant, vertebrate, and arthropod taxa. Among arthropod taxa, aphids (Hemiptera) are commonly found in both natural and agricultural ecosystems, where some species cause substantial crop damage. Here, we provide a novel and unique dataset, AphidFunga, compiling associations between fungi and aphids extracted from 412 scientific publications, spanning 167 years and covering 85 countries. Fungal and aphid taxonomies were revised to recent nomenclature, whereas association types were updated based on current knowledge. The AphidFunga database currently contains 2993 aphid-fungal association records, linking 365 aphid host taxa (species or genera) with 149 fungal taxa, 95% of which are entomopathogenic. The database is available in three formats: a combined comma-separated data table, a set of R data frames, and a MySQL relational database. The AphidFunga database lays the foundation for further research on fungus-mediated ecosystem processes and functions, and supports conservation science, policy development, and applications in crop protection and environmental management.

Electric cues (ECs) permeate microbial habitats, yet electrosensing, the ability of microorganisms to detect and respond to these cues, remains largely overlooked. We distinguish four principal EC types [electric fields (EFs), electrode potentials, redox signals, and electromagnetic induction] and map each to its biological sensing mechanism. Recent findings reveal that cable bacteria respond to dynamic EFs through electromagnetic induction, a candidate sensing mechanism that is absent from existing models. We synthesize conserved sensing strategies primarily in bacteria, with emerging evidence in eukaryotes, and assess applications in bioenergy, bioremediation, and electroceutical therapy. Realizing this potential requires moving beyond static-field models toward experimental frameworks that capture the full temporal complexity of natural electric landscapes.

Microbial biofilm-based hydrovoltaic electricity generators (BioHEGs) exemplify low-cost and facile manufacturing platforms for hydrovoltaic energy, albeit with relatively low power output that is unsatisfactory for practical applications. Herein, in situ surface polymerization of polyaniline (PAni) on Shewanella oneidensis (S. o o) is verified to boost the hydrovoltaic performance of the biohybrid system. Notably, the S. o o@PAni BioHEG unit achieves an ultra-high stable power density of ca. 168.6 mW & sdot;m(-2), which outperforms all BioHEGs hitherto documented by an order of magnitude. Specifically, the output voltage and current density of S. o o@PAni BioHEG are significantly enhanced due to the formation of Schottky junctions at the interface between the microbial biofilm and electrode. Moreover, the synergistic effect of extracellular polymeric substances and PAni induces accelerated electron transfer, thereby lowering the electrical resistance in the system. This work unambiguously provides a reliable strategy for advancing the performance of BioHEGs toward more comprehensive and practical scenarios.

Foliar diseases seriously limit tea productivity and leaf quality, highlighting the need for sustainable cultivation strategies that improve disease management, yield, and product quality. In this study, we evaluated how tea–soybean intercropping affects foliar disease occurrence, tea production, quality-related traits, and associated phyllosphere microbial and apoplastic metabolic changes. Compared with monoculture, intercropping markedly reduced the occurrence and disease index of major foliar diseases, especially anthracnose, and improved yield and quality-related traits. These agronomic benefits were accompanied by shifts in phyllosphere bacterial communities, including increased epiphytic bacterial richness and enrichment of Pseudomonas taxa. Apoplastic metabolomic analysis further revealed coordinated metabolic shifts under intercropping, including increased accumulation of salicylic acid, p-hydroxycinnamic acid, and tropolone, which showed positive correlations with Pseudomonas taxa. Culture-dependent isolation further recovered eight antagonistic Pseudomonas strains from tea leaves, several of which inhibited the anthracnose pathogen in vitro and reduced lesion development under pot conditions. Field application of a SynCom composed of these strains was associated with lower anthracnose severity than the control and also altered tea quality related metabolism, increasing water extract, flavonoids, and soluble sugars while reshaping catechin composition. These results indicate that tea–soybean intercropping represents a potential ecological cultivation strategy for improving tea production and reducing foliar disease pressure, while phyllosphere microbial and metabolic changes provide insights into the mechanisms underlying these benefits.

Groundwater pollution of antibiotic resistance genes (ARGs) constitutes a critical One Health concern, with metal-induced co-selection exacerbating associated public health risks. Yet the roles of cross-kingdom microbes (bacteria, protists, and fungi) and their interactive effects in shaping groundwater resistomes under long-term geogenic chromium (Cr) stress in deep aquifer systems remain unknown. Here, we characterized the cross-kingdom microbiomes, potential human pathogenic bacteria and antibiotic resistomes in deep aquifers with geogenic Cr(Ⅵ) up to 231 μg/L using a high-throughput ARG chip together with 16S rRNA, 18S rRNA, and ITS amplicon sequencing. Bacteria and protists exhibited stronger responses to elevated Cr(Ⅵ) and to key hydrochemical variables (TDS, ORP, and groundwater depth) than fungi. Protists were strongly correlated with ARGs and potential human pathogenic bacteria, acting as the second most important drivers of resistome variation after bacteria. Consumer protists dominated the protistan community (60.2%) and significantly influenced antibiotic resistomes and pathogenic bacteria via protist-bacteria interactions. Elevated Cr(VI) concentrations (>50 μg/L) dramatically increased the proportion of protist-associated multidrug resistance genes (13.2% to 74.5%) and enriched high-risk ARGs (Q1) nearly fivefold (6.1% to 29.0%), indicating geogenic Cr(VI) stress amplifies groundwater antibiotic resistance risks through coupled geochemical-biological interactions. Our findings highlight groundwater protists as underexplored ecological amplifiers of antibiotic resistance, emphasizing their critical role in influencing resistome risks in geogenically contaminated aquifer systems.

High levels of antimony (Sb) adversely affect plant growth and development. We aimed to uncover the harmful effects of different forms of Sb on root morphology, physiology and expression profiles of genes encoding functions associated with roots. Rice plants grown in ½ Hoagland nutrient solution were exposed to Sb(III) and Sb(V) at concentrations of 10 and 20 mgL−1 for one week. Results demonstrated that higher concentrations of Sb(III) significantly impaired root morphological traits, with high toxicity observed at 20 mgL−1 Sb(III) and 10 mgL−1 Sb(V). The application of Sb(III) led to reduced uronic acid levels in hemicellulose-II (HCII) with cell organelle and cytosol displaying substantial accumulation of Sb(III). Enzymatic activity revealed that high levels of Sb(III) disrupted the activity of cellulase (CE) and pectin methylesterase (PME), while augmenting the activity of Xyloglucan endotransglycosylase hydrolase (XTH). Additionally, polygalacturonase (PG) was significantly reduced under Sb(V) 10 mgL−1 exposure. Pearson’s correlation coefficient was used for continuous data to draw a linear trend between studied parameters. Shoot biomass displayed a negative correlation with root and shoot Sb. Shoot XTH had a positive correlation with shoot Sb. Furthermore, root and shoot Sb showed a positive association with root diameter and XTH. Hemicellulose-1 (HCI) was negatively associated with PME, PG and pectin, suggesting that HCI was a suitable binding site for uronic acid in the context of Sb contamination. Additionally, to elucidate the molecular mechanisms underlying root structural alterations, the expression profiles of key cell wall-related genes—Expansin, Cellulase synthase, XTH8 (xyloglucan endotransglucosylase/hydrolases) and Pectinesterase—were systematically analyzed using qRT-PCR. All genes were up-regulated in response to different forms of Sb exhibiting resistance. Xylanase was down-regulated, showing its role in the containment of Sb in roots. Further studies are advised for elucidating the mechanism of action of Sb on different tissues of rice plants.

Chorion peroxidase plays a crucial role in the hardening of insect eggshells, yet its potential as a target for pest control in Spodoptera frugiperda, a globally destructive pest that rapidly develops resistance to conventional insecticides, remains unexplored. In this study, we functionally characterized the S. frugiperda chorion peroxidase (SfCPO) gene and its roles in development, reproduction, and its indirect association with gut microbiota. Phylogenetic analysis revealed strong evolutionary conservation of SfCPO across species. The expression profile showed that SfCPO was highly expressed in ovaries and eggs, indicating a strong maternal contribution during early embryogenesis. RNA interference (RNAi)-mediated silencing of SfCPO reduced hatchability by 45%, lowered female fecundity by 42%, and disrupted the larval-pupal transition and adult emergence. Knockdown of SfCPO perturbed gut microbiota, reducing diversity and depleting beneficial genera such as Lactobacillus and Enterococcus, while enriching Pseudomonas. These findings identify SfCPO as a dual-function target for sustainable pest management.

Pathogenic fungi cause economic loss to many crops including strawberry, highlighting the need for control using sustainable eco-friendly strategies. Earthworm casts effectively reduce the occurrence of soil-borne diseases. However, the interactions between earthworms and soil-borne pathogenic fungi and their underlying mechanisms remain insufficiently understood in strawberry. This study investigated the effects of the pathogenic fungi Fusarium oxysporum and Alternaria alstroemeriae on the structure and composition of the microbial communities in the drilosphere soil and earthworm gut using high-throughput sequencing. The impact of these pathogenic fungi on functional gene expression in earthworms was determined using transcriptomic analysis. Applying F. oxysporum and A. alstroemeriae with earthworms significantly altered the physicochemical properties of the drilosphere soil, reduced the fungal alpha diversity therein, and increased the abundance of potentially beneficial Pseudomonas spp. and Bacillus spp. The presence of the pathogenic fungi increased the alpha diversity and habitat niche breadth of the fungal community in the earthworm gut. However, there was a significant reduction in the relative abundance of potentially pathogenic fungi to plants and animals in the earthworm gut. Earthworms had a positive legacy effect on the abundance of beneficial bacteria in the rhizosphere and enhanced strawberry biomass. Transcriptomic analysis demonstrated that earthworms activated α-linolenic acid and glycerophospholipid metabolism but downregulated the Toll-like receptor pathway, mitigating excessive immune responses. In summary, earthworms suppress soil-borne pathogenic fungi in strawberry via an integrated mechanism involving the restructuring of the gut microbiota, enrichment of biocontrol agents in the drilosphere, and coordination of host immunity, offering a novel paradigm for pest management and sustainable means for strawberry cultivation.

Different forms of antimony (Sb) show different toxicities to plants, which are hypothesized to be partially due to the disorders of lipid and saccharide synthesis. Hydroponic experiments were conducted using a rice plant (Yangdao 6) exposed to antimonite (Sb(III)) and antimonate (Sb(V)). We monitored the following (1) saccharide concentration and enzymatic activities associated with synthesis/degradation of sucrose and starch; (2) changes in cell ultrastructure of rice leaves; and (3) differentially expressed metabolites (DEMs) associated with lipids. The results showed that when compared to the control, Sb(III/V) (1) increased the concentrations of starch, soluble sugars, sucrose and fructose as well as the activities of cell-wall binding acid invertase (B-AI) in rice leaves; (2) mainly affected the abundance of unsaturated lipids of fatty acids (FAs), prenol lipids, glycerolipids, and glycerophospholipids, especially for Sb(III); and (3) negatively affected the abundance of DEMs associated with alpha-linolenic acid metabolism and xanthophyll formation. Relative to Sb(V), Sb(III) (1) showed great negative effects on the activities of fructose-1, 6-diphosphatase (FBP), triose-phosphate isomerase (TPI), alpha-glucosidase, and sucrose-phosphate synthase (SPS); (2) significantly narrowed the shape of starch granules and increased the thickness of cell walls; (3) increased numbers and abundance of DEMs associated with toxins (belonging to sphingolipids), flavonoids (polyketides), and biomarkers (corticosteroid hormones); and (4) increased the numbers of FAs whose abundance was upregulated. This study showed a complex regulatory network associated with saccharide synthesis/degradation and lipid constitution in response to Sb toxicity.