The high-dosage and high-frequency application of organic fungicides has resulted in environmental contamination. Additionally, greenhouse gas emissions, especially nitrous oxide (N2O), pose significant environmental challenges. Nanoscale zero-valent iron (nZVI) can reduce organic contamination and affect soil nitrogen (N) cycling, while the nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) can reduce the N2O emissions. We investigated the effects of nZVI and DMPP on soil fungicide residues, N2O emissions and microbial communities. The DMPP application significantly decreased the carbendazim residues by 44.34%. This might be attributed to the increased soil pH and ammonium N, which likely promoted the growth of the specific microbes, such as Chloroflexi, Acidobacteriota and Sphingomonas. Furthermore, the DMPP reduced the soil N2O emissions by 54.98%. The nZVI decreased N2O emissions by reducing the biomass of N2O-producing fungi Aspergillus and Neocosmospora, while enriching N2O-consuming bacteria Streptomyces. The nZVI enhanced the positive effects of DMPP on bacterial community and biomass but hindered DMPP-mediated carbendazim degradation. The soil bacteria and fungi might be the substantial contributors to decreasing soil carbendazim residues and N2O emissions, respectively. This study broadened our understanding of the ecological implications of the nZVI and nitrification inhibitors for reducing organic pollution and greenhouse gas emission.

Albic soils, characterized by a prominent, compact, and nutrient-poor albic horizon, represent a major low-productivity soil type in Northeast China. Despite the development of various amelioration strategies, a systematic synthesis of their theoretical underpinnings and integrated application, particularly from a soil health perspective, is currently lacking. This limits our ability to design context-specific, sustainable management systems for these degraded soils. This review systematically analyzes the interconnected physical, chemical, and biological constraints that govern the low productivity of Albic soils. It further synthesizes and evaluates synergistic management strategies aimed at holistic soil health enhancement, drawing upon both empirical field studies and mechanistic research. The key constraints include poor structure, shallow rooting depth, acidity, nutrient deficiency, and impoverished biological activity. Effective amelioration requires integrated approaches. Physical engineering (e.g., subsoil mixing) enhances soil structure, including aggregate stability, porosity, and water infiltration, thereby increasing crop yield by 2.2–20

Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.

Human activity intensifies the spread of antibiotic resistance genes (ARGs), threatening environmental and public health. Plant metabolite-microbe interactions play a crucial role in mitigating ARGs by shaping the soil environment. However, the role of mosses and their metabolites in mitigating ARG risks in natural settings remains largely unexplored. In this study, we conducted paired surveys of moss-covered and bare soils across urban and suburban parks, and found that moss cover significantly reduced ARG abundance. This mitigation effect was most pronounced in urban parks, where human-induced changes led to significant enrichment of Enterobacterales, the primary microbial host within ARG profiles strongly correlated with ARG levels. Moss presence led to the suppression of these high-risk hosts through the selective accumulation of the moss secondary metabolite, cristacarpin, in the underlying soil. Microcosm experiments further confirmed that cristacarpin reduced both Enterobacterales and ARGs, while molecular simulations suggested that this effect may be associated with cristacarpin binding to MlaC, a protein involved in outer membrane lipid transport and integrity. Comparison of published data from 2938 soil samples across the globe confirmed that Enterobacterales were consistently enriched in areas under higher anthropogenic pressure, highlighting the potential of mosses to mitigate the spread of ARGs in human-impacted areas worldwide. Our findings support the consideration of mosses as a scalable, nature-based, contribution to limiting the spread of ARGs, offering novel opportunities to mitigate antimicrobial resistance risks in anthropogenically-disturbed environments worldwide.

Casimicrobiaceae strains inhabit various environments, but their ecological roles in natural soils remain mostly unclear. By actively targeting specific high-altitude datasets during our Global Mollisols Genomic Atlas (GMGA) mining efforts, we discovered a previously unknown lineage within this family. This novel group is represented by five metagenome-assembled genomes (MAGs) recovered from oligotrophic soils in the Southern Brazilian Highland Grasslands, a unique environment within the broad Pampas black soil region. Phylogenetic and comparative genomic analyses showed these five MAGs form a distinct monophyletic clade within Casimicrobiaceae. Their novel taxonomic status is supported by Average Nucleotide Identity (ANI) thresholds, showing clear divergence from all known reference genomes. Functional annotations suggest a chemoorganotrophic lifestyle with microaerobic respiration capacity, while trace-gas scavenging genes indicate potential lithoheterotrophy for maintenance energy under nutrient limitation. Additionally, an autonomous ACC deaminase system and specialized nutrient scavenging pathways (organophosphonate and taurine utilization) highlight its adaptive capacity for rhizosphere interactions and survival in oligotrophic environments. Screening 22,976 public metagenomes demonstrated a widespread global distribution, primarily inhabiting diverse soil (86.4%) and plant-associated (7.0%) environments. Based on these analyses, we propose the name Edaphobacterium genomatis gen. nov., sp. nov. for this novel taxon following the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data) rules. Our results uncover hidden species diversity and highlight the specific functional roles of uncultured microbes in nutrient-limited highland niches within fertile black soil regions.

Soil acidification has become a major constraint on agricultural productivity, and conventional lime application offers limited recovery of overall soil health. Here, we systematically compared the effects of three soil amendments-humic-based (LYPH1), lime-based (LYPH2), and alkaline organic-inorganic fertilizer (LYPH3)-against a conventional fertilization control (CK) to elucidate the multidimensional mechanisms by which they improve acidified soils. A field experiment was conducted to evaluate soil physicochemical and biological parameters and to calculate the Soil Health Index (SHI). The study assessed the impact of the three amendments (LYPH1, LYPH2, and LYPH3) as well as the control (CK) on the soil’s health and its microbiome. Metagenomic analyses were performed to identify the enriched microbial taxa and key functional genes involved in nutrient cycling. Results showed a clear gradient of improvement following the trend LYPH3 > LYPH1 > LYPH2 > CK, with LYPH3 exhibiting the strongest enhancement of soil health. Metagenomic analyses revealed the functional potential of LYPH3 to significantly enrich core functional taxa, including Gammaproteobacteria, Gemmatimonadetes, Nitrospira_D, and Reyranella, which were associated with the enrichment of key functional genes involved in carbon stabilization(SDHC, tfrB), nitrification(amoC_B), and phosphorus activation (phoC, htxA). This coordinated enrichment of microbial taxa and functional genes coincided with enhanced microbially mediated carbon stabilization, nitrogen transformation, and phosphorus mineralization. Through the synergistic optimization of soil physicochemical properties and microbial attributes, LYPH3 achieved a substantial improvement in soil health in acidified croplands. The evidence for these mechanisms is primarily association-based, linking specific microbial taxa and their associated genes to key biogeochemical processes. Overall, our findings demonstrate that the alkaline organic–inorganic amendment (LYPH3) enhances soil health by selectively enriching a consortium of core microbial taxa and functional genes involved in C, N, and P cycling, thereby promoting these key nutrient cycling processes. This strategy represents an effective and sustainable approach for restoring acidified agricultural soils.

Soil microbial carbon metabolism plays a critical role in the global carbon cycle through regulating carbon sequestration andrelease processes. This study explored the millennium-scale dynamics of carbon metabolism functional genes along a coastal land reclamation chronosequence. We analyzed soil samples from sites ranging from 10 to 1000 years of reclamation, utilizing high-throughput metagenomic sequencing and statistical modeling to explore the diversity, abundance, and functional shifts in carbon metabolism pathways. Prolonged reclamation significantly enhanced the diversity and abundance of carbon metabolism genes, accompanied by a gradual decrease in soil salinity (from 2.5% to 0.2%) and a consistent increase in total carbon (from 0.2% to 1.6%). A notable shift in pathways from carbon fixation and methane metabolism to carbohydrate metabolism occurring after 50 years of reclamation. Notably, multiple regression modeling revealed that salinity (R2 = 0.842) and nitrogen levels, specifically dissolved organic nitrogen (R2 = 0.180) and total nitrogen (R2 = 0.151), were identified as key environmental drivers influencing these shifts. Key microbial taxa, including Proteobacteria, Actinobacteria, and Methylomirabilota, were identified as important contributors to these functional transitions. These findings offer valuable guidance for optimizing carbon sequestration in similar coastal ecosystems under long-term agricultural management.

ABSTRACT Aims The latitudinal diversity gradient (LDG), a foundational pattern describing increasing biodiversity towards the Equator, has been extensively documented for aboveground organisms. However, whether this pattern holds for belowground biodiversity, the largest component of Earth's biodiversity remains unclear. Location Globe. Time Period Present. Major Taxa Studies Soil Archaea, Bacteria, Fungi, Protists, and Invertebrates. Methods We put together two data collections (amplicon and metagenomics) encompassing over 5,000 soil samples published online across multiple trophic levels, including archaea, bacteria, fungi, protists, and invertebrates. Results Our results demonstrate that multitrophic soil biodiversity deviates substantially from the classical LDG, with most taxa showing no decline in diversity with increasing latitude. We further found that local‐scale edaphic properties (e.g., soil carbon, nitrogen, and pH) and global‐scale climatic variables (e.g., rainfall and temperature), largely override latitude in explaining soil biodiversity variations. Multi‐group structural equation modelling indicated that local diversity was primarily governed by regional diversity and soil nitrogen availability, suggesting that nutrient supply mediates spatial variation in community assembly across regions. Conclusions Our findings challenge the universality of the classical LDG pattern and advance our understanding of the mechanisms shaping global soil biodiversity patterns.

Soil-borne microbiomes harbour vital genetic resources, encompassing gene richness and dissimilarity, an indicator of the degree of diversity and distinctiveness exhibited by the gene repertoire of the soil microbiome. These genetic resources underlie key microbial traits and enzyme profiles that support terrestrial ecosystem functioning, including nutrient cycling, plant productivity and soil health. Despite their importance, global patterns and protection status of such resources remain poorly resolved. Here we compile 1,609 soil metagenomes to map global patterns of microbial functional gene richness and dissimilarity. Hotspots of gene dissimilarity concentrate in tropical regions, whereas gene richness hotspots are more widely distributed. Areas combining both high richness and dissimilarity are rare, covering only 5.5% of the terrestrial surface of the Earth, while drylands emerge as prominent hotspots for microbial traits and enzyme profiles. Fewer than 25% of hotspots for soil microbial genetic resources fall within designated protected areas. Notably, the global patterns of soil microbial functional profiles are largely decoupled from those of bacterial and fungal taxonomic diversity, suggesting that taxon-based conservation policies may not adequately safeguard belowground genetic resources. Our work provides an actionable baseline to integrate soil microbial genetic resources into global biodiversity targets and protected-area planning. Soil microbiomes harbour diverse genetic resources that underpin their capacity to provide crucial ecosystem services (for example, nutrient cycling). Here the authors map global hotspots of soil microbial genetic resources from 1,609 soil metagenomes to inform actionable targets for their protection.

Accurate phage–host prediction underpins ecological interpretation and experimental validation of uncultivated phages, yet most current approaches rely heavily on metagenome-assembled genomes (MAGs). This reliance implicitly assumes that MAG-level quality metrics, such as completeness and contamination, ensure scaffold-level correctness. Here, we demonstrate that this assumption is frequently violated. Tetranucleotide frequency (TNF) analyses reveal that CRISPR-associated regions often diverge compositionally from their host genomes, increasing the risk of misbinning, while experimentally validated phage–host genome pairs show consistent TNF separation between phages and their hosts, challenging compositional binning assumptions. Through controlled simulations, we further show that the incorporation of substantial amounts of TNF-matched, non-host phage sequences into high-quality MAGs does not substantially alter standard completeness and contamination estimates, rendering such errors largely undetectable. Together, these results expose a systematic and underappreciated source of bias in MAG-based phage–host inference and highlight the need for explicit scaffold-level validation beyond conventional genome-quality metrics. We further propose a practical scaffold-level validation framework that integrates structural linkage and taxonomic consistency to improve the reliability of phage–host inference from MAGs.

Soil microorganisms are the biological engines of terrestrial ecosystems. The development of molecular technologies has overturned the ‘everything is everywhere’ paradigm, revealing that at the strain-level, soil microbes exhibit distinct biogeographical patterns governed by environmental selection, dispersal, diversification, and drift. In this review, we first summarize the major progresses in soil microbial biogeography. Then, we discuss the potential limitations, including the constraints of space-for-time substitution, the disconnect between statistical correlation and ecological causality, and the inherent challenges in mapping and scaling microbial distributions. Finally, we propose a strategic framework centered on three directions: (1) Enhancing prediction, by integrating microbial traits into Earth System Models to forecast the responses of soil microbes and their associated functions to global change; (2) Deciphering mechanisms, by bridging multi-omics approaches with rigorous experimental validation to establish causality between structure and function; and (3) Achieving manipulation, by leveraging synthetic ecology and core taxa to engineer microbiomes for practical application in One Health initiatives. Moving from pattern description to mechanistic understanding and functional manipulation will enable soil microbial biogeography to provide actionable solutions for sustainability in a rapidly changing world.

Rice blast, caused by the fungal pathogen Pyricularia oryzae, remains one of the most destructive diseases threatening global rice production. Although the deployment of resistant cultivars is widely regarded as the most effective and sustainable control strategy, resistance based solely on host genetics often has limited durability due to the rapid adaptation of the pathogen. Increasing evidence suggests that plant-associated microbial communities contribute to host health and disease resistance, yet the role of seed-associated microbiota in shaping rice blast resistance remains insufficiently understood. In this study, we investigated seed endophytic bacterial communities across multiple indica–japonica hybrid rice varieties from the Yongyou series that exhibit contrasting levels of resistance to rice blast. By integrating amplicon sequencing, we identified distinct seed bacterial assemblages associated with blast-resistant and blast-susceptible varieties were identified. Notably, the microbial communities in blast-resistant varieties exhibited significantly higher Shannon index, with a median value of 3.478 compared to 2.654 in susceptible varieties (p < 0.001), indicating a greater diversity and more balanced community structure compared to those in susceptible varieties. Several bacterial taxa consistently enriched in resistant varieties showed negative ecological associations with P. oryzae, both at the local scale and across publicly available global metagenomic datasets. These findings indicate that seed endophytic bacterial communities are non-randomly structured in relation to host resistance phenotypes and may contribute to rice blast resistance through persistent ecological interactions with the pathogen. This work highlights the potential importance of seed-associated microbiota as intrinsic components of varietal resistance and provides a microbial perspective for improving durable disease resistance in rice breeding programs.

Methane cycling in soils is governed by the balance between microbial methane production and oxidation, yet the functional redundancy of these processes across ecosystems remains poorly understood. Here, we analyzed 2531 global soil samples spanning five ecosystem types to investigate the biogeography, environmental drivers, and ecological significance of functional redundancy in methane-cycling communities. We quantified the normalized functional redundancy (nFR) of overall methane metabolism, methanogenesis, and methane oxidation using a genomic content network approach. Functional redundancy varied substantially across ecosystems and between processes, with methane oxidation exhibiting significantly higher nFR than methanogenesis. Forest soils exhibited the highest overall methane-metabolism redundancy, whereas wetlands and paddy fields showed lower redundancy, indicating that functional redundancy is not directly predicted by taxonomic diversity or abundance. Environmental factors such as soil moisture and sand content exerted opposing effects on methanogenesis and methane-oxidation redundancy. Overall methane-metabolism redundancy was primarily driven by the methanotrophic guild and maintained by a limited set of core genera, with rare taxa contributing disproportionately. Across ecosystems, higher methane-metabolism redundancy was associated with methane flux stability under warming, suggesting that microbial functional redundancy may buffer ecosystem methane cycling against climate perturbation. Together, these results demonstrate that functional redundancy in methane-cycling communities is ecosystem-specific, process-dependent, and linked to the stability of soil methane flux, highlighting microbial functional redundancy as an important but underappreciated dimension of methane-cycle regulation under climate change.

Abstract Accurate phage–host prediction underpins ecological interpretation and experimental validation of uncultivated phages, yet most current approaches rely heavily on metagenome-assembled genomes (MAGs). This reliance implicitly assumes that MAG-level quality metrics, such as completeness and contamination, ensure scaffold-level correctness. Here, we demonstrate that this assumption is frequently violated. Tetranucleotide frequency (TNF) analyses reveal that CRISPR-associated regions often diverge compositionally from their host genomes, increasing the risk of misbinning, while experimentally validated phage–host genome pairs show consistent TNF separation between phages and their hosts, challenging compositional binning assumptions. Through controlled simulations, we further show that the incorporation of substantial amounts of TNF-matched, non-host phage sequences into high-quality MAGs does not substantially alter standard completeness and contamination estimates, rendering such errors largely undetectable. Together, these results expose a systematic and underappreciated source of bias in MAG-based phage–host inference and highlight the need for explicit scaffold-level validation beyond conventional genome-quality metrics. We further propose a practical scaffold-level validation framework that integrates structural linkage and taxonomic consistency to improve the reliability of phage–host inference from MAGs.

Anaerobic oxidation of methane (AOM) can mitigate global warming by converting methane into either carbon dioxide or soil organic carbon (SOC). However, it is unclear whether soil viruses influence AOM and the associated carbon sequestration processes. Here we quantify the impact of viruses on the carbon sink formed through AOM and reveal the underlying mechanisms using C-13 labelling and metagenomics. Our findings show that viruses can substantially increase SOC associated with AOM and alter the amount of iron-bound organic carbon (Fe-bound OC). However, the magnitude and direction of these effects depend on the type of virus. Specifically, mitomycin C-induced viruses contributed 54.5% of the newly formed SOC and caused a 73.1% loss of C-13-Fe-bound OC by facilitating the survival of related microbes, such as iron-reducing bacteria, under anaerobic conditions. In contrast, free extracellular viruses increased both C-13-SOC (+115.5%) and C-13-Fe-bound OC (+35.8%) via viral lysis, due to the high affinity of lysate dissolved organic matter for sorption onto iron(hydr)oxides. These results highlight the substantial impact of soil viruses on the stabilization of methane-derived carbon in soils, and advance our understanding of viral-controlled soil carbon biogeochemical cycles.

Microbial dehalogenation governs the fate of persistent pollutants frequently detected globally-organohalides (OHs) in soils, and is a critical process for mitigating threats to ecosystem health. However, conventional research focused on rare specialist bacteria cannot account for the widespread, low-level OH turnover observed globally. This review applies a potential evolutionary ecology framework, reframing dehalogenation as a community-wide trait that originated from versatile ancestral enzymes and disseminated via horizontal gene transfer (HGT). This evolutionary history highlights the important ecological role of abundant non-specialists, such as methanogens, which capable of perform dehalogenation at certain condition as a secondary metabolic function. These organisms face metabolic trade-offs, allocating resources between primary growth and secondary dehalogenation. This resource partitioning links OH fate to major biogeochemical cycles, challenging traditional remediation approaches for complex environmental media such as soil. To advance the field, future research must quantify in situ fluxes using multi-omics and stable isotope techniques, and develop predictive models to elucidate these trade-offs. Ultimately, we advocate a shift from simple bioaugmentation to predictive ecological engineering—managing soils by manipulating environmental conditions and designing synthetic microbial consortia. This strategy aims to enhance polluted soil resilience and multifunctionality, aligning remediation with the broader goals of sustainable soil health.

Arsenic (As), a toxic element widespread in paddy soils worldwide, is mobilized by microbial processes, posing risks to environmental quality, food safety and human health. The rice rhizosphere is a dynamic environment with day-night cycles in chemical conditions and microbial activity. However, how arsenic itself changes over these daily cycles remains unexplored. Here we conduct metatranscriptomic and biogeochemical analyses in a greenhouse study to investigate the diurnal rhythms of As dynamics in the rice rhizosphere. We observed consistent diel fluctuations in arsenite (As(III)) concentrations, increasing from 1.8 to 2.9 mg l(-1) at night, alongside a 24.9% rise in ferrous iron (Fe(II)). Redox potential decreased to similar to 100 mV at night, promoting As/Fe reduction. Transcriptional activity of key functional genera involved in dissimilatory As/Fe reduction (for example, Geomobilimonas and Geobacter) increased at night, reflected in higher transcript abundances of reduction genes (arrA, omcS, omcZ and mtrC), without corresponding changes in relative abundance. These patterns were confirmed in a field study. Under constant darkness, these diel patterns disappeared. Together, these findings suggest managing rice cultivation to align with natural daily cycles may reduce contamination risks and optimize nutrient management.

Filamentous fungi harbor a vast potential for secondary metabolite (SM) biosynthesis, yet the biological functions of numerous biosynthetic gene clusters (BGCs) remain obscure. In Fusarium graminearum, a devastating cereal pathogen, SMs are best known as virulence factors, but their broader contributions to fungal physiology are poorly defined. Here, we present a genome-scale functional dissection of 53 predicted SM-BGCs by constructing a knockout library targeting cluster backbone genes and systematically quantifying 24 phenotypic traits, generating 1,272 phenotypic measurements. This dataset reveals that secondary metabolism is not a dispensable metabolic burden; instead, SM-BGCs are broadly integrated into vegetative growth, asexual development, and abiotic stress adaptation. Transcriptome analyses further uncover pronounced spatiotemporal regulation and tissue-dependent requirements of SM-BGCs during infection of wheat heads versus coleoptiles, thereby revealing an ecological dimension of pathogenesis. Mechanistic investigation identified two previously uncharacterized clusters, PKS-type BGC36 and NRPS-type BGC47, as critical for full virulence. BGC36 positively regulates deoxynivalenol (DON) biosynthesis, whereas disruption of BGC47 compromises cell wall/membrane stress tolerance and is associated with reduced phosphorylation of the kinase Mgv1, impaired DON-toxisome formation, and reduced DON production. Together, our findings establish fungal secondary metabolism as a core physiological buffer against environmental fluctuations that supports homeostasis and virulence, and they provide a comprehensive genetic resource for dissecting the chemical biology of Fusarium.

Albic soils are a typical problematic soil type distributed worldwide. These soils are characterized by a thin humus layer, low organic matter content, nutrient insufficiency, and weak microbial activity. Therefore, microbial-based approaches hold great potential for the amelioration of Albic soils. This review synthesizes microbial characteristics, influencing factors, amelioration mechanisms, and related technical efficacy of Albic soils. Microbial communities of Albic soils exhibit distinct regional characteristics, with Acidobacteriota and Proteobacteria dominating the bacterial community. Reasonable agricultural management practices—including deep plowing and subsoil mixing, combined organic fertilization and straw return—can increase microbial biomass by 62–248% and enhance enzyme activities by 12–303%, ultimately increasing crop yield by 1.5–13%. Such practices drive fertility enhancement and ecological functional improvement in Albic soils. Inoculation with functional microbes (e.g., Arbuscular Mycorrhizal Fungi, Trichoderma) alleviates Albic soil acidification by 1.1–3.8%, activates recalcitrant nutrients, and accelerates Soil Organic Matter (SOM) decomposition. Through extracellular polymeric substance secretion, such inoculation promotes aggregate formation, improving soil permeability and structural stability. However, challenges remain for current research, including difficult microbial agent colonization, unstable amelioration effects, and a lack of long-term field studies. Future research should utilize bio-omics technologies, artificial intelligence, and big data technologies to analyze microbial functions and regulate soil quality for cultivated land improvement and sustainable agriculture development.

Respiratory burst oxidase homolog D (RBOHD)-dependent reactive oxygen species (ROS) in Arabidopsis are well known to suppress pathogen colonization, but their influence on beneficial microbes remains unclear. Here, we found that the beneficial rhizobacterium Pseudomonas anguilliseptica was significantly less enriched in the rhizosphere of rbohD mutants than in that of wild-type plants. Conversely, elevated rhizosphere ROS levels, either triggered by pretreatment with pathogenic Dickeya solani bacteria or caused by mutations in ROS scavenging genes (e.g., in apx1 and cat2 mutants), promoted the rhizosphere recruitment of P. anguilliseptica. This promoting effect was abolished by catalase treatment. In situ microfluidic chemotaxis assays further revealed that P. anguilliseptica exhibits a chemotactic response to low concentrations of hydrogen peroxide ( ≤ 500 nM), accompanied by upregulated expression of chemotaxis- and motility-related genes. Notably, inoculation of P. anguilliseptica effectively suppressed D. solani-induced disease symptoms, and this protective effect was attenuated by catalase treatment. Collectively, these findings reveal a previously unrecognized role of ROS in recruitment beneficial microbiota to enhance plant growth and suppress disease symptoms. ROS produced by RBOHD play a crucial role in shaping the rhizosphere microbiome. This study reveals that rhizosphere ROS attract the beneficial bacterium Pseudomonas anguilliseptica to the roots, thereby promoting plant growth and suppressing disease symptoms in Arabidopsis. In Arabidopsis, ROS produced by RBOHD not only inhibit pathogens but also recruit beneficial rhizobacteria, enhancing plant resistance to disease.