Tianjie Yang

Strigolactones (SLs) are carotenoid-derived hormones that regulate plant development and abiotic stress responses, but their role in regulating plant–microbe interactions remains unclear. Here, we show that Arabidopsis thaliana loss-of-function mutants of two SL biosynthetic genes, MORE AXILLARY GROWTH 3 (MAX3) and MAX4, exhibit opposite responses to soil-borne pathogen Ralstonia solanacearum, with max3 mutants displaying enhanced resistance, whereas max4 mutants are hypersusceptible. Exogenous SL analog rac-GR24 restores resistance in max4 mutants supporting a role for canonical SL-dependent immunity, while max3 mutants mediated resistance is SL-independent. Multi-omics analyses suggest that MAX3 deficiency is associated with enhanced abscisic acid (ABA) and flavonoid pathways under natural conditions, coinciding with the enrichment of beneficial Pseudomonas in rhizosphere. Both in vitro and in planta validations suggest that the ABA-flavonoid axis cooperatively enhances Pseudomonas-mediated niche competition and antibiotic biosynthesis, thereby potentially contributing to pathogen suppression. Our findings support a model in which MAX3 is associated with the modulation of rhizosphere-mediated defense, linking hormone signaling, secondary metabolism, and microbiome assembly in the context of soil-borne disease resistance.

Fungal pathogens threaten the health of humans, animals, and plants. ITS sequencing offers an effective approach for detecting fungal pathogens; however, a comprehensive pathogen database and associated tailored pipeline are still lacking. This study introduces the multiple fungal pathogen detection (MFPD) pipeline, which incorporates an accurate and high‐speed sequence alignment algorithm for broad‐habitat pathogen identification. The curated MFPD database includes 95 660 full‐length ITS sequences from 4924 reported fungal pathogen species. In silico experiments show that the full‐length ITS achieves the highest accuracy in pathogen detection (average 99.34%), outperforming both the ITS1 and ITS2 subregions. Benchmarking against existing tools, including FUNGuild, FungalTraits, and ISHAM‐ITS, shows that MFPD achieves the highest F1 scores in mock communities (0.89 for both plant and human–animal pathogens) and detects the broadest spectrum of pathogenic taxa in real samples. In addition to identifying causal pathogens, MFPD can also detect coinfecting pathogens in biological and environmental samples. Together, our work supports pathogen surveillance across diverse sectors, including clinical, agricultural, and livestock systems within a One Health framework.

Potassium (K) is a vital nutrient for fruit quality in pears ( Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype‐dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE ( Pyrus betulaefolia and Pyrus ussuriensis ) using integrated pot and long‐term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low‐K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB , and COG3158 ) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia ‐grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K‐deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low‐K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K⁺ transporter (e.g., NRT2.4 ) expression, and activating calcium‐dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype‐driven enrichment of Bacillaceae ‐dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome‐based bioinoculants and breeding of “microbiome‐responsive” rootstocks for sustainable fruit production under K‐limiting conditions.

Background: Rare microbial communities represent an important component of biodiversity in soil ecosystems, co‐existing with abundant species to drive ecosystem multifunctionality and maintain its stable operation. However, knowledge remains limited regarding the geographical distribution patterns and potential driving factors of microorganisms, especially rare species, in soil ecosystems. Result: Using the CycloneSEQ WT sequencing platform, we systematically investigated soil bacterial communities across 160 sampling sites in southern Jiangxi Province. Abundant and rare taxa exhibited significant compositional differences. Abundant taxa displayed stronger distance‐decay relationships and were primarily driven by climatic factors. In contrast, rare taxa demonstrated higher sensitivity to spatial factors, while the influence of soil pH was substantially stronger on rare taxa than on abundant taxa. While stochastic processes predominantly governed community assembly for both taxa, rare taxa showed greater susceptibility to homogeneous selection, whereas abundant taxa were more strongly influenced by variable selection and dispersal limitation. Network analysis indicated that abundant taxa formed tighter connections internally, while rare taxa established more extensive but looser interactions with other nodes in the network. Conclusions: This study reveals different biogeographic patterns between abundant and rare bacterial taxa. Abundant taxa exhibited strong distance‐decay driven by environmental heterogeneity and dispersal limitation, whereas rare taxa showed weak distance‐decay governed by homogeneous selection, providing theoretical support for maintaining microbial diversity in agricultural soils.

Understanding how plant-associated microbiomes resist phytopathogen invasion remains a key challenge in natural ecosystems. Here we combined genome-scale metabolic models with synthetic community experiments, both in vitro and in planta, to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization profiles to fully capture their metabolic capacities. Trophic interactions inferred from models effectively predicted pathogen invasion outcomes across diverse microbial communities and nutrient environments. Importantly, considering both substrate and metabolite features provided a more holistic understanding of pathogen suppression. In particular, cross-feeding metabolites within the native community emerged as crucial yet often overlooked predictors of community resistance, disproportionally favouring native species over invaders. This study lays the foundation for designing disease-resistant microbiomes, with broad implications for mitigating pathogen exposure in diverse environments.

Bacterial wilt caused by Ralstonia solanacearum is one of the most severe plant diseases all over the world. Currently, many scientists are using SynCom (s

Root exudates are key mediators in maintaining plant health by mediating interactions with the rhizosphere microbiome. Plants release specific exudates to defend against pathogens, either directly by inhibiting pathogen growth or indirectly through alterations in the microbial community. However, the mechanisms by which root exudates influence the rhizosphere microbiome to enhance plant resistance remain poorly understood. In this study, we evaluated the effects of 23 root exudates on the growth of the pathogen Ralstonia solanacearum and tomato bacterial wilt. Seventeen of the exudates reduced the disease index, with most having neutral or even promotive effects on R. solanacearum growth. Notably, succinic acid (SA) completely suppressed bacterial wilt without directly affecting the pathogen or tomato plants in the absence of the rhizosphere microbiome. We further explored the impact of SA on the rhizosphere bacterial community in both tomato rhizosphere and bulk soil. Only the bacterial community in the rhizosphere responded significantly to SA addition, with indicator species and network analyses identifying Sphingomonas sp. WX113 as the key taxa associated with this response. A subsequent greenhouse experiment showed that co-applying Sphingomonas sp. WX113 with SA achieved 100% biocontrol efficiency, outperforming either treatment alone. In vitro assays further demonstrated that SA enhanced the antagonistic activity of Sphingomonas sp. WX113 against R. solanacearum. Our findings emphasize the host-mediated role of root exudates, such as succinic acid, in selectively promoting beneficial Sphingomonas sp., thereby enhancing plant resistance to bacterial wilt. These results offer new perspectives on the combination of beneficial microbes and their matching compounds for soil-borne diseases management.