Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe’s occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops.

The plant holobiont—an integrated unit of the host and its microbiome—has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles—priority effects, keystone taxa, and functional redundancy—that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling—including genome-scale metabolic models, dynamic flux balance analysis, and machine learning—to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.

Declining soil quality and microecological imbalances were evaluated in larch plantations in this study. One potential solution to this problem is the cultivation of mixed coniferous and broad-leaved plantations. However, it is unclear whether and how soil microbial community structure and nutrient cycling function would be affected by mixed plantations and soil depths. In this study, we used high-throughput sequencing technology to investigate bacterial 16S and fungal ITS regions for comparisons of soil microbial diversity among plantation types (aLarix gmeliniipure plantation, aFraxinus mandshuricapure plantation, aLarix–Fraxinusmixed plantation within theLarixrow, theFraxinusrow, and between theLarixandFraxinusrows) and soil depths (0–10, 10–20, and 20–40 cm). These data were used to evaluate variations in microbial communities and nutrient cycling function with the determining environmental factors. Our results indicated that bacteria had a stronger spatial dependence than did fungi, while plantation types significantly affected the fungal community. The relative abundance ofGaiellaceae, as well as bacterial ligninolysis, nitrate ammonification, and nitrite ammonification functions significantly increased with increasing soil depth. Compared with other plantations, the relative abundance ofInocybaceaewas significantly higher in theLarixplantation. Distance-based redundancy analysis (db-RDA) showed thatGaiellaceaeandInocybaceaeabundances were positively correlated with ammonium nitrogen content, available phosphorus content, and phosphatase activity. Our findings indicate that variations in soil available phosphorus are closely related to the relative abundances ofGaiellaceaeat different soil depths andInocybaceaein different plantation types. Mixed plantations might change the availability of soil phosphorus by controlling the relative abundance ofInocybaceae. We recommend that fungal community changes be considered in the sustainable management of mixed plantations.

Stress caused by pathogens strongly damages plants. Developing products to control plant disease is an important challenge in sustainable agriculture. In this study, a heat-killed endophytic bacterium (HKEB), Bacillus aryabhattai, is used to induce plant defense against fungal and bacterial pathogens, and the main defense pathways used by the HKEB to activate plant defense are revealed. The HKEB induced high protection against different pathogens through the salicylic and jasmonic acid pathways. We report the presence of gentisic acid in the HKEB for the first time. These results show that HKEBs may be a useful tool for the management of plant diseases.