Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity of the fungal community significantly increased, while Bray–Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.

Macadamia decline poses a serious economic threat to the macadamia industry. It exhibits either a slow decline due to infection by Kretzschmaria clavus or Ganoderma lucidum, or a quick decline caused by pathogens like Phytophthora spp., Lasiodiplodia spp., Neofusiccocum spp., Nectria rugulosa, Xylaria arbuscula, Phellinus gilvus, Acremonium recifei, and Rosellinia spp. Chemical strategies, resistant cultivars, and agronomic measures have been widely adopted to control macadamia decline, but effective biological control measures have rarely been applied. This paper proposes two key steps for implementing biological control strategies, i.e., the isolation and selection of biological control agents from healthy plants, or from the disease-suppressive soil for the construction of synthetic microbial communities, and the integration of synthetic microbial communities with various strategies, including seed coating, root dipping, seedling substrate, soil drenching, foliar spraying, and application as a bio-organic fertilizer. By adopting these strategies, we aim to provide proactive and efficient approaches for combating macadamia decline and safeguarding the health of macadamia orchards.

Sugarcane smut, caused by the fungal pathogen Sporisorium scitamineum, leads to significant economic losses in the global sugarcane industry. Bio-organic fertilizers (BF) offer a promising and sustainable strategy to mitigate smut incidence and enhance sugarcane growth. While the application of BF is known to modulate root exudates and rhizosphere microbial community structure, thereby promoting disease resistance, the precise mechanisms underpinning BF-mediated suppression of sugarcane smut remain largely unclear. This study investigated the microbiological mechanisms of smut suppression using a pot experiment, comparing a novel BF treatment (composted substrate enriched with Bacillus subtilis, Bacillus altitudinis, Bacillus cereus, Trichoderma harzianum, and Trichoderma longibrachiatum, biochar, and calcium carbonate) with a control receiving only conventional organic fertilizer. BF application significantly increased plant height (by 95.2%), dry weight (137.5%), fresh weight (253.3%), and sugar content (43.1%) relative to the control. Furthermore, the BF treatment enhanced catalase activity by 167.8% and peroxidase activity by 102.3% in sugarcane leaves, while the control effectiveness against the incidence of smut disease reached 88.0%. Analysis of the rhizosphere microbiome revealed that BF application significantly altered microbial alpha- and beta-diversity. Specifically, the BF treatment notably enriched beneficial genera such as Pseudomonas and Meyerozyma. Beta-diversity analysis revealed distinct microbial community structures in BF-treated rhizosphere soil compared to the control. Correlation and random forest analyses identified Pseudomonas and Meyerozyma as key taxa that were positively associated with sugarcane growth parameters and negatively correlated with smut incidence. These findings elucidate the dual role of this novel BF in enhancing sugarcane growth and suppressing smut incidence through the strategic reshaping of the rhizosphere microbiome.

The effectiveness of microbial inoculants in agriculture is often limited by their unstable colonization in dynamic soil environments. We investigated the impact of application timing and continuity of a four-member synthetic microbial community (SynCom) on pepper (Capsicum annuum L.) productivity and rhizosphere microbiome dynamics under greenhouse conditions. Four treatments were included: no inoculation (control), single inoculation at the seedling stage (T1; 5 days post-emergence), single inoculation at the potting stage (T2; 14 days post-transplant), and sustained inoculation at both stages (T3). T3 significantly enhanced plant dry weight (113.4%), root activity (267.8%), fruit sugar (43.9%), and yield (29.0%) relative to the control; and profoundly reshaped the rhizosphere microbiome, enriching functional pathways for nutrient cycling (e.g., phosphorus, nitrogen, and potassium metabolism) and phytohormone synthesis (e.g., indoleacetic acid pathway). Co-occurrence network analysis indicated a significant alteration in microbial interaction patterns, revealing a new community architecture with key taxa such as Neocosmospora, Dyella and the Rhizobium group emerging as central hubs in the T3 network. Our findings underscore that application continuity is a critical factor for optimizing bio-inoculant efficacy, providing a strategy to enhance crop productivity through microbiome engineering in sustainable agriculture.