Trichoderma yunnanense strain TM10 was isolated from rhizosphere soil of rice plants cultivated under system of rice intensification (SRI) practises in West Java, Indonesia. It exhibits significant potential as a plant growth promoter and biocontrol agent in rice plants. Although this strain has shown promise in promoting plant growth and suppressing phytopathogens under in vitro and in planta conditions, there is still a lack of genomic data to elucidate the molecular mechanisms underlying its plant growth-promoting and biocontrol capabilities. This study reports the whole genome sequence of T. yunnanense strain TM10. The genome of the fungus was sequenced using the MGI DNBSEQ-G400 high-throughput sequencing platform. The assembled genome of T. yunnanense strain TM10 was approximately 36 Mbp in length, comprising 385 contigs with a GC content of 48 % and a sequencing coverage of 43.8×. This genomic data provides a foundation for harnessing the plant growth-promoting and biocontrol potential of this strain. The complete genome sequence has been deposited at the National Center for Biotechnology Information (NCBI) under Bioproject accession number PRJNA1181959, BioSample ID SAMN44575400, and genome accession number JBIYZQ000000000. These data are valuable for further research into the biotechnological potential of this strain and for exploring the molecular mechanisms underlying its plant growth-promoting and biocontrol activities.
Climate change has intensified abiotic stresses such as drought, heat, and salinity, posing major threats to agricultural productivity and global food security. Conventional strategies to improve crop tolerance often face limitations in efficiency, sustainability, and environmental adaptability, underscoring the need for innovative approaches. This review focuses on the plant holobiont, which views plants and their associated microbiomes as an integrated functional unit in governing stress adaptation. Abiotic stress can disrupt plant-associated microbial communities, leading to dysbiosis and reduced holobiont resilience. Beneficial microorganisms, including plant growth-promoting rhizobacteria, endophytes, and arbuscular mycorrhizal fungi, can enhance stress tolerance by improving nutrient acquisition, regulating phytohormone signaling, strengthening antioxidant defenses, maintaining osmotic balance, and modulating stress-responsive gene expression. Emerging evidence suggests that these interactions contribute to the establishment of holobiont stress adaptation through biochemical signaling, microenvironmental modification, and epigenetic regulation, enabling plants to respond more effectively to recurrent stress. Advances in microbiome engineering, particularly through the development of synthetic microbial communities (SynComs), offer promising opportunities to restore microbial functions and enhance crop resilience under changing climatic conditions. The integration of multi-omics technologies, artificial intelligence, and precision agriculture is expected to accelerate the development of microbiome-based solutions for sustainable crop production. Collectively, microbiome engineering represents a promising, environmentally sustainable strategy to enhance the holobiont's adaptive resilience and improve long-term plant performance under abiotic stress.