Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant–microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly, microbial community functions, plant–microbe communication, and microbiome-mediated stress resistance in agricultural ecosystems. Current approaches to plant-associated soil microbiome manipulation and engineering, including microbial inoculants, synthetic microbial communities (SynComs), microbiome transplantation, rhizosphere steering, and synthetic biology-based interventions, are critically examined. The review further discusses the growing role of metagenomics, metabolomics, metatranscriptomics, machine learning (ML), and precision agriculture technologies in improving microbiome characterization, prediction, and management. Particular attention is given to the application of microbiome-based solutions for sustainable crop production, nutrient management, biological control, climate-smart agriculture, and ecosystem restoration. Despite significant progress, challenges related to field-scale variability, colonization stability, biosafety, regulatory frameworks, and data integration continue to limit large-scale implementation. Future advances in precision microbiome engineering are expected to combine ecological principles, multi-omics technologies, AI, and synthetic biology to develop predictive and resilient microbiome-based solutions for sustainable and climate-resilient agriculture.
A. Sadanov, G. Baimakhanova, B. Baimakhanova et al.· Microorganisms· 0 citations
This study compared the effects of a single-strain microbial inoculant, Brevundimonas diminuta NH1, and a synthetic microbial community (FSQN) composed of Bacillus amyloliquefaciens FH1, Ochrobactrum tritici S112, Gluconacetobacter liquefaciens QZR14, and B. diminuta NH1 on the rhizosphere soil and root microbiomes of rice (Oryza sativa) to investigate how these inoculation strategies differ in microbiome regulation and growth promotion. High-throughput sequencing was used to assess microbial α- and β-diversity, community composition, predicted bacterial and fungal functions, and correlations between microbiome shifts and rice growth traits. We found that neither inoculant significantly affected microbial α-diversity, but both significantly altered β-diversity in rhizosphere soil and roots. Compared with the control, the single-strain treatment mainly enriched Mortierella, Glaciozyma, and Bovista in rhizosphere soil, and Clostridium sensu stricto, Cronobacter, Exiguobacterium, Kosakonia, and Pseudomonas in roots. The synthetic community mainly enriched Mortierella, Tausonia, Fusarium, and Glomerella in rhizosphere soil, and Exiguobacterium, Pseudomonas, and Rhodotorula in roots. Functional prediction indicated that the single-strain inoculant enhanced sulfur respiration, ureolysis, xylanolysis, and denitrification-related functions, whereas the synthetic community enhanced ectomycorrhizal, endomycorrhizal, and plant-saprotrophic functions. Shoot height and dry weight were may positively associated with enriched taxa and functions, particularly Mortierella, Exiguobacterium, and endophytic functions.
B. Kossalbayev, Jingjing Wang, Mo Wei et al.· Functional Plant Biology· 0 citations
This study examines the influence of varying vermicompost application rates (0 %, 10 %, and 20 % of the substrate volume) on the growth, development, and yield of cucumber (Cucumis sativus) and tomato (Solanum lycopersicum) cultivated under greenhouse conditions in the Turkestan region of the Republic of Kazakhstan. The research is conducted within the framework of chemical and technological transformation of organic matter in soil substrates. The results indicate that the incorporation of vermicompost leads to notable changes in the physicochemical characteristics of the substrate, including an increase in organic matter content, stabilization of substrate pH, and improved availability of key macronutrients such as nitrogen, phosphorus, and potassium. These modifications contribute to more active mineralization processes and enhanced biochemical transformation of nutrients, which in turn stimulate root system development, promote vegetative growth, and increase crop yield. The highest overall productivity was recorded at a vermicompost application rate of 20 %, demonstrating its maximum agronomic effectiveness. At the same time, the 10 % application rate also showed a consistently positive effect, suggesting that it represents a balanced and economically viable option for greenhouse cultivation. Overall, the findings support the use of vermicompost as an efficient organic component in the chemical technology of soil substrate improvement for greenhouse vegetable production.
Nurlan Akhmetov, D. Yuldashbek, Yokubzhan Satanov et al.· Hydrometeorology and ecology· 0 citations