AP26193911 – Scientific substantiation, development and testing of synthetic microbiomes from bacteria producing ACC deaminase to reduce ethylene stress in plants

Objective of the project – to explore metagenomic and metatranscriptomic data from extreme ecosystems to identify and expand a collection of microorganisms with unique metabolic capabilities, forming a foundation for the development of innovative and environmentally sustainable biofuel technologies.

Relevance: The relevance of this project is driven by the growing impact of climate change, including rising temperatures, drought, and soil salinization, which negatively affect plant growth and reduce agricultural productivity. Stress-induced ethylene production further suppresses plant development, while intensive use of chemical fertilizers degrades soil quality and fertility. Kazakhstan faces an urgent need to transition toward environmentally friendly agriculture, making organic farming and biofertilizers a strategic priority. However, existing biofertilizers, especially imported ones, are often ineffective under the specific conditions of saline and arid regions. The project addresses this gap by developing synthetic microbiomes based on ACC deaminase-producing bacteria adapted to extreme environments, which can enhance plant stress tolerance and growth. Therefore, the project is highly relevant as it supports sustainable agriculture, reduces environmental impact, and contributes to food security and the development of local biotechnologies.

Scientific supervisor: Ph.D., Associate Professor, Kossalbayev Bekzhan Duisenbiuly

Expected and achieved results: The project successfully carried out a comprehensive collection and analysis of soil samples from extreme ecosystems across Kazakhstan. A total of 20 soil samples were collected from diverse environments, including saline, alkaline, sandy, thermophilic, and heavy metal-contaminated soils in Almaty, Turkestan, Zhambyl, and Kyzylorda regions. These samples provided a representative coverage of extreme ecological niches suitable for identifying plant growth-promoting bacteria (PGPB). All samples underwent microbiological analysis, including 16S rRNA sequencing to assess taxonomic diversity and identify potentially beneficial microorganisms associated with ACC deaminase activity. Additionally, deep metagenomic sequencing was performed, revealing that at least three samples had a high abundance of the acdS gene and related markers. These samples were selected as priority sources for further strain isolation. Based on transcriptomic profiles, the most metabolically active microbial taxa were identified within the extreme soil microbiomes. From selected samples, pure cultures of plant growth-promoting bacteria were successfully isolated using multiple nutrient media, including TSB, LB, DF, and minimal DF. More than 500 bacterial isolates were obtained using an automated QPix system, ensuring efficient and high-throughput selection. The isolates were identified through 16S rRNA gene analysis and grouped into approximately 50 species. The dominant genera included Aeromonas, Bacillus, Pseudomonas, Enterobacter, Halomonas, and others known for their biotechnological potential. These results created a solid foundation for selecting high-activity ACC deaminase-producing strains and developing synthetic microbial communities. Overall, the project achieved significant progress in identifying and isolating promising bacterial resources for sustainable agricultural applications.