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Microorganisms
Volume 14
Issue 8
10.3390/microorganisms14081648
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Review

Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications

by
Amankeldi K. Sadanov
1,
Gul Baimakhanova
1,
Baiken B. Baimakhanova
1,
Saltanat Orazymbet
1,
Irina Ratnikova
1,
Irina Smirnova
1,
Mamytova Nurgul
2,
Sydykbekova Raikhan
2,
Bekzhan D. Kossalbayev
3,4,
Gulzat S. Aitkaliyeva
3,* and
Ayaz M. Belkozhayev
3,5,*
1
LLP “Research and Production Center for Microbiology and Virology”, Almaty 050010, Kazakhstan
2
Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
3
Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan
4
Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh Turkish University, Turkistan 161200, Kazakhstan
5
M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty 050012, Kazakhstan
*
Authors to whom correspondence should be addressed.
Microorganisms 2026, 14(8), 1648; https://doi.org/10.3390/microorganisms14081648
Submission received: 2 July 2026 / Revised: 21 July 2026 / Accepted: 24 July 2026 / Published: 28 July 2026
(This article belongs to the Special Issue Insect–Plant–Microbe Interactions and Sustainable Agriculture)
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Abstract

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.
Keywords: plant-associated soil microbiome; rhizosphere microbiome; microbiome manipulation; microbiome engineering; plant–microbe interactions; synthetic microbial communities; sustainable agriculture plant-associated soil microbiome; rhizosphere microbiome; microbiome manipulation; microbiome engineering; plant–microbe interactions; synthetic microbial communities; sustainable agriculture
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MDPI and ACS Style

Sadanov, A.K.; Baimakhanova, G.; Baimakhanova, B.B.; Orazymbet, S.; Ratnikova, I.; Smirnova, I.; Nurgul, M.; Raikhan, S.; Kossalbayev, B.D.; Aitkaliyeva, G.S.; et al. Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications. Microorganisms 2026, 14, 1648. https://doi.org/10.3390/microorganisms14081648

AMA Style

Sadanov AK, Baimakhanova G, Baimakhanova BB, Orazymbet S, Ratnikova I, Smirnova I, Nurgul M, Raikhan S, Kossalbayev BD, Aitkaliyeva GS, et al. Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications. Microorganisms. 2026; 14(8):1648. https://doi.org/10.3390/microorganisms14081648

Chicago/Turabian Style

Sadanov, Amankeldi K., Gul Baimakhanova, Baiken B. Baimakhanova, Saltanat Orazymbet, Irina Ratnikova, Irina Smirnova, Mamytova Nurgul, Sydykbekova Raikhan, Bekzhan D. Kossalbayev, Gulzat S. Aitkaliyeva, and et al. 2026. "Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications" Microorganisms 14, no. 8: 1648. https://doi.org/10.3390/microorganisms14081648

APA Style

Sadanov, A. K., Baimakhanova, G., Baimakhanova, B. B., Orazymbet, S., Ratnikova, I., Smirnova, I., Nurgul, M., Raikhan, S., Kossalbayev, B. D., Aitkaliyeva, G. S., & Belkozhayev, A. M. (2026). Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications. Microorganisms, 14(8), 1648. https://doi.org/10.3390/microorganisms14081648

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