Omics Bioprospecting of Beneficial Microorganisms in Sustainable Agriculture

Sergio de los Santos-Villalobos is the director of the Microbial Resource Biotechnology Laboratory at Instituto Tecnológico de Sonora, Mexico, where his research spans microbial ecology, plant–microorganism–soil interactions, microbial inoculant production, and agro-ecosystem conservation using isotopic techniques. His work integrates ecological, physiological, biochemical, and genetic approaches, from in vitro studies to field-level application. He has organized and taught numerous workshops, served as President of international scientific congresses, and spoken as a plenary speaker at conferences worldwide. His contributions have been recognized by Mexico's National System of Researchers (Level 2), a special mention in the 2013 AgroBio Award, and the 2014 Tecnos Award for contributions to biotechnology. He serves on expert panels focused on soil conservation and microbial inoculant development and currently acts as Associate Editor for several journals in the field. Fannie Isela Parra Cota earned her PhD in Plant Biotechnology from the Center for Research and Advanced Studies of the National Polytechnic Institute (IPN) and is currently a Principal Researcher at the National Institute of Forestry, Agriculture, and Livestock Research (INIFAP). Her work focuses on agricultural biotechnology, particularly the study of plant–microorganism–soil interactions, the isolation and characterization of microorganisms with an agro-biotechnological approach, and the resistance mechanisms of wheat and maize to biotic stress (phytopathogenic fungi) and abiotic stress (drought, salinity, and heat). She is a Level I member of Mexico's National System of Researchers (SNI), contributing to advancements in sustainable agriculture and crop resilience. Valeria Valenzuela Ruiz is a researcher at the Laboratory of Microbial Resource Biotechnology at the Technological Institute of Sonora (ITSON), specializing in transcriptomic analysis of beneficial bacteria linked to biocontrol activity and plant growth promotion. She earned her Ph.D. from ITSON, where her work focused on the biocontrol mechanisms of Bacillus species against phytopathogenic fungi, with the aim of advancing sustainable agricultural practices. Her research integrates transcriptomic analysis and whole-genome mining to understand and enhance beneficial microbial traits in agriculture. Dr. Valenzuela Ruiz continues to contribute to the advancement of microbial biotechnology, promoting the development of bioinoculants and effective solutions for crop protection and growth enhancement.

• Section 1: Bioprospecting and omic sciences in agriculture1. Bioprospecting and its role in agriculture2. Importance of beneficial microorganisms in crop production and soil health3. Omics sciences and their agricultural applications4. Overview of agricultural challenges addressed by microbial bioprospecting through omics techniques5. Genomics: identifying plant beneficial microbial genes6. Transcriptomics: understanding gene expression in plant–microbe interactions7. Proteomics: studying functional proteins in soil and plant health8. Metabolomics: identifying bioactive compounds for crop protection9. Metagenomics: exploring soil and rhizosphere microbial communitiesSection 2: Bioprospecting plant-growth-promoting bacteria10. Role of rhizobacteria (PGPRs) in soil fertility and crop yield improvement11. Microalgae and nitrogen-fixing bacteria, including cyanobacteria, and their genomic insights12. Phosphate-solubilizing bacteria and their role in sustainable fertilization13. Potassium, calcium, and other nutrient-solubilizing bacteria and their role in crop production14. Biocontrol bacteria against plant pathogens in the omics era15. Polyphasic taxonomy for discovering novel taxa16. Metagenomic approaches for discovering novel bacterial action modesSection 3: Fungal bioprospecting for sustainable agriculture17. Mycorrhizal fungi and their role in enhancing plant nutrient uptake18. Omics-based discovery of biocontrol fungi against crop diseases19. Endophytic fungi and their potential for plant stress resistance20. Bioprospecting phyllosphere fungi for sustainable agriculture21. Deciphering soil fungi for biocontrol of plant diseases22. Trichoderma as a biological control agent23. Fungal secondary metabolites for natural pesticides and biofertilizersSection 4: Beneficial insects and viruses in agricultural biocontrol24. Microbial symbionts of insects and their role in natural pest control25. Metagenomic studies on insect microbiota for sustainable crop protection26. Omics-driven discovery of insect-based biofertilizers27. Bacteriophages for biocontrol of bacterial plant pathogens28. Viral interactions in soil microbiomes and their agricultural implications29. Potential of plant-associated viruses in enhancing crop resilienceSection 5: Success stories, challenges, and future trends in omic-driven agricultural microbial innovations30. Omics contributions to agricultural microbial bioprospecting31. Ethical and regulatory aspects of bioprospecting for agriculture32. Safety, stability, and scalability of microbial-based agricultural solutions33. Integrating multi-omics approaches for precision agriculture34. Advancements in synthetic biology for agricultural microbial engineering35. The role of omics in climate-resilient crop production36. The future of microbiome-based sustainable agriculture