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The intricate interplay between SMCs and agroecosystems has garnered substantial attention in recent decades due to its profound implications for agricultural productivity, ecosystem sustainability, and environmental health. Understanding the distribution of SMCs is complemented by investigations into their functional roles within agroecosystems. Soil microbes play pivotal roles in nutrient cycling, organic matter decomposition, disease suppression, and plant‒microbe interactions, profoundly influencing soil fertility, crop productivity, and ecosystem resilience. Elucidating the functional diversity and metabolic potential of SMCs is crucial for designing sustainable agricultural practices that harness the beneficial functions of soil microbes while minimizing detrimental impacts on ecosystem services. Various molecular techniques, such as next-generation sequencing and high-throughput sequencing, have facilitated the elucidation of microbial community structures and dynamics at different spatial scales. These efforts have revealed the influence of factors such as soil type, land management practices, climate, and land use change on microbial community composition and diversity. Advances in high-throughput methodological strategies have revolutionized our ability to characterize SMCs comprehensively and efficiently. These include amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics, which provide insights into microbial taxonomic composition, functional potential, gene expression, and protein profiles. The integration of multiomics approaches allows for a more holistic understanding of the complex interactions within SMCs and their responses to environmental perturbations. In conclusion, this review highlights the significant progress made in mapping, understanding the distribution, elucidating the functions, and employing high-throughput methodological strategies to study SMCs in agroecosystems.

Secondary metabolites, bioactive compounds produced by living organisms, can unveil symbiotic relationships in nature. In this study, soilborne entomopathogenic nematodes associated with symbiotic bacteria (Xenorhabdus stockiae and Photorhabdus luminescens) were extracted from solvent supernatant containing secondary metabolites, demonstrating significant inhibitory effects against E. coli, S. aureus, B. subtilus, P. mirabilis, E. faecalis, and P. stutzeri. The characterization of these secondary metabolites by Fourier transforms infrared spectroscopy revealed amine groups of proteins, hydroxyl and carboxyl groups of polyphenols, hydroxyl groups of polysaccharides, and carboxyl groups of organic acids. Furthermore, the obtained crude extracts were analyzed by high-performance liquid chromatography for the basic identification of potential bioactive peptides. Gas chromatography–mass spectrometry analysis of ethyl acetate extracts from Xenorhabdus stockiae identified major compounds including nonanoic acid derivatives, proline, paromycin, octodecanal derivatives, trioxa-5-aza-1-silabicyclo, 4-octadecenal, methyl ester, oleic acid, and 1,2-benzenedicarboxylicacid. Additional extraction from Photorhabdus luminescens yielded functional compounds such as indole-3-acetic acid, phthalic acid, 1-tetradecanol, nemorosonol, 1-eicosanol, and unsaturated fatty acids. These findings support the potential development of novel natural antimicrobial agents for future pathogen suppression.