Microbial Symbioses Under Agricultural Pressure: From Community Structure Profiling to Synthetic Microbiome Construction

Agricultural soils sustain intricate symbiotic networks among plants, bacteria, fungi, and other microorganisms, including plant growth-promoting rhizobacteria (PGPR), nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and endophytes, that collectively drive nutrient cycling, organic matter formation, aggregate stability, and pathogen suppression. Intensive farming practices, characterized by excessive synthetic chemical inputs, monoculture regimes, and continuous tillage, progressively disrupt these critical symbioses, leading to soil acidification, organic matter depletion, and loss of beneficial microbial diversity. The collapse of functional plant-microbe partnerships not only degrades soil quality but also threatens long-term agricultural productivity and ecosystem resilience.Recent advances in high-throughput sequencing and multi-omics technologies now enable precise, culture-independent profiling of soil symbiotic communities, linking their composition and assembly to functional soil quality indicators such as enzyme activities, nutrient mineralization rates, carbon sequestration capacity, and suppression of soilborne pathogens. These monitoring insights are opening new pathways toward the rational design of synthetic microbiomes—engineered consortia of functionally complementary symbionts capable of restoring disrupted soil functions. However, a critical gap remains: translating community-level monitoring data into predictable, stable, and function-specific synthetic microbiomes that can reliably establish and perform in competitive native soil environments.This Research Topic aims to synthesize current knowledge on soil plant-microbe and microbe-microbe symbioses in agricultural contexts, and to advance monitoring frameworks and synthetic microbiome strategies for sustainable soil management. We welcome Original Research, Reviews, Mini Reviews, Methods, Perspectives, and Opinion articles addressing, but not limited to, the following themes:o Diversity, assembly, and host specificity of beneficial soil symbionts in agricultural systemso Mechanisms of symbiosis establishment, competitive colonization, and partner selection in the rhizosphere and bulk soilo Multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) for monitoring soil symbiotic community structure and functiono Linking symbiotic community dynamics to soil quality indicators: enzyme activities, nutrient cycling, carbon storage, and pathogen suppressiono Principles and strategies for designing synthetic microbial consortia with defined symbiotic functions targeting soil restorationo Integration of synthetic symbiotic communities into soil bioremediation and circular agriculture frameworks Topic editors: Dongming Wu, Peng Zhang, Shang Wang, Mengmeng Chen, Jiwei Luo Source: https://www.frontiersin.org/research-topics/82515/microbial-symbioses-under-agricultural-pressure-from-community-structure-profiling-to-synthetic-microbiome-construction