Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions

Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.