Microbiome-Driven Strategies for Alleviation of Biotic and Abiotic Stresses in Agriculture

Agricultural systems worldwide are increasingly challenged by both biotic stresses, such as pathogens, pests, and weeds, and abiotic stresses, including drought, salinity, temperature extremes, and nutrient deficiencies. Collectively, these stresses threaten global food security by causing substantial yield and quality losses. Traditional responses, like the overuse of agrochemicals, offer temporary relief but contribute to long-term ecological damage, such as soil degradation, decreased biodiversity, and the development of resistant pathogen strains. Genetic modification has provided solutions for single gene traits, but falls short in addressing broader ecological and acceptance issues. In this context, microbiome-based strategies present a promising, sustainable alternative. Through natural, eco-friendly enhancements of crop resilience, these strategies leverage stress-tolerant cultivars and wild plant relatives that host beneficial microbiota. These microbe-mediated capabilities can be transferred to crops lacking such microbiomes, offering more robust stress resilience.

This Research Topic aims to gather the latest research focused on plant-microbe interactions under stress conditions. By promoting innovative microbiome-based strategies, the goal is to enhance crop resilience, minimize chemical inputs, and promote sustainable agricultural practices. Specific interests include studies on field or greenhouse trials that demonstrate the impact of microbiome interventions on crop performance under various stress conditions, as well as omics-based investigations into the microbiome structures and functions in stress-tolerant plants, such as xerophytes and halophytes. Such efforts are crucial in developing scalable and eco-friendly solutions for agriculture in the era of climate change.

The scope of this Research Topic is to explore microbiome-driven agricultural innovations while illuminating their range and limitations. Articles addressing, but not limited to, the following themes are welcome:

• Harnessing rhizosphere and endophytic microbiomes to bolster crop resilience to stress

• Exploring plant microbiomes for biocontrol of pathogens and pests

• Utilizing plant-associated microbiomes to enhance soil health under stress

• Investigating Metagenome Assembled Genomes (MAGs) of uncultured microbial groups for stress resilience

• Field evaluation of microbiome-based biostimulants to boost crop performance under various stresses

We invite submissions of original research papers, reviews, mini-reviews, methods, and perspectives articles related to these topics.

Keywords: Microbiome, Amplicon sequencing, MAGs (Metagenome Assembled Genomes), Core Microbiome, Host-Microbe interactions, ASVs (Amplicon Sequence Variants), OTUs (Operation Taxonomic Units), 16S rRNA gene, Salinity stress, Drought stress, Pathogen stress

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.