# Plant–soil–microbiome interactions: mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems

## TL;DR

This paper reviews how plant-soil-microbiome interactions support sustainable agriculture and healthy ecosystems by improving soil quality and plant resilience.

## Contribution

The paper synthesizes recent advances in understanding microbiome functions and their role in climate-resilient agriculture.

## Key findings

- Microbiomes enhance plant health and soil quality through nutrient cycling and stress mitigation.
- Biofertilizers and microbial consortia improve soil properties and reduce greenhouse gas emissions.
- Multi-omics approaches are critical for predicting plant diseases and modeling soil microbiome changes.

## Abstract

The focus of this article is to summarize current knowledge of plant-associated microbiomes, which play a key role in plant health and in maintaining soil quality. Such microbiomes, comprising bacteria, fungi, archaea, algae, nematodes, and protists, perform various functions, including nutrient transformation, pathogen protection, and stress mitigation. Microbial communities are commonly used as an indicator of ecosystem health. Soil microbiome diversity depends on environmental factors (including biotic and abiotic stresses), which can alter microbial composition, thereby modifying microbial interactions and plant resilience. Biofertilizers, biopreparations, and microbial inoculants or consortia have been utilized in agriculture to enhance soil properties, such as microbial diversity and enzymatic activity, and to prime plant immune responses, thereby promoting plant growth and health. Biofertilizers can significantly help plants adapt to environmental stresses and climate change, mitigating drought stress and reducing greenhouse gas emissions. Recent advances in DNA sequencing technologies, the computing power available to scientists, and the development of bioinformatics tools have made microbial community studies widely accessible. These tools enable the research and modeling of changes in the soil microbiome, plant disease susceptibility, and soil health. Multi-omics approaches to microbiomes are key to characterizing the microbiome and predicting plant diseases. Future research should focus primarily on understanding the interactions among soil, plants, and microbiomes. This approach will help develop climate-resilient plants and improve the health and functionality of agroecosystems. Key efforts closely aligned with the European Union’s goals and biodiversity strategies for sustainable agriculture and soil health restoration, as presented in this review, include studying the structures and functions of soil microbiomes, developing new assays, and designing and investigating microbial consortia to restore healthy communities. These strategies address contemporary challenges in agriculture, including vertical and urban farming and superfood production.

Infographic illustrating soil microbiome ecosystem services for climate change mitigation, featuring interconnected diagrams of carbon sequestration, stress resistance, biodiversity enhancement, and GHG emission mitigation, with detailed soil research methodologies and examples like intercropping, manuring, and agroforestry.