Plant-Soil-Microbiome Interactions: Mechanisms, Advances, and Challenges in Sustainable Agriculture and Healthy Agroecosystems

Jacek Panek¹Agata Gryta¹Wiktoria Maj¹Mateusz Mącik¹Karolina Oszust¹Giorgia Pertile¹Michał Pylak¹Dominika Siegieda¹Moritz Hallama²Ryusuke Hatano³Ellen Kandeler²Shamina Imran Pathan⁴Giacomo Pietramellara⁴Eligio Malusà⁵Jerzy Weber⁶Katarzyna Turnau⁷Sylwia Różalska⁸Magdalena Frąc^1*

• ¹Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
• ²Universitat Hohenheim, Stuttgart, Germany
• ³Hokkaido Daigaku, Sapporo, Japan
• ⁴Universita degli Studi di Firenze, Florence, Italy
• ⁵Instytut Ogrodnictwa - Panstwowy Instytut Badawczy, Skierniewice, Poland
• ⁶Uniwersytet Przyrodniczy we Wroclawiu, Wrocław, Poland
• ⁷Uniwersytet Jagiellonski w Krakowie, Kraków, Poland
• ⁸Uniwersytet Lodzki, Łódź, Poland

The focus of this article is to summarise 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 utilised 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 modelling 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.