INTRODUCTION
Soil microbial communities are crucial to the “one health” concept because they connect the health of ecosystems, the microbial communities associated with plants, animals, and humans (Fig. 1), functioning as a ‘second genome’ (an ‘extended genotype’ or an ‘eco-holobiont’). The microbial communities of different organisms are interconnected in a manner that influences the fitness and performance of the different prokaryotic and eukaryotic organisms (Banerjee & van der Heijden, 2023). Similar functions can be attributed to microbial communities in the human gut and plant rhizosphere including nutrient uptake, modulating host immunity, prevention of pathogen colonization, and improving overall health. Harnessing the second genome for food production can also lower the environmental impact and residual effect of chemicals on the food chain because they influence nutrient recycling and pollutant degradation, thereby increasing crop resilience to climate variabilities (Trivedi, Batista, Bazany, & Singh, 2022).
Plants have evolved efficient strategies to avoid infection by microbial pathogens such as restricting microbe entry and multiplication. However, plant-microbiome associations go far beyond pathogens, the overall diversity of microbial symbionts, commensals, and amensals being pivotal to the overall health of the biosphere. In particular, the root-driven sequestration of carbon is attributable to the exchange and transport of nutrients between the roots of perennial plants, particularly trees, and rhizosphere bacteria and fungi. Soil microbes are the key drivers of carbon storage in soils, surpassing other soil processes. Since, microbial carbon use efficiency (CUE) is a major determinant of global soil organic carbon storage, understanding the plant-microbe interactions that underpin processes such as CUE can improve nature-based solutions to climate change.
The plant-microbe community includes a diverse range of endophytes, that asymptomatically colonize the internal tissues of almost all plants (endosphere), as well as inhabiting the outside (ectosphere) plant organs (Ghatak, Chaturvedi, Waldherr, Subbarao, & Weckwerth, 2023; Sohrabi, Paasch, Liber, & He, 2023). The plant-beneficial bacteria (PBB), arbuscular mycorrhizal fungi (AMF), and plant-growth promoting microorganisms (PGPM) stimulate plant growth and development under optimal and stress conditions through a range of mechanisms (Fig. 2). Rhizosphere establishment and the persistence of beneficial microbes rely on efficient root colonization wherein they feed on the carbohydrates and other exudes. In turn, they assist in the uptake of essential nutrients, particularly nitrogen (N), phosphorus (P) and potassium (K), and produce phytohormones such as indole-3-acetic acid (IAA), cytokinins (CK) and gibberellins, and also siderophores and thereby enhance plant fitness and resilience to environmental stresses (Bai et al., 2022; Ghatak et al., 2023; Turner, James, & Poole, 2013), such as salt (Chakraborty et al., 2021; Li, La, Zhang, Gao, & Tian, 2021) and drought (Bazany, Wang, Delgado-Baquerizo, Singh, & Trivedi, 2022; de Vries, Griffiths, Knight, Nicolitch, & Williams, 2020).
Seed microbiota including epiphytes that inhabit the seed coat and endophytes that colonize the endosphere, including the embryo, endosperm, aleurone, and perisperm, are central to plant establishment (Nelson, 2018; Nelson, Simoneau, Barret, Mitter, & Compant, 2018). This microbial community not only pioneers next-generation functions in the seedling establishment but also facilitates subsequent microbial colonization from the spermosphere (Fig. 2A). Microbe-assisted solutions to combat the negative impact of climate change may improve plant survival, in a world faced with an increased frequency of heat waves, floods, droughts and contamination of toxic heavy metals. However, a much deeper understanding of inter-organism communication is required to tailor the microbial community for maximizing plant growth and productivity, especially under realistic field scenarios. Building on a firm foundation of previous reviews on this topic such as Saad et al. (2020); Ke et al. (2021) and Banerjee & van der Heijden (2023), we present a synthesis of current research information, while highlighting the constraints to practical feasibility.