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.