Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a “back to the roots” framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
Highlights
Plants rely on their rhizosphere microbiome for functions and traits related to plant growth, development and health (Berendsen et al 2012; Mendes et al 2013)
Cook et al (1995) postulated that natural selection resulted in only few examples of plant genetic resistance against belowground pathogens and that plant rely, in part, on the natural defence provided by rhizosphere microorganisms
At least in part, on the rhizosphere microbiome as a product of natural selection, modern cultivars of crop plants may have lost some of the traits needed to recruit host-specific root microbiota as compared to their wild relatives, which are genetically more diverse and adapted to pre-agricultural soils (Wissuwa et al 2009; Bulgarelli et al 2013)
Summary
Plants rely on their rhizosphere microbiome for functions and traits related to plant growth, development and health (Berendsen et al 2012; Mendes et al 2013). Members of the rhizosphere microbiome harbour a range of beneficial properties contributing to nutrient acquisition, enhanced stress tolerance, protection against soil borne pathogens and host immune regulation (Berendsen et al 2012; Bakker et al 2013; Mendes et al 2013; Turner et al 2013a; Berg et al 2014; Lakshmanan et al 2014) In this context, Cook et al (1995) postulated that natural selection resulted in only few examples of plant genetic resistance against belowground pathogens and that plant rely, in part, on the natural defence provided by rhizosphere microorganisms. The lack of a co-evolutionary trajectory between plants, microbial communities and pathogens in dissimilar agricultural landscapes, made human interventions even more critical to maintain a healthy and productive crop (Fig. 2)
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