Interactions between plants and soil shaping the root microbiome under abiotic stress

Abstract

Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

“…Actinobacteria are grampositive (G + ), monoderm bacteria. G + bacteria are thought to accumulate under drought, and the cell wall is thought to improve cell drought tolerance by increasing their ability to resist desiccation [6,46]. Our data also show that G + bacteria were signi cantly enriched in the rhizosphere under drought conditions (Fig.…”

“…Similarly, Santos-Medellín et al reported root-associated community in rice in which several OTUs belonging to the phyla Actinobacteria and Chloro exi were signi cantly enriched under drought, whereas OTUs from the phylum Acidobacteria and classes Deltaproteobacteria were generally depleted [42]. Of note, many works focusing on the root bacterial microbiomes of rice [42], sorghum [43], and diverse lineages of plant species [44,45] under drought stress have reported enrichment of bacteria from the phylum Actinobacteria [6]. Actinobacteria are grampositive (G + ), monoderm bacteria.…”

“…Drought not only decreases the water available to soil microbial communities and plants but also changes in nutrient availability, speci cally N and P uptake [6]. Moreover, microbial communities control many biogeochemical processes [7].…”

“…The plant creates nutrient-rich conditions by exuding complex carbon compounds, mucilage, sloughed root border cells and microbe signaling hormones to recruit the soil microbiota to the rhizosphere. Then, host-plant genetic factors screen a subset of microbiota into the root endosphere [6,17,18]. Plants shape their associated microbiota by employing a combinatorially complex system of receptors and signals; conversely, the microbiota can have wide-ranging effects on host plant tness, including on host drought tolerance and nutrient uptake [17,[19][20][21][22].…”

Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering

“…Western diet versus Mediterranean or vegetarian diet) [18] or addition of specific nutrients such as resistant starch [19]. In plants, alterations in soil microbiomes happen in response to biotic and abiotic stresses, such as those listed above [20]. More than one hundred dysbioses have been related to human diseases [21], and disease-suppressing soils -defined by their microbial composition -are studied to promote plant resistance to pathogens [22].…”