Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

Abstract

Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.

Microbial interactions: ecology in a molecular perspective

“…Reinhold-Hurek et al, 50 proposed a model for microorganism colonization. In bulk soil, the microbial community presents a great diversity and is influenced only by soil type and environmental factors.…”

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

“…For example, symbionts such as the N 2 -fixing Bradyrhizobium japonicum and pathogens such as Phytophthora sojae are attracted by specific plant flavonoids (Philippot et al, 2013). In more general terms, a step-wise selection model has been proposed for root microbiota differentiation (Bulgarelli et al, 2013; Reinhold-Hurek et al, 2015). In the initial soil, edaphic factors (e.g., soil pH and structure) determine the composition of the soil microbial community.…”

“…The first selection step takes place in the rhizosphere, the thin soil layer directly surrounding the roots, where rhizodeposits and root cell wall features promote the growth of mainly organotrophic microorganisms and thereby initiate a shift in the soil microbiome. In a second and third step, a host genotype-dependent selection takes place close to and within the root corpus, respectively, and thereby fine-tunes community profiles thriving on the rhizoplane (i.e., the root surface) and within plant roots (Bulgarelli et al, 2013; Reinhold-Hurek et al, 2015). …”

Effects of strategic tillage and plant hormone treatments on wheat-associated microbial communities

“…Two-and three-step models for the plant's recruitment of bacteria have been proposed (Bulgarelli et al, 2013;Reinhold-Hurek et al, 2015). It seems that the ectorhizosphere, rhizoplane and plant immune system may serve as the first, second and the third screening points, respectively.…”

“…Surface sterilization by disinfecting with sodium hypochlorite and ethanol as well as mechanical removal of microbes closely attached to the root surface by vigorous shaking with glass beads or ultrasonication have been used for this purpose Reinhold & Hurek, 1989). The chemical disinfection seems to be more effective but may underestimate the presence of bacteria as it damages DNA (Reinhold-Hurek et al, 2015). A diverse range of bacteria have been isolated from surface-sterilized plant tissues, such as roots, tubers, stems, leaves, seeds, flowers, fruits and legume nodules (Compant et al, 2011;Deng et al, 2011;Marques et al, 2015;Rosenblueth & Martínez-Romero, 2006;Truyens et al, 2015).…”