Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

Abstract

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.

Antibiotic resistance genes in manure-amended soil and vegetables at harvest

“…Previous studies have reported appreciable numbers of antibiotic resistant members on the consumer-ready vegetables, such as lettuce and spinach leaves [17,46,47]. Root endophytes can be recruited from common soil bacteria and survived in the interior of the root [48,49], which allow ARGs transferring from soil into plant. Microorganisms can also be colonized in leaf tissue as leaf endophytes [50].…”

Spatio Temporal Influence of Isoflavonoids on Bacterial Diversity in the Soybean Rhizosphere

“…When combined with quantitative and high-resolution bacterial profiling methods such as pyrosequencing, some of these variations can be directly correlated to the level of silencing to better interpret the results. Previous studies used sonication to either separate rhizosphere soil from nonrhizosphere soil or to isolate one region of the rhizosphere (Bulgarelli et al 2012;Doi 2007). We used successive sonication to reproducibly isolate different soil fractions with specific bacterial composition.…”

“…A number of studies have identified the influence of plant genotype and the environment on the composition and diversity of rhizosphere microbiota (Bulgarelli et al 2012;Gottel et al 2011;Peiffer et al 2013;Philippot et al 2013). In addition, either the roles of specific compounds in rhizodeposits, the roles of specific cellular transport machinery on rhizosphere microbial diversity, or both have been investigated (Bais et al 2006;Walker et al 2003).…”

Endophytic actinomycetes: promising source of novel bioactive compounds

“…It is well known that many kinds of bacteria live in and around plant roots, including the phyla Proteobacteria, Actinobacteria (Gram-positive high G+C bacteria), Bacteroides and Verrucomicrobia, which have been detected by pyrosequencing. [3][4][5] Over 40 genera of filamentous Actinobacteria (actinomycetes) have been detected from Triticum aestivum roots alone by terminal restriction fragment length polymorphism. 6 Bacteria exist on the surface and inside of plant roots, as demonstrated by fluorescence in situ hybridization, scanning electron microscopy or detection of target genes.…”

“…6 Bacteria exist on the surface and inside of plant roots, as demonstrated by fluorescence in situ hybridization, scanning electron microscopy or detection of target genes. [7][8][9][10] Numerous bacteria live in rhizospheres, up to 10 6 cells per mm 3 , including filamentous bacteria with actinomycetes accounting for an estimated 4% of the total. 9 This shows the relationship that exists between actinomycetes and plants.…”