Rhizosphere bacterial communities associated with disease suppressiveness stages of take‐all decline in wheat monoculture

Abstract

International audience• The decline of take-all disease (Gaeumannomyces graminis var. tritici), which may take place during wheat monocropping, involves plant-protecting, rootcolonizing microorganisms. So far, however, most work has focused on antagonistic fluorescent pseudomonads. Our objective was to assess the changes in rhizobacterial community composition during take-all decline of field-grown wheat. • The study was based on the development and utilization of a taxonomic 16S rRNA-based microarray of 575 probes, coupled with cloning–sequencing and quantitative PCR. Plots from one experimental field grown with wheat for 1 yr (low level of disease), 5 yr (high level of disease) or 10 yr (low level of disease, suppressiveness reached) were used. • Microarray data discriminated between the three stages. The outbreak stage (5 yr) was mainly characterized by the prevalence of Proteobacteria, notably Pseudomonas (Gammaproteobacteria), Nitrosospira (Betaproteobacteria), Rhizobacteriaceae, Sphingomonadaceae, Phyllobacteriaceae (Alphaproteobacteria), as well as Bacteroidetes and Verrucomicrobia. By contrast, suppressiveness (10 yr) correlated with the prevalence of a broader range of taxa, which belonged mainly to Acidobacteria, Planctomycetes, Nitrospira, Chloroflexi, Alphaproteobacteria (notably Azospirillum) and Firmicutes (notably Thermoanaerobacter). • In conclusion, take-all decline correlated with multiple changes in rhizobacterial community composition, far beyond the sole case of pseudomonads

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

“…3), but also at phylum (Table 6) and genus levels (Tables S1 & S2). Sanguin et al (2009) showed that Verrucomicrobia was one of the prevalent phyla during the outbreak of wheat take-all disease, which was different from the finding in the present study that the abundance of this phylum was higher in healthy (5.06 % in rhizosphere soil and 0.40 % in roots) than diseased plants (2.85 % in rhizosphere soil and 0.32 % in roots). This may be explained by the low relative abundance of Verrucomicrobia accounted for the total sequences, 3.96 % in rhizosphere soil and 0.36 % in roots on average, variation in the initiator of different soil-borne diseases (Van Elsas et al 2002) and difference in land management (Rescia et al 1994).…”

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

“…As others have found in community-based analyses of suppressive soils (Sanguin et al, 2009;Mendes et al, 2011;Rosenzweig et al, 2012), no single phylum was uniquely associated with disease suppression in the strawberry wilt microbiome (Table 1 and Supplementary Tables S4, S5 and S6). Instead, our identification of antibiotic-producing Streptomyces as participating in the suppression of Fusarium wilt also required culture-based approaches that have long implicated specific microorganisms in those instances where the etiology of specific soil suppressiveness has been at least partially resolved.…”

“…have long been known to contribute to the suppression of common scab of potato caused by pathogenic Streptomyces spp. (Bowers et al, 1996;Lorang et al, 1989), community-based studies of such soils have shown that multiple taxa are associated with suppression but have not resolved functionally active agents at the species or subspecies level in either pathosystem (Sanguin et al, 2009;Rosenzweig et al, 2012). A third study, guided by a community-based approach and on which our work was modeled, also identified multiple phyla in a soil suppressive of damping-off disease caused by Rhizoctonia solani, but culturebased methods were needed to identify specific strains of an antibiotic-producing Pseudomonas inhibitory to the pathogen (Mendes et al, 2011).…”

“…These are soils in which, because of their microbial makeup and activity, a pathogen does not establish or persist, establishes but causes little or no disease or establishes and causes disease at first but then the disease declines with successive cropping of a susceptible host crop (Cook and Rovira, 1976;Raaijmakers and Weller, 1988;Weller et al, 2002;Sanguin et al, 2009;Kwak and Weller, 2012). Suppressive soils have reemerged as a major topic of research because of the growing emphasis on sustainable and organic agriculture, recognition of the need to reduce the use of chemical pesticides and the fact that they provide control of soil-borne pathogens with little or no offfarm inputs.…”

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

“…However, if we consider bacterial-fungal biofilms, it is clear that fungi can promote distinct differences in bacterial development by contributing to a distinctive ecological niche, within which bacteria exhibit physiological differences, such as resistance to antibiotics, stress, and an altered expression of virulence genes, compared to free-living bacteria (153,154,306). There is also body of literature that points to the influence of fungi on bacterial community structure at both the taxonomic and functional levels, notably in the mycorrhizosphere and pathorhizosphere (119,332,370) but also in other contexts, such as cheese and wine production (2,58,173,261,386). However, it is a significant challenge to make the link between cell-cell communication in BFIs and community-level organization.…”