Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

Abstract

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.

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).…”

The Minimal Rhizosphere Microbiome

“…38) provide a very good 'model system'to unravel and design the optimal microbial consortium to protect plants from infection by soil-borne pathogens. Studies by Kyselkova et al (2009);Mendes et al (2011) and Rosenzweig et al (2012) on soils suppressive to different fungal and bacterial plant pathogens pinpointed multiple bacterial genera that were more abundant in the suppressive than in the corresponding disease conducive soils. Although the potential role of the identified bacterial communities in disease suppressiveness was addressed for only a few genera, these studies do provide a framework to reconstruct microbial consortia for disease control.…”

Pumpkin powdery mildew disease severity influences the fungal diversity of the phyllosphere

“…Previous studies have reported that there are usually more unique 245 OTUs in the rhizosphere of healthy soil than in diseased soil (Rosenzweig et al, 2012). In the 246 phyllosphere, there may be same phenomenon as the soil.…”