Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab

Abstract

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Micronutrients and Soil Microorganisms in the Suppression of Potato Common Scab

“…Similarly, CS-suppressive soils were enriched in total Mg compared to CS-conducive soils [27]. A connection of Mg and CS suppression was also found in a resistant potato cultivar that also had a higher Mg content in the periderm compared to a susceptible cultivar [28]. However, in another study, the number of thaxtomin gene copies (txtB) representing the quantity of the pathogens in potato periderm was found positively correlated to periderm Mg content [32].…”

“…Ca relationships to CS are some of the most studied, in combination with soil pH. High total calcium levels in soil and also composed exchangeable Ca are often positively correlated with CS severity [17,27,28,37]. However, addition of Ca and K to acidic and neutral soils increased CS severity only in the neutral soil, showing that pH and Ca:K ratio are more important than the content of Ca in soil alone [38].…”

“…The composition of microbial communities in the rhizosphere is also influenced by the invasion of pathogens, which poses consequences not only for the particular disease but also for the functioning of the whole community [127]. Then, suppressive soils may act differently than conducive soils with respect to microbial community changes [22,28]. Furthermore, the suppressive effect is differentiated between induced suppressive soils of long-term monoculture and natural suppressive soils that undergo regular crop rotation [27,31,128,129].…”

“…Induced suppressive soils for CS contained a higher proportion of Acetobacteraceae, Bacillaceae and Lysobacter (Xanthomonadaceae) but also non-pathogenic Streptomyces (Actinobacteria) and lower proportions of some Acidobacteria, Nocardioidaceae and Pseudomonadaceae [130]. The naturally suppressive soils were enriched in Pseudomonadaceae, Bradyrhizobiaceae, Acetobacteraceae and Paenibacillaceae, which are all families of known plant growth-promoting microbes [28]. Some of the taxa occurring in suppressive soils were also enriched in soils supplemented with organic matter, which also led to CS suppression.…”

“…Most of the generally known microbial activities connected to plant disease control were also observed in CS-related interactions, particularly in suppressive soils [27][28][29][30]. Extensive research was conducted with supplementation of antagonistic strains to soil or improvement of the whole microbial communities using organic substrates reviewed in [31].…”