Abstract
The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.
Highlights
The domestication of plants began with the identification of wild plant species exploitable for food, animal feed, or other domestic purposes
MOLECULAR FINGERPRINTS OF 16S rRNA GENES OF THE BACTERIAL COMMUNITIES Molecular fingerprints were performed by Single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes amplified from DNA obtained from all samples to gain first insight into the bacterial communities
Bacterial fingerprints of potting soil samples (SB-PS and PS) comprised fewer but more dominant bands compared to the SSCP profiles from WB-coastal drift lines (CS), sugar beets cv. BERETTA (SB)-CS, and CS, where a higher number of SSCP bands were detected (Figure S1)
Summary
The domestication of plants began with the identification of wild plant species exploitable for food, animal feed, or other domestic purposes. Selective crop breeding programs are mainly oriented toward increasing food production and high-yielding varieties, percentage of usable plant parts, and resistance against diseases (Akhalkatsi et al, 2012). In contrast to many other crops, the ancestor of domesticated sugar beets (trivial name: wild or sea beet) differs significantly from domesticated sugar beet lines (Dohm et al, 2014). It shows high variation at the vernalization B-locus, and most of the plants are perennials in contrast to all cultivated lines, which have a biennial life cycle enabling seed production (Dohm et al, 2014). Several studies analyzing sugar beet-associated bacterial communities already exist (Zachow et al, 2008; Mendes et al, 2011; Shi et al, 2014), little is known about the relation of the microbiome to existing cultivars and their wild relatives
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