The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens

Abstract

BackgroundAlthough the plant microbiome is crucial for plant health, little is known about the significance of the seed microbiome. Here, we studied indigenous bacterial communities associated with the seeds in different cultivars of oilseed rape and their interactions with symbiotic and pathogenic microorganisms.ResultsWe found a high bacterial diversity expressed by tight bacterial co-occurrence networks within the rape seed microbiome, as identified by llumina MiSeq amplicon sequencing. In total, 8362 operational taxonomic units (OTUs) of 40 bacterial phyla with a predominance of Proteobacteria (56%) were found. The three cultivars that were analyzed shared only one third of the OTUs. The shared core of OTUs consisted mainly of Alphaproteobacteria (33%). Each cultivar was characterized by having its own unique bacterial structure, diversity, and proportion of unique microorganisms (25%). The cultivar with the lowest bacterial abundance, diversity, and the highest predicted bacterial metabolic activity rate contained the highest abundance of potential pathogens within the seed. This data corresponded with the observation that seedlings belonging to this cultivar responded more strongly to the seed treatments with bacterial inoculants than other cultivars. Cultivars containing higher indigenous diversity were characterized as having a higher colonization resistance against beneficial and pathogenic microorganisms. Our results were confirmed by microscopic images of the seed microbiota.ConclusionsThe structure of the seed microbiome is an important factor in the development of colonization resistance against pathogens. It also has a strong influence on the response of seedlings to biological seed treatments. These novel insights into seed microbiome structure will enable the development of next generation strategies combining both biocontrol and breeding approaches to address world agricultural challenges.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0310-6) contains supplementary material, which is available to authorized users.

Mycobiota of maize seeds revealed by rDNA‐ITS sequence analysis of samples with varying storage times

“…Among the host‐specific factors, the genetic background of seeds may be the most important. Species‐specific, cultivar‐specific, and even genotype‐specific components have been found within the plant microbiome (Andreote & Pereira E Silva, ; Berg & Smalla, ; Cardinale, Grube, Erlacher, Quehenberger, & Berg, ; Lundberg et al., ; Rybakova et al., ; Smalla et al., ), suggesting that the genetic background of plants plays a key role in modulating the composition and structure of the seed mycobiota (Oren, Ezrati, Cohen, & Sharon, ; Peiffer et al., ). Our multi‐year seed stocks were all the same maize variety (Zheng58) and thus shared the same host genetic background.…”

“…A vast diversity of microorganisms colonize all organs of plants; these microorganisms constitute the plant microbiome and play an integral role in plant growth and health (Berg, Rybakova, Grube, & Koberl, ; Mendes et al., ; Rybakova et al., ; Sánchez‐Cañizares, Jorrín, Poole, & Tkacz, ). Recently, great efforts have been made to understand the plant microbiome, and the microbiota diversity of different tissues and developmental stages has been described for many plants, including major crops such as rice (Edwards et al., ), maize (Peiffer et al., ), barley (Bulgarelli et al., ), and soybean (Han et al., ; Liu et al., ; Sugiyama, Ueda, Takase, & Yazaki, ).…”

Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory

“…However, the underlying mechanism is unclear. Recent studies confirm that some endophytic bacterial genera such as Enterobacter, Pantoea, Pseudomonas, and Citrobacter present in seeds are derived from the rhizosphere microbial community of plant hosts (Johnston-Monje and Raizada, 2011; Adam et al, 2018;Rybakova et al, 2017). Enterobacter asburiae from seeds of different maize (Zea mays) cultivars was established in the rhizosphere after seeding (Johnston-Monje and Raizada, 2011).…”

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: the case of theLeptosphaeria maculans-Brassica napuspathosystem

“…Furthermore, host genetics has been shown to influence the plant and root microbiome strongly (Rybakova et al, 2017;Sapkota et al, 2015;Wagner et al, 2016), mostly because the cultivars considered differ for other traits in addition to resistance to a plant pathogen. The use of nearisogenic lines differing only by the presence or absence of a specific resistance gene was therefore expected to limit the 'genotype' effect (Newton et al, 2010) and appeared to be the best technical solution in this case.…”