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.

Due to the lack of foliar fungicide use, the organic production of Brassica seeds free of Alternaria spp. is difficult. Therefore, effective seed treatments certified for use in organic farming are needed to eradicate or at least effectively reduce the seed-borne inoculum. We here report results of greenhouse and field experiments in which non-chemical seed treatments were tested for control of A. brassicicola on cabbage seeds naturally infested with the pathogen. In greenhouse experiments, significant improvements were obtained by seed treatment with some commercialised and experimental microbial biocontrol agents, an emulsion of thyme oil in water (0.1%) and by the tested physical seed treatments methods (i.e. hot water, aerated steam and electron seed treatment). Resistance inducers tended to increase the percentage of healthy plants, but the effects were statistically not significant. Generally the combination of physical treatments with the effective agents did not result in improved performance. Positive effects on crop establishment and yield by the same treatments were also observed in field tests. Overall the results indicate that several options for non-chemical control of A. brassicicola on Brassica seeds exist that are comparable in efficacy to the chemical standard Aatiram (active ingredient thiram) used in this study.

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Heyman, F., Blair, J. E., Persson, L., and Wikström, M. 2013. Root rot of pea and faba bean in southern Sweden caused by Phytophthora pisi sp nov. Plant Dis. 97:461-471..'.>/' F i>-A root rot disease of pea and faba bean caused by a Phytophthora sp. was observed in fields and field soil samples in southern Sweden.Observations of the disease in pea root rot greenhouse assays were systematically recorded, and incidence and geographic distribution data were compared with the pea root rot caused by Aphanomyces euteiches. Following one successful isolation of the pathogen, isolation procedures and selective media were optimized to retrieve more isolates. Phylogenetic analysis showed that the isolates belong to a novel lineage, closely related to Phytopitthora sojae, and proposed here as a new species, P. pisi sp. nov. In a collection of 13 isolates from separate fields, intraspecific variation was detected in both nuclear and mitochondrial loci. Pathogenicity tests on a range of crop plants and wild legumes suggest that the host range of the pathogen is restricted to a group of legumes closely related to pea which, in addition to pea, include the crop species faba bean, lentil, common vetch, and chickpea. Morphology, growth requirements, and pathogenicity traits indicate that the species may be identical to the organism previously described as P. erythroseptica var. pisi. The work characterizes a novel Phytophthora sp. causing root rot of legume crops.

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