Background and aims Plant breeding activities shape the rhizosphere microbiome but less is known about the relationship of both with the seed microbiome. We analyzed the composition of bacterial communities of seeds and rhizospheres of Styrian oil pumpkin genotypes in comparison to bulk soil to elucidate specific microbial signatures to support a concept involving plant-microbe interactions in breeding strategies. Methods The seed and rhizosphere microbiomes of 14 genotypes of oilseed pumpkin and relatives were analyzed using a 16S rRNA gene amplicon sequencing approach, which was assessed by bioinformatics and statistical methods. Results All analyzed microhabitats were characterized by diverse bacterial communities, but the relative proportions of phyla and the overall diversity was different. Seed microbiomes were characterized by the lowest diversity and dominant members of Enterobacteriaceae including potential pathogens (Erwinia, Pectobacterium). Potential plant-beneficial bacteria like Lysobacter, Paenibacillus and Lactococcus contributed to the microbial communities in significant abundances. Interestingly, strong genotype-specific microbiomes were detected for seeds but not for the rhizospheres. Conclusions Our study indicates a strong impact of the Cucurbita pepo genotype on the composition of the seed microbiome. This should be considered in breeding of new cultivars that are more capable of exploiting beneficial indigenous microbial communities.

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40–83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.

Summary Soybean crop management have not been studied much in Central Europe as compared with cereals. We assessed the effect of variety, row spacing, seeding rate and nitrogen (N) fertilization on yields and yield components of soybean in a two-year experiment in Gleisdorf, Austria. The varieties Lenka, Naya and Xonia were tested in row spacings of 13 cm, 38 cm and 76 cm with 30 germinable seeds m−2. Additionally, 60 seeds m−2 were tested at 13 cm row spacing, and 38 cm row spacing was additionally established with N fertilization. Faster soil coverage was obtained with a high seeding rate or narrower row spacings. First pod height differed between varieties and increased with higher seeding rate. Grain yield was not affected by treatments but yield components differed. The widest row spacing resulted in a lower plant density but more pods plant−1, grains plant−1, grains pod−1 (in one year) and a higher thousand kernel weight (TKW). The higher seeding rate resulted in a higher plant density but less pods plant−1 whereas grains pod−1 and TKW did not differ. N fertilization did not affect the grain yield. Correlation analysis showed a high adaptability of soybean to different seeding rates and row spacings through modulation of yield components.

Background Global warming and issues in favour of a more sustainable agriculture suggest a reconsideration of minor cereals in European agrosystems. Compared to other summer crops, proso millet has a remarkable drought resistance and could be used to improve crop rotation and biodiversity. Proso millet is also increasingly sought by industry to produce novel foods such as those designed for coeliac patients. In this study, a thorough characterization of 11, commercially available, proso millet (Panicum miliaceum L.) varieties was carried out as a preliminary step for crop reintroduction and breeding in Western Europe. Methods The cultivars under evaluation were introduced from Austria, Poland, Russia, and the USA (University of Nebraska–Lincoln). Plants were grown at Udine (NE Italy) and Gleisdorf (Styria, Austria), under greenhouse and field conditions, respectively. Yield components and a range of morphophysiological characters were recorded in both locations. In parallel, 85 SSR markers were tested on DNA samples extracted from randomly chosen plants of each variety and the 12 responsive markers used to genotype the whole variety set. Results Morphometric analyses showed that varieties have several diverging phenotypic traits and architectures. In all instances, yields recorded at field level were much lower than potential yields. In this respect, US selections were comparable to earlier developed European varieties, suggesting that breeding for an increased adaptation is the keystone for a stable reintroduction of millet in Western Europe. Molecular analyses uncovered remarkably low genetic differences and heterozygosity levels within cultivars, confirming millet as an essentially autogamous species; in contrast, large genetic distances were noted among cultivars selected in different environments. Results of SSR genotyping combined with those originating from phenotypic analyses indicated possible crosses to source the genetic variability necessary for selection. Conclusions This study enabled the identification of cultivars that could be used to revitalize the crop in Western Europe and to produce genetically variable hybrid progenies exploitable by breeding.