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Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and 2 generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and internal transcribed spacer (ITS) regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e., generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a “core microbiome” was detected consisting of 5 bacterial and 12 fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.

Seed are reproductive units that transfer genetic information to the next generation and harbor microbial communities that may interact with a host plant at all stages of its development. Here, we assessed the effect of the environment and plant genotype on the seed microbiome of eight spring Brassica napus lines harvested from four site years in Saskatchewan, Canada: one location each in 2016 and 2017 and two additional locations in 2017. Seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S ribosomal RNA and fungal internal transcribed spacer regions. Our results revealed that microbial communities were predominantly shaped by the environment, with location explaining 34% of bacterial and 43% of fungal total variance. Meanwhile, genotype had a smaller effect, accounting for only 9% of bacterial and 13% of fungal variance. The seed microbiome of B. napus predominantly contained members of Enterobacteriales and Pseudomonadales bacterial orders as well as Pleosporales and Capnodiales fungal orders. Additionally, common taxa, including Enterobacteriales, Pseudomonadales, Micrococcales, Sphingomonadales, Pleosporales, Capnodiales, Tremellales, Filobasidiales, and Sporidiobolales, were detected across all site years. Our results demonstrate that the environment plays a dominant role in shaping spring B. napus seed microbiomes, with more subtle contributions related to host plant genotype. Information collected in this study may contribute to the development of novel and sustainable breeding and agricultural strategies that consider microorganisms carried by seed.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. We sequenced the bacterial 16S ribosomal RNA gene generating a total of 127.7 million reads and the fungal internal transcribed spacer (ITS) region generating 113.4 million reads. 14,944 unique fungal amplicon sequence variants (ASV) were detected, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. We detected 10,882 unique bacterial ASVs with an average of 249 ASVs per sample. Temporal, site-to-site, and line-driven variability were key determinants of microbial community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.