Influence of Environment and Host Plant Genotype on the Structure and Diversity of the Brassica napus Seed Microbiota

Abstract

Seeds are involved in the transmission of microorganisms from one plant generation to the next and consequently act as reservoirs for the plant microbiota. The driving processes influencing seed microbiota assemblage have not been yet deciphered because of confounding factors related to environmental location, agricultural practices, and host genotype selection. Nine genotypes were chosen among a large panel of genetically diverse Brassica napus accessions. The taxonomic structure of the seed microbiota was monitored by amplification and subsequent high-throughput sequencing of gyrB and internal transcribed spacer 1 markers for two successive years on seed lots collected from self-pollinated plants. Seed germination capacities were compared between all seed lots. Although harvesting year was the main driver of seed microbiota composition, the host genotype also significantly altered the structure of seed microbial assemblages. The core microbiota of B. napus included nine fungal taxa shared between all the genotypes and years, while no bacterial taxa were conserved across all genotypes and years. The harvesting year had the major effect on seed germination but with some differences between genotypes. The study demonstrated the relative contribution of host- and environmental-filtering on the assemblage of the seed microbiota. It suggested some influence of these assemblages on seed germination.

Crop, genotype, and field environmental conditions shape bacterial and fungal seed epiphytic microbiomes

“…Significant differences in richness and diversity between parents and offspring were found in most lines analyzed, reflecting that environmental conditions such as field location and potentially, agricultural management practices are contributing factors in seed-associated microbial assemblage. Similar results were reported by Klaedtke et al (2016) and Rochefort et al (2019) in the seed microbiome of P. vulgaris L. and B. napus collected from different locations and years. More generally, bacterial and fungal richness were determined by both crop type and generation, whereas diversity was driven only by the crop type.…”

Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth

“…Harvesting year and plant genotypes are significant drivers of the diversity structure of the B. napus seed microbiota (35). Two B. napus genotypes (Boston and Major) collected during two harvest years (Y1 and Y2) were selected for this work.…”

“…Amplicon libraries were constructed with the primer sets gyrB_aF64/gyrB_aR553 (24) and ITS1F/ITS2 (37), following the experimental procedure previously described in Rochefort et al (35). A blank extraction kit control and a PCR-negative control were included in each PCR plate.…”

“…More specifically, we investigated ( i ) what is the main source of microbial transmission to seedlings; ( ii ) does seed microbiota composition and soil diversity impact the assembly of seedling microbiota; and (iii) does the initial taxon abundance in the source influence its transmission success? To answer these questions, we selected seed lots of different genotypes of the winter oilseed rape Brassica napus, which harbored contrasting seed microbiota (35). We simulated a total of eight different coalescence events by sowing the four seed lots in two soils of different microbial diversities.…”

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

“…The idea of vertical transmission, the direct transfer of a microorganism from a parent to its progeny, is a universal phenomenon in animals (Funkhouser and Bordenstein, 2013; Berg and Raaijmakers, 2018). Since seeds are considered the plant progeny, the majority of studies on vertical transmission in plants have focused on the composition and assembly of the seed's microbial community, rather than the dynamics of establishment and transmission during seedling development, despite the latter being a crucial step in maintaining the continuity of the plant microbiome and a potential bottleneck in vertical transmission (Gundel et al ., 2011; Hodgson et al ., 2014; Bergna et al ., 2018; Shahzad et al ., 2018; Hardoim, 2019; Rochefort et al ., 2019; Wassermann et al ., 2019; Rodríguez et al ., 2020) (Fig. 1A).…”