Emergence shapes the structure of the seed microbiota

Abstract

Seeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment of gyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

FIG 1

Estimation of bacterial and fungal diversity. Richness (aOTUs) and diversity (Simpson's inverse index [invsimpson]) were estimated in seeds (H0), germinating seeds (H24), and seedlings with 16S rRNA gene, gyrB, and ITS sequences. Each sample is represented by a green line, while the gray area represents the estimation of the distribution (created via Beanplot [71]).

FIG 2

Emergence influences the microbial β-diversity NMDS ordination of Bray-Curtis dissimilarity matrix obtained with 16S (A, B), gyrB (C, D), and ITS (E, F) aOTUs. Each dot represents a microbial community observed in samples derived from H0 (red), H24 (blue), and H96 (green). Stress values and total variance are indicated for each NMDS ordination.

FIG 3

Dynamics of microbiota composition during germination-emergence. Krona radial space-filling (44) charts show the mean relative abundances of bacterial and fungal taxa in seeds (H0), germinating seeds (H24), and seedlings (H96).

FIG 4

Correlation networks observed between aOTUs. Correlation networks obtained with 16S rRNA gene (A, B, C), gyrB (D, E, F), and ITS (G, H, I) sequences. Nodes correspond to aOTUs, and connecting edges indicate correlations between them. Correlations between aOTUs were calculated with the Sparse Correlations for Compositional data algorithm (SparCC) (48) implemented in mothur. The effect of uneven sampling was corrected by dividing sequence counts by total library size. Only correlations with values less than −0.30 (blue) or larger than 0.30 (orange) were represented in the network using the R package qgraph (49). While graphics in panels A, D, and G represent all the aOTUs, graphics in panels B, C, E, F, H, and I are restricted to aOTUs with negative or positive correlations. Blue and orange nodes (B, E, and F) represent aOTUs with decrease and increase in relative abundance during transition from seeds to seedlings. Node colors (C, F, and I) represent the different bacterial and fungal classes.