Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat

Abstract

Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the rhizosphere, particular operational taxonomic units (OTUs) in the culture-dependent fraction were absent from the culture-independent fraction, indicating that deeper sequence analysis is required for this approach to be exhaustive. We also found that the microbial seed load defined the endosphere, but not rhizosphere, community structure for plants grown in soil which was not wheat adapted. Together, these findings increase our understanding of the importance of land management and microbial seed load in shaping the root microbiome of wheat and this knowledge will facilitate the exploitation of plant-microbe interactions for the development of novel microbial inoculants.

Keywords: embryo; endosphere; microbiome; rhizosphere; seed; wheat.

FIGURE 1

Scheme representing the setup of the experiment to recover culturable rhizosphere (brown) and endosphere (green) bacteria from complete wheat seeds (dark color) and embryos (light color) in arable soil (square) and bare fallow soil (circle).

FIGURE 2

PCoA based on Bray–Curtis distance matrix was performed on culture-independent bulk soil samples collected in 2011 (triangle) and 2013 (inverted triangle) and rhizosphere samples (circle) collected in 2012 showing the structure of bacterial communities from the Highfield experiment under three types of land management: continuous arable (yellow), conversion of bare fallow to arable (brown), and conversion of grassland to arable (green).

FIGURE 3

Venn diagram showing the number and proportion of shared OTUs (C) (at 97% similarity) detected with both unculturable (A) and culturable (B) methods in the wheat rhizosphere. Pie charts correspond to the percentage of bacterial phyla and classes of Proteobacteria assigned to each OTU. “Others” include 26 phyla corresponding to <1%, which include: BJ-169, BRC1, Candidatus Berkelbacteria, Chlamydiae, Chlorobi, Deinococcus–Thermus, Elusimicrobia, FBP, FCPU, Fibrobacteres, Gracilibacteria, Ignavibacteriae, Latescibacteria, Microgenomates, Nitrospirae, Omnitrophica, Parcubacteria, Peregrinibacteria, Saccharibacteria, Spirochaetae, SR1, Tectomicrobia, Tenericutes, TM6, WS2, and WWE3.

FIGURE 4

PCoA plots based on Jaccard distance matrix of culturable bacterial communities from the rhizosphere (A) and endosphere (B) of wheat grown in continuous arable or bare fallow soil. The percentage shown on each axis corresponds to the proportion of variation explained. Solid squares represent continuous arable soil and solid circles represent bare fallow soil. Light brown color represents wheat rhizosphere samples derived from the culturing of excised embryos and brown color indicates samples from the rhizosphere of complete seed-derived wheat plants. Dark green color represents samples obtained from the endosphere of complete seed-derived wheat plants and light green color represents samples from endosphere of wheat plants generated from excised embryos.