The effect of the growth substrate on cultivable and total endophytic assemblages of Arabidopsis thaliana

Abstract

Aims We investigated the effect of different growth substrates, frequently used during production of Arabidopsis thaliana seeds, on the endophytic assemblage of this plant. Methods Arabidopsis thaliana was grown on sand and on a mixture of sand and potting soil. Seeds harvested on both substrates were sown again on the same substrate until the radicle emerged and until there were 3 week-old leaves. Cultivable soil bacteria and endophytic bacteria from seeds, radicles and leaves were isolated and identified using 16S rRNA gene sequencing. Total bacterial assemblages were investigated using a direct DNA extraction from soil, seeds, radicles and leaves, and pyrosequencing of the V5-V7 hypervariable region of the 16S rRNA gene. Results Despite differences in the soil bacterial assemblages, seed and radicle endophytic assemblages were similar. The leaf endophytic assemblage was mainly derived from the environment and not from the seed. The endophytic genera most abundant in the cultivable assemblage coincide with the genera frequently detected in the total assemblage. Conclusions Our results indicate that plants can select their seed endophytes. During plant growth, bacteria seem to be recruited from the environment to complement the endophytic population from which the seed endophytes of the next generation can again be selected.