Colonization of beet by rhizosphere bacteria takes place in discreet phases regardless of bioinculation with wild sea beet root community

Abstract

Abstract Background: Bioinoculation can increase crop yields under environmental stress. Inoculants consisting of microbial communities instead of single strains may be of broader use than the latter ones, as different plants might recruit specific organisms from a large pool. Inoculation influences rhizosphere and endophytic community structure modifying community assembly process, which is driven by selection due to the host and by microbe-microbe interactions. Plant colonization by microbes is an instance of succession, with its distinct phases differing in community structure and diversity. This process needs to be studied to determine the optimal timing for bioinoculation and studying its effects. We wanted to learn if, and if so, when stable bacterial communities form during axenic beet plants colonization by bacteria from soil, either inoculated with wild beet bacterial community or non-inoculated and if this process depends on beet genotype and soil. Results: Here we show that regardless of bioinoculation, soil type and plant genotype bacteria colonize axenic beets rhizosphere and tissues in two phases differing in bacterial load, degree of nestedness, community structure, diversity as well as assembly mechanisms and aligned with taproot development. Both rhizosphere and endosphere communities remain stable after five weeks of growth in soil. Alpha-diversity was higher and bacterial load was lower in late samples than in early ones. Communities were more similar at the level of predicted functional potential than at the level of amplicon sequence variants (ASVs). Time, soil type and genotype determined community structure but not alpha-diversity, bacterial load, nestedness or assembly mechanisms both in rhizosphere and in endosphere. Inoculation slightly but significantly changed community structure both in rhizosphere as well as in roots and leaves. Pseudomonadota (formerly Proteobacteria) and Bacillota (formerly Firmicutes) of low abundance coming from the inoculant were found to be recruited by beets. Conclusions: Axenic beets colonization runs through phases similar to those in other instances of microbial succession and bacteria are recruited mostly randomly. Transition from the early to late phase involves drop of bacterial load in plant tissues, which may be linked to plant growth and bacterial cells division arrest. Therefore, early inoculation seems to be the right choice. Five weeks of growth in soil enable formation of stable bacterial communities both in rhizosphere and endosphere. Inoculation influence seems to be mostly indirect, probably due to microbe-microbe interactions.