Response of Plant-Associated Microbiome to Plant Root Colonization by Exogenous Bacterial Endophyte in Perennial Crops

Abstract

The application of bacterial inoculums for improving plant growth and production is an important component of sustainable agriculture. However, the efficiency of perennial crop inoculums depends on the ability of the introduced endophytes to exert an impact on the host-plant over an extended period of time. This impact might be evaluated by the response of plant-associated microbiome to the inoculation. In this study, we monitored the effect of a single bacterial strain inoculation on the diversity, structure, and cooperation in plant-associated microbiome over 1-year period. An endophyte (RF67) isolated from Vaccinium angustifolium (wild blueberry) roots and annotated as Rhizobium was used for the inoculation of 1-year-old Lonicera caerulea (Haskap) plants. A significant level of bacterial community perturbation was detected in plant roots after 3 months post-inoculation. About 23% of root-associated community variation was correlated with an application of the inoculant, which was accompanied by increased cooperation between taxa belonging to Proteobacteria and Actinobacteriota phyla and decreased cooperation between Firmicutes in plant roots. Additionally, a decrease in bacterial Shannon diversity and an increase in the relative abundances of Rhizobiaceae and Enterobacteriaceae were detected in the roots of inoculated plants relative to the non-inoculated control. A strong effect of the inoculation on the bacterial cooperation was also detected after 1 year of plant field growth, whereas no differences in bacterial community composition and also alpha and beta diversities were detected between bacterial communities from inoculated and non-inoculated roots. These findings suggest that while exogenous endophytes might have a short-term effect on the root microbiome structure and composition, they can boost cooperation between plant-growth-promoting endophytes, which can exist for the extended period of time providing the host-plant with long-lasting beneficial effects.

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Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils

“…Bray–Curtis distance matrices were then subjected to an analysis of variance using distance matrices statistical method (ADONIS test), through which their values were fitted to a linear regression to determine what proportion of variance in community structure could be attributed to different niches. Non-metric multidimensional scaling (NMDS) of bacterial communities was performed on Bray–Curtis matrices using Vegan R package [ 32 , 33 ]. The graphics were created through RStudio (Version 1.2.5001, RStudio Inc., Boston, MA, USA) using the qiime2R package and plotted using ggplot2 [ 34 ].…”

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“…The application of endophytic Rhizobium sp. RF67 isolated from Vaccinium angustifolium resulted in rootassociated bacteria variation, which boosted cooperation of plant-growth-promoting endophytes (Yurgel et al, 2022). Moreover, Piriformospora indica recruited the member of Firmicutes and decreased Proteobacteria in rice roots, resulting in enhancement of rhizosheath and improvement of drought tolerance (Xu F. Y. et al, 2022).…”