Abiotic treatment to common bean plants results in an altered endophytic seed microbiome

Abstract

12We performed a pilot study in a controlled growth chamber to investigate how the seed microbiome of 13 the common bean (Phaseolus vulgaris L. (var. Redhawk)) was altered under abiotic treatments relevant 14 for crop management with changing climate. Bean plants were subjected to one of three treatments: 1566% water withholding to simulate mild drought, 50 % Hoagland nutrient solution to simulate 16 fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene 17 amplicon sequencing and ITS amplicon sequencing of the endophytic metagenomic DNA to assess seed 18 bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed 19 microbiome structure was high while alpha diversity was low, with tens of taxa present. Water 20 withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal 21 communities as compared to the untreated control, and each treatment resulted in a distinct 22 microbiome structure. There were no statistically supported differences in the fungal microbiome across 23 treatments. While we discuss several limitations of this study, the promising results suggest that further 24 and more comprehensive investigation is needed to better understand abiotic stress-induced changes in 25 2 the seed microbiome, the mechanisms that drive those changes, and the implications of seed 26 microbiome changes for the health and stress responses of the next plant generation. 27 28

Endophytic microbiome variation at the level of a single plant seed

“…As is true for other plant compartments, different plant species or divergent crop lines/varieties/cultivars often have different seed microbiome composition or structure (Wassermann et al 2019; Klaedtke et al 2016; Johnston-Monje and Raizada 2011; López-López et al 2010). However, many seed microbiome studies have reported generally high variability across seed samples from the same plant type and treatment (Bergna et al 2018; López-López et al 2010; Bintarti et al 2020), with strong explanatory value of either seed origin/seed lot, geographic region or soil edaphic conditions (Chartrel et al 2021; Klaedtke et al 2016; Johnston-Monje and Raizada 2011; but see also Adam et al 2018 for an exception). While these insights may call into question the proportion of “inherited” versus acquired seed microbiome members, the high microbiome variability may be in part due to methods applied to extract the microbial DNA from the seed compartment, and different methods applied across studies.…”