The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root‐associated microbial communities

Abstract

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems.Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosatetreated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS).Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host

Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full‐length 16S rDNA amplicon and metatranscriptomic analyses

“…Understanding the mechanisms by which bacteria colonize the root‐associated niches is crucial for processes related to the application of the beneficial bacteria, including the screening of strains with efficient root colonization ability and directed strain improvement (Yang et al, 2022 ). By characterizing the colonization abilities of single gene deletion mutants or high‐throughput transposon mutagenesis libraries of the beneficial strains after being inoculated into the sterilized plants, or profiling the transcriptome of strains stimulated by root exudates, recent studies have identified several genes involved in bacterial root colonization, such as those involved in the biosynthesis of chemotaxis system, flagella, and lipopolysaccharides (LPS) (Cole et al, 2017 ; Coutinho et al, 2015 ; Feng et al, 2021 ; Ishizawa et al, 2022 ; Knights et al, 2021 ; Wallner et al, 2022 ).…”