Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Abstract

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions

“…On the other hand, in agricultural soils and the rhizosphere of tomato plants, Chloroflexi was the fourth and fifth phyla represented. Chloroflexi has already been described in the soil and in the rhizosphere of several plant species including tomato [ 23 , 30 , 56 , 57 ]. Although reported in numerous microbiome studies, there is little information on Chloroflexi because, together, Acidobacteria and Planctomycetes require more than 12 weeks to grow and form very small colonies on culture media and are therefore very difficult to isolate [ 58 ].…”

Source and acquisition of rhizosphere microbes in Antarctic vascular plants

“…Strains of Devosia have been isolated from the rhizosphere of Cq and display a high tolerance to salt, where in vitro experiments have demonstrated that this bacteria can improve the osmotic and physiological performance of the Antarctic vascular plants ( Gallardo-Cerda et al, 2018 ). Additionally, this genus is globally abundant in soil and has been found enriched in the rhizospheres of various plants of economic interest ( Delgado-Baquerizo et al, 2018 ; Wang et al, 2022 ). Finally, representative genus Galbitalea has not been obtained from vascular plant rhizospheres; however, several isolates have been obtained from Antarctic lichens ( Noh et al, 2021 ).…”

A 16S rRNA amplicon approach to the structural and functional diversity of bacterial communities associated with horse gram crop for drought mitigation and sustainable productivity

“…The databases used were SILVA, GREENGENES and NCBI. Each read was classified according to the percentage coverage and identity (Wang et al, 2021). METAGENassist was used for performing the comparative genomics of bacterial populations.…”