2025-07-30
ENA first public
ERC000047
ENA-CHECKLIST
EMG
INSDC center name
public
INSDC status
ERS25336102
SRA accession
SRR17295755_binner12_Refined_168
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaspades_v3.15.3
assembly software
default
binning parameters
MGnify-genomes-generation-pipeline_v1.0.0
binning software
soil
broad-scale environmental context
EBI-EMG
broker name
2020-02-08
collection date
55.54
%
completeness score
CheckM2_v1.0.1
completeness software
1.07
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run SRR17295755 of study SRP351931.
description
tomato
environmental medium
not provided
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
rhizosphere metagenome
isolation_source
rhizosphere
local environmental context
rhizosphere metagenome
metagenomic source
uncultured Thalassospira sp.
organism
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 seven-fold 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.
project name
SAMN24146842
sample derived from
uncultured Thalassospira sp.
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: SRR17295755_binner12_Refined_168
title