2025-08-08
ENA first public
ERC000047
ENA-CHECKLIST
EMG
INSDC center name
public
INSDC status
ERS25424756
SRA accession
ERR14720254_concoct_57
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaspades_v3.15.5
assembly software
default
binning parameters
MGnify-genomes-generation-pipeline_v1.0.0
binning software
soil
broad-scale environmental context
EBI-EMG
broker name
2019-06-12
collection date
88.77
%
completeness score
CheckM2_v1.0.1
completeness software
0.57
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR14720254 of study ERP166136.
description
tomato
environmental medium
Ecuador
geographic location (country and/or sea)
-4.43805200
DD
geographic location (latitude)
-79.58501800
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
rhizosphere metagenome
isolation_source
rhizosphere
local environmental context
rhizosphere metagenome
metagenomic source
uncultured Enterobacteriaceae bacterium
organism
Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Alike genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that contribute to crop growth and health.
project name
SAMEA116999260
sample derived from
uncultured Enterobacteriaceae bacterium
scientific_name
Illumina MiSeq
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: ERR14720254_concoct_57
title