U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

Metagenome-assembled genome: ERR2144884_bin.2_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA13911885; SRA: ERS11512321
Organism
uncultured Herbaspirillum sp.
cellular organisms; Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Herbaspirillum; environmental samples
Attributes
collection date1978-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextPlants
environmental mediumPlants
geographic locationUSA
investigation typemetagenome-assembled genome
isolation sourceplant metagenome
project nameDinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by nitrogen isotope determinations of fern biomass and detection of N2O released. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct near full-length Rhizobiales genomes were identified from leaf-pocket enriched samples from ditch grown A. filiculoides. Annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface sterilized ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.
sample nameERR2144884_bin.2_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA13911885
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:31:52Z
INSDC last update2023-01-03T00:31:52Z
INSDC statuspublic
Submitter IdERR2144884_bin.2_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwarespadesv3.11.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score99.95
completeness softwareCheckM
contamination score0.4
geographic location (latitude)0.0
geographic location (longitude)0.0
metagenomic sourceplant metagenome
sample derived fromSAMEA104288478
scientific_nameuncultured Herbaspirillum sp.
sequencing methodIllumina HiSeq 2000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2144884 of study ERP021566.

BioProject
PRJEB51079 Large-scale analysis of novel cellular microbes from the plant biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA13911885
ID:
32555210

BioProject Nucleotide

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center