Metagenome-assembled genome: SRR3997477_bin.48_CON... - BioSample

Metagenome-assembled genome: SRR3997477_bin.48_CONCOCT_v1.1_MAG

Identifiers: BioSample: SAMEA14081972; SRA: ERS11685108

Organism: Sphingobacterium mizutaii
cellular organisms; Bacteria; Pseudomonadati; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Sphingobacteriia; Sphingobacteriales; Sphingobacteriaceae; Sphingobacterium

Attributes

collection date	2014-03-17
broad-scale environmental context	Engineered
local-scale environmental context	Engineered
environmental medium	Engineered
geographic location	South Africa
investigation type	metagenome-assembled genome
isolation source	metagenome
project name	Gold mining and other industrial activities make extensive use of cyanide (CN-) and produce large volumes of thiocyanate- (SCN-) contaminated wastewater that must be treated before reuse in mining processes. Furthermore, contaminated wastewater stored in tailings dams may pose an environmental threat through the potential for leakage into local groundwater. Microbial communities are often used for biodegradation and environmental remediation, however, little is known about the membership and metabolic potential of SCN-degrading consortia. Application and improvement of the remediation strategy will benefit from an understanding of organisms that can contribute to the breakdown of SCN- into sulfur, carbon and nitrogen compounds. To this end, we performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN- and CN- degradation by established microbial consortia. Community analysis revealed the dominance of Thiobacillus spp. whose genomes harbor a previously unreported operon for SCN- degradation. Metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed, but using energy gained from oxidation of the sulfur compounds produced during SCN- degradation. Heterotrophs compose a smaller portion of the reactor bacterial community, and predation by phage and eukaryotes is predicted to affect community dynamics. Furthermore, genes for ammonium oxidation and denitrification were detected, possibly allowing removal of nitrogen as required for complete remediation of wastewater. These findings suggest possible optimization strategies for reactor design such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.
sample name	SRR3997477_bin.48_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14081972
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:32:16Z
INSDC last update	2023-01-03T00:32:16Z
INSDC status	public
Submitter Id	SRR3997477_bin.48_CONCOCT_v1.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaspadesv3.12.0
binning parameters	Default
binning software	CONCOCT v1.1
broker name	EMG broker account, EMBL-EBI
completeness score	78.68
completeness software	CheckM
contamination score	4.59
geographic location (latitude)	-33.9575
geographic location (longitude)	18.4606
metagenomic source	metagenome
sample derived from	SAMN05509838
scientific_name	Sphingobacterium mizutaii
sequencing method	Illumina HiSeq 2500
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR3997477 of study SRP056932.

BioProject: PRJEB51072 Large-scale analysis of novel cellular microbes from the engineered biome
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Submission: EBI; 2023-01-04

Accession:: SAMEA14081972
ID:: 32559268

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Metagenome-assembled genome: SRR3997477_bin.48_CONCOCT_v1.1_MAG

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