2024-12-11
ENA first public
ERC000047
ENA-CHECKLIST
CMR
INSDC center name
public
INSDC status
ERS22192312
SRA accession
SRP226684_co1_2
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes;3.15.4;default
assembly software
coverage and kmer
binning parameters
MetaBAT2;2.15;default
binning software
engineered
broad-scale environmental context
2018-11
collection date
90.13
%
completeness score
CheckM2;1.0.2;default
completeness software
0.41
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR10333328,SRR10333329 of study SRP226684.
description
engineered
environmental medium
China
geographic location (country and/or sea)
not provided
DD
geographic location (latitude)
107.1424
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
mine drainage metagenome
isolation_source
mine drainage biome
local environmental context
mine drainage metagenome
metagenomic source
Candidatus Micrarchaeota archaeon
organism
A unique terrace with sharp gradient of environmental conditions was selected to study the microbial response and survival strategies to the extreme environments introduced by acid mine drainage (AMD) contamination. A combination of geochemical analyses, metagenomic sequencing, in-situ microcosm setups, and statistical analyses were used to investigate the environment-microbe interactions. The microbial communities and metabolic potentials along the terrace were studied by focusing on the genes associated with C, N, S cycling and metal resistance. Results show that the variations of geochemical parameters substantially shaped the microbial communities. Autotrophic microorganisms prevailed in more contaminated fields while heterotrophic microorganisms dominated in less contaminated fields. Sharp environmental gradients also impacted the metabolic potentials, especially for C, N, and S cycling. Although the relative abundances of carbon fixing genes did not significantly vary along the environmental gradients, the taxa for carbon fixation varied significantly in more contaminated fields versus less contaminated fields, indicating the effects of AMD contamination on the autotrophic microbial communities. AMD input also influenced the N cycling, especially for nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Nitrogen fixation as an important biogeochemical process in mining environments is of great interest and ex situ experiments were undertaken to evaluate the effects of AMD contamination on nitrogen fixation rates. Random Forest (RF) analysis indicated that nitrate, pH, total N, TOC exhibited positive correlations with the rates of nitrogen fixation while total Fe, Fe(III), and sulfate showed negative effects. TOC were identified as one of the most important factors affecting the DNRA. In addition, Fe- and S-related environmental parameters showed significant positive effects on the genes associated with dissimilatory sulfate reduction. The current study provides an understanding for microbial response to AMD contamination and lays the foundation for future potential AMD bioremediation.
project name
SAMN12995754,SAMN12995753
sample derived from
Candidatus Micrarchaeota archaeon
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: SRP226684_co1_2
title