Metagenome-assembled genome: SRP226684_co1_183
uncultured Ktedonobacteraceae bacterium
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR10333328,SRR10333329 of study SRP226684.
ENA first public
2024-12-11
INSDC center name
CMR
INSDC status
public
Submitter Id
SRP226684_co1_183
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes;3.15.4;default
binning parameters
coverage and kmer
binning software
VAMB;3.0.2;default
broad-scale environmental context
engineered
collection date
2018-11
completeness score
78.97
completeness software
CheckM2;1.0.2;default
contamination score
4.81
environmental medium
engineered
geographic location (country and/or sea)
China
geographic location (latitude)
not provided
geographic location (longitude)
107.1424
investigation type
metagenome-assembled genome
isolation_source
mine drainage metagenome
local environmental context
mine drainage biome
metagenomic source
mine drainage metagenome
project name
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.
sample derived from
SAMN12995754,SAMN12995753
sample name
SRP226684_co1_183
scientific_name
uncultured Ktedonobacteraceae bacterium
sequencing method
Illumina HiSeq 2500
taxonomic identity marker
multi-marker approach