title: Metagenome-assembled genome: SRP226684_co1_16
organism: uncultured Acidimicrobiaceae bacterium
description: This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR10333328,SRR10333329 of study SRP226684.
attributes.tag: ENA first public
attributes.value: 2024-12-11
attributes.tag: INSDC center name
attributes.value: CMR
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: SRP226684_co1_16
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaSPAdes;3.15.4;default
attributes.tag: binning parameters
attributes.value: coverage and kmer
attributes.tag: binning software
attributes.value: MetaBAT2;2.15;default
attributes.tag: broad-scale environmental context
attributes.value: engineered
attributes.tag: collection date
attributes.value: 2018-11
attributes.tag: completeness score
attributes.value: 86.29
attributes.tag: completeness software
attributes.value: CheckM2;1.0.2;default
attributes.tag: contamination score
attributes.value: 2.03
attributes.tag: environmental medium
attributes.value: engineered
attributes.tag: geographic location (country and/or sea)
attributes.value: China
attributes.tag: geographic location (latitude)
attributes.value: not provided
attributes.tag: geographic location (longitude)
attributes.value: 107.1424
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: mine drainage metagenome
attributes.tag: local environmental context
attributes.value: mine drainage biome
attributes.tag: metagenomic source
attributes.value: mine drainage metagenome
attributes.tag: project name
attributes.value: 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.
attributes.tag: sample derived from
attributes.value: SAMN12995754,SAMN12995753
attributes.tag: sample name
attributes.value: SRP226684_co1_16
attributes.tag: scientific_name
attributes.value: uncultured Acidimicrobiaceae bacterium
attributes.tag: sequencing method
attributes.value: Illumina HiSeq 2500
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach