ArticleThe ISME journal2015
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.
Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
99 citing papers in PubMed, 273 citations in OpenAlex.
- Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.Scientific reports · 2026Article
- Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota.National science review · 2026Article
- Diverse microbial metal resistance and novel metal cycling organisms in copper/nickel mine tailings.Metallomics : integrated biometal science · 2026Article
- Halophilic Anaerobic Cultures Enriched with COMicrobial ecology · 2026Article
- Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.ISME communications · 2026Article
- Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.Journal of oral microbiology · 2026Article
- Antibiotic Resistance Crisis: From Bacterial Bioprospecting to Artificial Intelligence.Environmental microbiology reports · 2025Review
- Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.Nature microbiology · 2025Article
- Shrub Expansion Impacts on Carbon, Nitrogen, and Sulfur Cycles and Microorganism Communities in Wetlands in Northeastern China.Microorganisms · 2025Article
- Current state of the heavy metal pollution, microbial diversity, and bioremediation experiments around the Qixia Mountain lead-zinc mine in Nanjing, China.RSC advances · 2025Article
- Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.Innovation (Cambridge (Mass.)) · 2025Article
- ComammoxiMeta · 2025Article
- Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes.Scientific data · 2025Article
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- Quantifying the contribution of the rare biosphere to natural disturbances.The ISME journal · 2025Article
- Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.FEMS microbiology ecology · 2024Article
- Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota.Nature communications · 2024Article
- Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, hereinNational science review · 2024Article
- Methods for studying microbial acid stress responses: from molecules to populations.FEMS microbiology reviews · 2024Review
- Statistical Modelling of Thermostable Cellulase Production Conditions of ThermophilicIndian journal of microbiology · 2024Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.