ArticleThe ISME journal2016
Predicting taxonomic and functional structure of microbial communities in acid mine drainage.
Article in The ISME journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed.
- A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.International journal of molecular sciences · 2017Trial
- Faster turnover of taxonomic over functional bacterial composition during vermicomposting indicates increasing functional redundancy.PloS one · 2026Article
- Bayesian networks for network inference in biology.Journal of the Royal Society, Interface · 2025Review
- Environmental stress mediates groundwater microbial community assembly.Nature microbiology · 2024Article
- A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems · 2024Article
- pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments.Frontiers in microbiology · 2024Article
- Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste.Environmental microbiome · 2023Article
- Predicting microbial community compositions in wastewater treatment plants using artificial neural networks.Microbiome · 2023Article
- Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province.Microorganisms · 2023Article
- Impact of Petroleum Contamination on the Structure of Saline Soil Bacterial Communities.Current microbiology · 2022Article
- Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.Nature communications · 2022Article
- Microbial diversity in extreme environments.Nature reviews. Microbiology · 2022Review
- Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles.Journal of fungi (Basel, Switzerland) · 2022Article
- Composition and Functional Characteristics and Influencing Factors of Bacterioplankton Community in the Huangshui River, China.Microorganisms · 2021Article
- High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.Applied and environmental microbiology · 2021Article
- Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning.ISME communications · 2021Article
- Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning.Scientific reports · 2021Article
- High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments.Microbial biotechnology · 2021Review
- Insights into the Metabolism and Evolution of the GenusmSystems · 2020Article
- Sediment Bacterial Community Structure Under the Influence of Different Domestic Sewage Types.Journal of microbiology and biotechnology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.
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.