ArticleThe ISME journal2015
Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities.
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 22 papers.
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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.
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Who cites it
22 citing papers in PubMed, 79 citations in OpenAlex.
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- Comparative Genomics of Sigma Factors inMicroorganisms · 2025Article
- Insights into the role of cyclopropane fatty acid synthase (CfaS) from extreme acidophile in bacterial defense against environmental acid stress.Extremophiles : life under extreme conditions · 2024Article
- Renaissance for magnetotactic bacteria in astrobiology.The ISME journal · 2023Review
- The evolution of alkaliphilic biofilm communities in response to extreme alkaline pH values.MicrobiologyOpen · 2022Article
- Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments.Microbial cell factories · 2021Review
- Insights into the Metabolism and Evolution of the GenusmSystems · 2020Article
- Expanding magnetic organelle biogenesis in the domain Bacteria.Microbiome · 2020Article
- Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic.Extremophiles : life under extreme conditions · 2020Article
- Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies.Current microbiology · 2020Review
- Validation of Genetic Markers Associated to Oxygen Availability in Low-Grade Copper Bioleaching Systems: An Industrial Application.Frontiers in microbiology · 2019Article
- Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Low-Abundance Members of theFrontiers in microbiology · 2018Article
- Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.Microbiome · 2017Review
- Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps.Frontiers in microbiology · 2017Article
- Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France.Microbial ecology · 2016Article
- Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale.Microbial ecology · 2016Article
- Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets.Microbial ecology · 2016Article
- Article
- Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.Proteomics · 2015Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ∼ 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time.
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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.