ArticleFrontiers in microbiology2018
Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.
Article in Frontiers in microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A global perspective on bacterial diversity in the terrestrial deep subsurface.Microbiology (Reading, England) · 2023Pooled it
- Multi-Year Biofilm Formation on Granitic Surfaces Reveals Dynamic Microbial Communities in Fennoscandian Shield Deep Groundwaters.Microbial ecology · 2026Article
- Ecological Processes Underpinning Microbial Variability in Archean Granitoids Beneath the Deccan Traps: Evidence From Deep Drilling in Koyna, India.Environmental microbiology reports · 2026Article
- Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential COScientific reports · 2026Article
- The Microbiology and Geochemistry of the Shallow-Water Hydrothermal Vents of the Gulf of Naples, Italy.Environmental microbiology · 2026Article
- From CRISPR-Cas to Argonautes: Defense systems of bacteria and archaea in the hydrothermal deep subsurface.ISME communications · 2026Article
- The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time.Environmental microbiome · 2025Article
- Guidelines for preventing and reporting contamination in low-biomass microbiome studies.Nature microbiology · 2025Review
- Resilience of deep aquifer microbial communities to seasonal hydrological fluctuations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere.Nature communications · 2025Article
- Ubiquitous microbial contaminants associated with scientific ocean drilling.Access microbiology · 2025Article
- Genotype and culture condition effects on single-cell diatom microbiomes: enhanced detection of low-abundance taxa with CRISPR-Cas9.ISME communications · 2025Article
- A global deep terrestrial biosphere core microbiome.ISME communications · 2025Article
- Article
- Heterogeneity of rock-hosted microbial communities in a serpentinizing aquifer of the Coast Range Ophiolite.Frontiers in microbiology · 2025Article
- A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.Science advances · 2024Article
- Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.Nature communications · 2024Article
- An Update on Implant-Associated Malignancies and Their Biocompatibility.International journal of molecular sciences · 2024Review
- Impact of root canal preparation using two single-file systems on the intra-radicular microbiome of teeth with primary apical periodontitis.Clinical oral investigations · 2024Article
- Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy.Environmental microbiology reports · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were
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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.