ArticleApplied and environmental microbiology2013
Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.
Article in Applied and environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 116 citations in OpenAlex.
- Environmental Adaptation Strategies of Deep-Sea Fungi.Journal of fungi (Basel, Switzerland) · 2026Review
- Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland.FEMS microbiology letters · 2026Article
- Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.Frontiers in microbiology · 2026Article
- Deep-sea viral diversity and their role in host metabolism of complex organic matter.Nature communications · 2025Article
- A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.Science advances · 2024Article
- Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.Advanced biotechnology · 2024Review
- Development of a genetic system forApplied and environmental microbiology · 2024Article
- Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses.Journal of advanced research · 2024Article
- Scientific novelty beyond the experiment.Microbial biotechnology · 2023Article
- Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems.PloS one · 2023Article
- The Viral Susceptibility of theViruses · 2022Article
- Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece.Frontiers in microbiology · 2022Article
- Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea.Frontiers in microbiology · 2022Article
- The global ocean size spectrum from bacteria to whales.Science advances · 2021Article
- Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin.ISME communications · 2021Article
- Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes.Microorganisms · 2021Article
- Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.Microbiology and molecular biology reviews : MMBR · 2021Review
- Cellular and Genomic Properties ofFrontiers in microbiology · 2021Article
- Global diversity of microbial communities in marine sediment.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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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
There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.
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