ArticleApplied and environmental microbiology2015
Quantitative microbial ecology through stable isotope probing.
Article in Applied and environmental microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed, 305 citations in OpenAlex.
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
- Soil microbial growth rate, trophic strategy, and the oligotroph-copiotroph continuum.Applied and environmental microbiology · 2026Article
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- A Review of Rumen Biohydrogenation and Efficient, Green Production of High-Quality Ruminant Products: Mechanisms, Opportunities and Challenges.Animals : an open access journal from MDPI · 2026Review
- Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.mSystems · 2026Article
- Seasonal thawing of high Arctic soils triggers selective microbial growth and predation.mSystems · 2026Article
- Fungi enhance microbial carbon retention in high Arctic fjord sediment.PLoS biology · 2026Article
- Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.Nature communications · 2026Article
- Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.Microbiome · 2026Article
- Key role of moss in supplementing nitrogen for plant growth under warming in a permafrost ecosystem.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hypoxia increases microbial carbon assimilation of taurine in a seasonally anoxic fjord.The ISME journal · 2026Article
- Widespread marine and freshwater distributions of active sulfoquinovose-degrading bacteria.The ISME journal · 2026Article
- SIPdb: a stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using reverse ecology.ISME communications · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Fungi without borders: cross-ecosystem decomposition of riparian leaf litter.ISME communications · 2026Article
- Fungal Community Responses to Natural Humus Amendment Potentially Facilitate the Enhancement of Saline-Alkali Soil Multifunctionality.Microorganisms · 2025Article
- Cosmopolitan marine bacteria facilitate a vast phytoplankton-derived sulfonate-based carbon flow through sulfoquinovosidases.Nature communications · 2025Article
- DNA stable isotope probing reveals hidden microbial carbon processing pathways in agricultural soils.Applied and environmental microbiology · 2025Article
- Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.Environmental microbiome · 2025Article
- Ecosystem consequences of a nitrogen-fixing proto-organelle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
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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.