Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
Open accessAbstract
Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.
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Because RNA extractions were performed, the study examined active prokaryotic communities.
“As we performed RNA extractions, we studied active prokaryotic communities (Blazewicz et al., 2013).”
From Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp <i>Litopenaeus stylirostris</i> : possible influence of the rearing water and more (2021) · cites this paper as Blazewicz et al., 2013
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- Authors
- Blazewicz, S. J., Barnard, R. L., Daly, R. A., & Firestone, M. K.
- Affiliations
- United States Geological Survey (US)
- Agroécologie (FR)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Blazewicz, Steven J
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-07-04
- Volume
- 7
- Issue
- 11
- Pages
- 2061-2068
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC3806256
- OpenAlex
- W1978468198
- Cited by
- 878
- References
- 79
- Citations by year
- 2026: 61 · 2025: 47 · 2024: 49 · 2023: 46 · 2022: 60 · 2021: 100 · 2020: 64 · 2019: 78 · 2018: 122 · 2017: 83 · 2016: 59 · 2015: 65 · 2014: 40 · 2013: 3
- FWCI
- 49.20
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The ISME Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy (DE-PS02-09ER09-25)
- European Commission (219357)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- ribosomal RNA, microbial activity, microbial growth rate, life history strategies, microbial assemblages, environmental microbial communities
- MeSH terms
- Bacteria, Ecology, Environmental Microbiology, RNA, Ribosomal, Ecosystem, Microbiota
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