The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed
Open accessAbstract
For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.
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“However, the prediction of process rates from the presence and quantity of genes and transcripts is yet to be clearly established (Rocca et al., 2015).”
From Soil quality – A critical review (2018) · cites this paper as Rocca et al., 2015
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Embracing the unknown: disentangling the complexities of the soil microbiome
Fierer, N. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.87 · Cited by 3,579
Soil quality – A critical review
Bünemann, E. K., Bongiorno, G., Bai, Z., Creamer, R. E., De Deyn, G., de Goede, R., Fleskens, L., Geissen, V., Kuyper, T. W., Mäder, P., et al. (2018) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2018.01.030 · Cited by 2,960
Malik, A. A., Martiny, J. B. H., Brodie, E., Martiny, A. C., Treseder, K. K., & Allison, S. (2019) · The ISME Journal · doi:10.1038/s41396-019-0510-0 · Cited by 1,244
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Metadata
- Authors
- Rocca, J. D., Hall, E. K., Lennon, J. T., Evans, S. E., Waldrop, M. P., Cotner, J. B., Nemergut, D. R., Graham, E. B., & Wallenstein, M. D.
- Affiliations
- Colorado State University (US)
- Natural Resource Ecology Laboratory, Colorado State University , Fort Collins, CO, USA
- Indiana University Bloomington (US)
- Michigan State University (US)
- United States Geological Survey (US)
- University of Minnesota (US)
- Duke University (US)
- Corresponding author
- Rocca, Jennifer D
- ORCID
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-12-23
- Volume
- 9
- Issue
- 8
- Pages
- 1693-1699
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC4511926
- OpenAlex
- W2024344827
- Cited by
- 398
- References
- 45
- Citations by year
- 2026: 66 · 2025: 32 · 2024: 34 · 2023: 24 · 2022: 48 · 2021: 38 · 2020: 35 · 2019: 30 · 2018: 32 · 2017: 25 · 2016: 28 · 2015: 6
- FWCI
- 2.13
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The ISME Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Geological Survey
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- gene abundance, mRNA levels, enzyme activity, carbon cycle, nitrogen cycling, transcription and translation, metagenomics, metatranscriptomics, ecosystem processes
- MeSH terms
- Carbon, Catalysis, Dosage Compensation, Genetic, Nitrogen, Transcription, Genetic, Gene Expression Regulation, Bacterial, Ecosystem, Gene Dosage, Gene Expression Profiling, Biocatalysis
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