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Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed
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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).”
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Cites
Conducting Meta-Analyses in R with the metafor Package
Viechtbauer, W. (2010) · Journal of Statistical Software · doi:10.18637/jss.v036.i03 · Cited by 20,464
Meta-Analytic Procedures for Social Research
Rosenthal, R. (1991) · doi:10.4135/9781412984997 · Cited by 4,635
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Meta-Analytic Procedures for Social Research.
Metcalfe, A., & Rosenthal, R. (1994) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.2307/2348600 · Cited by 4,249
Effect size, confidence interval and statistical significance: a practical guide for biologists
Nakagawa, S., & Cuthill, I. C. (2007) · Biological Reviews · doi:10.1111/j.1469-185x.2007.00027.x · Cited by 3,835
Principles of Terrestrial Ecosystem Ecology
Chapin, F., Matson, P., & Mooney, H. A. (2002) · Springer: New York · doi:10.1007/b97397 · Cited by 3,714
Rotthauwe, J.-H., Witzel, K.-P., & Liesack, W. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.12.4704-4712.1997 · Cited by 2,900
Isolation of an autotrophic ammonia-oxidizing marine archaeon
Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., & Stahl, D. A. (2005) · Nature · doi:10.1038/nature03911 · Cited by 2,864
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., & Oakley, B. B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506625102 · Cited by 2,426
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
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Duan, R., Gao, W., He, Q., Zhai, Z., Zong, Y., Zhang, D., Shi, X., Hao, X., & Li, P. (2026) · Journal of Cleaner Production · doi:10.1016/j.jclepro.2026.148585 · Cited by 1
Govednik, A., Jones, C. M., Hallin, S., & Suhadolc, M. (2026) · Applied Soil Ecology · doi:10.1016/j.apsoil.2026.107165 · Cited by 1
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Robinson, J. M., Guentas, L., & Breed, M. F. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001777 · Cited by 1
Xue, R., Li, J., Hu, S., Ding, J., Wang, C., Ke, W., Li, C., Corvini, P. F.-X., & Cui, L. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag250 · Cited by 2
Yan, W., Wang, W., Chen, W., Cui, K., Zhang, X., Shangguan, Z., & Zhong, Y. (2025) · Global Ecology and Biogeography · doi:10.1111/geb.70058 · Cited by 1
Koos, J. M. A. (2018) · doi:10.33915/etd.7201 · Cited by 1
Tree microbiomes and methane exchange in upland forestsPreprint
Gewirtzman, J., Arnold, W., Taylor, M., Burrows, H., Merenstein, C., Woodbury, D. J., Whitlock, N., Kraut, K., González, L. F., Brodersen, C. R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.679632 · Cited by 1
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Thieffry, S., Aubert, J., Beguet, J., Devers‐Lamrani, M., Martin-Laurent, F. A., Pesce, S., Romdhane, S., Rouard, N., Siol, M., & Spor, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.21.707176 · Cited by 1
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Rousk, J., & Hicks, L. C. (2021) · doi:10.5194/egusphere-egu21-14139
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(2022) · SOIL · doi:10.5194/soil-2021-148-rc2
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Li, S., Yan, X. D., Ndayishimiye, J. C., Smirnov, A. V., Tsyganov, A. N., Nassonova, E., Mazei, N. G., Mazei, Y., & Yang, J. (2025) · Journal of Environmental Sciences · doi:10.1016/j.jes.2025.07.053
Duan, D., Sacks, E. J., & Kent, A. D. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5524923
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Preheim, S. P., Morris, S., Zhang, Y., Holder, C., Arora‐Williams, K., Gensbigler, P. A., Hinton, A., Jin, R., Pradal, M., Buchanan, M., et al. (2025) · Journal of Geophysical Research Biogeosciences · doi:10.1029/2025jg009066
de Araújo, V. L. V. P. (2024) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
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Hu, X., Wang, Z., Liu, Z., Gao, Z., Zhang, X., Du, L., Gao, W., Jia, M., Han, G., & Zhang, G. (2026) · Ecological Engineering · doi:10.1016/j.ecoleng.2026.107976
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Domeignoz‐Horta, L. A. (2016) · theses.fr (ABES) · doi:10.70675/0fc7d78dz937bz46adzabb7z88ee4c1c3bd4
Zhang, Q., He, G., Guo, Z., He, Y., Xiong, J., He, T., & Lee, S. L. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05008-7
Mishra, P., Mishra, U., Singh, A., Panda, D., & Srivastava, P. K. (2026) · Bioresource Technology · doi:10.1016/j.biortech.2026.134945
Chen, D., Ibrar, M., Yan, F., Sun, G., Xue, R., Jia, A., Zhou, J., Gao, Y., Ma, C., Wang, M., et al. (2026) · Journal of Environmental Management · doi:10.1016/j.jenvman.2026.130022
Yuan, G., Zhou, M. Y., Xiong, C., Bai, R., Cao, F., Yuan, Y., Zhang, W., & Bai, W. (2026) · New Phytologist · doi:10.1111/nph.71342
Wang, L., Gao, H., Fu, S., Xu, L., Zhang, L., Li, H., You, C., Liu, S., Xu, H., Li, J., et al. (2026) · Plant and Soil · doi:10.1007/s11104-026-08744-9
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Li, S., Rigon, L., Chiodi, C., Gavinelli, F., Ravi, S., Celletti, S., Zardinoni, G., Maucieri, C., Giordano, M., Giagnoni, L., et al. (2026) · Agriculture · doi:10.3390/agriculture16131410
Kim, H.-R., Lim, J., Jung, H.-K., Shim, J.-M., Kim, J., Kim, S.-Y., & Kim, I. (2026) · Biogeosciences · doi:10.5194/bg-23-4719-2026
Liu, Z., Gao, D., Wang, C., Zhu, Y., Liu, X. G., & Liu, S. (2026) · Geoderma · doi:10.1016/j.geoderma.2026.117935
Yin, X., Gurieff, N. B., & Oehmen, A. (2026) · Journal of Environmental Management · doi:10.1016/j.jenvman.2026.130497
He, D., Xu, C., Shi, J., Niu, H., Lian, J., Wang, Q., Xing, W., Ruan, H., Wang, L., & Yuan, Y. (2026) · Applied Soil Ecology · doi:10.1016/j.apsoil.2026.107318
Li, Y., Han, M., Qu, Z., Gong, Z., Gao, T., Wang, J., Ren, A., & Zhao, N. (2026) · European Journal of Soil Biology · doi:10.1016/j.ejsobi.2026.103853
Song, M., Wang, J., & Mu, C. (2026) · Forests · doi:10.3390/f17080899
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Liu, J., Clough, T., Carrick, S. T., Luo, J., Podolyan, A., Wells, N. S., Shen, J., Li, P., Du, L., Pan, H., et al. (2026) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2026.110286
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Küsel, K., Singavarapu, B., Human, Z. R., Patoine, G., Heintz‐Buschart, A., Bei, Q., Wegner, C., Eisenhauer, N., Buscot, F., Guerra, C. A., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-9962094/v1
Wang, T., Li, Z., Shao, S., Sun, Y., & Wang, J. (2026) · Land · doi:10.3390/land15081474
Chen, R., Ruan, S., Liu, C., Chen, F., Zhang, Y., Gao, D., & Yang, P. (2026) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2026.120270
Yao, L., Shao, B., Gu, L., Li, W., Ma, B., Gao, X., & Wang, W. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7315746
Sébilo, M., Redon, B., Ousselin, E., Longchamp, M., Chalder, L., Devarieux, A., Jean-Louis, P., & Gros, O. (2026) · European Journal of Soil Science · doi:10.1111/ejss.70396
Feng, J., Sun, X., Zhang, R., Xu, S., Wan, Y., Li, T., Zhang, Y., Alnaimy, M. A., 伍延正, Meng, L., et al. (2026) · Agriculture · doi:10.3390/agriculture16171832
Cai, X., Chen, L., Chen, C., Zhu, X., Singh, A. K., & Liu, W. (2026) · CATENA · doi:10.1016/j.catena.2026.110553
Li, R., Zhang, C., Miao, Y., Li, F., Zhang, G., Sun, Q., Hua, T., Pang, Z., & Lin, X. (2026) · Microorganisms · doi:10.3390/microorganisms14091907
Elevated water levels drive greenhouse gas mitigation in the riparian zone profile
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Hou, H., Lan, X., Xiao, J., Lv, Z., Liu, X., Liu, Y., & Ji, J. (2026) · Soil Ecology Letters · doi:10.1007/s42832-026-0465-9
Impact of Chamaecrista rotundifolia cover cropping on soil elemental cycling in karst agroecosystems
Yue, Z., Sheng, S., Peng, L., Xu, W., Zhang, J., Wu, D., Liu, B., Li, Q., Dong, R., Cheng, H., et al. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1906173
Kwon, H., Wang, Q., Riveros, A., Li, Y., & Jiang, D. (2026) · Environmental Research · doi:10.1016/j.envres.2026.125626
Jiayi, Z., Jiacheng, T., Fang, F., Yanting, Z., Li, S., Dandan, M., ShunBao, L., & Yanjie, Z. (2026) · Plant and Soil · doi:10.1007/s11104-026-09067-5
Sai, J., Deng, Z., Ni, Q., Wang, C., Dan, X., Hu, J., Bao, H., Jin, C., Yue, Z., Zhu, Q., et al. (2026) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2026.125132
Guo, X., He, Z., Wang, X., Ren, H., Ren, B., Zhang, J., Liu, P., Song, Z., & Zhao, B. (2026) · Journal of Environmental Management · doi:10.1016/j.jenvman.2026.130951
Wang, P., Sun, X., Li, W., CaiYan, D., Liu, H., Yuan, S., Jintrawet, A., Wang, B., Tang, L., & Wang, Z. (2026) · European Journal of Agronomy · doi:10.1016/j.eja.2026.128340
Pedersen, M. L., Jørgensen, H. M., Andersen, A. G., Priemé, A., Jiménez, J. D. L. C., & Pedersen, O. (2026) · Research Square · doi:10.21203/rs.3.rs-10971694/v1
Yin, Y., Ma, Y., Wang, Y., 高配科, Jia, C., Li, C., Yang, Q., Zhang, F., Bo, H., Wang, R., et al. (2026) · RSC Advances · doi:10.1039/d6ra03694e
Yao, L., Shao, B., Gu, L., Li, W., Ma, B., Gao, X., & Wang, W. (2026) · Bioresource Technology · doi:10.1016/j.biortech.2026.136019
Dong, H., Ren, K., Lan, J., Peng, C., Pan, X., Tu, C., Song, C., 张文平, & Cao, J. (2026) · Environmental Research · doi:10.1016/j.envres.2026.125870
Wang, L., Zhang, S., Luo, Y., Sui, P., Liu, X., Li, Q., Liang, Y., Wang, H., 蔡红光, Ren, Y., et al. (2026) · Agriculture Ecosystems & Environment · doi:10.1016/j.agee.2026.110791
Yang, X., Li, Y., You, K., Liu, Y., Rensing, C., & Li, Y. (2026) · Agricultural Environment and Sustainability · doi:10.1016/j.ages.2026.100047
Ding, E., Zhao, L., Hu, Y., Zhang, J., Zafar, A., Wang, S., Li, X., Wang, X., & Shen, W. (2026) · Ecological Engineering · doi:10.1016/j.ecoleng.2026.108185
Gu, Y., Liu, Z., Qian, H., Zhao, X., Ji, Y., Zeng, X., Shi, Y., Niyatbekov, T., Yang, Y., Baozhan, 王. W., et al. (2026) · Geoderma · doi:10.1016/j.geoderma.2026.118091
Youxin, H., 渠祁, Li, Z., Liang, J., Smith, A., Smith, M. N., Gao, D., Jing, L., & Lu, W. (2026) · Agricultural and Forest Meteorology · doi:10.1016/j.agrformet.2026.111542
Wang, Y., Huang, Y., 沈仕洲, Ren, T., & Du, H. (2026) · Applied Soil Ecology · doi:10.1016/j.apsoil.2026.107540
Lepcha, A., Dogra, S., Kumar, R., Yadav, S. K., & Pati, A. M. (2026) · Biomass and Bioenergy · doi:10.1016/j.biombioe.2026.110210
Wang, A., Sun, Y., Feng, X., Zhang, L., Cai, Y., & Wang, C. (2026) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2026.125633
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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