University of Oulu

Lavrinienko, A., Jernfors, T., Koskimäki, J. J., Pirttilä, A. M., & Watts, P. C. (2021). Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities? Trends in Microbiology, 29(1), 19–27.

Does intraspecific variation in rDNA copy number affect analysis of microbial communities?

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Author: Lavrinienko, Anton1; Jernfors, Toni1; Koskimäki, Janne J.2;
Organizations: 1Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
2Ecology and Genetics, University of Oulu, 90014 Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.2 MB)
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Language: English
Published: Elsevier, 2021
Publish Date: 2021-03-05


Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, the rDNA is dynamic and can exhibit substantial interspecific and intraspecific variation in copy number in prokaryotes and, especially, in microbial eukaryotes. As change in rDNA copy number is a common response to environmental change, rDNA copy number is not necessarily a property of a species. Variation in rDNA copy number, especially the capacity for large intraspecific changes driven by external cues, complicates analyses of rDNA amplicon sequence data. We highlight the need to (i) interpret amplicon sequence data in light of possible interspecific and intraspecific variation, and (ii) examine the potential plasticity in rDNA copy number as an important ecological factor to better understand how microbial communities are structured in heterogeneous environments.

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Series: Trends in microbiology
ISSN: 0966-842X
ISSN-E: 1878-4380
ISSN-L: 0966-842X
Volume: 29
Pages: 19 - 27
DOI: 10.1016/j.tim.2020.05.019
Type of Publication: A1 Journal article – refereed
Field of Science: 1183 Plant biology, microbiology, virology
Funding: This work was supported by the Academy of Finland (to P.C.W. projects 287153 and 329334; to A.M.P. and J.J.K. project 308766), University of Oulu Graduate School (A.L.), and Finnish Cultural Foundation (T.J.).
Academy of Finland Grant Number: 308766
Detailed Information: 308766 (Academy of Finland Funding decision)
287153 (Academy of Finland Funding decision)
Copyright information: © 2020 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (