Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Lavrinienko, Anton; Jernfors, Toni; Koskimäki, Janne J.; Pirttilä, Anna Maria; Watts, Phillip C.

doi:10.1016/j.tim.2020.05.019

Cited by 96 publications

(77 citation statements)

References 75 publications

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“…Finally, we also compared the relative read abundances of the different marker genes against the proportional biovolume for each taxon (Figure 3). Although the copy number of rRNA marker genes was previously proposed as proxy of cell biovolume (due to a positive association between rDNA content and cell size in some marine protist taxa (Lavrinienko et al 2021)), the correlation of biovolume against rRNA gene relative abundances were not stronger than those against psbO (Figures 3 and S5). The relative read abundances for Prochlorococcus and eukaryotic picophytoplankton based either on 16S rDNA or psbO were higher than their proportional biovolume in the same samples, while the opposite occurred for Synechococcus.…”

Section: Comparison With Imaging Dataset Suggested That Psbo Is a Robust Marker Gene For Estimating Relative Cell Abundance Of Phytoplankmentioning

confidence: 84%

“…Biovolume is a proxy of biomass, which is a relevant variable for studies of energy and matter fluxes such as food web structures and biogeochemical cycles. However, there is still little consensus for the use of rRNA gene as a biovolume estimator due to the poor correlations reported in many studies (Lamb et al, 2019;Lavrinienko, Jernfors, Koskimäki, Pirttilä, & Watts, 2021;Santoferrara, 2019;van der Loos & Nijland, 2021). Instead, there are attempts to infer relative cell abundances from rRNA gene metabarcoding by correcting the copy number variation.…”

Section: Introductionmentioning

confidence: 99%

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A robust approach to estimate relative phytoplankton cell abundance from metagenomes

Pelletier

Zinger

et al. 2021

Preprint

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Phytoplankton account for >45% of primary production on Earth, and hence have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found across many of the major clades of the tree of life, including prokaryotes (cyanobacteria) and multiple eukaryotic lineages. Phytoplankton communities are generally studied by PCR amplification of rRNA marker genes from DNA extracted from environmental samples and high-throughput sequencing of the amplicons. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa and the fact that rRNA do not provide insights into metabolic traits such as photosynthesis (i.e., it is sometimes difficult to distinguish an rRNA sequence of a phytoplanktonic species from a phylogenetically close non-photosynthetic species). In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously, thus hampering assessment of the entire phytoplankton community. Here, we propose to use the core single-copy photosynthetic gene psbO extracted from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is present in both prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed in most cases improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine communities of dinoflagellates. To facilitate the incorporation of psbO in future molecular-based surveys, we released a curated database including >26,000 sequences. Overall, psbO appears to be a promising new gene marker for improving molecular-based evaluations of phytoplankton communities.

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Section: Comparison With Imaging Dataset Suggested That Psbo Is a Robust Marker Gene For Estimating Relative Cell Abundance Of Phytoplankmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

A robust approach to estimate relative phytoplankton cell abundance from metagenomes

Pelletier

Zinger

et al. 2021

Preprint

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“…Another aspect that prevents data analyses from being fully quantitative is the potential of multiple copies of marker genes present per organism, which may also vary across taxa. For example, the 16S rRNA gene copy number per bacterial cell can vary between 1 and 18 and can additionally show variation within different strains of the same species (Stoddard et al, 2014;Coenye and Vandamme, 2003;Lavrinienko et al, 2021). Therefore, relying solely on the number and diversity of markers such a 16S rRNA genes can lead to inaccurate estimates of the relative abundance and diversity of microbial communities.…”

Section: Compositionality Necessitates Careful Data Processingmentioning

confidence: 99%

A critical perspective on interpreting amplicon sequencing data in soil ecological research

Alteio

Séneca

Canarini

et al. 2021

Preprint

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Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing studies in soil and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation and availability to improve the rigor of future studies.

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“…rDNA is abundant in many eukaryotic genomes, typically varying from tens to thousands of copies depending upon the species Parks et al, 2018;Prokopowich et al, 2003;Symonová, 2019). Moreover, rDNA copy number can vary widely among individuals within a species (Lavrinienko, Jernfors, et al, 2020;Symonová, 2019;Weider et al, 2005), and geographic variation in rDNA content has been documented in diverse taxa (reviewed by Weider et al, 2005), for example, among plant populations that differ in altitude and latitude (Strauss & Tsai, 1988), in Daphnia (Harvey et al, 2020), and among human populations (Parks et al, 2018). As a tandemly repeating locus, rDNA is prone to copy-number mutations, a feature that is exacerbated by topological stress from opening of the helical DNA structure and collisions between replication and transcription machinery due to frequent transcription (Salim & Gerton, 2019).…”

Section: Introductionmentioning

confidence: 99%

Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides

Jernfors

Danforth

Kesäniemi

et al. 2021

Ecology and Evolution

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Altered copy number of certain highly repetitive regions of the genome, such as satellite DNA within heterochromatin and ribosomal RNA loci (rDNA), is hypothesized to help safeguard the genome against damage derived from external stressors. We quantified copy number of the 18S rDNA and a pericentromeric satellite DNA (Msat‐160) in bank voles ( Myodes glareolus ) inhabiting the Chernobyl Exclusion Zone (CEZ), an area that is contaminated by radionuclides and where organisms are exposed to elevated levels of ionizing radiation. We found a significant increase in 18S rDNA and Msat‐160 content in the genomes of bank voles from contaminated locations within the CEZ compared with animals from uncontaminated locations. Moreover, 18S rDNA and Msat‐160 copy number were positively correlated in the genomes of bank voles from uncontaminated, but not in the genomes of animals inhabiting contaminated, areas. These results show the capacity for local‐scale geographic variation in genome architecture and are consistent with the genomic safeguard hypothesis. Disruption of cellular processes related to genomic stability appears to be a hallmark effect in bank voles inhabiting areas contaminated by radionuclides.

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Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Cited by 96 publications

References 75 publications

A robust approach to estimate relative phytoplankton cell abundance from metagenomes

A robust approach to estimate relative phytoplankton cell abundance from metagenomes

A critical perspective on interpreting amplicon sequencing data in soil ecological research

Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides

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