Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

By Thorsten Stoeck, David Bass, M. Nebel, Richard Christen, Meredith D. M. Jones, H. Breiner, T. Richards. Molecular Ecology, 2010

1,499 citations recorded by the source corpus.

Sequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour‐intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High‐throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers—the variable V4 and V9 regions—from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4f9ae5f3e32dfb1539de8c681fe0c6dbd82d8acf

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Citations in the corpus

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future (2013, background): “Using NGS it is now possible to recover thousands of DNA (or RNA) sequences directly from environmental samples (e.g. Sogin et al. 2006; Stoeck et al. 2010).”
The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps (2013, background): “…for assessing microbial diversity (Guillou 236 Downloaded from https://academic.oup.com/plankt/article-abstract/35/2/235/1436132 by guest on 28 July 2018 et al., 2008; Not et al., 2009; Cheung et al., 2010; Countway et al., 2010; Scheckenbach et al., 2010; Stoeck et al., 2010; Caron et al., 2012).”
Mesocosm Experiments as a Tool for Ecological Climate-Change Research (2013, background): “Microscopic diversity is currently at the forefront of DNA-based approaches to taxonomy in marine (Stoeck et al., 2010), freshwater (Medinger et al.”
Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem (2017, neutral): “…et al., 2016), targeting metazoans exclusively; COI, ca. 315 bp, (Leray et al., 2013), targeting eukaryotes], and Frontiers in Marine Science | www.frontiersin.org 2 January 2017 | Volume 3 | Article 283 one nuclear ribosomal gene [18S, ca. 385 bp, (Stoeck et al., 2010), targeting eukaryotes].”
Microbial colonization of microplastics in the Caribbean Sea (2020, methodology): “2016) to amplify the V4–V5 region of bacterial 16S rRNA genes and primers eukv4F and eukv4R (Stoeck et al. 2010) to amplify the V4 region of eukaryotic 18S rRNA genes.”
Next‐generation sequencing technologies for environmental DNA research (2012, background): “Marine eukaryotic microbiota were investigated through NGS analysis of 18S rDNA amplicons (Stoeck et al. 2010).”
Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes (2014, background): “, 2011) that has been recently extended to eukaryotes (Fonseca et al., 2010; Stoeck et al., 2010; Bik et al., 2012; Logares et al., 2014) and the expanding field of environmental DNA analysis (Hajibabaei et al.”
Protist diversity along a salinity gradient in a coastal lagoon (2015, methodology): “The reverse primer used here was found to amplify a larger fraction of protists (85% of all classes), especially Haptophyta — compared to the V4R primer used previously (Stoeck et al. 2010) — using testprime (www. arb-silva . de/ search/ testprime/).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “In contrast, slightly more studies conducted in marine habitats focused on sediments (e.g. Nagahama et al. 2011; Pawlowski et al. 2011; Dong et al. 2015) compared to water samples (e.g. Stoeck et al. 2010; Thomsen et al. 2012a; Pochon et al. 2013).”