Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Abstract

DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n = 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high-resolution taxonomy of groups problematic in conventional surveys (e.g., larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

“…Researchers have used metabarcoding (the amplification and sequencing of marker genes) of single-celled organisms in water samples for over thirty years to describe the diversity and composition of environmental microbial and phytoplankton communities (Hugenholtz, Goebel, & Pace, 1998;Pace, 1997;Pace, Stahl, Lane, & Olsen, 1986;Pedro, Di, Massana, Marina, & De, 2001). These methods have recently expanded to encompass multicellular organisms by taking advantage of the fact that all organisms leave traces of their genetic material in the environment as environmental DNA (eDNA) through shedding and depositing waste (Deagle, Clarke, Kitchener, Polanowski, & Davidson, 2018;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012). Since the majority of eDNA is found in the 1-10 µm size fraction, a 0.22 µm filter effectively captures both single-celled organisms and particulate organic matter left behind by multicellular individuals (Sassoubre, Yamahara, Gardner, Block, & Boehm, 2016;Turner et al, 2014).…”

Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding

“…Thus, when extracting DNA from bulk samples containing rare or small taxa with little biomass, those might be overshadowed by biomass rich taxa that contribute a large amount of DNA in the extraction. This natural variation in biomass can jeopardize the detection of small and rare specimens (Deagle et al, 2018), especially when taking PCR effects into account (Kelly, Shelton and Gallego, 2019). To maximise taxa detection in bulk samples showing substantial specimen biomass variation (Aylagas et al, 2016), size sorting might be required (Liu et al, 2019).…”

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

“…Few recent studies have employed the mitochondrial cytochrome c oxidase subunit I (COI) marker region to offset the limited taxonomic resolution of ribosomal genes (Deagle et al, ; Lacoursière‐Roussel et al, ; Leray & Knowlton, ). The COI “barcode” region (Hebert, Ratnasingham, & deWaard, ) is one of the most commonly used DNA fragments for the analysis of species diversity among marine animals (Bucklin, Steinke, & Blanco‐Bercial, ).…”

“…DNA-based methods are revolutionizing the analysis of biodiversity, as they offer advantages over traditional, visual, and morphological survey methods (Thomsen &Willerslev, 2015). Accordingly, eDNA metabarcoding approaches have been successfully employed to characterize specific marine plankton communities in natural seawater samples, such as zooplankton, mesozooplankton, and full eukaryotic plankton diversity (Chain, Brown, MacIsaac, & Cristescu, 2016;Deagle, Clarke, Kitchener, Polanowski, & Davidson, 2017;de Vargas et al, 2015;Djurhuus et al, 2018;López-escardó et al, 2018;Villarino et al, 2018), as well as benthic communities from both soft (Guardiola et al, 2015;Lejzerowicz et al, 2015;Pawlowski, Esling, Lejzerowicz, Cedhagen, & Wilding, 2014) and hard (Leray & Knowlton, 2015;Wangensteen, Cebrian, Palacín, & Turon, 2018;Wangensteen, Palacín, Guardiola, & Turon, 2018) bottom habitats.…”