ICES Journal of Marine Science - Special Issue

Patterns of Biodiversity of Marine Zooplankton Based on Molecular Analysis

MZG JMS Special Issue

A Themed Set (aka "special issue") of 15 publications; with 7 co-authored by WG157 MetaZooGene members.

WG157 Themed Set motivators:  Ann Bucklin, Katja Peijnenburg, Ksenia Kosobokova, Tyuji Machida


Authors Title Abstract

Theme Set Introduction

Bucklin, Ann; Peijnenburg, Katja T.C.A.; Kosobokova, Ksenia; Machida, Ryuji J.



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New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches

Marine zooplankton are key players in pelagic food webs, central links in ecosystem function, useful indicators of water masses, and rapid responders to environmental variation and climate change. Characterization of biodiversity of the marine zooplankton assemblage is complicated by many factors, including systematic complexity of the assemblage, with numerous rare and cryptic species, and high local-to-global ratios of species diversity. The papers in this themed article set (TS) document important advances in molecular protocols and procedures, integration with morphological taxonomic identifications, and quantitative analyses (abundance and biomass). The studies highlight several overarching conclusions and recommendations. A primary issue is the continuing need for morphological taxonomic experts, who can identify species and provide voucher specimens for reference sequence databases, which are essential for biodiversity analyses based on molecular approaches. The power of metabarcoding using multi-gene markers, including both DNA and RNA templates, is demonstrated. An essential goal is the accurate identification of species across all taxonomic groups of marine zooplankton, with particular concern for detection of rare, cryptic, and invasive species. Applications of molecular approaches include analysis of trophic relationships by metabarcoding of gut contents, as well as investigation of the underlying ecological and evolutionary forces driving zooplankton diversity and structure.

Authors Title Abstract

Theme Set Contributed Papers

Brandão, Manoela (proxy) (contact); Comtet, Thierry; Pouline, Patrick; Cailliau, Caroline; Blanchet-Aurigny, Aline; Sourisseau, Marc; Siano, Raffaele; Memery, Laurent; Viard, Frederique; Nunes, Flavia



Oceanographic structure and temporal variations contribute to high heterogeneity in mesozooplankton over small spatial scales The coastal oceans can be highly variable, especially near ocean fronts. The Ushant Front is the dominant oceanographic feature in the Iroise Sea (NW Atlantic) during summer, separating warm stratified offshore waters from cool vertically-mixed nearshore waters. Mesozooplankton community structure was investigated over an annual cycle to examine relationships with oceanographic conditions. DNA metabarcoding of COI and 18S genes was used in communities from six sites along two cross-shelf transects. Taxonomic assignments of 380 and 296 OTUs (COI and 18S respectively) identified 21 classes across 13 phyla. Meroplankton abundances peaked in spring and summer, particularly for polychaete and decapod larvae respectively, corresponding to the reproductive periods of these taxa. Meroplankton was most affected by season, while holoplankton varied most by shelf position. Copepods with a mixed feeding strategy were associated with the most offshore sites, especially in the presence of the front, while filter-feeding or carnivorous copepods were associated with nearshore sites. In sum, mesozooplankton communities in well-mixed coastal waters were distinct from those found in the Ushant Front (high thermal stratification and chlorophyll-a). Furthermore, the benthic compartment, through its partial life cycle in the water column, contributed to high heterogeneity in planktonic communities over short temporal and spatial scales.

Bucklin, Ann (proxy) (contact); Questel, Jennifer; Frenzel, Alexandra; Smolenack, Sara; Wiebe, Peter



Population connectivity of the euphausiid, Stylocheiron elongatum, in the Gulf Stream (NW Atlantic Ocean) in relation to COI barcode diversity of Stylocheiron species The euphausiid genus Stylocheiron includes species that exhibit broad and disjunct biogeographical distributions, spanning multiple ocean basins. Variation of the mitochondrial cytochrome oxidase I (COI) barcode region within and between eight species of Stylocheiron revealed marked differences in geographical patterns of variation. One circumglobal species, S. elongatum, showed low barcode variation (<1%) among ocean basins, and was examined for population connectivity along the Gulf Stream System in the NW Atlantic Ocean using short regions of COI and mitochondrial cytochrome b (CYB). Specimens were identified from samples collected in the Florida Current (February, 1993) and Gulf Stream Meander Region (April, 1993). Phylogeographic analysis supported a migration pathway along the Gulf Stream and revealed small-but-significant genetic differentiation between the regions. Both gene regions showed high haplotype diversity and low nucleotide diversity, consistent with departures from neutral expectations and recent (post-glacial) population expansion. These results indicate that even dynamic current systems may not result in genetic homogenization (panmixis) of marine zooplankton populations. Global-scale studies of population genetic diversity and connectivity are needed to evaluate the ecological and evolutionary consequences of circumglobal distributions of Stylocheiron species.

Di Capua, Iole (proxy) (contact); Piredda, Roberta; Mazzocchi, Maria Grazia; Zingone, Adriana




Metazoan diversity and seasonality through eDNA metabarcoding at a Mediterranean long term ecological research site Metabarcoding of filtered environmental DNA has provided striking insights into the diversity of marine microbes. With this approach, we assessed the diversity of metazoan assemblages and their temporal variations in surface waters of the Long Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples (Mediterranean Sea). The Illumina sequencing of the V4-18S rDNA fragment from 48 samples collected in 2011-2013 produced a total of 5,011,047 marine metazoan reads. The normalized dataset was generally dominated by copepods (60.3%), followed by anellids (34.7%) mostly represented by the invasive benthic polychaete Hydroides elegans. Non-copepod holoplankton were mainly represented by siphonophores, rotifers and appendicularians, with occasional outbursts of jellyfish. The rest of meroplankton (mainly mollusks, anellids and anthozoans) showed a high diversity, covering all 11 zooplankton phyla, from Porifera to Craniata. A high number of copepod genera were identified, with seasonal recurrence matching patterns observed in years of studies in the Gulf of Naples. Despite limitations related to the molecular marker and reference dataset, the study provided valuable insights into diversity and seasonal pattern of the whole metazoans assemblage, expanding the knowledge on rare or hardly identifiable taxa and confirming DNA metabarcoding as a powerful approach to be integrated at LTER sites.

Ershova, Elizaveta (proxy) (contact); Wangensteen, Owen; Descoteaux, Raphaelle; Barth-Jensen, Coralie; Præbel, Kim



Metabarcoding as a quantitative tool for estimating biodiversity and relative biomass of marine zooplankton Although metabarcoding is a well-established tool for describing diversity of pelagic communities, its quantitative value is still controversial, with poor correlations previously reported between organism abundance/biomass and sequence reads. In this study, we explored an enhanced quantitative approach by metabarcoding whole zooplankton communities using the highly degenerate Leray-XT primer set for the mitochondrial marker COI and compared the results to biomass estimates obtained using the traditional morphological approach of processing zooplankton samples. As expected, detected species richness using the metabarcoding approach was 3-4 times higher compared to morphological processing, with the highest differences found in the meroplankton fraction. 75% of the species identified using microscopy were also recovered in the metabarcoding run. Within the taxa detected using both approaches, the relative numbers of sequence counts were highly and significantly correlated with their relative biomass, estimated from length-weight regressions, for a wide range of metazoan taxa. The highest correlations were found for crustaceans and the lowest for meroplanktonic larvae. Our results show that the reported approach of using a metabarcoding marker with improved taxonomic resolution, universal coverage for metazoans, reduced primer bias and availability of a comprehensive reference database, allow for rapid and relatively inexpensive processing of hundreds of samples at a higher taxonomic resolution than traditional zooplankton sorting. The described approach can therefore be widely applied for monitoring or ecological studies.

Hirai, Junya (proxy) (contact); Hidaka, Kiyotaka; Nagai, Satoshi; Shimizu, Yugo



DNA/RNA metabarcoding and morphological analysis of epipelagic copepod communities in the Izu Ridge off the southern coast of Japan The Izu Ridge off the southern coast of Japan is composed of many seamounts and knolls and is an important fishery ground and hatchery of commercially important fish. Since pelagic copepods link lower and higher trophic levels, we investigated the epipelagic copepods in the Izu Ridge using 28S DNA/RNA metabarcoding and microscopic approaches. In comparison with off-ridge regions, a low water temperature and high chlorophyll a concentration were observed in the Izu Ridge, possibly attributed to high levels of nutrients supplied by strong turbulence around complex topography. We observed unique copepod communities with a large total biomass in the Izu Ridge, owing to the increased dominance of large copepod species. The rRNA:rDNA (28S ratio) of these large species mainly showed positive correlations with chlorophyll a concentration, suggesting a rapid response to food supply and an increase in metabolism. Migrating copepods were less dominant around the Izu Ridge with shallow water depth. Additionally, higher species diversity and more rare species were detected in the Izu Ridge, which might be maintained by complex environment conditions with temporal and spatial variation in this region. The combined approach thus characterized copepod community structure and diversity supporting the rich pelagic ecosystems in the Izu Ridge.

Käse, Laura (proxy) (contact); Metfies, Katja; Kraberg, Alexandra; Neuhaus, Stefan; Meunier, Cédric; Wiltshire, Karen; Boersma, Maarten



Metabarcoding analysis suggests that flexible food web interactions in the eukaryotic plankton community are more common than specific predator-prey relationships at Helgoland Roads, North Sea Various field studies on plankton dynamics have broadened our understanding of the species succession patterns. Additionally, feeding experiments have shown that certain predators are selective grazers. While both approaches can give us a good understanding of the ecosystem and its dynamics, drawbacks in identification and coverage of species have left open questions, which might be important for future ecosystem understanding. We, therefore, investigated water samples taken at Helgoland Roads by metabarcoding to describe seasonal succession patterns of plankton. By use of network analysis we also tried to identify predator-prey dynamics. The strong seasonality typically found for temperate waters was seen in our dataset. Small and abrupt changes, such as pronounced blooms and random appearance of autotrophs, can cause seasons to be quite different in an inter year comparison, however a stable background community survives strong fluctuations. While we found copepods, ciliates and dinoflagellates as main predators, dinoflagellates were most abundant during the three years. Furthermore, our results suggest that zooplankton predators might favour specific prey during certain time periods but seem to be quite opportunistic otherwise throughout the year. The variability and potential for many different relationships in the plankton community might be indicative of resilience in the system.

Kulagin, Dmirty (proxy) (contact); Lunina, Anastasia; Simakova, Ulyana; Vereshchaka, Alexander



Speciation caught in the act: a phylogeny and biogeography of the mesopelagic Nematoscelis (Crustacea: Euphausiacea) in the Atlantic Evolutionary mechanisms driving diversification of pelagic animals remain poorly understood, partly due to the high levels of gene flow in the open ocean. We use molecular phylogenetics, morphological, and phylogeographic approach to test the allopatric speciation model in respect to the Atlantic krill genus Nematoscelis. We show three progressing stages of the ongoing speciation: (1) geographically separated populations, divergence occurring in the mitochondrial COI gene only (N. megalops, one lineage of N. tenella); (2) same, morphological difference added (lineages of N. microps and N. atlantica); (3) same, divergence in the nuclear H3 gene added (lineages of N. tenella). Our results confirm allopatric expectations and the dispersal-limiting speciation model. We show that the primary driver of diversification is the geographic isolation coupled with hydrology-linked gene barriers at ~14-22º N (new) and ~30º S. The second driver preventing hybridization of diverged lineages is linked to external morphology, i.e. enlarged photophores and chitin saddles on the pleon of males, which provide a sexual selection by female choice. Same male forms, even belonging to different species, rarely co-occur, which makes the selection effective and not biased. Our results implicate a significant role of non-copulatory characters in Nematoscelis speciation.

Machida, Ryuji (proxy) (contact); Kurihara, Haruko; Nakajima, Ryota; Sakamaki, Takashi; Lin, Ya-Ying; Furusawa, Kazushi



Bias in the taxonomic methods used to estimate the zooplankton diversity Community-based diversity analyses, including metagenetic analyses and metabarcoding, are increasingly popular in the field of metazoan community ecology. The advantage of this method is that it requires neither the isolation of individuals nor morphological identification. However, certain methodological uncertainties remain, such as the potential inflation of diversity estimates resulting from contamination by pseudogene sequences. Furthermore, taxonomic composition might be skewed during PCR caused by primer affinity to the specific taxonomic groups. In the present study, we estimated species richness, Shannon’s H', and the phylum-level taxonomic composition of samples from a coastal zooplankton community using four taxonomic approaches: cDNA and gDNA mitochondrial COI gene amplicon, metatranscriptome sequencing, and morphological identification. As a result, it is strongly indicated that diversity inflation occurred from the samples amplified from gDNA because of mitochondrial pseudogene contaminations. The unique taxonomic compositions observed in the case of the cDNA and gDNA COI amplicons indicated that taxonomic amplification bias had occurred during the PCR. It is accordingly recommended that PCR-based approaches not be used when taxonomic composition is an important aspect of the analysis.

Martinez, Miguel; Hereu, Clara; Arteaga, María; Jiménez-Rosenberg, Silvia P. A.; Herzka, Sharon; Saavedra-Flores, Anaid; Robles-Flores, Javier; Gomez-Reyes, Ricardo; Batta-Lona, Paola; Gasca-Pineda, Jaime; Galindo-Sánchez, Clara (proxy) (contact)



Epipelagic zooplankton diversity in deep waters of the Gulf of Mexico: A metabarcoding survey Zooplankton is a key component in marine ecosystem health assessment. Here we present a taxonomically comprehensive description of the zooplankton community (0-200 m) based on metabarcoding of the V9 hypervariable region of the 18S rRNA gene of 47 samples collected in the Gulf of Mexico (GoM) during summer 2015. Fourteen phyla were identified: Arthropoda, were dominant, with Calanidae, Metridinidae and Euphausiidae as the most conspicuous families. Other abundant phyla were Cnidaria (Hydrozoa), Chordata (Tunicata) and Chaetognatha. The V9-18S sequence data were clustered into 1,888 Operational Taxonomic Units (OTUs), of which 41 were cosmopolitan and belonging to various phyla, suggesting the presence of a core community with high local diversity throughout the GoM. Evaluation of metabarcoding sequences abundance showed overall positive correlations with morphologically quantified abundances except for specific groups. Cluster analysis of OTU distributions indicated two primary biographically distinctive groups of stations: one restricted to the Bay of Campeche, while the other occurred in the Central-West GoM, similar to previous descriptions of regional variation of the GoM based on environmental variables. Together these results provide a foundation for broad-scale zooplankton molecular biodiversity assessments in the southern GoM allowing evaluation of the effects of environmental changes on zooplankton communities.

Matthews, Stephanie (proxy) (contact); Goetze, Erica; Ohman, Mark



Recommendations for interpreting zooplankton metabarcoding observations and integrating molecular methods with morphological analyses  Metabarcoding analyses of zooplankton communities are becoming more common, but molecular results must be interpreted carefully and for some applications, validated with traditional morphology-based analyses. To evaluate the robustness of our metabarcoding approach within the California Current Ecosystem, we tested whether physical subsampling and PCR replication affects observed community composition, and whether pH neutralization of ethanol with ammonium hydroxide affects molecular diversity. In addition, we tested whether zooplankton community composition resolved by metabarcoding is comparable to morphological analyses by comparing multi-marker metabarcoding with enumerations by digital imaging. We found that 1) PCR replication was important to accurately resolve alpha diversity and that physical subsampling can decrease sensitivity to rare taxa; 2) ammonium hydroxide had no effect on molecular diversity; and 3) there were significant correlations between relative read abundance and proportions of carbon biomass for most taxonomic groups analyzed, but such relationships showed better agreement for the more dominant taxonomic groups. Together, these results indicate that with appropriate replication, paired metabarcoding and morphological analyses can characterize zooplankton community structure and biomass, and that metabarcoding methods are to some extent indicative of relative community composition when absolute measures of abundance or biomass are not available.

Pappalardo, Paula (proxy) (contact); Collins, Allen; Pagenkopp Lohan, Katrina; Hanson, Kate; Truskey, Sarit; Jaeckle, William; Ames, Cheryl; Goodheart, Jessica; Bush, Stephanie; Biancani, Leann; Strong, Ellen; Vecchione, Michael; Harasewych, M.; Reed, Karen; Lin, Chan; Hartill, Elise; Whelpley, Jessica; Blumberg, Jamie; Matterson, Kenan; Redmond, Niamh; Becker, Allison; Boyle, Michael; Osborn, Karen



The role of taxonomic expertise in interpretation of metabarcoding studies The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analyzed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1-2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1,042 COI and 1,108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys.

Parry, Helen (proxy) (contact); Atkinson, Angus; Somerfield, Paul; Lindeque, Penelope



What does conventional plankton monitoring miss? A metabarcoding comparison of taxonomic richness, composition and density between the water column and the benthic boundary layer Zooplankton monitoring in shelf seas uses nets that miss the Benthic Boundary Layer (BBL) just above the seabed. However, this boundary between pelagic and benthic assemblages can be faunistically rich, having its own distinct fauna and acting as a low-light refuge for overwintering or dielly-migrating zooplankton. To compare species richness, composition and density between pelagic and BBL habitats we sampled a long-term monitoring site in the Western English Channel seasonally. Metabarcoding methods applied to vertical net samples (top 50 m in a ~54 m water column) and those from an epibenthic sledge generated >100,000 sequences clustered into 294 Operational Taxonomic Units (OTUs). Of these, 215 were found in the BBL and 170 in the water column. Some key taxa (e.g. mysids) were native to the BBL, while others (e.g. Chaetognaths), showed strong seasonal concentrations there. By contrast, other delicate taxa (e.g. Ctenophores) seemed to avoid the BBL. The major contrasts in plankton composition related to the seasonal cycle rather than to pelagic-BBL differences, suggesting that the basic dynamics of the site are captured by our weekly-resolution monitoring. Overall, metabarcoding approaches, applied to both water column and BBL, provide an independent view of plankton dynamics, and augment the existing traditional methods.

Semmouri, Ilias (proxy) (contact); De Schamphelaere, Karel; Willemse, Stijn; Vandegehuchte, Michiel; Janssen, Colin R.; Asselman, Jana



Metabarcoding reveals hidden species and improves identification of marine zooplankton communities in the North Sea Zooplankton are crucial organisms both in terms of biodiversity and their unique position in aquatic food webs. As such, it is crucial that we improve our insights into how anthropogenic and natural factors may affect them. Although easily collected in large numbers, the subsequent processing and identification of specimens has usually been a barrier to large-scale biodiversity assessments. DNA barcoding, the use of standardized short gene regions to discriminate species, has been increasingly used by non-taxonomists to identify specimens. Here, we measured the diversity and community composition of zooplankton in the Belgian Part of the North Sea over the course of one year. We identified zooplankton using both a traditional approach based on morphological characteristics, and by metabarcoding of a 650 bp fragment of the V4 and V5 region of the 18S rRNA gene using nanopore sequencing. We found a distinguishing taxonomic resolution offered by long rDNA sequences across a broad taxonomic scale. Using both methods, we compared community composition and obtained diversity metrics. Diversity indices were not significantly correlated between the two data types. Metabarcoding allowed for comparisons of diversity and community composition, but not all groups (cumaceans, harpacticoid copepods) were successfully sequenced. Additionally, some disparities existed between relative abundances of the most abundant taxa based on traditional counts and those based on sequence reads. Overall, we conclude that for zooplankton samples, metabarcoding is capable of detecting taxa with a higher resolution, regardless of developmental stage of the organism. Combination of molecular and morphological methods results in the highest detection and identification levels of zooplankton.

Snyder, Richard (proxy) (contact); Moss, Joseph; Santoferrara, Luciana; Head, Marie; Jeffrey, Wade



Ciliate microzooplankton from the Northeastern Gulf of Mexico Microzooplankton mediate a critical juncture of autotrophic and heterotrophic microbial production in the water column. Taxonomic and ecological work on this group has been substantial, yet few reports exist for the offshore Gulf of Mexico. This report focuses on protists in the phylum Ciliophora collected at stations spanning the continental shelf in the northeastern Gulf of Mexico. Samples were obtained by plankton net for microscopy and by filtration of seawater for DNA extraction and ciliate-specific clone sequencing. Microscopy and molecular analysis recovered 46 and 160 taxa respectively. Some visually identified taxa were missing from the sequence analysis and sequences from unknown species dominated molecular results. Differences were apparent with both dominant and rare taxa between February and July sampling and across a trophic gradient from coastal influenced stations to those more representative of the offshore environment. This report provides new data on ciliate microzooplankton richness and distribution in the Gulf of Mexico, and adds to our understanding of microzooplankton diversity in the open oceans.