Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer

Abstract

Arctic regions have experienced pronounced biological and biophysical transformations as a result of global change processes over the last several decades. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. The effects on ecosystem function and services, particularly when invasive or toxigenic harmful species become dominant, can be expressed over a wide range of temporal and spatial scales in plankton communities. Our study focused on the comparison of molecular biodiversity of three size-fractions (micro-, nano-, picoplankton) in the coastal pelagic zone of West Greenland and their association with environmental parameters. Molecular diversity was assessed via parallel amplicon sequencing the 28S rRNA hypervariable D1/D2 region. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano-and microplankton. In multidimensional scaling analysis, community composition of all three size fractions correlated with cell size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX). Individually, each size fraction community composition also correlated with other different environmental parameters, i.e. temperature and nitrate. We observed a more homogeneous community of the picoplankton across all stations compared to the larger size classes, despite different prevailing environmental conditions of the sampling areas. This suggests that habitat niche occupation for larger-celled species may lead to higher functional trait plasticity expressed as an enhanced range of phenotypes, whereas smaller organisms may compensate for lower potential plasticity with higher diversity. The presence of recently identified toxigenic harmful algal bloom (HAB) species (such as Alexandrium fundyense and A. ostenfeldii) in the area points out the potential risk for this vulnerable ecosystem in a changing world.

Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)

“…OTUs of studies using LSU (Elferink et al, 2017) and/or ITS sequences (Lutz, McCutcheon, McQuaid, & Benning, 2018). Concomitantly, taxa such as Peridiniella, Sphaerodinium and Tyrannodinium, of which only LSU sequences are known at present, are subsequently undetectable using dinoref (however, †Leonella and †Posoniella are also missing, although SSU reference sequences are already available).…”

“…Due to a huge number of reads, and the diversity of organisms captured by HTS of environmental DNA, initial OTU annotation using reference databases usually allows for confident taxonomic classifications only up to coarser taxonomic ranks (such as phylum, class, or order: Quast et al, 2013). This method has been recently used in barcoding and biomonitoring projects of protists (Elferink et al, 2017;Keck, Vasselon, Rimet, Bouchez, & Kahlert, 2018;Medinger et al, 2010;Vergin et al, 2013). family, genus, or species), is the phylogenetic placement of reads in reference trees, which also offers the advantage of estimating statistical support values for annotations, regardless of the read's length (Dunthorn et al, 2014).…”

“…family, genus, or species), is the phylogenetic placement of reads in reference trees, which also offers the advantage of estimating statistical support values for annotations, regardless of the read's length (Dunthorn et al, 2014). This method has been recently used in barcoding and biomonitoring projects of protists (Elferink et al, 2017;Keck, Vasselon, Rimet, Bouchez, & Kahlert, 2018;Medinger et al, 2010;Vergin et al, 2013).…”

Harmful Algal Blooms in Fjords, Coastal Embayments, and Stratified Systems: Recent Progress and Future Research

“…In particular, recent attention to HAB biodiversity and biogeography has begun to focus on frontier locations within and adjacent to fjords in the Arctic and sub-Arctic, where the effects of climate change are anticipated to be most rapid and dramatic and may yield evidence of regime shifts in these habitats. Application of metagenomic and metatranscriptomic approaches by parallel amplicon sequencing of 28S rRNA in comparative Arctic fjords reveals differential patterns of molecular diversity in plankton size fractions and identifies links between the occurrence of particular HAB taxa and their toxins (Elferink et al, 2016).…”

Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding

“…It uses the amplified sequence from a short, standardised DNA locus as diagnostic characters for species identification (Lin et al 2009;Shokralla et al 2012). Loci tested for dinoflagellates include the nuclear small ribosomal subunit (18S rRNA) ), large ribosomal subunit (28S rRNA; D1/D2 region) (Elferink et al 2017), internal transcribed spacers (Stern et al 2012) and the mitochondrial cytochrome c oxidase subunit I and cytochrome b (Lin et al 2009). The mitochondrial genes cannot be easily amplified from all dinoflagellate taxa (Stern et al 2012) and, amongst the nuclear loci, 18S rRNA remains the most well-sequenced marker in public databases due to their widespread use in dinoflagellate systematics (Mordret et al 2018).…”