A metabarcode based (species) inventory of the northern Adriatic phytoplankton

Abstract

The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method. This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea.

First regional reference database of northern Adriatic diatom transcriptomes

“…The NA phytoplankton is largely dominated by diatoms, and species from the genera Skeletonema , Pseudo-nitzschia and Chaetoceros are known to be an important component of the NA phytoplankton community with some species occasionally forming very high abundances and toxic blooms 8 , 48 , 54 – 62 . The characterisation of the NA diatom community was mainly studied using classical light microscopy methods for species identification and physiological experiments 8 , 19 , 48 , 61 , 63 while studies using high-throughput sequencing methods of molecular species identification and functional characterisation are still rare for the field 64 – 66 . Transcriptome and metatranscriptome studies of the diatom community are lacking for the NA.…”

Coastal Eukaryotic Plankton Diversity of the Southern Adriatic as Revealed by Metabarcoding

“…Brandtodinium was only recently described as a new dinoflagellate genus [65], and this metabarcoding record represents a new occurrence for the Southern Adriatic. As Brandtodinium has only recently also been metabarcoded for the northern Adriatic [24], this may indicate a wider and more common occurrence in the Adriatic that was previously hidden due to microscopic identification limitations. While species of the genus Eucyrtidium have been described in previous studies as characteristic of the euphotic layer in the Southern Adriatic [66], the genera Sphaerozoum (Sphaerozoum trigenimum and Sphaerozoum fuscum), Disolenia (Disolenia quadrata) and Collozoum (Collozoum sp.)…”

“…In addition to Brandtodinium (Brandtodinium nutricula), Pelagodinium (Pelagodinium beii) as a foraminifera symbiont [65,69] and Ellobiopsis (Ellobiopsis chattonii) as a common parasite of pelagic marine copepods (Acartia, Calanus, Centropages) [70] were recorded for the first time in the Southern Adriatic. As Pelagodinium has only recently been metabarcoded for the Northern Adriatic [24], its detection in the Southern Adriatic may indicate a broader and more common occurrence in the Adriatic, which was previously hidden due to microscopic identification limitations. Blastodinium, Syndinium and Chytriodinium are cosmopolitan genera of parasitic dinoflagellates, also known as copepod parasites in the gut or lipid-rich copepod eggs [71,72].…”

“…Metabarcoding studies have described spatial and temporal variation in complete eukaryote plankton assemblages [6][7][8], but more often studies have focused on selected plankton taxa [9][10][11][12][13][14][15]. As at the global scale, only those groups and taxa representative of the Adriatic plankton community have been analysed using metabarcoding [16][17][18][19][20][21][22][23][24], neglecting insight into the eukaryotic plankton community as a whole. For the Southern Adriatic, previous plankton research in this area also included mainly zooplankton and phytoplankton studies on certain representative groups.…”