Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study

Abstract

Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

“…Interestingly, another toxin-producing dinoflagellate species, Protoceratium reticulatum, was not detected in the samples, although the cysts of this species have been reported from the sediments throughout Tokyo Bay (Matsuoka et al 2003). In a study from the Baltic Sea, the species could be successfully identified from eDNA samples using the same marker (Sildever et al 2021). Thus, the lack of detection in this study could result from collecting data from only a single station, which does not capture the entire diversity of the Bay.…”

“…was identified from several samples by metabarcoding and HTS, but had a lower similarity (94%) with the best taxonomic match from the database. Therefore, targeting several genes and usage of genus-specific primers may improve species detection (Gran-Stadniczeñko et al 2017;Nagai et al 2017;Smith et al 2017;Sildever et al 2019Sildever et al , 2021. The low identification of those taxa could also be related to the overall lower number of sequences obtained per sample in 2018 (average 14,508 ± 3,592 sequences after bioinformatics treatment) compared to 2017 (26,781 ± 3,709 sequences after bioinformatics treatment).…”

“…Metabarcoding has also been applied for investigating the diversity of microalgae, which has uncovered the presence of previously unknown HAB species/genera for the sampling area (e.g. Dzhembekova et al 2017;Elferink et al 2017;Moreno-Pino et al 2018;Gran-Stadniczeñko et al 2019;Sildever et al 2019Sildever et al , 2021Sze et al 2019;Liu et al 2020).…”

“…Furthermore, eDNA metabarcoding has been successfully applied to reveal appearance patterns for several organism groups ranging from bacteria to mammals (Nagai et al 2016;Hirai et al 2017;Sigsgaard et al 2017;Stoeckle et al 2017;Berry et al 2019;Zhang et al 2020;Sildever et al 2021;Alter et al 2022), including the HAB species (Nagai et al 2017(Nagai et al , 2019Sildever et al 2019). As several genes or markers can be amplified from the same sample, co-appearance patterns and associations amongst species and groups can also be investigated (Lima-Mendez et al 2015;Sawaya et al 2019;Djurhuus et al 2020).…”

Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types—Weir and Stream

“…Cordier et al (2022) [ 18 ] explored the assemblage of 0.24 million eukaryotic ASVs in 1.95 billion DNA reads, representing the plankton diversity in deep-ocean sediments throughout the world. The 18S V9 primers showed potency to locate different species exclusively from the larger assemblage group to the minor fractions, including novel species of phytoplankton, fungi, and zooplankton [ 19 , 20 , 21 ] and different faunal communities [ 22 , 23 , 24 ]. Gut content profiles using eDNA analysis have dramatically increased in the context of taxonomic diversity ecology.…”