Dataset Information

Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.

ABSTRACT: Operational taxonomic units 94%-95% similar to the known Pedinophyceae were found as a result of high-through sequencing of 18S rDNA V4 amplicons of environmental DNA from the summer picophytoplankton samples from the White Sea. Partial sequence of a ribosomal operon (the 5,298 bp includes partial 18S and 28S rDNA, complete 5.8S rDNA, ITS1, and ITS2 sequences) and a partial 2,112 bp chloroplast 23S rDNA sequence White Sea Pedinophyceae was amplified from metagenomic DNA by specific primers and sequenced. A new phylotype was designated as uncultured Pedinophyceae WS. On Chlorophyta phylogenetic trees the discovered phylotype occupies a basal position in the Marsupiomonadales clade. The synapomorphic base substitutions in rRNA hairpins confirm the relationship of Pedinophyceae WS to Marsupiomonadales and its difference from known genera of the order. The obtained results extend knowledge of picophytoplankton diversity in subarctic waters.

SUBMITTER: Milyutina IA

PROVIDER: S-EPMC6813492 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.

Milyutina Irina A IA Belevich Tatyana A TA Ilyash Lyudmila V LV Troitsky Aleksey V AV

MicrobiologyOpen 20190611 10

Operational taxonomic units 94%-95% similar to the known Pedinophyceae were found as a result of high-through sequencing of 18S rDNA V4 amplicons of environmental DNA from the summer picophytoplankton samples from the White Sea. Partial sequence of a ribosomal operon (the 5,298 bp includes partial 18S and 28S rDNA, complete 5.8S rDNA, ITS1, and ITS2 sequences) and a partial 2,112 bp chloroplast 23S rDNA sequence White Sea Pedinophyceae was amplified from metagenomic DNA by specific primers and s ...[more]

PMID: 31184446

Similar Datasets

Project description:Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity-especially in polar ecosystems.

Project description:The waters around Iceland, bounding the Northern North Atlantic and the Nordic seas, are a region characterized by complex hydrography and seabed topography. This and the presence of the Greenland-Iceland-Faroe-Scotland ridge (GIFR) are likely to have a major impact on the diversity and distribution of the benthic fauna there. Biodiversity in this region is also under increasing threat from climate-induced changes, ocean warming and acidification in particular, affecting the marine realm. The aim of the present study was to investigate the biodiversity and distributional patterns of amphipod crustaceans in Icelandic waters and how it relates to environmental variables and depth. A comprehensive data set from the literature and recent expeditions was compiled constituting distributional records for 355 amphipod species across a major depth gradient (18-3,700 m). Using a 1° hexagonal grid to map amphipod distributions and a set of environmental factors (depth, pH, phytobiomass, velocity, dissolved oxygen, dissolved iron, salinity and temperature) we could identify four distinct amphipod assemblages: A Deep-North, Deep-South, and a Coastal cluster as well as one restricted to the GIFR. In addition to depth, salinity and temperature were the main parameters that determined the distribution of amphipods. Diversity differed greatly between the depth clusters and was significantly higher in coastal and GIFR assemblages compared to the deep-sea clusters north and south of the GIFR. A variety of factors and processes are likely to be responsible for the perceived biodiversity patterns, which, however, appear to vary according to region and depth. Low diversity of amphipod communities in the Nordic basins can be interpreted as a reflection of the prevailing harsh environmental conditions in combination with a barrier effect of the GIFR. By contrast, low diversity of the deep North Atlantic assemblages might be linked to the variable nature of the oceanographic environment in the region over multiple spatio-temporal scales. Overall, our study highlights the importance of amphipods as a constituent part of Icelandic benthos. The strong responses of amphipod communities to certain water mass variables raise the question of whether and how their distribution will change due to climate alteration, which should be a focus of future studies.

Dataset Information

Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.

Publications

Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets