Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabarcoding of plankton dynamics

ABSTRACT: Universal metabarcoding of pico- mesoplankton reveals seasonal dynamics and a bacterial bloom

PROVIDER: PRJEB13126 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1333500.fastq.gz	Fastqsanger.gz
	ERR1333510.fastq.gz	Fastqsanger.gz
	ERR1333520.fastq.gz	Fastqsanger.gz
	ERR1333501.fastq.gz	Fastqsanger.gz
	ERR1333511.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 27

Similar Datasets

Protist plankton dynamics in the Skagerrak

Project description:Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities

| PRJEB28373 | ENA

Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding.

Project description:Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge. Here, we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA (eDNA) metabarcoding. The three ecosystems include a long-term cut-off river, a short-term connected river after EWR, and long-term connected rivers. We analyzed community stability by investigating species composition, stochastic and deterministic dynamics interplay, and ecological network robustness. We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton, altered their community dynamics, and lessened the variation within the community. Moreover, EWR disrupted the deterministic patterns of community organization, favoring dispersal constraints, and aligning with trends observed in naturally connected rivers. The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance, whereas, in permanently connected rivers, both forces concurrently influenced community assembly. The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems. This shift markedly bolstered the resilience of the ecological network. The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions, which could be critical in assessing the effects of river restoration projects throughout their life cycle.

| S-EPMC10987827 | biostudies-literature

Metabarcoding on plankton along the Baltic salinity gradient

Project description:Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea

| PRJEB12362 | ENA

Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy.

Project description:Protist community composition and seasonal dynamics are of major importance for the production of higher trophic levels, such as zooplankton and fish. Our aim was to reveal how the protist community in the Skagerrak changes through the seasons by combining high-throughput sequencing and microscopy of plankton collected monthly over two years. The V4 region of the 18S rRNA gene was amplified by eukaryote universal primers from the total RNA/cDNA. We found a strong seasonal variation in protist composition and proportional abundances, and a difference between two depths within the euphotic zone. Highest protist richness was found in late summer-early autumn, and lowest in winter. Temperature was the abiotic factor explaining most of the variation in diversity. Dinoflagellates was the most abundant and diverse group followed by ciliates and diatoms. We found about 70 new taxa recorded for the first time in the Skagerrak. The seasonal pattern in relative read abundance of major phytoplankton groups was well in accordance with microscopical biovolumes. This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.

| S-EPMC6587730 | biostudies-literature

Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding.

Project description:DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.

| S-EPMC6781235 | biostudies-literature

Universal dynamics of cohesin-mediated loop extrusion

Project description:Universal dynamics of cohesin-mediated loop extrusion

| PRJNA1140881 | ENA

Colesdalen metabarcoding

Project description:Colesdalen metabarcoding

| PRJEB71945 | ENA

Kola metabarcoding

Project description:Kola metabarcoding

| PRJEB71946 | ENA

marine plankton metagenome

Project description:Monitoring harmful algal bloom species and their appearance in Tokyo Bay, Japan, using metabarcoding and high-throughput sequencing approach

| PRJDB12693 | ENA

Seasonal eukaryotic dynamics in Alaskan sea ice

Project description:Seasonal eukaryotic dynamics in Alaskan sea ice

| PRJEB23427 | ENA