SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site

High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, asignificant proportion of which remains uncharacterized. Here we use a temporal approach tounderstanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcusand Synechococcus grazers, and traditional oceanographic parameters. We also exploit ourability to track OTUs temporally to evaluate the ability of 18S sequence-based OTU assignmentsto meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic interms of both species richness and composition, though proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughoutthe year. This study has resulted in a temporal dataset of eukaryotic 18S sequences that cover a wide range of taxa and offers insights into the pier microbial community and how it changes with time.

Biome: root:Environmental:Aquatic:Marine:Coastal
Protists in Havre-aux-Maisons Lagoon, Magdalen Islands, Quebec, Canada

Seasonal monitoring, 454-sequencing 18S rDNA V4 region

Biome: root:Environmental:Aquatic:Marine:Coastal
the assembly of abundant and rare bacterioplankton subcommunities in three subtropical bays

Contribution of selective and neutral processes to the assembly of abundant and rare bacterioplankton subcommunities

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbial diversity in the Tongyeong-Geoje coastal area of Korea

Investigate the potential interactions among the bacterial species, phytoplankton, and environmental parameters

Biome: root:Environmental:Aquatic:Marine:Coastal
Distribution of the Roseobacter clade

The aim of this study was to investigate the distribution of the Roseobacter clade in water and sediment samples which were taken along a latitudinal gradient from Germany to Norway.

Biome: root:Environmental:Aquatic:Marine:Coastal
Coastal seawater influenced by the municipal effluents Raw sequence reads

Coastal seawater influenced by the municipal effluents

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbial diversity in the Tongyeong-Geoje coastal area of Korea2

Investigate the potential interactions among the bacterial species, phytoplankton, and environmental parameters

Biome: root:Environmental:Aquatic:Marine:Coastal
Temporal dynamics of the particle-attached and free-living microbial communities from coastal seawater

We examined the particle-attached and free-living microbial communities from coastal seawater at the Pivers Island Coastal Observatory (PICO) monthly from July 2013-August 2014. Partial 16S rRNA gene libraries were used to identify bacteria found in four size fractions of seawater >63m (zooplankton and large particles), 63-5m (particles), 5-1m (small particles/ dividing cells) and <1m (free-living bacteria).

Biome: root:Environmental:Aquatic:Marine:Coastal
Distributions and Abundances of Sublineages of the N2-Fixing Cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) in the Noumea Lagoon

UCYN-A sequences from the Noumea Lagoon time-series (July 4, 2012 - April 3, 2014).

Biome: root:Environmental:Aquatic:Marine:Coastal
Nahant Collection

This collection includes whole genome sequences of purified isolates of marine bacteria, isolated on Vibrio-selective media, and viruses infecting a subset of these strains. All derive from seawater collected in the marine littoral zone at Canoe Cove in Nahant, MA, USA.

Biome: root:Environmental:Aquatic:Marine:Coastal
seawater metagenome Metagenome

Environmental metagenomic dataset originating from seawater collected near Anvers Island (Antarctic Peninsula). Dataset consist of short reads produced via the Illumina HiSeq 2500 platform. The complete dataset was used to assess metazoan community composition through the application of environmental DNA (eDNA).

Biome: root:Environmental:Aquatic:Marine
marine metagenome Raw sequence reads

Raw bacterial 16S rRNA sequences from 3 North Atlantic water masses, amended and unamended with high molecular weight organic matter (cruise EN584).

Biome: root:Environmental:Aquatic:Marine
marine plankton metagenome Targeted loci environmental

Study the pigmentation composition and taxonomic composition of Synechococcus communities in the South China Sea and East China Sea

Biome: root:Environmental:Aquatic:Marine
microbes in coastal sea

microbial biogeography

Biome: root:Environmental:Aquatic:Marine
Diazotroph Community Structure and Distribution in the Kuroshio Current along the Tokara Strait Raw sequence reads

Diazotroph Community Structure and Distribution in the Kuroshio Current along the Tokara Strait

Biome: root:Environmental:Aquatic:Marine
Niche separation of ammonia-oxidizing archaea by the Kuril Islands in the subarctic Northwestern Pacific


Biome: root:Environmental:Aquatic:Marine
Picocyanobacterial diversity in spring in the East China Sea and the East Sea (Targeted loci environmental)

To understand a distribution pattern of picocyanobacterial diversity during spring season in seas around Korean peninsula, their genetic diversity were studied using barcoded amplicon sequencing approaches in the East Sea and the East China Sea.

Biome: root:Environmental:Aquatic:Marine
Assessing the microbial diversity in Cape Comorin ocean water

Cape Comorin is a site located at the southern-most point of the Indian Peninsula, where the Bay of Bengal, Arabian Sea and the Indian Ocean meet. This study aims to explore the microbial diversity present in the ocean water at this site.

Biome: root:Environmental:Aquatic:Marine
North Sea plastic incubation and reference communities, raw sequence reads

The study investigated the influence of seasonal and biogeographical factors on composition and structure of microbial communities colonizing plastic water bottles in the North Sea. Additionally, glass slides and background seawater were sampled.

Biome: root:Environmental:Aquatic:Marine
Marine bacterium Metagenome

Analyze the potential utilization of EPS

Biome: root:Environmental:Aquatic:Marine
Surface samples of the NW Pacific Ocean Targeted Locus (Loci)

Diversity of DMS-producing dddP genes in the NW Pacific Ocean

Biome: root:Environmental:Aquatic:Marine
ETSP OMZ nirS Metagenome

nirS amplicon sequences from the Eastern Tropical South Pacific

Biome: root:Environmental:Aquatic:Marine
Picocyanobacterial diversity in temperate marginal seas

To elucidate the seasonal and spatial changes in picocyanobacterial diversity in temperate waters, baccoded amplicon pyrosequencing of 16S-23S internal transcribed spacer sequences was applied.  Synechococcus and Prochlorococcus diversity in the East Sea and the East China Sea.

Biome: root:Environmental:Aquatic:Marine
Bacteria community in the southern East China Sea

Bacterial community analysis in the southern East China Sea.  V6 region of 16s rRNA amplification for bacterial community in the southern East China Sea.

Biome: root:Environmental:Aquatic:Marine
Phaeobacter inhibens host-attached and free-living communities

The aim of the study was to investigate the microbial communities succession on the surface of a diatom and the surroundings

Biome: root:Environmental:Aquatic:Marine
Particulate methane monooxygenase diversity on an Arctic shelf

Analysis of particulate methane monooxygenase diversity from natural seawater and methane-ammended sea water incubations via amplicon sequencing of the pmoA subunit.

Biome: root:Environmental:Aquatic:Marine
microbial diversity Raw sequence reads

microbial diversity of Bohai Sea

Biome: root:Environmental:Aquatic:Marine
18S-V4 amplification of dinoflagellate cyst communities in the South China Sea

We employed both the newly developed high-throughput sequencing-based metabarcoding method and traditional morphological identification to characterize dinocyst communities collected from the South China Sea.

Biome: root:Environmental:Aquatic:Marine
seawater metagenome Genome sequencing and assembly

particle-attached and free-living bacteria

Biome: root:Environmental:Aquatic:Marine
Microbial communities in the phycosphere environment

understand the mechanisms that shape microbial diversity in the algal bloom process

Biome: root:Environmental:Aquatic:Marine
Herbicide-incubated GBR lagoon microbiomes Targeted loci environmental

Year-long incubation of microbiomes from the Great Barrier Reef lagoon using the diuron herbicide. Profiling using 16S rRNA amplicon profiling.

Biome: root:Environmental:Aquatic:Marine
marine metagenome

23 seawater microbiomes collected from the aquaculture areas, Laoshan Bay, the Yellow Sea, China

Biome: root:Environmental:Aquatic:Marine
Microbial diversity

Analysing microbial diversity

Biome: root:Environmental:Aquatic:Marine
Diatom Community Composition CCS Diel

Diatom and other Stramenopile community composition from targeted amplicon sequencing of V4 region of 18S from incubated seawater collected in upwelled waters off the coast of Oregon. Incubation treatments included UV and no UV natural light treatments as well as dark treatments and were collected at 3 time points.

Biome: root:Environmental:Aquatic:Marine
Marine biomonitoring: predicting biotic indices from eDNA metabarcoding

We investigated the possibility of using supervised machine learning (SML) algorithms to build predictive models from eDNA metabarcoding data targeting groups that are not commonly used for benthic monitoring. We tested our approach on benthic foraminifera, a group of unicellular eukaryotes known to be sensitive to organic enrichment associated with marine aquaculture

Biome: root:Environmental:Aquatic:Marine
Arctic sea-ice and sub-ice seawater raw sequence reads

Arctic sea-ice and sub-ice seawater crude oil microcosms

Biome: root:Environmental:Aquatic:Marine
Vertebrate eDNA survey in nearshore marine environment

This study compared the presence/absence and relative abundance of marine fishes and mammals in different nearshore habitats using environmental DNA (eDNA) versus visual surveys (SCUBA). We determined the spatial resolution of eDNA as well as the false-negative rate compared to the dive surveys.

Biome: root:Environmental:Aquatic:Marine
Characterization of bacterial communities associated With toxic Dinoflagellates: pyrodinium bahamense Var. compressum

The publication should report the findings of bacteria communities associated with toxic dinoflagellate, pyrodinium bahamense Var. Compressum based on 16S rRNA Metagenomic sequencing

Biome: root:Environmental:Aquatic:Marine
Bacterial community composition in the naturally iron-fertilized region off Kerguelen Island (Southern Ocean). Targeted Locus (Loci)

The KEOPS2 cruise sampling strategy covered spatially diverse iron-fertilized stations at early bloom stages in the Kerguelen plateau and ocean region (Oct-Nov 2011). KEOPS2 data showed that natural iron fertilization of the Southern Ocean at the scale of hundreds of thousands km2 produced a mosaic of blooms, and that the biological and biogeochemical response to fertilization was diverse. The objective of this study was to explore the bacterial community structure using 16S rRNA gene tag pyrosequencing during the onset of spring phytoplankton blooms in the context of natural Fe fertilization of the Southern Ocean.

Biome: root:Environmental:Aquatic:Marine
Microbial eukaryote community structure during early phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean) Targeted Locus (Loci)

The KEOPS2 cruise sampling strategy covered spatially diverse Fe-fertilized stations at early bloom stages in the Kerguelen plateau and ocean region (Oct-Nov 2011). KEOPS2 data showed that natural iron fertilization of the Southern Ocean at the scale of hundreds of thousands km2 produced a mosaic of blooms, and that the biological and biogeochemical response to fertilization was diverse. The objective of this study was to explore the microbial eukaryotic community structure using 18S rRNA gene tag pyrosequencing during the onset of spring phytoplankton blooms in the context of natural Fe fertilization of the Southern Ocean. The hypothesis tested was that the protistan communities would differ between the Fe-fertilised blooms and the HNLC waters and also between the blooms. The use of pyrotags provided a unifying approach for assessing the breadth of protistan communities including the groups that are quasi impossible to characterize using traditional approaches of microscopy and culture (e.g MAST, MALV, Fungi..).

Biome: root:Environmental:Aquatic:Marine
DOM nutrient stress experiment bacterial communities

These sequences include bacterioplankton 16S rDNA amplicons both environmental samples from the Santa Barbara Channel, CA, USA, and from subsequent remineralization bioassays. Bioassays were amended with dissolved organic carbon from nutrient-stressed diatoms.

Biome: root:Environmental:Aquatic:Marine
Santa Barbara Channel cruise SBDOM11 bacterioplankton 16S rDNA

This sample includes environmental bacterioplankton DNA from the SBDOM11 cruise in the Santa Barbara Channel, California, USA, in May 2011, as well as associated experimental samples from remineralization bioassays. This project traced the bacterial response to the DOM produced by an upwelling-driven phytoplankton bloom, from recently upwelled water through the onset of nutrient stress.

Biome: root:Environmental:Aquatic:Marine
Microbial community of Red Sea (16S amplicon) Targeted Locus (Loci)

16S pyro-sequencing of samples from multiple places in Red Sea

Biome: root:Environmental:Aquatic:Marine
Nanticoke Harbour, ON, Canada (plankton SSU 454 sequencing)


Biome: root:Environmental:Aquatic:Marine
Bayside Harbour, NS, Canada (plankton SSU library 454 sequencing)


Biome: root:Environmental:Aquatic:Marine
Marine phytoplankton Metagenome

Marine phytoplankton in the northern ECS and coastal waters near Jeju from April 24~30th, 2011

Biome: root:Environmental:Aquatic:Marine
Ascidian and Seawater Metagenome

Diversity, structure and host-specificity of microbial associates in ascidians (tunic tissue).

Biome: root:Environmental:Aquatic:Marine
Microbial eukaryotes in an Arctic under-ice spring bloom north of Svalbard.

In this study, we investigated microbial eukaryote diversity and community compositional differences in an under-ice spring bloom north of Svalbard. Our mainobjectives were to: 1) Identify the community of microbial eukaryotes in two ice-coveredstations, 2) to unravel the influence of water masses of different characteristics and historyversus local processes on the composition of the microbial protist communities, and 3) tostudy the metabolically active fraction of the community by comparing inventories based onrRNA and the rRNA gene.

Biome: root:Environmental:Aquatic:Marine
Characteristics of eukaryotic plankton community in the Coastal Waters of Rongcheng by Illumina sequencing

Plankton community structure and diversity in the coastal waters of Rongcheng, China

Biome: root:Environmental:Aquatic:Marine
marine metagenome Targeted Locus (Loci)

The goal of this project is to examine and integrate taxonomic, genetic, and functional diversity in marine lakes in Palau and Indonesia. Samples have been collected at multiple depths in multiple lakes since 2010. DNA was extracted from filtered water samples, and archaeal/bacterial 16S rRNA genes were amplified and then sequenced (using 454 in 2010 and Illumina thereafter).

Biome: root:Environmental:Aquatic:Marine
Polyamine-transforming bacterioplankton in seawater

This study investigated the taxonomic compositions of PA-transforming bacterioplankton in surface seawater collected from nearshore to shelf break stations on the South Atlantic Bight of the United States.

Biome: root:Environmental:Aquatic:Marine
Surface water bacteria Targeted Locus (Loci)

Study of diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations

Biome: root:Environmental:Aquatic:Marine
Marine plankton Metagenome

Changes of Bacteria community composition in the water column of Igoumenitsa Gulf, Ionian Sea, Greece, over a year

Biome: root:Environmental:Aquatic:Marine
Bacteria Metagenome

This study presented the bacterial diversity in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, and provided reference for the investigating of the function of the Antarctic ecosystem.

Biome: root:Environmental:Aquatic:Marine
Canada Basin Metagenome

The Canada Basin is a deep oceanic basin within the Arctic Ocean. To investigate the bacterial diversity in seawater from the Canada Basin, water samples were collected from five stations in the Canada Basin during the 3rd Chinese Arctic Scientific Expedition in 2008. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V3 region of the 16S rRNA gene sequences were analyzed, the bacterial diversity of sea water from the Canada Basin was generally achieved.

Biome: root:Environmental:Aquatic:Marine
Microbial eukaryotes Metagenome

This study presented the molecular diversity of microbial eukaryotes in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, and provided reference for the investigating of the function of the Antarctic ecosystem.

Biome: root:Environmental:Aquatic:Marine
Plankton sample collected from Nanaimo Harbour Targeted Locus (Loci)

Nanaimo Harbour, BC, Canada (plankton SSU library 454 sequencing)

Biome: root:Environmental:Aquatic:Marine
Active picoeukaryotes in the Eastern Mediterranean Sea

Response of active picoeukaryotes to the deposition of Saharan dust and European aerosols in the Eastern Mediterranean Sea revealed by 454 pyrosequencing

Biome: root:Environmental:Aquatic:Marine
Enrichment metagenome

Genetic and Cultured diversity of free living marine Spirochaetes

Biome: root:Environmental:Aquatic:Marine
Amplicon-Based Illumina Sequencing Reveals High Diversity of Phytoplankton in the Coastal Waters of Qinhuangdao

plankton community structure and diversity in the coastal waters of Qinhuangdao

Biome: root:Environmental:Aquatic:Marine
Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

This study compared the presence/absence of marine fishes and mammals at 10 different sites in the Monterey Bay National Marine Sanctuary. We tested for differences in marine vertebrate communities at different water sampling depths and whether a station was located on the shelf or in a canyon on Monterey Bay. We also compared OTUs identified in biological triplicates.

Biome: root:Environmental:Aquatic:Marine
marine metagenome

Romanian coastal Black Sea Bacteria

Biome: root:Environmental:Aquatic:Marine
May 2013 DNA-SIP marine seawater bacteria metagenomic assembly

Illumina bacteria and archaea 16S rRNA genes

Biome: root:Environmental:Aquatic:Marine
Meiobenthos nSSU metagenetic meiobenthic data

nSSU meiobenthic diversity - nSSU meiobenthic samples from UK, EU and Gambia from 454 GS FLX.

Biome: root:Environmental:Aquatic:Marine
Island Metagenome

Actinobacterial Diversity

Biome: root:Environmental:Aquatic:Marine
Seawater sample Targeted Locus (Loci)

Heterotrophic nanoflagellate (HNF) grazing is one of the main factors shaping the structure of the prokaryotic communities in the marine environments as an important source of microbial mortality. It strongly affects prokaryotic abundance, diversity and taxonomic composition. We analyzed the effects of predation exerted by heterotrophic nanoflagellates (HNF) on bacterioplankton assemblages from a surface coastal station in the North Adriatic Sea, evaluating also the effects of smaller HNF (<3 m) which are known to constitute an important link between bacteria and larger protists. We coupled the traditional dilution method with 454 sequencing of 16S rRNA gene, providing qualitatively and quantitatively evaluations of the grazing process occurring in marine microbial communities.

Biome: root:Environmental:Aquatic:Marine
ETNP Targeted Locus (Loci)

Bacterial communities in filtered seawater isolated from the Eastern Tropical North Pacific (ETNP).

Biome: root:Environmental:Aquatic:Marine
Metagenetic analysis of copepod community in the tropical and subtropical Pacific

A large-scale biogeographic study of copepods is challenging in the tropical and subtropical Pacific due to inaccessibility, high species diversity and limitation by morphological identification. In this study, spatial patterns of epipelagic copepod community structure was revealed using 28S metagenetic method at 19 stations in Kuroshio, North Pacific subtropical gyre, eastern tropical Pacific and South Pacific subtropical gyre. The copepod communities were the most correlated to chlorophyll a, and community structure in subtropical gyres was different from those in Kuroshio and eastern tropical Pacific. The metagenetic analysis also could detect copepod diversity, and high copepod diversity was observed in oligotrophic North and South Pacific subtropical gyres with peak in North Pacific subtropical gyre. This is first metagenetic study of copepods covering wide-area and could serve as a basis of the understanding of diversity and biogeography of copepods in the tropical and subtropical Pacific.

Biome: root:Environmental:Aquatic:Marine
A metagenetic approach for revealing community structure of marine planktonic copepods

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We developed a method for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) through analysis of an artificial copepod community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads per MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. MOTUs were successfully classified at the family level at 97% similarity; similar patterns of species richness and biomass within families were revealed with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

Biome: root:Environmental:Aquatic:Marine
California Current System Long Term Ecological Research P1604 (CCS_LTER_P1604) Targeted loci environmental

Using metabarcoding of 16S and 18S rRNA, we evaluate variability of prokaryotic and protistan communities in the water column and on particles collected in sediment traps across an inshore-offshore environmental gradient in the California Current System.

Biome: root:Environmental:Aquatic:Marine
uncultured prokaryote Raw sequence reads

To study the 16S phylogeny in the upwelling water, which was caused by the intrusion of Kuroshio Current

Biome: root:Environmental:Aquatic:Marine