SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Spatial variation of bacterioplankton in south Atlantic Bight

The continental shelf ecosystem off the Georgia coast i.e., the South Atlantic Bight (SAB), is among the most productive marine environments that hosts many hard or live bottom areas and are homes to large number of phytoplankton, sponges, corals and many species of tropical and subtropical fishes. From the Georgia bank seaward, the coastal, shelf, slope and Gulf Stream waters represent a natural gradient of many environmental parameters, including decreased nutrients and increased salinity. Extensive efforts have surveyed the major macroorganisms in the region, however, little is known yet on the dynamics of bacteria, which are the major conduits in the energy and nutrient flow within the system. This study investigated the spatial and temporal dynamics of bacterioplankton community composition along transects from the coast bank of Georgia to Gulf Streams on the SAB.

Biome: root:Environmental:Aquatic:Marine
Seawater free living bacterioplankton

To study the relationships between bacterioplankton community composition and environmental factors between different sampling scales.

Biome: root:Environmental:Aquatic:Marine
ARK26/3_Station212 Targeted Locus (Loci)

ARK26/3_Station212_Protist

Biome: root:Environmental:Aquatic:Marine
Santa Barbara Basin Raw sequence reads

Microbial community of the benthic boundary layer of the Santa Barbara Basin.

Biome: root:Environmental:Aquatic:Marine
Eastern Mediterranean Sea Lignin and Xylan enrichments

A set of microcosms inoculated with a consortia of microbes from the eastern Mediterranean sea and incubated with lignin and xylan as a sole carbon source in artificial seawater medium. Consortia was investigated for their potential to produce lignin degrading enzymes.

Biome: root:Environmental:Aquatic:Marine
Pyrosequencing, the South Sea, May 2009

Analysis of microbial diversity and spatial distribution patterns of microbial community structure in seawater samples

Biome: root:Environmental:Aquatic:Marine
sea water bacteria Raw sequence reads

Here, we use high throughput sequencing to investigate bacterial diversity and community structure in seawater of the of Zhoushan archipelago. The large amount of data that was obtained and will lay foundations for further biological research in the east china sea.

Biome: root:Environmental:Aquatic:Marine
water sample Raw sequence reads

water microbial diversity in the Zhoushan Archipelago Sea Area

Biome: root:Environmental:Aquatic:Marine
Ecological Genomics of the Eastern Tropical South Pacific Oxygen Minimum Zone Metagenome

Oxygen minimum zones (OMZs) are oxygen deficient regions of the ocean that are hotspots for nutrient and climate active trace gas cycling. Forming at intermediate depths (~1001000 m) in response to high biological oxygen demand and reduced ventilation, OMZs occur naturally in regions of high productivity and nutrient-rich upwelling. Global climate change and enhanced run-off from our farms and cities also contributes to OMZ formation and expansion. An expansive and permanent OMZ persists in the Eastern Tropical South Pacific (ETSP) along the coast of northern Chile and Peru. Studies in the ETSP-OMZ have been critical in charting the microbial communities and metabolic processes driving coupled biogeochemical cycling in coastal and open ocean OMZs throughout the global ocean.

Biome: root:Environmental:Aquatic:Marine
Magadalen Islands Spatio Temporal (MIST) Large Fraction

Farm and control large fraction protists samples pyrosequencing 454 raw sequence reads

Biome: root:Environmental:Aquatic:Marine
Copepod induced bacterial community Raw sequence reads

Live copepods from the North Atlantic subtropical gyre were collected and rinsed to be used in bioassay-type experiments. Bacteria present in various seawater and copepod treatments were analyzed by targeting the 16S rRNA V3-V4 region. In this study, copepods were observed to increase growth of bacteria which were released to their surroundings. Additionally, copepods may be responsible for inhibiting or inducing growth of specific bacterial groups.

Biome: root:Environmental:Aquatic:Marine
Sea microbial community Metagenome

Taxonomic description of the Azov Sea microorganisms

Biome: root:Environmental:Aquatic:Marine
Amplicon sequences from naphthalene biodegradation in Arctic and temperate seawater

Seawater samples from Arctic and temperate area were collected and used directly as inoculum for microcosm scale (1 L) biodegradation experiments. Two set of naphthalene biodegradation experiments were carried out at four different incubation temperatures (0.5, 4, 8, 15 C) with Arctic and temperate seawater. DNA was extracted and amplicon libraries were prepared from the two original seawater samples and one exposed sample at each incubation temperature.

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

To understand the succession of phytoplankton-associated bacteria in correlation with phytoplankton bloom

Biome: root:Environmental:Aquatic:Marine
Marine photic zone, New Caledonia Lagoon raw sequence reads, nitrogenase amplicons

The VAHINE mesocosm experiment, conducted in the low-nutrient low-chlorophyll waters of the Noumea Lagoon (coastal New Caledonia) was designed to trace the incorporation of nitrogen (N) fixed by diazotrophs into the food web, using large volume (50 m3) mesocosms. This experiment provided a unique opportunity to study the succession of N2-fixing microorganisms (diazotrophs) and calculate in situ net growth and mortality rates in response to fertilization with dissolved inorganic phosphate (DIP) over a 23-day period, using both polymerase chain reaction (PCR) amplification of nitrogenase genes (nifH) and quantitative PCR (qPCR) assays targeting known marine diazotroph lineages.

Biome: root:Environmental:Aquatic:Marine
Antarctic Hypersaline Brine Raw sequence reads

Antarctic brine sampled in the Boulder Clay site (74  44 ''S, 164  01'' E), located in Northern Victoria Land. The aim was to identify the biodiversity differences in hypersaline brines; understanding the reasons of these differences, considering that brines might contain DNA and RNA molecules that remain trapped inside for long geological eras, thus representing a key to reconstruct past ecosystems.

Biome: root:Environmental:Aquatic:Marine
16S rDNA amplicon of Bacteria and Archaea Metagenome

16S rDNA sequencing of Bacteria and Archaea in the NW Mediterranean sea (transect from coast to open ocean and vertical profiles)

Biome: root:Environmental:Aquatic:Marine
The Nanoeukaryotic plankton Raw sequence reads

This research in molecular biology techniques for research method, on the east sea tiny eukaryotic analyze and evaluate the diversity of plankton, using multidisciplinary technology to create a data platform, environmental impact factors of miniature eukaryotic phytoplankton were discussed.

Biome: root:Environmental:Aquatic:Marine
atmospheric depositon effect on bacterial diversity

Atmospheric inputs from mineral and anthropogenic sources are nowadays increasing globally due to desertification in one hand and industrialization on the other. In this context, it is important to understand how atmospheric particles can favor the growth of certain bacterioplankton groups of the ocean over others, as these changes will affect the ratio between primary and heterotrophic production, and consequently the concentration of atmospheric carbon that can be fixed (or released) in the surface layer of the ocean. As aerosol composition varies seasonally and locally, we evaluated the effect of both types of atmospheric particles on different locations of the northwestern Mediterranean and at different times of the year.

Biome: root:Environmental:Aquatic:Marine
Marine eukaryotes Targeted loci environmental

18S rRNA gene was targeted in environmental samples from the subsurface chlorophyll maximum (SCM) in the Arctic Ocean and the Atlantic (Scotian Shelf) to assess diversity of the eukaryotic protist community.

Biome: root:Environmental:Aquatic:Marine
Spatial and environmental variation in whole microbial communities in Fildes Bay, King George Island, Antarctica Raw sequence reads

To explore the photosynthetic eukaryotic and bacterial diversity using NGS, statistics analysis and ecological studies in Fildes Bay, King George Island, Antarctica.

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

This project examines the effects of        inorganic phosphorus addition to water column (within water tanks)        bacterioplankton community structure.  All samples from all tanks and experimental days.  Control mesocosm 1, experimental day zero - Control mesocosm 2, experimental day zero.  Samples were collected from seawater in Eastern        Mediterranean from polluted and nearby unpolluted coastal areas.

Biome: root:Environmental:Aquatic:Marine
SAR amplicon from community incubated with various nanophytoplankton in microcosm

To address the impact of prey (bottom-up) on protist communities, we combine insights from two methods  DGGE to assess abundant ciliates, and HTS sequencing of SAR (Stramenopila, Alveolata, Rhizaria) communities  in marine microcosms. Here are the resulting read generated for this project with our SAR primers.

Biome: root:Environmental:Aquatic:Marine
Seawater bacteria Metagenome

The study goal is the investigate the bacteria genera and species changes with small peptide incubation in seawater.

Biome: root:Environmental:Aquatic:Marine
suspended particulate matter Raw sequence reads

Analysis of microbial diversity in the Black Sea water column

Biome: root:Environmental:Aquatic:Marine
White sea picoplankton Metagenome

Phototrophic picoeukaryotes are important constituents of marine ecosystems. The aim of this study was to determine the molecular diversity and community structure of phototrophic picoeukaryotes in the water and ice of the White Sea in different seasons.

Biome: root:Environmental:Aquatic:Marine
Microcosms Metagenome

Interactive effects

Biome: root:Environmental:Aquatic:Marine
Marine Metagenome

16S Barcode pyrosequence

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
AllDist Targeted Locus (Loci)

All samples from all sites

Biome: root:Environmental:Aquatic:Marine
Trichodesmium spiralis associated microbiome Targeted loci

We sequenced 16S rRNA gene amplicons of samples collected from Trichodesmium spiralis colonies and filtered seawater obtained concomitantly to determine the microbiome of this Cyanobacterium in comparison with the community structure of the surrounding seawater.

Biome: root:Environmental:Aquatic:Marine
Species-specific associations between bacterioplankton and photosynthetic picoeukaryotes

We used flow cytometry sorting of raw seawater to identify novel bacterial phylotypes found in physical association with photosynthetic picoeukaryotes. In total, five samples were collected at the Santa Cruz wharf on Monterey Bay during summer and fall, 2014. The phylogeny of associated microbes was assessed through Illumina MiSeq sequencing of amplicons of the 16S rRNA gene from unsorted seawater <10 m >0.2 m as well as triplicate samples of 1000 sorted photosynthetic picoeukaryote cells.

Biome: root:Environmental:Aquatic:Marine
Sea water microorganisms Raw sequence reads

To investigate the microbial diversity at the SEATS station in South China Sea.

Biome: root:Environmental:Aquatic:Marine
blocking PCR amplification of metazoan DNA for protistan diversity

Protists form the basis of marine food webs. However, the understanding of protistan diversity is typically impeded by the predominance of metazoans, especially when employing universal primers in samples from large size fractions. In order to block the amplification of metazoan DNA in PCR, we designed 3 blocking primers and tested the performance using pure cultures and environmental samples. Furthermore, blockimg primers were applied to samples from a large size fraction, which is insufficiently studied due to the dominance of metazoans.

Biome: root:Environmental:Aquatic:Marine
sea water Picoeukaryotic Community Raw sequence reads Raw sequence reads

Little is known regarding the diversity and distribution of picoeukaryotes in the east China Ocean, although these organisms are vital components of their environment. Here, we used High throughput sequencing technology to assess the seasonal 18S r RNA diversity of picoeukaryotes at six sampling sites in Carbon sink Time Series Station at Zhoushan

Biome: root:Environmental:Aquatic:Marine
Magdalen Island Spatio Temporal (MIST) Raw sequence reads

Mussels culture impact on protists community in Magadlen Islands Havre-aux-Maisons lagoon (Gulf of St-Lawrence, Canada) in 2010

Biome: root:Environmental:Aquatic:Marine
SCS SEATS Raw sequence reads

Marine Group II only dominated shallow water column (<75 m) at the central basin (SEATS) station and was replaced by the dominance of Marine Group I in deeper water, which has commonly been observed in global oceans.

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

Mesocosm experiment with water from Bothnian Bay: the effect of temperature and terrestrial DOC

Biome: root:Environmental:Aquatic:Marine
16S rRNA sequences of bacterioplankton spatial distributions in the Baltic Proper

The overall goal of this spatial sampling of marine bacterioplankton was to observe the distribution of populations from coastal to offshore. In relation to bacterial production and primary production such information is relevant for investigating coastal to offshore food web efficiency and the role of bacterioplankton community composition in food web dynamics.

Biome: root:Environmental:Aquatic:Marine
Oceanic microplankton do not adhere to the latitudinal diversity gradient

A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged with regard to the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. This investigation has evaluated microbial planktonic communities along a ~15,400 km Pacific Ocean transect with DNA from samples aquired every 2 degrees of latitude within a three month period between late August to early November, 2003. Next generation sequencing targeted Bacteria, Archaea, and Eukarya rDNA sequences.Beta analysis of ~10.8 million high quality sequences showed significant geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. Despite regional clustering, none of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters; whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on these analyses, constraints on macrofaunal response to factors related to latitude may not be defining prokaryotic and eukaryotic microorganism diversity patterns in the global ocean.

Biome: root:Environmental:Aquatic:Marine
marine Archaea metagenome

Vertical profiles of archaeal diversity in water columns

Biome: root:Environmental:Aquatic:Marine
Bacterial communities from the water column and the surface sediments along a transect in the East Sea (Sea of Japan)

We determined the composition of water and sediment bacterial assemblages from the East Sea using 16S rRNA gene sequencing. Total bacterial reads were greater in surface waters (<100 m) than in deep seawaters (>500 m) and sediments. However, total OTUs, bacterial diversity, and evenness were greater in deep seawaters than in surface waters with those in the sediment comparable to the deep sea waters. Proteobacteria was the most dominant bacterial phylum comprising 67.3% of the total sequence reads followed by Bacteriodetes (15.8%). Planctomycetes, Verrucomicrobia, and Actinobacteria followed all together consisting of only 8.1% of the total sequence. Candidatus Pelagibacter ubique considered oligotrophic bacteria, and Planctomycetes copiotrophic bacteria showed an opposite distribution in the surface waters, suggesting a potentially direct competition for available resources by these bacteria with different traits. The bacterial community in the warm surface waters were well separated from the other deep cold seawater and sediment samples. The bacteria exclusively associated with deep sea waters was Actinobacteriacea, known to be prevalent in the deep photic zone. The bacterial group Chromatiales and Lutibacter were those exclusively associated with the sediment samples. The overall bacterial community showed similarities in the horizontal rather than vertical direction in the East Sea.

Biome: root:Environmental:Aquatic:Marine
water Raw sequence reads

microbial diversity in the water

Biome: root:Environmental:Aquatic:Marine
Eukaryotic natural population from Northern Baffin Bay - Raw sequence reads

This BioProjects contain raw sequences reads of 18S rRNA and rDNA from natural populations in Northern Baffin Bay from surface and 20m depth.

Biome: root:Environmental:Aquatic:Marine
Microbial diversity associated with copepods in the North Atlantic subtropical gyre

To characterize microscale spatial heterogeneity, microbial community composition of microzooplankton, primarily small copepods, was investigated in comparison to bacterioplankton in surrounding seawater from the oligotrophic open ocean. Zooplankton individuals were collected at or above the deep chlorophyll maximum in the North Atlantic Subtropical Gyre, and the diversity of microbial communities was investigated using 16S rRNA gene amplicon pyrosequencing targeting the V5-V9 region. Zooplankton studied included the copepods Undinula vulgaris, Pleuromamma spp., Sapphirina metalina, Pseudocalanus spp., and Tigriopus sp., and an amphipod, Phrosina semilunata. High -diversity was observed among samples, with zooplankton taxa-specific bacterial communities distinct from the communities in the surrounding seawater. The taxonomic composition of the microbial communities suggests both external and internal associations are present. Copepod association is a unique microbial niche that may play a role in biogeochemical cycling in the oligotrophic open ocean.

Biome: root:Environmental:Aquatic:Marine
15N methylamine SIP (WCO station L4)

Methylated amine compounds such as methylamine are important sources of nitrogen for microorganisms in marine habitats. Methylamine is a volatile organic compound generated by degradation of organic matter. The biodegradation of methylamine by marine microorganisms is a major factor modulating the emission of this compound into the atmosphere, where methylamine influences global climate processes. As methylamine contains carbon as well as nitrogen, it can serve as a source of both elements for microorganisms So far, little is known about the identity of the active methylamine oxidisers in marine habitats, especially regarding organisms that use methylamine as a nitrogen source. In this study, Stable Isotope Probing using 15N labelled methylamine was combined with 16S rRNA and functional gene amplicon sequencing as well as metagenome sequencing to identify bacteria that are involved in methylamine degradation or assimilation of methylamine derived nitrogen in samples obtained from the Western Channel Observatory station L4.

Biome: root:Environmental:Aquatic:Marine
Microbial associations in temperate marine copepods from the Gulf of Maine

16S rRNA amplicon sequencing with the Illumina MiSeq platform on seawater and copepods from the Gulf of Maine.

Biome: root:Environmental:Aquatic:Marine
Northern Gulf of Mexico Hypoxic Zone Raw sequence reads

Northern Gulf of Mexico Hypoxic Zone. Water column samples collected July 2013. Average depth 18 m.

Biome: root:Environmental:Aquatic:Marine
Water and Sediment samples Targeted loci environmental

Water and Sediments samples from multiple locations in Panama

Biome: root:Environmental:Aquatic:Marine
INVESTIGATING THE MICROBIAL EUKARYOTIC COMMUNITIES IN THE SURFACE WATERS OF THE ARAFURA SEA AND CORAL SEA

WE INVESTIGATED THE DIVERSITY OF MICROBIAL EUKARYOTES IN THE SURFACE WATERS OF THE ARAFURA SEA, TORRES STRAIT AND CORAL SEA, USING FLOW CYTOMETRY AND HIGH-THROUGHPUT SEQUENCING OF THE V9 REGION OF THE 18S rRNA GENE.

Biome: root:Environmental:Aquatic:Marine
ocean bacteria Metagenomic assembly

Bacterial DNA was isolated from two water samples: 1 location in the Bering Strait from the chlorophyll max layer (7m depth) and 1 location in the Chukchi Sea from bottom water (55m depth). The samples were collected with the purpose of sequencing the metagenome to serve as a protein identification database for a metaproteomics study.

Biome: root:Environmental:Aquatic:Marine
Vibrio-specific 16S rRNA sequences from seawater, sediment, and oyster hatchery samples

Vibrionaceae rRNA sequences from seawater, sediment, and oyster hatchery samples. Vibrio-specific 16S rRNA genes were amplified using VF169 and 680R primers (Yong et al. 2006, Thompson et al. 2004) and sequenced on the Illumina MiSeq.

Biome: root:Environmental:Aquatic:Marine
Bacterial Diversity in the East China Sea

This study aims to determine bacterial community structures using illumina MiSeq paired-end sequencing (for 16S rDNA) in the East China Sea.

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

Study of spatial and temporal variation in marine bacterial communities.

Biome: root:Environmental:Aquatic:Marine
Protist Diversity in the East China Sea

This study aims to determine protist community structures using illumina MiSeq paired-end sequencing (for 18S rDNA) in the East China Sea.

Biome: root:Environmental:Aquatic:Marine
Sea spray aerosols at Three California Beaches

While the diversity and identity of microorganisms in water and sand at the beach have been well documented, few studies have investigated microorganisms in sea spray aerosols (SSA) at the beach. We characterized the microbial communities in SSA, water, and sand of three beaches in central California (Cowell Beach, Baker Beach, and Lovers Point) by sequencing the V4 region of the 16S rRNA gene.

Biome: root:Environmental:Aquatic:Marine
IMPACT OF SAHARAN DUST DEPOSITION ON BACTERIOPLANKTON IN MARINE SURFACE WATER

Microcosm Experiments Performed in Florida Keys, field season 2015

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

The main goals of this study were to establish a baseline of the microbial organisms present in surface water samples in Port Everglades Inlet in Fort Lauderdale, FL

Biome: root:Environmental:Aquatic:Marine