SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial communities associated with ferromanganese nodules and the surrounding sediments

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
a seamount and adjacent deep-sea plains in the western Pacific Ocean Metagenome

Using high-throughput DNA sequencing, we investigated their diversity and community composition in different sediment layers of a seamount and an adjacent deep-sea plain in the tropical western Pacific Ocean with water depths ranging between 813 m and 4,566 m.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
marine metagenome Raw sequence reads

the diversity of aoa in the South China Sea

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine picocyanobacterial community structure

A surprising recent observation is that one of the smallest types marine phytoplankton, picocyanobacteria of the genus Synechococcus, can contain concentrations of silicon rivaling those found in diatoms. As part of an NSF-funded project exploring the implications of this observation, entitled ''Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle'', we used PacBio sequencing of a PCR-amplified fragment of the petB gene to describe the diversity and structure of the cyanobacterial community in seawater samples collected at several locations in the North Atlantic ocean. We used this information to determine whether there is a relationship between the content of biogenic silica in the <3 micron size fraction and the types of picocyanobacteria present.

Biome: root:Environmental:Aquatic:Marine:Oceanic
dust metagenome Raw sequence reads

Evaluating the impact of atmospheric depositions on dinitrogen fixation in the Eastern Mediterranean Sea- A mesocosm approach

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

18S rDNA sequences from the southern East China sea

Biome: root:Environmental:Aquatic:Marine:Oceanic
Microbial communities in the ocean Raw sequence reads

understand the mechanisms that shape microbial diversity in the global-scale ocean ecosystem

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

Bacterial 16S rDNA sequences in the southern East China Sea

Biome: root:Environmental:Aquatic:Marine:Oceanic
16S marine bacteria Raw sequence reads MEDEA2

dataset includes deep sea bacteria from the deep northern North Atlantic ocean including mesopelagic, and bathypelagic samples.

Biome: root:Environmental:Aquatic:Marine:Oceanic
seawater metagenome Raw sequence reads

The study wants to reveal the influence of solitary wave to bacterial community

Biome: root:Environmental:Aquatic:Marine:Oceanic
Bacterial community diverisity

Bacterial community diversity of seawater in East China Sea

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

South China Sea sediment core microbial diversity

Biome: root:Environmental:Aquatic:Marine:Oceanic
Sea ice and seawater Raw sequence reads

Fungi are vastly understudied in the marine realm and the extent of their functionality as nutrient cyclers and parasites is constrained by the current understandings of fungal distribution and drivers on global scales. To investigate fungal distributions, high throughput sequencing of the 18S and 28S rRNA genes were examined from across the western Arctic and sub-Arctic.

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

Microbial dicersity

Biome: root:Environmental:Aquatic:Marine:Oceanic
Microbial eukaryote Metagenome

The central Arctic Ocean has been covered by heavy sea ice, thus the condition of the underlying ecosystem has remained uncertain. To investigate the microbial eukaryotes diversity in seawater from the central Arctic Ocean, water samples were collected from five stations during the 3rd Chinese Arctic Scientific Expedition in 2008. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V4 region of the 18S rRNA gene sequences were analysis, the molecular diversity of microbial eukaryotes of sea water from the central Arctic Ocean was generally achieved.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine protists Metagenome

A study of the genetic diversity of protists in the central Arctic Ocean in late summer 2011.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Benham Rise 16S raw sequence reads

16S rDNA raw sequencing reads from prokaryotes isolated from the water column of Benham Rise, Philippines

Biome: root:Environmental:Aquatic:Marine:Oceanic
aquatic bacterial metagenome Raw sequence reads

Bacterioplankton metacommunity structure across thermal effluent gradients

Biome: root:Environmental:Aquatic:Marine:Oceanic
CTD water column metabarcoding

Water column metabarcoding of 16S rRNA from South Atlantic

Biome: root:Environmental:Aquatic:Marine:Oceanic
Surface ocean Targeted Locus (Loci)

18S rRNA gene was targeted in environmental samples from surface water in the Chukchi Sea to assess diversity of the eukaryotic protist community.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Ocean Acidification baceria sample Targeted loci environmental

A microcosm experiment was done in the western pacific ocean to investigate the response of bacterial community to the ocean acidification.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Ocean Water Metagenome

Microbes from water column samples and "non-lethal" sediment traps were collected on 0.2 uM micron filters to look at diversity and richness of bacterial community dynamics within an annually recurring spring phytoplankton bloom.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Green Edge microcosms Raw sequence reads

We investigate the response of Arctic bacterial communities to the addition of phytoplankton derived dissolved organic matter through biodegradation experiments conducted during a cruise in the Baffin Bay in June-July 2016

Biome: root:Environmental:Aquatic:Marine:Oceanic
16S amplicons Subtropical Frontal Zone New Zealand

This study consists of samples collected from 8 surface water stations along a 48 km transect. Samples were taken between January 2014 and April 2015.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Southern Ocean microorganisms Targeted Locus (Loci)

Bacteria and archaea from filtered Southern Ocean seawater.  Filtered and size-fractionated (0.1 m, 0.8 m, 3.0 m) seawater from the Southern Ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic
16S rRNA amplicon from marine Bacteria Raw sequence reads

The contribution of different bacterial phylotypes to the ocean biogeochemical cycles depends on their activity and biomass. However, little is known about active bacteria in the deep ocean, the largest habitat on Earth.

Biome: root:Environmental:Aquatic:Marine:Oceanic
DEEPEND: Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples. Cruises DP03 and DP04 from Jan 2016 - December 2016

Seawater will be collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters will be stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions will be generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0  1500 m, assess seasonal variation, and examine variation related to nektonic vertical migration. Microbiome analyses will also consider environmental variables unique to the GOM, such as Mississippi river green water inputs, mesoscale features, or microbiomes of associated GOM marine fauna as part of community ecology profiles. When possible, correlations will be made to other environmental factors such as nutrient concentrations.

Biome: root:Environmental:Aquatic:Marine:Oceanic
rDNA amplicon sequencing of Western North Atlantic microbial community

Targeted amplicon sequencing of the 16S V4 and 18S V4 rRNA genes from microplankton DNA collected via filtration of seawater. Samples obtained from 24 sampling stations across the Western North Atlantic as part of work conducted for NSF Award #1350710: "Method Development for High-Resolution Underway N2 Fixation Measurements", with the goal of characterizing the marine microplankton community and relating community structure to measured productivity and nitrogen fixation rates.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Shallow-water pockmarks diversity Targeted Locus (Loci)

Shallow-water pockmarks are associated with hydrocarbon ascent through the muddy sediment blanjet in world-wide continental shelves. We investigated the prokaryotic diversity in the sediment of several shallow-water pockmarks.

Biome: root:Environmental:Aquatic:Marine:Neritic zone:Sediment
13C methanol SIP (WCO station L4)

Methanol is a biochemically active, volatile organic compound that plays an important role in tropospheric oxidant photochemistry. It has recently been suggested that the global ocean, where surface methanol concentrations are in the ~30-400 nM range, is a net sink for atmospheric methanol. In the marine environment, this (and other) one-carbon compound is used as an energy and carbon source by bacteria known as methylotrophs. So far, little is known about the identity of the active methanol oxidisers in marine habitats. In this study, Stable Isotope Probing using 13C labelled methanol was combined with 16S rRNA and functional gene amplicon sequencing as well as metagenome sequencing to identify methylotrophic bacteria that are responsible for methanol assimilation in samples obtained from the Western Channel Observatory station L4.

Biome: root:Environmental:Aquatic:Marine:Neritic zone
California Current Cruise CCE-P1408 Process Cruise #6

Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. In this work, we use DNA metabarcoding of 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem. The PITs included formalin-fixed and 'live' traps to investigate compositional changes associated with consumption and remineralization processes. Sequences affiliated to Radiolaria, mainly Spumellaria and Acantharia, dominated the eukaryotic assemblage in fixed-traps (90%) with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased markedly in live-traps (<3%), possibly due to selective consumption by large copepods, heterotrophic nanoflagellates and amoeboid phaeodarians that were heavily enriched in these traps. These patterns were consistent across the coastal-to-open water masses surveyed, despite major differences in productivity and trophic structure of the epipelagic plankton community. Our findings indicate that in addition to more commonly considered phytoplankton and crustacean zooplankton, the role of rhizarians can be significant for POM vertical export and cycling in the CCE and potentially in other oceanic ecosystems.

Biome: root:Environmental:Aquatic:Marine:Neritic zone
16S rRNA amplicon sequences of Baltic Sea bacterioplankton

The aim of this study was to investigate interactions between bacterioplankton and phytoplankton during the Baltic Sea spring bloom. These datafiles include the 16S rRNA amplicon sequences of the bacterioplankton.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
ARMS Jeddah sample Raw sequence reads

To assess cryptic benthic diversity in three reefs in the Jeddah region of the Red Sea we undertook a metabarcoding (using 18S rRNA primers) approach to survey the eukaryotes found in Autonomous Reef Monitoring Structures (ARMS)

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
A long-standing complex tropical dipole shapes marine microbial biogeography

Dipole eddies are mesoscale oceanographic features consisted of a cyclonic eddy and an anticyclonic eddy that function as a two-way biological pump, accumulating plankton production by pumping nutrient into the euphotic zone and accelerating the transport of organic matter into deep ocean, respectively. Dipoles happened frequently in the ocean with a duration from a few days to several months, resulting in significant impacts on local and global oceanic biological, ecological and geochemical processes. To better understand how dipole shape microbial community, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated the dipole had a substantial influence on the microbial distributions and community structures both vertically and horizontally. Large Alpha- and Beta- diversity differences were observed between anticyclonic eddy and cyclonic eddy in surface and subsurface layers, consistent with distribution changes of major OTUs in the dipole with effects of uplifted, downward transported, enriched, depleted, horizontally transported. The edge of dipole might also cause strong vertical water movement indicated by Prochlorococcus and Synechococcus. Our findings suggest that dipole with its unique physical features might act as a driver for the distribution and diversity of microbial community.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
uncultured marine picoeukaryote strain:Peuk_V4_NWP2 Raw sequence reads

We aim to determine spatial and temporal distribution and diversity of marine picoeukaryotes in marginal seas of the northwestern Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
Anammox bacteria in sediment cores of Daya Bay, China

16S rRNA gene of anammox bacteria

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
Marine bacteria metagenome

16S metagenome of marine bacteria from marginal East China Sea

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
uncultured marine picoeukaryote strain:Peuk_V4_NWP1 Raw sequence reads

We aim to determine spatial and temporal distribution and diversity of marine picoeukaryotes in marginal seas of the northwestern Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
Microbial community in permeable intertidal sediment

The microbial community in permeable intertidal sediment, Gloucester Point

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
E1 Targeted Locus (Loci)

Reveal the diverse bacterial community in intertidal sediments of Fildes Peninsula

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Sediment surface microbial community changes due to phytoplankton addition

Changes in microbial community in the sediment surface after addition of phytoplankton biomass.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Stromatolite Type 1 HBC Metagenome

Samples were isolated from stromatolitic microbial mats from Bahamas.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
HBC thrombolite metagenome

Metagenome of a intertidal thrombolitic mat community from Highborne Cay, Bahamas.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Sediment Metagenome Raw sequence reads

Metagenomic sequences of Archaea, Bacteria and Eukarya originating from Spiekeroog salt marsh sediment

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Chandeleur Island 2016 Amplicon Study Raw sequence reads

These amplicon sequences were generated from year 2 of an ongoing study of Chandeleur Islands saltmarsh habitats.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)

Microbial communities play a crucial role in microbial loop process that constitute the foundation of the ecosystem structure and function. The goal of this study was to monitor a shift in the bacterial community following treatment with MC252 oil.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Salt Marsh Sediments Raw sequence reads

A study looking at the effects of sediment depth and nitrogen enrichment on bacterial communities

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
US East Coast Salt Marshes Targeted Locus (Loci)

This work is aimed at elucidating the extent of microbial diversity and biogeography in US east coast salt marshes using 16s tag sequencing.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Little Sippewissett Marsh Targeted Locus (Loci)

Anthropogenic impacts and fecal populations at Little Sippewissett Marsh.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Wetland soil Targeted Locus (Loci)

At the salt marsh Dongtan, the effect of Spartina alterniflora invasion on the structure of archaea were investigated at three points where the first was uninvaded, the second was partially invaded and the third was completely displaced.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Metagenomic study of Alchichica microbialites

We performed a comparative metagenomic analysis of microbialite samples along a depth gradient to characterise the functional profile of the microbialite-associated microbial communities.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Microbialites
Diversity of denitrifying bacteria in Sanya mangrove sediments

This study aims to evalue the diversity of denitrifying bacteria in Sanya mangrove sediments from China.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Diversity of diazotrophic bacteria in Sanya mangrove sediments

This study aims to assess the structure and driving factors of diazotrophic bacteria in Sanya mangrove sediments from China

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
mangrove rhizosphere sediment Metagenome Raw sequence reads

To provide the comprehensive diversity and structure of diazotrophic and bacterial communities in the rhizospheres of mangroves

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
mcrA singapore mangrove Raw sequence reads

Spatial variations of methanogenic communities in the tropical mangroves

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Fungal diversity in Sanya mangrove sediments, China

This study aims to investigate the diversity pattern and driving factors of fungi in mangrove sediments from Sanya, China.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Diversities of bacteria and archaea in Sanya mangrove sediments

Study on the diversities of bacteria and archaea in Sanya mangrove sediments.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Enriched mixed culture from mangrove sediment with capability of producing 1,3-PDO from glycerol genome sequencing and assembly

This project investigated the impact of increasing initial concentration of pretreated crude glycerol over the microbial community in mixed culture and metabolic products distribution.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
South China Normal University mangrove sediment Targeted Locus (Loci)

South China Normal University mangrove sediment samples

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Cataloging the Microbial Diversity of Sundarbans in the Backdrop of Climate Change

The influence of temporal and spatial variations on the microbial population in sediments of Sundarbans has been assessed using 16S rRNA gene pyrosequencing. The extraction of DNA from the sediment samples collected from the surface (2 cm) and subsurface (16 cm) layers in two seasons (monsoon and post monsoon) and the direct application of the 16S rRNA gene pyrosequencing resulted in approximately 117 Mbp of data from three sampling stations (Jharkhali, Sahidnagar and Godkhali). The taxonomic analysis of the pyrosequencing data grouped the sequences into 24 different phyla. In general, Proteobacteria were the most dominant phyla and further analysis revealed the dominance of Deltaprotaobacteria, Alphaproteobacteria and Gammaproteobacteria within the sediments. To our knowledge, this is the first detailed analysis of the microbial diversity in the world''s largest mangrove sediment of Sundarabns.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
marine metagenome Raw sequence reads

The microbial community of Sundarban Mangrove marine water samples

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
Marine planktonic ciliates (phylum Ciliophora, subclasses Oligotrichia and Choreotrichia): SSU rDNA

This study focuses on the richness and taxonomic composition of ciliate protists in marine plankton of a large temperate estuary (Long Island Sound, USA).

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Benthic Ocean Acidification

Investigation of the impact of elevated CO2 and temperature on microbial community composition within a muddy sediment mesocosm.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Po river Prodelta and Mar Piccolo of Taranto surface sediments bacterial communities targeted loci


Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Patagonian fjord prokaryote community

Time series of prokaryote community composition in waters of a Patagonian fjord

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Coral Spawn Degradation, Bocas del Toro, Panama - Raw sequence reads

The goal of this study was to identify bacterial communities that were labeled with a thymidine analog, bromodeoxyuridine, for investigating active bacterial communities during a coral mass-spawn degradation study off coastal Panama.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Effects of triclosan on bacterial community composition in natural seawater microcosms

The main objective of this study was to analyze the impact of triclosan on bacterial communities in seawater microcosms from Looe Key Reef, FL, Keys, USA.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Localized impact of aquaculture effluent on Red Sea coral reef water nutrients and microorganisms

We examined the impact of an aquaculture effluent canal in Al Lith, Saudi Arabia on the nutrients and picoplankton community overlying coral reefs in the Red Sea. Across 24 sites representing 0  21 km from the effluent, we measured nutrient concentrations, quantified microbial cell abundances, and utilized high-throughput sequencing of bacterial and archaeal small subunit ribosomal RNA (SSU rRNA) to examine microbial community composition.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef