SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial Diversity in Antarctic marine sediments (Admiralty Bay and Bransfield Strait)

We assessed the composition and structure of bacterial and archaeal communities at 15 stations in Admiralty Bay and Bransfield Strait, Antarctica.

Biome: root:Environmental:Aquatic:Marine:Sediment
Archaea diversity in marine sediment

To study archaeal diversity in global marine sediment

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

to compare the differences among these environmental samples

Biome: root:Environmental:Aquatic:Marine:Sediment
envinronment Metagenome

We used a 16S and 18S rRNA based pyrosequencing approach to characterize the sediment bacterial and microeukaryote communities in mud volcanoes (MVs) with differential activity in the Gulf of Cadiz

Biome: root:Environmental:Aquatic:Marine:Sediment
gas hydrate bearing sediment Raw sequence reads

By investigating the microbial community structure in the gas hydrate bearing cores, we can understand some of in situ biochemistry processes. It is useful to get to know how microbial involved in forming high-saturation microbial origin gas hydrates.

Biome: root:Environmental:Aquatic:Marine:Sediment
Anammox bacteria in surface sediments of South China Sea

Raw sequences of anammox bacteria in South China Sea.

Biome: root:Environmental:Aquatic:Marine:Sediment
Archaea

archaea communitites

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial diversity of marine sediments from Ross Sea

To understand the microbial diversity of marine sediments along the depth

Biome: root:Environmental:Aquatic:Marine:Sediment
Aarhus Bay sediment PCR amplified product sequencing

To identify acetate-assimilating/utilizing microbes in marine sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
Nitrate-storing microorganisms in sediments of the Bornholm Basin

The objective of this study is to examine the distribution of nitrate-storing microorganisms along a transect towards deeper water depths in the hypoxic Bornholm Basin. Nitrate-storing microorganisms were identified by amplicon sequencing (Illumina MiSeq) of Eukaryotes and diatoms (18S rRNA gene). The organisms that were identified by sequencing were evaluated in regard to their ability and capacity to store intracellular nitrate.

Biome: root:Environmental:Aquatic:Marine:Sediment
Queensland Marine Sediment

Characterization of bacterial communities in marine sediments from Gladstone and Heron Island

Biome: root:Environmental:Aquatic:Marine:Sediment
Deep mud-volcano biosphere in the Nankai accretionary wedge

Submarine mud-volcanoes are globally distributed in the plate convergent margins1,2. The mud-volcanism transports deep-sourced fluids and hydrocarbons to the seafloor3, which upward supply often supports chemosynthetic benthic life and microbial communities that play significant ecological roles in biogeochemical carbon cycle4,5. Yet, geochemical and microbiological characteristics of the deep mud-volcano subsurface remain largely unknown. Here, we studied an active submarine mud-volcano in the Nankai Trough by drilling down to 200 meters from the summit. Cell count and molecular analyses indicate that relatively small (102~105 cells/cm3) but phylogenetically diverse microbial populations are present throughout the cored sediment. In the pore water, carbon isotopic compositions of bicarbonate and acetate are notably 13C-enriched up to the maximum value of +40 and -25, respectively. High concentrations of hydrogen (up to 1,800 nM) are observed, suggesting a thermodynamically feasible condition for microbial acetogenesis via CO2 reduction. Radiotracer experiments consistently showed that acetogenesis activities are generally 2-3 orders of magnitude higher than those of methanogenesis. These data indicate that the deep biosphere in the submarine mud-volcano is characterized by tectonic and sedimentolgoical regimes of the oceanic accretionary wedge, and hence different from the stratified sedimentary biosphere.

Biome: root:Environmental:Aquatic:Marine:Sediment
Taxonomic study of endospores in a marine sediment

This study mapped the taxonomy and diversity of endospores and vegetative bacteria in a marine sediment. We further investigated potential sources of endospore accumulation in the seabed.

Biome: root:Environmental:Aquatic:Marine:Sediment
marine sediment metagenome Metagenome

China sediments from the northern slope of the South China Sea archaeal 16S rRNA gene groups, metagenomic data, deep-sea sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
eDNA_Subseafloor

PMA-DNA study of subseafloor sediment

Biome: root:Environmental:Aquatic:Marine:Sediment
SCHEMA_Sediment

GoM-SCHEMA: Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology and Archaeology Project

Biome: root:Environmental:Aquatic:Marine:Sediment
marine sediment metagenome Metagenome

In this study, we investigated marine sediment from around the Okinawan 'Kaichu-Doro' Causeway, which was constructed 44 years ago to connect three islands (Henza-jima, Miyagi-jima, Hamahiga-jima) to Okinawa. The construction of this causeway has been shown to influence the surrounding marine ecosystem via fragmentation and the loss of water circulation. In this research, we collected 10 sediment cores (5 cores from each side) 60-80 cm length from 1 m water depth and divided into layers (each layer 15 cm) to examine differences in environmental DNA from areas around the causeway. We examined the vertical diversity of microbial communities and metabolite to elucidate and estimate the correlation between metabolites and microbial communities among marine sediment layers.

Biome: root:Environmental:Aquatic:Marine:Sediment
Extracellular DNA marine sediment Targeted Locus (Loci)

To assess the diversity of eukaryotes in Red Sea sediments via amplicon sequencing of extracellular DNA.

Biome: root:Environmental:Aquatic:Marine:Sediment
Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (1330?cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 39 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.

Biome: root:Environmental:Aquatic:Marine:Sediment
Zostera Marina Ammonification environmental

In the Fall of 2014, Jessica Abbott (from Jay Stachowiczs lab) and Susan Williams performed an ammonification experiment in Bodega Bay, CA. The experiment involved 72 different plots containing either two or six known genotypes of Zostera marina. The rate of ammonification was measured in sediment from these plots at several different time points post field collection. We are working to determine the microbial community composition of this sediment with the goal of identifying which member(s) of the community might be responsible for the ammonification rates observed.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial diversity studies of Arabian Sea sediment

Marine ecosystems are distinctive ecological niche, with a variety of microbes playing important roles in nutrient recycling and other ecological processes, thereby requiring a thorough exploration of their microflora. Similarly Arabian Sea sediments are hotspots for microbial diversity and therefore requires a detailed investigation. Bacterial diversity profiles of marine metagenome were brought to light by the present studies based on Illumina sequencing trageting the V3 regions of 16S rRNA gene, revealing the roles of different bacteria in nutrient cycling and organic matter degradation. The analysis also revealed the existence of many unknown sequences, indicating a large untapped bacterial diversity in these areas.

Biome: root:Environmental:Aquatic:Marine:Sediment
Characteristics of SOB community in Sediments from the East China Sea by high-throughput sequencing

The diversity and composition of SOB in sediments from the East China Sea was investigated based on the high-throughput sequencing analyses of the soxB gene

Biome: root:Environmental:Aquatic:Marine:Sediment
marine seawater and sediment Raw sequence reads

bacterial diversity

Biome: root:Environmental:Aquatic:Marine:Sediment
ANME-2a Genome sequencing

To understand the ecological roles of ANME-2a

Biome: root:Environmental:Aquatic:Marine:Sediment
Temperature shifts simulating secondary oil recovery

The germination of endospore forming bacteria in response to temperature shifts encountered during secondary oil recovery was investigated. Relevance for the mitigation of reservoir souring.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Tyne oil spill snorkels Raw sequence reads

Bioelectrochemical bioremediation to accelerate hydrocarbon biodegradation in anoxic marine sediments, using "oil-spill snorkels". The snorkels (rods of conductive material) were positioned to create an electrochemical connection between the anoxic contaminated sediment and the oxic overlying water. In principle, the snorkel could take advantage of the capability of electro-active bacteria to anaerobically oxidize hydrocarbons with the snorkel serving as a respiratory electron acceptor.Fifty 16S rRNA amplicon libraries were generated representing microbial communities from the snorkel, no oil snorkel, control, no oil control and abiotic experiments at 175, 286 and 466 days during the incubation period, as well as from the initial sediments with and without oil (Time 0).

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
sediment metagenome Metagenome

Ecological effects assessments of spilled oils

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Sediment Microcosm Metagenome

Sediment Microcosm - Oil_contaminated*reduced_water_pH

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Gulf of Mexico open ocean Targeted Locus (Loci)

Influence of dispersants on pelagic microbial oil degraders. Microbial communities from deep seawater at a natural hydrocarbon seep in the northern Gulf of Mexico were exposed to Macondo oil; dispersed oil; or dispersants in laboratory experiments.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Survey of xoxF diversity in different marine environments

Methanol dehydrogenase is a key enzyme in methylotrophic bacteria, catalysing the oxidation of methanol to formaldehyde. In many methylotrophs, this is a well-characterised pyrroloquinoline quinone dependent enzyme consisting of two subunits, encoded by the genes mxaFI. A homolog of the large subunit MxaF is also present in most known methylotrophs, encoded by the gene xoxF. In several methylotrophs, this gene was found to be the only putative methanol dehydrogenase, but it is also present in several non-methylotrophs. This has led to a discussion over its potential role in methylotrophy and C1 cycling. This study aims to investigate the presence and diversity of the xoxF gene in the marine environment.

Biome: root:Environmental:Aquatic:Marine:Neritic zone
Mediterranean Contaminated Pelagic communities

Response of pelagic communities to an input of contaminated elutriate from sediments or to artificial pollution with a mix of pollutants

Biome: root:Environmental:Aquatic:Marine:Pelagic
Simulated crude oil seepage Caspian Sea Raw sequence reads

The response of the microbial community to a crude oil seepage simulated for 190 days under close-to-in situ conditions in a sediment core from Caspian Sea using a Sediment-Oil-Flow-Through (SOFT) system was studied by NGS sequencing. We hypothesize that specific taxa respond specifically to simulated crude oil seepage by an increase of their cell numbers resulting in a change of community composition.

Biome: root:Environmental:Aquatic:Marine:Oil seeps
bacterial community in the deep-sea surface sediments

bacterial community in the deep-sea surface sediments of the Eastern Indian Ocean

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Controls on microalgal community structures in cryoconite holes upon high Arctic glaciers, Svalbard

Glaciers are known to harbor surprisingly complex ecosystems. On their surface, distinct cylindrical holes filled with meltwater and sediments are considered as hot spots for microbial life. The present project addresses possible biological interactions5 within the community of prokaryotic cyanobacteria and eukaryotic microalgae (microal- gae) and relations to their potential grazers, additional to their environmental controls.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
uncultured prokaryote Targeted loci environmental

This study sequenced bacterial 16S ribosomal DNA from subseafloor sediment of the Bering Sea, in an effort to understand diversity in the deep subsurface.

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

This dataset contains the bacterial and archaeal 16S rRNA sequence information from the Methane Microbial Observatory for Seafloor Analysis (MIMOSA) deployment at GC600 from October 2013 (PE14-09) to March 2014 (PE14-14). The purpose of the deployment was to examine the in situ degradation of oil. The deployment contained flow-through chambers of sediment, one amended with oil and one unamended. Samples were collected from the beginning and end of the experiment.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Sediment bacteria in the Southern Ocean

The aim of the study was to investigate bacterial community structures sediment samples taken in the Southern Ocean around Elephant Island and the Antarctic Peninsula. Bacterial community structures were assessed by pyrotag sequencing targeting the bacterial 16S rRNA gene.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Caspian Sea Sediment - 16S Survey Targeted Locus (Loci)

The Caspian Sea is one of the most polluted seas in the world due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can impact the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe the microbial diversity of sediments collected from three sampling stations in the Caspian Sea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as remediation efforts are initiated to reduce pollution.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Marine sediment Raw sequence reads

A mesocosm-scale experiment to investigate the electrobioremediation of crude oil-contaminated marine sediments.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated sediments
Hydrocarbon biodegradation potential affected by geographical location, tempearture, and nutrient

Surface water samples from three different geographical locations were incubated with oil at a systematic set of temperature and nutrient conditions.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Dispersant experiment using Pensacola beach water

The project studies the impact of dispersant application in oil-contaminated seawater at environmental-related concentration

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Oil-water intephase microbial community analysis Raw sequence reads

Following the succession of microbial community changes at oil-seawater interphase during oil degradation

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Arctic benthos Targeted Locus (Loci)

Biogeography of Arctic benthic bacteria. This study examines the influence of global change on the structural and functional diversity of microbial communities in Arctic sediments.  Biogeography of Arctic benthic bacteria sampled at the deep-sea, long-term observatory HAUSGARTEN in the Arctic Ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Microbial eukaryotes

Little is known about the taxonomic and phylogenetic diversities, and the relative importance of historic processes and environmental gradients underlying the current diversity and community assembly, of single-celled eukaryotes in marine benthic habitats. By pyrosequencing ribosomal RNA genes and characterizing multiple environmental factors, we investigated temporal and spatial patterns of a- and -diversities of microeukaryotes in near-surface sediments of three basins of the Yellow Sea Large Marine Ecosystem.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
marine sediment metagenome Targeted loci environmental

Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W), respectively. This project consists of samples isolated at the sediment sites described above and inoculated into seawater medium in microcosm experiments to evaluate the influence of bicarbonate on community composition.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
Microbial Biogeography and Potential Ecological Function Deep Indian Ocean Ridge

The marine microbial biogeography is gradually emerging a consensus. However, knowledge of the biodiversity, the biogeographic patterns and the factors influencing the distribution of deep-marine prokaryotes in distinct habitats at large scale is far from adequate. In this study, 16S rRNA gene Miseq-sequencing was used to survey the diversity and biogeography of prokaryotes from 39 sites across a broad geographic range, containing two obvious different habitats, hydrothermal and non-hydrothermal sediments. The deep marine sediment communities were highly diverse and Proteobacteria, Thaumarchaeota, Planctomycetes, Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae and Bacteroidetes were dominant in both habitats with varied percentages. The composition of prokaryotic communities obviously diverged across environmental heterogeneity and large geographic distances.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
pyrosequencing  Raw sequence reads of deep-sea Archaea

water-sediment interface in the slope Mariana Trench

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
Global Malaspina 2010 deep ocean expedition - rRNA pyrotags

Amplicon sequencing of the 16S rRNA of deep oceanic Bacteria and Archaea from Malaspina 2010 Expedition

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
marine sediment metagenome Targeted loci environmental

Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W), respectively.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
Abyssal Baseline Study & Geophysical Survey (ABYSSLINE 02)_AB01_Re-sequenced Targeted loci environmental

Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49 N, 116 36 W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49 N, 116 36 W), respectively.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane