SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Gulf Oil Spill underwater oil plume samples Targeted Locus (Loci)

During late spring and summer of 2010, the Northern Gulf of Mexico (GoM) was exposed to an oil spill different in magnitude and scope from any previous spill. The Deepwater Horizon, an ultra-deep, offshore drilling platform, began working GoM oil fields in 2001. While working a well in Mississippi Canyon on April 20, 2010, a bolus of methane gas ascended the drill pipe and exploded at the surface. Two days later the platform sank and since then, substantial quantities of oil and gas have leaked from the damaged wellhead. This work addressed the offshore oceanic impacts of the BP spill.  Sediment microbial mediated processes are capable of oxidizing oil and methane in the environment. The PI''s examined the impacts of the Deepwater Horizon Oil Spill on microbially mediated processes in the deep waters and sediments in the vicinity of the spill site. The work complemented several funded or planned geochemical and microbiological sampling programs focused on the oil spill response. PI''s evaluated rates of water column methane oxidation and sediment sulfate reduction and methanogenesis at multiple sites around the spill site. Additional experiments quantified the impact of nutrients, oxygen and substrate concentrations on these important microbially mediated processes.  The Joye group participated in six research cruises during 2010 and received samples from another six cruises from the study area. On all cruises, water samples were collected using a CTD rosette and Niskin or Go-Flo bottles. Sediment samples were obtained by box coring, multi-coring, or using the manned submersible ALVIN.  The PI''s extended the monitoring/assessment program that was initiated through the NOAA National Institute of Undersea Science and Technology (NIUST) funded cruise and further leveraged by NOAA/NIUST (cruises in July 2010, October 2010) by conducting three major expeditions in 2010. This RAPID project directly supported the PI''s efforts for cruises in May/June 2010 (NSF Joye chief scientist); August 2010 (NSF Montoya, chief scientist); November/December 2010 (NSF Joye chief scientist); and July 2011 (NSF Montoya, chief scientist)

Biome: root:Environmental:Aquatic:Marine
Western Antarctic Peninsula Microbial Community Assembly


Biome: root:Environmental:Aquatic:Marine
Protistan communities of the upper Arctic Ocean (18S SSU-rRNA Targeted Locus)

Protistan communities of the upper Arctic Ocean (18S SSU-rRNA Targeted Locus), sampled during the MALINA cruise, August 2009.

Biome: root:Environmental:Aquatic:Marine
Seawater Metagenome

Microbial community in seawater sample

Biome: root:Environmental:Aquatic:Marine
UK coast natural seawater Genome sequencing

the aim of the project is to determine the effect of plastics on marine bacterial community

Biome: root:Environmental:Aquatic:Marine
Red Sea metagenomes

An expedition spanning nearly the entire eastern Red Sea. We sampled at eight stations along this route, sampling from the surface down to 500m.

Biome: root:Environmental:Aquatic:Lentic:Brackish
Baltic Sea Surface Water Metagenome

Surface water collected in the Baltic Proper, 10 km east of Oland in the Baltic Proper (N 5655.851, E 1703.640)

Biome: root:Environmental:Aquatic:Marine
seawater sample Metagenome

Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments Seawater samples collected from the Gulf of Mexico

Biome: root:Environmental:Aquatic:Marine
Hawaii Dissolved Organic Matter (HIDOM) microcosm perturbation experiments

Marine dissolved organic matter (DOM) contains nearly as much carbon as the Earths atmosphere. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of DOM, we followed the transcriptional responses of a surface water microbial assemblage to DOM derived from an axenic culture of Prochlorococcus marinus and high-molecular weight DOM concentrated from nearby surface waters.

Biome: root:Environmental:Aquatic:Marine
Gulf of Mexico water and sediments Metagenome

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km SW of the wellhead), one water column reference station outside of the affected area (37.77 km SE of the wellhead), and deep-sea sediments near the wellhead (3.66 km SE of the wellhead) were sampled one year after the capping of the well.

Biome: root:Environmental:Aquatic:Marine
Marine water Metagenome

Examine viral communities in ballast and harbor waters

Biome: root:Environmental:Aquatic:Marine
Marine eukaryotic metatranscriptomes

Metatranscriptome data

Biome: root:Environmental:Aquatic:Marine
Metagenome sequencing of marine membrane vesicles

Sequencing of DNA amplified from membrane vesicles isolated from the oceans

Biome: root:Environmental:Aquatic:Marine
sediment metagenome metagenome L-T

The objectives of this investigation were to assess TCS removal mechanisms in sediments from surface flow constructed wetlands planted with Lemnaminor.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
sediment metagenome Metagenome

The objectives of this investigation were to assess TCS removal mechanisms in sediments of surface flow constructed wetlands planted with Hornwort

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
Sediment microbial communities from Cattail constructed wetlands, Jinan, China - C-T Metagenome

The objectives of this investigation were to assess TCS removal mechanisms in sediments from surface flow constructed wetlands planted with emergent plant (Cattail)

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
XRCWU sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
XRCWD sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
XRM sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
Coastal marsh sediment alkB, pmoA, and P450 gene survey

This dataset includes high-throughput amplicons for alkane dehydrogenase (alkB) genes, particulate monooxygenase (pmoA) genes, and cytochrome P450, encoded by CYP153, genes amplified and sequenced from subtidal sediment and inland soil samples collected biannually (September 2011 to October 2014) from a marsh near Grand Isle, Louisiana. This marsh was affected by oil deposition following the Deepwater Horizon oil spill in 2010. The goals of this dataset are to 1) track changes in the phylogenetic diversity of genes that code for a key enzymes used for bacterial alkane oxidation, short and long chain, from the oil impacted sediments and soil, and 2) to contribute to an understanding of bacterial functional role in the degradation of weathered oil residues in a natural marsh system.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Marsh
Temporal effect of plant diversity and oiling on nitrogen cycling in marsh sediments

The effect of plant diversity on ecosystem recovery from oil spills and temporal effects on biogeochemical cycles needs to be investigated to identify key ecosystem processes as well as the various challenges associated with coastal ecosystem recovery. Oil spill effects on nitrogen cycling caused by either changes in species composition of primary producers or microbial community composition have also been documented. Although low to moderate oiling of coastal wetlands has been shown to impact ecosystem functions, studies focused on determining long term impacts of oil spills on marsh vegetation, microbial community composition and associated effects on nitrogen cycling are relatively limited. This project investigated temporal effects of plant diversity on denitrification and microbial community dynamics through mesocosm experiments. The mesocosms consisted of the black mangrove, Avicennia germinans, along with either a monoculture or polyculture of the smooth cord grass, Spartina alterniflora. The results presented were obtained using DNA extracted from replicate sediment cores sampled in April 2016, 6 months after the mesocosms were treated with oil to achieve a final concentration of 4000 ppm.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Marsh
sediment metagenome Raw sequence reads

The goal of the project is to differentiate storm and tsunami deposits by characterizing the microbial assemblage found in them.

Biome: root:Environmental:Aquatic:Freshwater:Storm water
microbial community in an integrated constructed wetland Raw sequence reads

microbial community in an integrated constructed wetland

Biome: root:Environmental:Aquatic:Freshwater:Sediment
lake sediment Raw sequence reads

methanotrophs diversity in lake sediments

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Amplicon sequencing of gyrA and parC in Escherichia communities in river/lake sediments

To describe the abundance of fluoroquinolone resistance mutations in environmental Escherichia communities, and investigate the link between abundance of resistance mutations and fluoroquinolone pollution.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Robertson Glacier Targeted Locus (Loci)

cbbL transcript amplicons from Robertson Glacier, Alberta, Canada subglacial sediment sampled in 2010

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Freshwater sediment Raw sequence reads

The study aims to find out the changes in microbial community structure of anode biofilm and sediment in sediment microbial fuel cells. The samples include original freshwater sediment that used in SMFCs and anode biofilm of SMFCs in which worms were observed or not.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Studies on archaeal communities from freshwater sediments based on 16S rRNA gene biomarker

Study of the abundance and diversity of archaeal communities inhabiting freswater sediments in basis of the 16S rRNA gene biomarker.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment samples Raw sequence reads

the Sediment samples and background Environmental microbial diversity

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Enhanced pyrene and benzo[a]pyrene degradation by plant root and SMFC

Toward Understanding Complex Interaction between Roots of Macrophyte Sweet Flag Acorus calamus and Anode of Microbial Fuel Cell for Pyrene and Benzo[a]pyrene Degradation in Freshwater Sediments

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Molecular Characterization of the Structural and Functional Microbial Community in Sediments of a Northern Utah, Basin-Fill Aquifer

Characterization of arsenic and Fe(III) reducing microbial communities at the cache valley sites

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal

Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal, assessed by 16S rRNA gene pyrosequencing

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Vertical profiles of bacterial community diversity in a drinking water reservoir

Bacterial community diversity in a drinking water reservoir

Biome: root:Environmental:Aquatic:Freshwater:Sediment
CPN Metagenome

Paired end illumine sequencing of V4 region of the 16S rRNA gene along with biolog ecoplate has been performed to systematically evaluate the bacterial community and their metabolic activity of cave sediments in Meghalaya, India

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Svalbard Targeted Locus (Loci)

This study compared microbial communities in sediments in streams that drain glaciated and unglaciated catchments in Svalbard

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Yangtze River bacteria Raw sequence reads

Abstract: the bacteria in the Yangtze River

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Brazoria Sediment Inocula and Fermentations of Carboxylate Biofuels Platform Targeted Locus (Loci)

Comparison of community compositions of different fermentation screen approaches conducted simultaneously with a shared inoculum source. Chemical engineers at Texas A&M use three fermentation screens to evaluate and model community performance at different scales, times, substrate concentrations, and product concentrations. To date, these screens have been used sequentially to optimize different features of the process while the inoculum has undergone selective pressure from storage conditions. We used four fresh, environmentally distinct, previously characterized sediment sources collected from Brazoria National Wildlife Refuge to simultaneously inoculate the three screens. We sequenced the communities in each screen to compare the communities that establish across the manipulated parameters.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Pond sediments Metagenome

Diversity of Bacterial and Archaeal 16S rRNA genes in sediment samples collected from biological stabilization ponds across different latitudes of China

Biome: root:Environmental:Aquatic:Freshwater:Pond:Sediment
magnetite Targeted Locus (Loci)

Pond sediment magnetite grains show a distinctive microbial community

Biome: root:Environmental:Aquatic:Freshwater:Pond:Sediment
Arctic Microbial response to oil and Corexit

The fate of oil and oil spill response chemicals in the Arctic is of critical importance as marine shipping and oil exploration are increasing due to receding sea ice cover. Using indigenous Arctic marine organisms in freshly collected seawater, we identified of bacterial taxa that increase in relative abundance in response to both oil and Corexit in Arctic seawater, suggesting that some taxa biodegrade components of both oil and dispersant. We then paried these microbial analyses with the chemical loss of oil and the surfactant components of Corexit 9500. These results allow for the first comparison between Arctic and temperate environments in regards to the fate of Corexit and the microbes involved in biodegrading dispersants and oil.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Hangzhou-sediment-sample Raw sequence reads

This is the result of amplicon sequencing of multiple microbial functional genes in sediment samples

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
ZRCWU sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
River sediments Metagenome

Mining activities have introduced contamination to surrounding aquatic and terrestrial environments, causing adverse impacts to human health and the environment. Indigenous microbial communities are responsible for biogeochemical cycling in diverse environments, indicating the potential to remediate the contamination introduced by the mining activities. Antimony has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. However, the microbial composition and structure in response to antimony contamination has remained overlooked. Here we selected a watershed heavily contaminated by an antimony tailing from an upstream mine. We obtained comprehensive geochemical data (specifically, physical-chemical properties and different antimony extraction fractions) from river water and sediments at different depths. In addition, the indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads).

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
sediment metagenome B2 Metagenome

The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
sediment metagenome metagenome A2

The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
sediment metagenome B1 Metagenome

The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
16S rDNA sequencing

Bacteria communiy abundance during PAHs degradation

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania

The goal of this study were to determine how hydraulic fracturing impacts bacteria in nearby streams by analyzing 16S rRNA data. Overall diversity and interactions among bacteria were examined to see how hydraulic fracturing may impact bacterial communities. Analysis was also done to identify pathways that were potentially enriched in streams near hydraulic fracturing and taxa that could be potential biomarkers for impacted streams. Therefore, this study generated data that increase our understanding of how hydraulic fracturing affects the surrounding environment.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Variation in freshwater stream sediment community 16S rRNA profiles along an urbanization gradient

We examined bacterial community change along an urbanization gradient in NE Ohio, USA to assess the effects on urbanization on bacterial community diversity.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Sediment river Genome sequencing and assembly

Bacterial community composition in sediment discharge at upper and lower reaches of Puyang river

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Microbial diversity in benthic stream sediment

The goal of this sequencing project is to identify putative methanotrophic organisms in benthic stream sediments.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Marine sediment metagenome

Study of bacterial diversity of Bhitarkanika sediment

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Enrichment of organohalide respiring bacteria

Organohalide respiring bacteria are difficult to enrich and isolate, which can limit research on these important organisms. The goal of this research was to develop a method to rapidly (minutes to days) enrich these organisms from a mixed culture or sediment sample. The method presented herein was based on the hypothesis that organohalide respiring bacteria would be more hydrophobic than other bacteria as a result of their niche dehalogenating hydrophobic compounds. To test this hypothesis, a method was developed to separate putative organohalide respiring bacteria at the interface between a hydrophobic organic solvent and aqueous media. This novel separation technique was tested with a sediment-free culture, a tetrachloroethene-enriched digester culture, and sediment from an uncontaminated lake.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Study of microbial diversity from sediment samples of the SaiGon-DongNai system

The main goal is to study the microbial diversity in polluted river affected by urban and industrial activities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
XRU sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
ZRCWD sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
ZRD sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
ZRM sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
ZRU sediment metagenome Metagenome

To investigate the influence of wetland types on the composition and structure of microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
PAH-contaminated sediment from the Lagos Lagoon, Nigeria

sediment metagenome

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Lakes ediments of the Amazon River system Raw sequence reads

There is a paucity of information on the composition of the methanogenic microbial communities in tropical lake sediments, and we decided to study methanogenic lake sediments from the Amazon in more detail.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Rifle sediment bacterial community Targeted Locus (Loci)

The objective of the research at the Rifle site is to gain a comprehensive and mechanistic understanding of the microbial factors and associated geochemistry controlling uranium mobility at the field scale so that DOE can confidently remediate uranium plumes as well as support stewardship of uranium-contaminated sites.  This subproject focuses on near-full-length amplification, high-throughput sequencing, and assembly of the bacterial 16S rRNA gene for community characterization.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
the under-explored coal gangue and the adjacent acid mine drainage creek soil Raw sequence reads

Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied. However, the microbial communities in the coal gangue that may generate the AMD and function as the seed bank of microbiota for AMD-related environments are still under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Appliaction of metagenomic technique for isolation of microbes from mangroves for potential use in biofertilization and bioremediation

The sequences submitted are the fingal ITS metagenomic. The mangrove ecosystem of Goa forms a very important bio-repository. Therefore, the ITS metagenomic DNA sequences obtained from Goa coastline will help to develop a gross idea about the fungal community members present in the mangrove sediments of North and South Goa. This is the first report of fungal metagenomic sequences for Mandovi &amp; Zuari mangrove ecosystem obtained through illumina Miseq platform.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment