SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial mats and sediments from Atacama

Atacama region in Chile is one of the most arid locations in the world. Extreme conditions in the area include: high UV irradiation, hypersalinity, drastic temperature changes, and desiccation. Hypersaline lakes can be found in this environment, and therein, bacterial communities thrive, forming different structures and colonizing varied niches. Given that the conditions in the lakes have important seasonal changes, including mainly temperature and dissecation, it is interesting to study the composition and evolution of these communities, and also its influence in the biogeochemical setting. In this dataset of bacterial diversity assessed by pyrosequencing V4 region of 16S rRNA gene, microbial mats and sediments from several lakes in Atacama region in Chile, including Coposa, Pucsa, Llamara, and Cejar, were analyzed.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
Llamara 1 evaporites metagenome

Domal evaporitic structures on Salar de Llamara are analyzed to study microbial diversity in the community inhabiting the evaporite.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
Raw sequence reads

Archaeal and bacterial 16S rRNA sequence from sediments sampled from Great Salt Lake, Utah, USA

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
Hypersaline sapropels Targeted loci environmental

The purpose of the present study was to describe and link the prokaryotic diversity in two disparate hypersaline sapropels (Transylvanian Basin, Central Romania), with nutrient and geochemical data in order to infer the role of the microbiome in their formation.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
Socompa Lake Stromatolite Shotgun Metagenomic Sequencing

With the altitude of 3570 m, this is so far the highest site where actively forming non-lithified stromatolites have been found, located at the shore of a volcanic, alkaline lake Socompa (Argentina). These microbial communities are a hotspot of biodiversity thriving under harsh environmental conditions that might be compared to Early Earth. This study uses a WGS strategy to understand the unique community composition and the mechanisms used by their members to withstand the extreme environment.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Antarctic Lakes Brine Raw sequence reads

The Tarn Flat area is the largest ice-free area (ca. 11  9 km) north to the McMurdo Dry Valley in Victoria Land (Antarctica). 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:Non-marine Saline and Alkaline:Hypersaline
Santa Pola Saltern Metagenome

Filtered water samples from hypersaline ponds of Santa Pola Saltern, Spain.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Soda Lakes Metagenome

The objective of this study was to explore the microbial diversity within the soda lakes in Kenya. Soda lakes represent some of the extreme but highly productive environments on earth. The microbial diversity on these environments is of interest in biotechnological applications. The data presented here give the first detailed study of the microbial taxa resident within lakes Magadi, Elmenteita, Crater Lake Sonachi and Bogoria in Kenya

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
Great Sippewissett Marsh Plot nirS Targeted Locus

nirS amplicon sequences from Great Sippewissett Marsh plot fertilization experiments

Biome: root:Environmental:Aquatic:Marine:Wetlands:Sediment
Biogeography of coastal wetland bacterial communities experiencing sudden vegetation dieoff

This study aims to describe how sediment microbial communities respond to the loss of vegetation through sudden vegetation die off (SVD) in two geographically separated wetlands. Further, samples were collected in the summer and fall to characterize temporal dynamics of the communities.

Biome: root:Environmental:Aquatic:Marine:Wetlands:Sediment
Sediment metagenome

Anaerobic methane oxidizing enrichment sampled from coastal tropical wetland

Biome: root:Environmental:Aquatic:Marine:Wetlands
Mud volcano Metagenome

Mud Volcano

Biome: root:Environmental:Aquatic:Marine:Volcanic
East China Sea environmental 16S rRNA gene pyrosequencing

To study the bacterial community structure of seawater samples of the ECS

Biome: root:Environmental:Aquatic:Marine:Sediment
cultured bacteria from enrichment culture Raw sequence reads

To targeted culture marine bacteria after enrichment culture

Biome: root:Environmental:Aquatic:Marine:Sediment
nirS-Encoding and nirK-Encoding Denitrifiers in the Sediment of Daya Bay Raw sequence reads

Surface sediments (upper 2 cm) were collected in spring (March 2016), summer (August 2016) and winter (December 2015) from four different locations in Daya Bay.

Biome: root:Environmental:Aquatic:Marine:Sediment
A comparison of eukaryote community composition in four contrasting sediments in the Celtic Sea

As part of the NERC funded Shelf Seas Biogeochemistry program, microbial structure, diversity and abundance was compared in four contrasting sediment types, from mud to sand. Samples were collected before (March 2015) and immediately after a spring diatom bloom (May) and also again in late summer (August). These data are 16S rRNA and 18S rRNA gene sequence sets from the four sediment types, and from the three sampling time points. Relative abundance and composition was determined using Illumina MiSeq (MrDNA, TX, USA). The V1V3 region of 16S rRNA was amplified using the PCR primers 27F (Vergin et al., 1998) and 519Rmod (Andreotti et al., 2011) using the PCR and sequencing conditions described in Tait et al. (2015). For 18S rRNA genes, the primers Euk7F and Euk570R were used.

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

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

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

Cores were collected over a year long period from sites associated with three transects in the northern Gulf of Mexico. Surface sediments were analyzed to determine patterns in Bacteria and Archaea within these samples and comparisons made to patterns observed for microeukaryotes. The study aimed to determine how location, season and sediment characteristics influence diversity and community structure. Similarities or differences in patterns among the three domains were identified.

Biome: root:Environmental:Aquatic:Marine:Sediment
Detection and diversity of nitrite oxidoreductase alpha subunit (nxrA) gene of Nitrospina in the marine sediments

nxrA gene abundance and diversity in sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
illumina high-throughput sequencing of AOB community

Microbial ecology of AOB community

Biome: root:Environmental:Aquatic:Marine:Sediment
Pyrosequencing of AOB community

Microbial ecology of ammonia-oxidizing bacteria

Biome: root:Environmental:Aquatic:Marine:Sediment
Denitrifying communities in marine sediments incubated under different oxygen regimes.

The aim of this study was to understand how oxygen regimes control denitrifying communities with the genetic capacity to reduce nitrous oxide. The study highlights importance of oxygen as a factor influencing the genetic potential for N transformations in marine sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Diversity of methyl alkyl succinate synthase genes in hydrocarbon seep sediments (Raw sequence reads)

In this study, the potential of hydrocarbon biodegradation in marine sediments was determined through the detection of a functional biomarker, the masD gene encoding (1-methyl-alkyl) succinate synthase, the key enzyme of anaerobic alkane degradation. We studied the masD diversity in 12 sampling sites from 7 methane, gas and hydrocarbon seeps differing in water depth, sediment depth, temperature, sulfate reduction rate and hydrocarbon composition (alkanes, aromatics) by parallel 454-tagged sequencing.

Biome: root:Environmental:Aquatic:Marine:Sediment
marine sample sequencing

microbial diversity

Biome: root:Environmental:Aquatic:Marine:Sediment
environmental sample sequencing

microbial diversity

Biome: root:Environmental:Aquatic:Marine:Sediment
Guaymas Basin and Sonora Margin sediment Targeted loci

Our proposed microbial analyses of Guaymas Basin and Sonora Margin subsurface sediments are guided by the working hypothesis that microbial communities will change in composition and metabolic potential, as hydrothermal activity decreases across the ridge flanks, chemical and thermal gradients are attenuated, and substrate availability changes. We propose that the distinctly different lithological and hydrothermal histories of these sediments, and their depositional contexts and changing quality and quantity of buried organic matter will affect the microbial community composition and activity.PI: Andreas Teske

Biome: root:Environmental:Aquatic:Marine:Sediment
Artificial stream sediment raw sequence reads

This study used artificial stream mesocosms to assess the effects of a single addition of nano-TiO2 (P25 at a final concentration of 1 mg L-1) on the abundance, activity and community composition of sediment-associated bacterial communities. The addition of nano-TiO2 resulted in a rapid (within one day) decrease in bacterial abundance in artificial stream sediments, but bacterial abundance returned to control levels within 3 weeks. Pyrosequencing of partial 16S rRNA genes did not indicate any significant changes in the relative abundance of any bacterial taxa with nano-TiO2 treatment, indicating that nano-TiO2 was toxic to a broad range of bacterial taxa and that recovery of the bacterial communities was not driven by changes in community composition.

Biome: root:Environmental:Aquatic:Marine:Sediment
Assessing the effects of salmon farming seabed enrichment using bacterial community diversity and high throughput sequencing

16S bacterial sequencing of DNA and RNA taken from around marine sediment under and around salmon farm cages.Published 2015 FEMS

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

Benthic communities in the aquatic ecosystem are influenced by both natural and anthropogenic stressors. To understand the ecogenomic responses of sediment communities to the multiple stressors of polluted environments, the bacteria, protistanand metazoan communities in sediments from marine and adjacent riverine areas of North Bohai Sea were characterized by environmental DNA meta-systematics, and their associations with environmental variables were assessed bymultiple statistical approaches. The structures of communities in sediments were shaped by both natural variables and anthropogenic contaminants, including DDTs, PAHs or metals. Particularly, the correlation network of multiple communities was modulated by the concentrationsof Na and DDTs at the family level.

Biome: root:Environmental:Aquatic:Marine:Sediment
Metagenome microbial communities of bottom sediments of the Kara Sea

Metagenomic analysis of the microbial community in the bottom sediments Kara Sea shelf Yenisei Gulf and Gyda Bay by pyrosequencing

Biome: root:Environmental:Aquatic:Marine:Sediment
Uncultered bacterium Targeted Locus (Loci)

In the context of global warming in the Arctic environment greater understanding of microbial-driven processes related to sediment and hydric transfers is of major importance where these are linked to erosion processes. To add to the research in this area, we investigated the structure of sedimentary microbial communities from three distinct samples collected along a short Glacier-River-Fjord transect in Kongsfjorden (Fjord of Svalbard) at the beginning of the active thaw using a metagenomic approach. A methodological approach was used based on the pyrosequencing of 16S rRNA genes coupled with multiple DNA extractions to overcome major methodological biases, namely DNA extraction and polymerase chain reaction (PCR).

Biome: root:Environmental:Aquatic:Marine:Sediment
Illumina high-throughput sequencing of bacterial community

Microbial ecology of bacterial community

Biome: root:Environmental:Aquatic:Marine:Sediment
Pyrosequencing of bacterial community

Microbial ecology of bacterial community

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

The microbial community influenced by bioturbation of macrofauna

Biome: root:Environmental:Aquatic:Marine:Sediment
2011 depth sediment Metagenome

2011 oil spilled sediment

Biome: root:Environmental:Aquatic:Marine:Sediment
Red Sea sediment 2011 Targeted Locus (Loci)

This study is to determine the eukaryotic microbial community structure in the sediment of Red Sea.

Biome: root:Environmental:Aquatic:Marine:Sediment
Narragansett Bay, RI Sediments Targeted Locus (Loci)

Goals were to investigate microbial community of sediment samples with acetylene and without

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

This study demonstrated that Dehalococcoides could be employed as a promising biomarker to test the present of organohalides in wastestreams or other environmental samples.

Biome: root:Environmental:Aquatic:Marine:Sediment
Eukaryote diversity assessment of sediments of the Western English Channel

Sediments were collected at monthly intervals from the Western English Channel (site L4) and environmental DNA extracted. The effect of season on the community composition and diversity of eukaryotes was assessed using in depth sequencing of 18S rRNA genes. This data will be compared with traditional techniques used to identify benthic species to assess the efficacy of eDNA biomonitoring as a tool for measuring biodiversity.

Biome: root:Environmental:Aquatic:Marine:Sediment
Arabian sea sediment samples with protist reads Metagenome

Protist paleome from Arabian sea

Biome: root:Environmental:Aquatic:Marine:Sediment
Benthic microbial communities in the sediments of the Southern Ocean

To investigation benthic microbial communities in the sediments of the Southern Ocean underlying Phaeocysis bloom.

Biome: root:Environmental:Aquatic:Marine:Sediment
A comparison of microbial community composition in four contrasting sediments in the Celtic Sea

As part of the NERC funded Shelf Seas Biogeochemistry program, microbial structure, diversity and abundance was compared in four contrasting sediment types, from mud to sand. Samples were collected before (March 2015) and immediately after a spring diatom bloom (May) and also again in late summer (August). These data are 16S rRNA and 18S rRNA gene sequence sets from the four sediment types, and from the three sampling time points. Relative abundance and composition was determined using Illumina MiSeq (MrDNA, TX, USA). The V1V3 region of 16S rRNA was amplified using the PCR primers 27F (Vergin et al., 1998) and 519Rmod (Andreotti et al., 2011) using the PCR and sequencing conditions described in Tait et al. (2015). For 18S rRNA genes, the primers Euk7F and Euk570R were used.

Biome: root:Environmental:Aquatic:Marine:Sediment
uncultured prokaryote Targeted Locus (Loci)

Analysis of community composition of sulfur-oxidizing bacteria in East China Sea using soxB as a functional molecular marker

Biome: root:Environmental:Aquatic:Marine:Sediment
Sediment microbial community Random survey

Assessment of Microbial Community Composition in Chesapeake Bay Sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
La Medee sediment - Microbial Metagenome Metagenome

SSU 16S pyrosequencing project of the microbial metagenome of a DHAB sediment (La Medee) from the Eastern Mediterranean.

Biome: root:Environmental:Aquatic:Marine:Sediment
Oxic sediment - Extracellular Metagenome

SSU 16S pyrosequencing project of the microbial metagenome of an oxic deep-sea sediment from the Eastern Mediterranean.

Biome: root:Environmental:Aquatic:Marine:Sediment
Baltic Sea Basin sediments diversity Raw sequence reads

Baltic Sea sediment from IODP X347 active community diversity through 16S RNA sequencing

Biome: root:Environmental:Aquatic:Marine:Sediment
dsrB gene diversity in marine coastal sediments in Aarhus Bay, Denmark

Sulfate-reducing microorganisms (SRM) are key players in the marine carbon and sulfur cycles, especially in coastal sediments. We identified and characterised SRM using dsrB gene sequencing in a marine coastal sediment in Aarhus Bay, Denmark.

Biome: root:Environmental:Aquatic:Marine:Sediment
SMAR-T Raw sequence reads

deep-sea sediments

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

surface coastal sediment

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

18S sequences from environmental samples using universal eukaryote primers. The goal of the study is to design and test eukaryote specific primers to be used in assessing biodiversity of eukaryotes.

Biome: root:Environmental:Aquatic:Marine:Sediment
deep marine subsurface Raw sequence reads

The deep sedimentary biosphere, extending hundreds of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Little is known about microbial eukaryotes in these habitats, however studies suggest that fungi dominate. Here we compared fungal ribosomal RNA signatures present in sediment core samples from 6 and 95mbsf from Peru Margin site 1229A. Fungal-specific PCR primers were used in this study.

Biome: root:Environmental:Aquatic:Marine:Sediment
Global phylogeography survey of thermophilic spores in marine sediments.

16S rRNA gene-based survey of thermophilic spores in marine sediments from globally distributed locations.

Biome: root:Environmental:Aquatic:Marine:Sediment
Eastern offshore environmental monitoring of Krishna Godavari Basin Bay of Bengal 2013-2016, Funded by: ONGC India

Environmental monitoring of Krishna Godavari Basin Bay of Bengal

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

Microbial diversity survey of shallow tropical marine sediment.

Biome: root:Environmental:Aquatic:Marine:Sediment
Marine sediment amplicon Targeted loci environmental

Marine sediment from Aarhus Bay

Biome: root:Environmental:Aquatic:Marine:Sediment
Metazoan sequencing

The present study provides a new data on the diversity of nematodes communities in sub-marine canyon.

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

Understanding the microbial diversity of deep sea marine sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
uncultured eukaryote Raw sequence reads

This study aims to reveal eukaryotic diversity in sediments from the South China Sea.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial community structure of chronically polluted marine sediments from a cold region of the southern hemisphere

This study is part of a larger initiative: Microbial Community Structure and Metabolic Potential of Chronically Polluted Marine Sediments from Cold Regions of the Northern and Southern Hemispheres (CSP-328, JGI-DOE). The goal of this larger project is to increase our understanding of the biogeographic distribution patterns and functional traits of microorganisms in cold, polluted costal sediments. In this study, we analized the structure and diversity of microbial communities of cold polluted coastal sediments from Ushuaia Bay.

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

The study of this paper was to characterize the characterization of depth-related microbial communities and their potential functions in the sediment ecosystem of the East China Sea.

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

This study was to characterize the structure and function of microbial communities in surface sediment from the East China Sea.

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

Marine microbial diversity study

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial communities in deep eastern Mediterranean Sea surface sediments

In order to elucidate spatial distribution of microorganisms in deep sea surface sediments and to reduce the general information deficiency regarding microbial community composition in sediments of the eastern Mediterranean Sea, sequences of surface sediment samples from 9 stations in the Levantine basin were produced by 454 massive tag sequencing and compared to each other.

Biome: root:Environmental:Aquatic:Marine:Sediment
Sinking bloom influences benthic microorganisms

Here, we analyzed the bacterial community structure of four abyssal sediments and one shallow reference site in the Atlantic sector of the Southern Ocean. The sediments differed in their exposure to phytoplankton blooms to investigate potential links between the blooms and benthic microorganisms. Our main hypotheses were (i) that an extended bloom situation in the surface ocean leads to shifts in the benthic microbial communities with short delay times and (ii) that certain key bacterial clades benefit from the organic matter input.

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

Environmental parameters driving the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt Region in the Gulf of Mexico

Biome: root:Environmental:Aquatic:Marine:Sediment
Mid-Atlantic Ridge sediment Raw sequence reads

The objective of this study was to determine the bacterial community structure within deeply buried marine sediments along the western flank of the mid-Atlantic ridge. Samples were collected during Integrated Ocean Drilling Program expedition 336 (Oct-Dec 2011).

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

Using environmental samples to study the microbial community structure in bohai sediment.

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

Using environmental samples to study the community structure of anammox bacteria in Bohai sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
sediment microorganisms nirK gene Raw sequence reads

We extract total DNA in sediment microorganisms from BoHai sediment, and we use illumina to study the nirK gene in total DNA.

Biome: root:Environmental:Aquatic:Marine:Sediment
dsrB sequencing of sulfate-reducing microbial communities in Skagerrak and Baltic sediment

Seabed communities of sulfate-reducing microorganisms were profiled by Illumina MiSeq sequencing of the dsrB gene from four different sites up to a depth of 5.3 meters below seafloor.

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

To investigate the methane-oxidation archaeal communities in the Canadian Beaufort Sea

Biome: root:Environmental:Aquatic:Marine:Sediment
16S_Sediment_Bolinao

V4-V5 sequences from sediments in Bolinao, Philippines

Biome: root:Environmental:Aquatic:Marine:Sediment
Studies of marine microbial dark matter

To analyze the culturable mechanisms of enrichment culture, and to establish a sequencing-based workflow that could be used as a platform for the culturing of marine bacteria throught 16S rRNA transcript amplicon sequencing.

Biome: root:Environmental:Aquatic:Marine:Sediment
resuscitation mechanisms during enrichment culture

To analyze the culturable mechanisms of enrichment culture, and to establish a sequencing-based workflow that could be used as a platform for the culturing of marine bacteria

Biome: root:Environmental:Aquatic:Marine:Sediment