SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Biogeography of Arctic picoeukaryotes during summer of 2012

Information on recent photosynthetic biomass distribution and biogeography of Arctic marine pico-eukaryotes (0.2  3 m) are needed to better understand consequences of environmental change for Arctic marine ecosystems. We analysed pico-eukaryote biomass and community composition in Fram Strait and larger parts of the central Arctic Ocean (Nansen Basin, Amundsen Basin) by chlorophyll a (Chl a) measurements, Automated Ribosomal Intergenic Spacer Analysis (ARISA), and 454-pyrosequencing. Samples were collected during summer 2012, the year with the latest record sea ice minimum. Chl a values were highest in eastern Fram Strait and pico-plankton accounted for 60-90% of Chl a biomass during the observation period. ARISA-patterns and 454-pyrosequencing revealed, that pico-eukaryote distribution is closely related to water mass distribution in the euphotic zone of the Arctic Ocean. Phaeocystaceae, Micromonas sp., Dinophyceae and Syndinales constitute a high proportion of sequence reads, while sequence abundance of autotrophic Phaeocystaceae and mixotrophic Micromonas sp. was inversely correlated. Highest sequence abundances of Phaeocystaceae were observed in the warm Atlantic waters in Fram Strait, while Micromonas sp. dominated the abundant biosphere in the arctic halocline. Our results are from particular interest, because there are hypotheses that environmental conditions in Nansen Basin might become more similar to the current conditions in Fram Strait. In regard to this we propose that in response biodiversity and biomass of pico-eukaryotes in Nansen Basin could resemble those currently observed in the Fram Strait in the future. This would significantly alter biogeochemical cycles in that area, that constitutes a large part of the central Arctic Ocean.

Biome: root:Environmental:Aquatic:Marine
Pyrosequencing reveals effect of increased pCO2 on bacterial assemblage
                shifts in response to glucose addition in Fram Strait seawater
                mesocosms

Ocean acidification (OA) may stimulate primary production through
                increased availability of inorganic carbon in the photic zone, which may in turn
                change the biogenic flux of dissolved organic carbon (DOC) and the growth potential
                of heterotrophic bacteria. In order to investigate the effects of OA on marine
                bacterial assemblages, a two-by-three factorial mescosom experiment was conducted
                using surface seawater from the East Greenland Current in Fram Strait.
                Pyrosequencing of the V1-V2 region of bacterial 16S ribosomal RNA genes was used to
                investigate differences in the endpoint (Day 9) composition of bacterial assemblages
                in mineral nutrient-replete mesocosms amended with glucose (0 M, 5.3 M and 15.9
                M) under ambient (250 atm) or acidified (400 atm) partial pressure of CO2 (pCO2).
                All mesocosms showed low richness and evenness by Chao1-estimator and Shannon-Wiener
                diversity index, respectively, with general dominance by Gammaproteobacteria and
                Flavobacteria. Non-metric multidimensional scaling analysis and two-way analysis of
                variance of the Jaccard dissimilarity matrix (97% similarity cut-off) demonstrated
                that the significant community shift between 0 M to 15.9 M glucose addition at 250
                atm pCO2 was eliminated at 400 atm pCO2. These results suggest that the response
                potential of marine bacteria to DOC input may be altered under acidified
                conditions.

Biome: root:Environmental:Aquatic:Marine
Protist communities in moored long-term sediment traps (Fram Strait, Arctic)  Preservation with mercury chloride allows for PCR-based molecular genetic analyses

Protist communities in moored long-term sediment traps (Fram Strait, Arctic)  Preservation with mercury chloride allows for PCR-based molecular genetic analyses

Biome: root:Environmental:Aquatic:Marine
Microbial community 16S rRNA from Fram Strait water samples PS85 2014

Several depths of the full water column of two stations (HGIV and N4) were sequenced in order to correlate the communities of the Fram Strait water column at HAUSGARTEN with benthic communities. DNA from CTD samples was extracted and the v3v4 region of the 16S rRNA was sequenced with Illumina MiSeq.

Biome: root:Environmental:Aquatic:Marine
Pelagic eukaryotic communities across Fram Strait

Water samples were collected in Fram Strait during the Polarstern cruise PS85 (June 6th 2014
                until July 3rd 2014) from eastern Greenland shelf to west coast of Spitsbergen. For assessing eukaryotic
                community composition 2 L of water were filtered using vacuum filtration (at 200 mbar) through
                successive membrane filters of 10 m , 3 m and 0.4 m. The extracted genomic eukaryotic DNA was pulled
                together from the different fractions and the hypervariable V4 (528iF - 964iR) region of the 18S rRNA
                was amplified and sequenced using Illumina MiSeq platform in a 2  300 bp paired-end run.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Pelagic bacterial communities across Fram Strait

Water samples were collected in Fram Strait during the Polarstern cruise PS85 (June 6th 2014
                until July 3rd 2014) from eastern Greenland shelf to west coast of Spitsbergen. For assessing bacterial
                community composition 2 L of water were filtered with peristaltic pump through successive membrane
                filters of 3 m and 0.22 m. The extracted genomic bacterial DNA was isolated and the hypervariable
                V3-V4 (341F - 785R) region of the bacterial 16S rRNA was amplified and sequenced using Illumina MiSeq
                platform in a 2  300 bp paired-end run.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Universal Amplicon Sequences (mixed 16S/18S) from GEOTRACES Cruises GA03 and GP13

Dedicated sampling campaigns such as JGOFS, CLIVAR, and GEOTRACES have quantified critical oceanic biogeochemical processes on a global scale. Integrating these measurements with microbial community composition data is highly desirable because it would allow hypotheses about biogeographic distributions to be tested or perhaps lead to the discovery of organisms responsible for a particular biogeochemical process. A promising strategy to generate this microbial community composition data comes from high-throughput sequencing of PCR amplicons generated with the 515Y/926R universal 16S/18S primer set. The two key advantages of the 515Y/926R primers are 1) their comprehensiveness - recovering amplicons from the entire cellular microbial community - and 2) their quantitative nature - recovering gene copy abundances as shown previously with microbial community standards. Compared to metagenomes, amplicons additionally have the advantage of more easily detecting rare community members that may be biogeochemically significant (e.g. diazotrophs). In this study, we applied the 515Y/926R primers to DNA from the recently published bioGEOTRACES metagenomic dataset, and use these results to describe microbial community composition across a longitudinal transect of the southern Pacific Ocean from Australia to Tahiti (GEOTRACES section GP13) and a longitudinal transect of the northern Atlantic from Massachusetts to the Canary Islands (GEOTRACES section GA03). In addition, we conducted intercomparisons with metagenomic taxa abundances and show the two techniques correspond strongly to one another for most samples (average R^2=0.97).

Biome: root:Environmental:Aquatic:Marine:Oceanic
The Indigo Project: a global citizen science Ocean survey

Sequencing the microbiome of the world''s Oceans with data collected by citizen sailing oceanographers

Biome: root:Environmental:Aquatic:Marine:Oceanic
EMG produced TPA metagenomics assembly of PRJNA419970 data set (Metagenomic analysis exploring soil microbial communities associated with Antarctic vascular plants).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA419970, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
Metagenomic analysis exploring soil microbial communities associated with Antarctic vascular plants

The Antarctic ecosystem is one of the most stressful natural habitats, especially for terrestrial plants. Likewise, only two vascular plants have colonized the Antarctic environment, Colobanthus quitensis (Caryophyllaceae) and Deschampsia antaractica (Poaceae). Although both plants colonize Antarctica, C. quitensis is mainly found growing in association with D. antarctica in more stressful areas, while D. antarctica is capable to grow alone in areas with higher abiotic stress. Positive inter-specific interactions play a pivotal role in the structure and functioning of several ecosystems in harsh environments, and possibly they play a role in Antarctic terrestrial ecosystems.In this study, we compare the rhizosphere microbiomes associated with Colobanthus quitensis, either growing alone or associated with Deschampsia antarctica, using shotgun metagenomic DNA sequencing technology for comparative metagenomics. This approach allows us to gain insight into the rhizospheric microbial community structure associated with C. quitensis and C. quitensis  D. antarctica, through the study of soil's microbial taxonomic diversity, including non-culturable organisms. Such analysis could also provide valuable information regarding microbial functional diversity. This functional diversity might be playing important roles in conferring different degrees of tolerance to Antarctica's harsh environmental conditions such as low temperatures, desiccation, and low water and nutrient availability, which could help to explain the enigma of the success of these plant species in such harsh environments.

Biome: root:Host-associated:Plants:Rhizosphere
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Biome: root:Host-associated:Amphibia
EMG produced TPA metagenomics assembly of PRJNA318384 data set (marine metagenome Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA318384, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

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

Marine plastic debris has become a significant concern in ocean ecosystems worldwide. Little is known however, about its influence on microbial community structure and function. In 2008, we surveyed microbial communities and metabolic activities in seawater and on plastic on an oceanographic expedition through the 'Great Pacific garbage patch'. The concentration of plastic particles in surface seawater within different size classes (2-5 mm and > 5 mm) ranged from 0.35-3.7 particles m-3 across sampling stations. These densities and the particle size distribution were consistent with previous values reported in the North Pacific Ocean. Net community oxygen production (NCP = gross primary production  community respiration) on plastic debris was positive and so net autotrophic, whereas NCP in bulk seawater was close to zero. Scanning electron microscopy and metagenomic sequencing of plastic-attached communities revealed the dominance of a few metazoan taxa, and a diverse assemblage of photoautotrophic and heterotrophic protists and bacteria. Bryozoa, Cyanobacteria, Alphaproteobacteria and Bacteroidetes dominated all plastic particles, regardless of particle size. Bacteria inhabiting plastic were taxonomically distinct from surrounding picoplankton, and appeared well adapted to a surface-associated lifestyle. Genes with significantly higher abundances among plastic-attached bacteria included che genes, secretion system genes and nifH genes, suggesting enrichment for chemotaxis, frequent cell-to-cell interactions and nitrogen fixation. In aggregate, our findings suggest that plastic debris forms a habitat for complex microbial assemblages that have lifestyles, metabolic pathways and biogeochemical activities that are distinct from free-living planktonic microbial communities.

Biome: root:Environmental:Aquatic:Marine
Natural product discovery via metatranscriptomic analysis of three Caribbean octocoral species.

Octocorals are an important source of bioactive natural products such as the pseudopterosin family of diterpene glycosides which exhibit potent anti-inflammatory activity. Despite the promising activity of these molecules their clinical development has been hampered by a lack of sustainable supply. Identification of the genes that direct natural product biosynthesis in octocorals would set the stage for further development of octocoral-derived natural products. Identification of these genes is complicated by the complex symbiotic assemblage hosted by octocorals, which is composed of both eukaryotic and prokaryotic symbionts. As a first step in elucidating natural product biosynthesis in octocorals we acquired metatranscriptomic datasets from two Caribbean octocorals. This data will be analyzed to identify transcripts related to natural product biosynthesis.

Biome: root:Host-associated:Cnidaria
EMG produced TPA metagenomics assembly of the Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces (Ecosystem functions in cryoconites) data set

The Ecosystem functions in cryoconites Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12327. This project includes samples from the following biomes : Freshwater.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
EMG produced TPA metagenomics assembly of PRJNA389280 data set (Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389280, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Prokaryotic Community Profiling of the Mt. Makiling Mudspring

This study aims to determine the prokaryotic community thriving in the Mt. Makiling Solfaratic Mudspring in Los Banos, Laguna, Philippines using 16S rRNA gene amplicon Next Generation Sequencing Technology.

Biome: root:Environmental:Terrestrial:Volcanic
Effect of zinc and alternative compound on pigs' microbiota

Samples have been taken to look at changes in the gut microbiome when weaning piglets are supplemented with zinc or with an alternative compound.

Biome: root:Host-associated:Mammals:Digestive system
MF_PPS5_Study_1

Study inside facility

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJDB4115 data set (Metgenomic analysis of human saliva microbiome from healthy subjects).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB4115, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Metgenomic analysis of human saliva microbiome from healthy subjects

Metgenomic analysis of human saliva microbiome from healthy subjects. Saliva microbiome from 6 healthy individual.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJEB37199 data set (Microbial community dynamics of a polyester film-degrading marine enrichment culture).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37199, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
Microbial community dynamics of a polyester film-degrading marine enrichment culture

In this study, we present a multiomics approach to elucidate the biodegradation mechanism of a commercial aromatic-aliphatic copolyester film by a marine microbial enrichment culture. Marine seawater and eulittoral sediment samples were collected from three different sources: Helgoland, Germany (5411 17.0" N 752 50.1" E), near Athens, Greece (3753 33" N, 2324 30" E) and Elba, Italy (4244 00.8" N 1009 14.4" E). The enrichment cultures were made by inoculating the seawater/sediment slurry in marine minimal medium containing the polyester film as sole C source. Community composition and function was examined by metagenome/transcriptome analysis a)of the plastic biofilm/free-living fractions separately, b) after a starvation period (t0) and addition of new plastic substrate after one hour (t1), 24 hours (t2) and seven days (t3). In addition to the plastic film, the culture was grown on each monomer separately and metagenomes were analysed for each different growth condition.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis (RA) data set.

The RA Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6997.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJEB28422 data set (The Salivary Microbiome in Health and Disease).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB28422, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
The Salivary Microbiome in Health and Disease

Several diseases have been associated with with shifts in the salivary microbiome. Here we explore such links in a case control cohort for colorectal cancer (see PMID:25432777, BioProject ERP005534 for matched fecal samples), amended by an independent time series of healthy controls (see PMID:25888008, BioProject ERP009422 for matched fecal samples).

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Samples of a study the Venice lagoon from a functional perspective via metagenomics.

The samples belong to a project aiming to study the Venice lagoon from a functional perspective via metagenomics.

Biome: root:Environmental:Aquatic:Estuary:Sediment
EMG produced TPA metagenomics assembly of PRJNA649273 data set (Kidney stone patient microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA649273, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJDB7293 data set (Metagenomic analysis of Kirishima hot springs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB7293, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Metagenomic analysis of Kirishima hot springs

Metagenomic sequencing analysis of the 9 hot springs in the Kirishima region in Kyushu's Kagoshima prefecture.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA335670 data set (Metagenomic Sequencing of Hot Springs from Central India).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA335670, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Metagenomic Sequencing of Hot Springs from Central India

The Sequencing of metagenomic samples from Hot Springs of Central India

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJEB39386 data set (Estuarine microbiome exposed to copper oxide nanoparticles).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB39386, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Estuary:Sediment.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Estuarine microbiome exposed to copper oxide nanoparticles

Nanomaterials usages are increasing in multiple fields. With a large spectrum of applications, the impact of nanomaterials on natural ecosystems is a growing concern in environmental science and management. Methods for nanomaterials removal from wastewaters are yet developing and currently a significant fraction of nanomaterials escapes treatment plants. As a result estuaries are becoming the final repository for nanomaterials. The implications of this towards biota have been assessed, but usually at higher concentrations than the environmentally-predicted. Moreover, the impact of nanoparticles towards ecosystem services has seldom been reported.
The aim of this project was to ascertain whether deposition of copper oxide nanoparticles (Cu NPs) in estuarine sediments will change metal speciation and bioavailability, which will in turn impact the composition and functionality of the estuarine microbial communities. For this project we selected the Douro River estuary (North Atlantic), which is of major importance in its geographical area as its watershed drains 17 % of the Iberian Peninsula.
We performed a series of microcosms enrichment experiments exposing estuarine sediments to Cu NPs, of size <50 nm, at a concentration of 10 ng/g, tested for 4 h, 7h and 24 h. The microcosms pH and dissolved oxygen was monitored, as well as concentrations of nitrate, nitrite and ammonium. DNA was extracted from the sediment and sequencing was performed using Illumina Hiseq Xten to acquire 150 bp paired-end sequences. This generated 18 Gbp per sample, after filtering adaptor sequences, contamination and low-quality reads. Links were identified between the microbial community and ecosystems services they might provide, namely the service of removing fixed nitrogen, which is critical in eutrophic ecosystems.

Biome: root:Environmental:Aquatic:Estuary:Sediment
EMG produced TPA metagenomics assembly of PRJNA628604 data set (Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA628604, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective

Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and to explain failure or success through microbiome analyses.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal