SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Marine subseafloor sediment Targeted Locus (Loci)

We examine the relationship between subseafloor microbial diversity and paleoceanographic conditions in samples from three sediment cores from the Eastern Mediterranean Sea and the Black Sea. All three cores record dramatic changes in oceanographic/limnic conditions resulting from oscillation between oligotrophic and euxinic condition, yet they also differ remarkably between sites. Our motivation for this study is based on the premise that paleoenvironmental conditions in the overlying water column are intimately linked to the composition of aquatic microbial communities and thus the inoculum for subseafloor communities. Our study will address the long-standing question to what degree the composition of subseafloor microbial communities is linked to paleoenvironmental conditions at time of deposition. The sample set at both Mediterranean sites is composed of carbonate-rich, organic-lean sediments and interspersed so-called sapropels, that is, organic-rich black layers that were deposited during climates that were probably warmer and more humid than today, when the Mediterranean was euxinic. The samples from the discovery basin are influenced by a highly saline brine and thus may select for halophilic sedimentary microbes. The Black Sea sample set is composed of organic-lean coccolith ooze deposited during the recent few thousand years, an organic-rich sapropel deposited during the early Holocene and below of sediment deposited during the late glacial/early Holocene when the Black Sea was still a freshwater lake. We examine both archaeal and bacterial diversity with a 454-based tag sequencing survey. We can address questions relating to the paleoenvironmental history at each site as well as to the relationship of microbial communities in sediments deposited during euxinic conditions at three sites along a salinity gradient remote to each other, in two different ocean basins. The sample set will be accompanied by an in-depth biogeochemical characterization of its sedimentary habitat. Sediment sampling and characterization are performed and mutually integrated on the same cruise (RV Meteor, M84-1, February 9-22, 2011) by the proponents of this proposal.

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

The application of fresh digestate, derived from the anaerobic treatment of animal wastes, is known to affect the short-term dynamics of microbial communities. A metagenomic study was carried out to test the effect of livestock-derived digestate amendment on an agricultural soil bacterial, yeasts and fungal community structure and dynamics.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Ocean crust Targeted Locus (Loci)

Much of the earth''s microbial biomass exists in the subsurface, and a sizable fraction of this is in oceanic igneous rocks. If microbial life in the igneous ocean crust extends to the depth of the ~120°C isotherm (the current upper temperature limit of life) then the volume of rock available for microbial colonization is about the same as the volume of the oceans. Most of this volume is difficult to sample but microorganisms have been identified from deep layers of the igneous ocean crust.  Additional understanding of the deep igneous biome comes from microorganisms extracted from subsurface fluids; although unattached microorganisms in aquifer fluids are not necessarily representative of the microorganisms attached to the host rocks. Another difficulty is that the ocean crust is mineralogically heterogeneous typically on the 0.01 mm to 10 mm scale and if the mineralogy influences or controls the microbial communities, then the ocean crust is microbially heterogeneous on the 0.01 to 10 mm scale. Community structure that is determined from bulk crustal rock samples will not be informative about how communities are associated with crustal minerals. Also, molecular and sample processing methods are not currently available to determine the community structure of minerals in igneous rocks.  In situ colonization of mono-mineralic substrates in the ocean crust is one method of determining microbial community structure of the minerals that make up the crust. We devised a method of incubating a wide variety of mono-mineral aggregates in the ocean floor simultaneously so that they all experienced the same temperature, water composition, and pressure. The mass of each incubated mineral was large enough to expect recovery of adequate amounts of DNA for analysis. The location chosen for this experiment was Integrated Ocean Drilling Program (IODP) borehole 1301A, which is located at 47° 45.210'' N, 127° 45.833'' W in 3.6 Ma old ocean crust in the northeast Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Bacterial population dynamics in a natural assemblage upon the addition of artificial alginate particles and alginolytic Alteromonas macleodii

Investigation of alginate degradation by marine bacterial communities from macroalgae-rich habitats in Southern California.

Biome: root:Environmental:Aquatic:Marine
CK1/MNPK1/NPK1 Targeted Locus (Loci)

The goal of present study is to examine what soil bacterial taxa were significantly affected by Cu amendments, and what taxa were the keystone organisms in Cu-contaminated soils using network analysis approach

Biome: root:Environmental:Terrestrial:Soil:Contaminated
soil metagenome Metagenome

Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (e.g. nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 varied Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP). Bacterial community composition of uncontaminated, diesel-contaminated, and diesel + MAP soils was assessed through multiplexed 16S rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by GC analysis. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.   Top 15 cm soils collected from across the Arctic, left untreated, or treated with diesel or diesel   nutrients.

Biome: root:Environmental:Terrestrial:Soil
Arable soil Targeted Locus (Loci)

Manure unspiked and spiked with SDZ in two different concentrations was applied three times, and the bacterial community composition in soil was monitored over a period of 193 days. To differentiate between short and longer-term effects, the soil was sampled 3 and 60 days after each manure application, respectively.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Diversity and abundance of Bathyarchaeota (MCG) in South China Sea sediments and the implication of its ecological roles

Diversity and abundance of Bathyarchaeota

Biome: root:Environmental:Aquatic:Marine:Sediment
Diet analysis of Pacific Bluefin Tuna larvae

Metagenetic analysis on gut contents of Pacific Bluefin Tuna larvae and planktons in environmental water

Biome: root:Environmental:Aquatic:Marine
Changes in microbiota composition in colitis-prone mdr1a mice

The symbiotic relationship between gut microbiota and the host is necessary for intestinal homeostasis.  Loss of tolerance to the gut microbiota results in chronic inflammatory bowel diseases (IBD), such as Crohn’s disease and Ulcerative colitis. The microbiota resides in two compartments-the gut lumen and mucus layer. Most published findings focus on luminal microbial communities in IBD pathogenesis with much less being understood about the bacteria resident in the mucus layer that abuts the epithelium. Thus, the precise interactions between microbiota and the intestinal mucosa during IBD development are still unknown. To address this, we investigated colitis progression in the mdr1a-/- spontaneous model of colitis. We examined microbiota composition in the mucus and lumen in mdr1a-/- mice and wild-type littermate controls at an early pre-colitic and a later post-colitic stage. We aim to identify if bacterial differences in specific niches  precede IBD development and progression. Our study provides valuable insight in microbiota-host interactions in normal and diseased states, revealing new approaches for the management of IBD.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Marine metagenome ICM_BSR

Examining the Free-Living and Particle-Associated Bacterial Community in the Black Sea''s Suboxic Zone.

Biome: root:Environmental:Aquatic:Marine
Microbial Processes and Biodiversity: OCEAN

Study of microbial communities (16S rRNA and 18S rRNA genes) in two coastal oceans observatories located in contrasting latitudes: (i) Equatorial Atlantic Ocean - Equatorial Atlantic Microbial Observatory (EAMO) and (ii) Mediterranean Sea - Blanes Bay Microbial Observatory (BBMO).

Biome: root:Environmental:Aquatic:Marine:Coastal
Diversity of Microbial Eukaryotes in Sea Waters From Fildes Peninsula,King George Island, Antarctica

To investigate molecular diversity of microbial eukaryotes in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, ten water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013. After pyrosequencing and analysis, the molecular diversity of microbial eukaryotes of sea water from Greatwall cove and Ardley cove was generally achieved.

Biome: root:Environmental:Aquatic:Marine:Coastal
Nutrient addition mesocosm experiment Targeted Locus (Loci)

Amplicon sequencing of environmental planktonic organisms to assess the interactions during a nutrient addition experiments.

Biome: root:Environmental:Aquatic:Marine:Coastal
South China Sea interfaces 16S amplicon sequencing

16S amplicon sequencing of microbial communities at geological interfaces in South China Sea marine sediments sampled during IODP expedition 349.

Biome: root:Environmental:Aquatic:Marine:Sediment
Arable and pasture soils spiked with anthracene Metagenome

Two soils were contaminated with 500 mg anthracene using acetone. Five different treatments were applied to the anthracene-contaminated soil. In a first treatment, soil was amended with two adult Eisenia fetida earthworms (0.35 g) and with a developed clitellum. The earthworms were fed 60 g carrot every two weeks. In a second treatment, soil was amended with 60 g organic material (carrot) every two weeks. As such, the effect of the earthworms on the removal of anthracene could be differentiated from that of the organic material applied. In a third treatment, soil was mixed for 10 min every 7 days. In a fourth treatment, soil was amended with 24.9 g kg-1 soil surfactant Surfynol® 485 and mixed. In a fifth treatment, soil was left unamended and served as control so that remediation capacity of the autochthonous microorganisms could be determined. Two more treatments were used in this study. In a first additional treatment, both soils were applied with the same amount of acetone used as carrier to contaminate the soil with anthracene and in a second additional treatment, unamended soil was used and served as control.

Biome: root:Environmental:Terrestrial:Soil
Marine planktonic ciliates: SSU rDNA

Diversity and biogeography of marine planktonic ciliates in the NW Atlanctic Ocean

Biome: root:Environmental:Aquatic:Marine:Oceanic
Benthic microbial communities associated with hypoxia on the Black Sea shelf break (NW Crimea)

The effect of varying oxygen conditions on benthic microbial communities was investigated at the North Western Crimean shelf break (Black Sea), at water depths between 105-207 m.  Sampling was performed with a TV-MUC on April-May 2010 on board of the RV Maria S. Merian (Cruise MSM 15-a) along gradient of oxygen bottom water concentrations between oxic (150 μmol L-1, station 464), variable hypoxic (3-60 μmol L-1 O2, stations 487 and 393) and anoxic, sulfidic conditions (station 448).

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

The nitrogen cycling bacterial community at 100 m depth in crystalline bedrock groundwater was investigated using nitrate and ammonium as substrates in a stable isotope probing study. The bacterial community was enriched with 15N ammonium or nitrate for 28 days after which the enriched community and the nitrogen assimilating communities were compared using 454 amplicon sequencing of the 16S rRNA genes

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Study on bacterial diversity and functionality in the Adriatic Sea

Study on bacterial diversity and functionality in the Adriatic Sea.  PCR amplified 16S rRNA genes from an inoculum in the Adriatic Sea and bacterial communities incubated in continuous cultures with different treatments.

Biome: root:Environmental:Aquatic:Marine:Coastal
Red Sea marine sponges and seawater Targeted Locus (Loci)

The genes and transcripts of 16S rRNA were amplified from seawater, S. carteri, and X. testudinaria DNA (originating the following datasets: WTD1-WTD3, ASD1-ASD3, and AXD1-AXD3; respectively) and cDNA (originating the following datasets: WTR1-WTR3, ASR1-ASR3, and AXR1-AXR3; respectively). Purified amplicons were pooled equally and sequenced on a Roche 454 GS FLX Titanium platform. Sponge samples from the species Stylissa carteri and Xestospongia testudinaria were collected. Seawater samples were collected during the same dive. Sample location is: Fsar reef (22°23'N; 39°03'E) at the coast of Thuwal, Saudi Arabia. Depth was at 8.5-12 meters.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJEB34453 data set (Atlantic Ocean Metagenomes).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34453, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
Marine fungi Raw sequence reads

biogeography and seasonality of benthic fungi

Biome: root:Environmental:Aquatic:Marine:Oceanic
Surfactant-associated bacteria in the near-surface layer of the ocean

Certain marine bacteria found in the near-surface layer of the ocean are expected to play important roles in the production and decay of surface active materials; however, the details of these processes are still unclear. Here we provide evidence supporting connection between the presence of surfactant-associated bacteria in the near-surface layer of the ocean, slicks on the sea surface, and a distinctive feature in the synthetic aperture radar (SAR) imagery of the sea surface. From DNA analyses of the in situ samples using pyrosequencing technology, we found the highest abundance of surfactant-associated bacterial taxa in the near surface layer below the slick. Our study suggests that production of surfactants by marine bacteria takes place in the organic-rich areas of the water column. Produced surfactants can then be transported to the sea surface and form slicks when certain physical conditions are met. This finding has potential applications in monitoring organic materials in the water column using remote sensing techniques. Identifying a connection between marine bacteria and production of natural surfactants may provide a better understanding of the global picture of biophysical processes at the boundary between the ocean and atmosphere, air-sea exchange of greenhouse gases, and production of climate-active marine aerosols.

Biome: root:Environmental:Aquatic:Marine:Oceanic
22V-SMAR-TVG01 Targeted Locus (Loci)

Analyzing the microbial diversity of the sediment

Biome: root:Environmental:Aquatic:Marine:Sediment
Aarhus Bay Station M5 sediment metagenome sequencing

ANME-1 draft genome binned from Aarhus Bay M5 sediment metagenome samples (Bioproject PRJNA305566)

Biome: root:Environmental:Aquatic:Marine:Sediment
Spirulina necromass degradartion in arctic marine sediments

Reveal the identity and population dynamics of responders to spirulina and acetate amendments to arctic marine sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
EMG produced TPA metagenomics assembly of the A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB1220.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbial communities in marine surface water

To investigate the biogeographic patterns of microbial communities in surface water from Indian Ocean to Chinese marginal seas

Biome: root:Environmental:Aquatic:Marine
16s rRNA profiling of Park Grass microbial community

16s rRNA amplicon sequencing of DNA isolated from the Park Grass soil

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Flores_forehead_EBI

Forehead skin samples from Flores_SMP for submission to EBI

Biome: root:Host-associated:Human:Skin
marine sediment metagenome Raw sequence reads


Biome: root:Environmental:Aquatic:Marine:Sediment
Diversity of SE Pacific benthic Bacteria and Archaea communities Targeted Locus (Loci)

Characterization of the benthic bacteria and archaea communities their inferred functions and biotechnological potential.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Sediment microbial diversity from samples of the lagoons of the Amvrakikos Gulf (Ionian Sea, Western Greece)

The aim of the present study was to explore the biodiversity patterns of microorganismic assemblages and to examine whether these patterns are associated with those of the contextual environmental parameters. For this purpose, sediment samples were collected from five lagoons (Rodia, Tsoukalio, Tsopeli, Mazoma, Logarou), located in Amvrakikos Gulf (Ionian Sea, Western Greece). In each lagoon, two sampling stations were chosen, with different connectivity degree with the sea. A number of abiotic parameters were measured for every station, including the sediment concentrations of heavy metals and elements. Microbial DNA was extracted from the sediment upper layer (0-2cm) and was further processed through deep sequencing of the V5-V6 region of the 16S rRNA gene by next generation sequencing.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Marine sediment microbial communities in the presence of macrophytes

In this study we examined the sediment microbial communities in the absence and presence of two marine macrophytes (Zostera muelleri - Zm, and Caulerpa taxifolia - Ct), and at low (L) and high (H) densities of the macrophytes.Three independent and randomly obtained samples were taken from each of the five treatment groups (absent, Zm-L, Zm-H, Ct-L, Zm-H), genomic DNA extracted and PCR conducted targeting the V4 region of the 16S gene. PCR amplicons were sequenced using Illumina MiSeq 2x250 bp, with paired-end sequencing.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial eukaryotes present in a Norwegian coastal ecosystem and in the gut content of Calanus copepods from Raunefjorden

Use metabarcoding to characterize the diversity of Calanus prey relative to the total microbial eukaryote diversity in the co-occurring seawater habitat

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

Microbial diversity in coastal areas of Sichang island in Thailand

Biome: root:Environmental:Aquatic:Marine
Geothermal Springs Targeted Locus (Loci)

Studies to date suggest that this temperature-diversity gradient relationship is weak or nonexistent for Bacteria and Archaea. To test the impact of temperature as well as pH on prokaryotic diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study.

Biome: root:Environmental:Terrestrial:Soil
marine sediment metagenome Targeted Locus (Loci)

The microbiological objectives of IODP Expedition 347 Baltic Sea Paleoenvironmentfocused on 1) how the phylogenetic diversity of the deep biosphere in this intracontinental sea differs from that of deep-ocean communities, and 2) are microorganisms that presently live in the deep sediments remnants of limnic and marine populations, or does the modern sedimentary environment select for thecommunity. The Expedition took place September 16, 2013 – November 1, 2013 on board the IODP Mission-Specific Platform Greatship Manisha. Cores were advanced for microbiological sampling at 4 locations: BSB-1, BSB-3, BSB-7, and BSB-9 (Figure 1) using Advanced Piston Coring (APC) and checked for contamination using perfluorcarbon tracers (PFTs).

Biome: root:Environmental:Aquatic:Marine:Sediment
Seawater coastal British Columbia

Examine the distribution of specific markers genes over time

Biome: root:Environmental:Aquatic:Marine
16S rRNA genes Random survey

Sequencing of 16S genes from fractions of 15N and 13C SIP experiments

Biome: root:Environmental:Aquatic:Marine
Diversity of archaeal amoA gene

Diversity of Archaeal amoA genes in sea water samples from Ardley cove, Fildes Peninsula, Antarctica

Biome: root:Environmental:Aquatic:Marine
Arabian Sea OMZ nirS Metagenome

nirS amplicon sequences from the Arabian Sea

Biome: root:Environmental:Aquatic:Marine
1)sediments; 2) coral floc Metagenome

Deep-sea sediments and coral flocculant material (floc) collected from a coral community impacted by the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of oil-degrading genes

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

microbe community and funtion

Biome: root:Environmental:Aquatic:Marine:Sediment
Goodrich_TwinsUK_Miseq_2

second half of Goodrich_MiSeq for EBI submission

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time and seeded with either acclimated or non-acclimated sludge

In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the effect of solids retention time (SRT) on the diversity and dynamics of total, dominant and rare bacterial taxa in eight replicate lab-scale sequencing batch reactors (SBRs) operated for a period of 78 days and seeded with either acclimated or non-acclimated sludge. Rank-abundance curves showed strong abundance of few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2d vs. 10d) on Shannon diversity index and OTU richness of both dominant and rate taxa. Nonmetric Multidimensional Scaling (NMDS) analysis showed that the total, dominant and rare bacterial taxa were highly dynamic during entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media. Moving-window analysis, Global ANOSIM and NMDS analysis revealed that the bacterial community structure in replicate SBRs seeded with acclimated or non-acclimated sludge was reproducible. Overall 16S rRNA gene pyrosequencing could reveal the dynamics of rare bacterial taxa that are normally left out using conventional molecular biology methods.

Biome: root:Engineered:Bioreactor:Continuous culture