SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Marine sediment metagenome ICM_FIS

Sands as microbial biodiversity hotspots: Investigating the effect of grain size and biofilm formation.

Biome: root:Environmental:Aquatic:Marine:Coastal
Antarctic soil watering experiment across a natural salinity gradient

The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change induced disturbances including the melting of massive buried ice, cutting through permafrost by streams, and warming events. These processes are increasing moisture across the landscape altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition (16S rRNA genes) and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment.

Biome: root:Environmental:Terrestrial:Soil
NEON Surface Water Microbe Marker Gene Sequences - 2014

This study provides the sequence data for the NEON data product, Surface water microbe marker gene sequences (NEON.DP1.20282). The goal of this project is to track changes in the diversity and composition of bacteria, archaea and fungi in planktonic aquatic ecosystems through space and time. NEON collects water column microbes from various depths at numerous sites distributed across the United States. Total genomic DNA is extracted and the 16S and ITS regions of the rRNA cistron are sequenced using high-throughput methods. For additional details and data, visit the NEON Data Portal at http://data.neonscience.org.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Oxygen minimal zone Targeted loci environmental

To study diversity of microbe community including bacteria, dizotrophs, and protist.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Effect of long term fertilization strategies on soil bacterial communities

Effect of long term fertilization strategies on soil bacterial communities

Biome: root:Environmental:Terrestrial:Soil:Agricultural
La Medee sediment - Extracellular Metagenome Metagenome

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

Biome: root:Environmental:Aquatic:Marine:Sediment
Arbuscular mycorrhizal fungi from soil samples Targeted Locus (Loci)

Sequence arbuscular mycorrhizal fungi from soil samples from the Andean region

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Diversity of archaeal and bacterial 16S rRNA gene in marine sediment in Aarhus Bay

This project is to study the diversity of Archaeal and bacterial 16S rRNA gene in marine sediments in Aarhus Bay.

Biome: root:Environmental:Aquatic:Marine:Sediment
nifH diversity in the North Pacific Ocean

This study was performed to elucidate community structure of nitrogen fixing bacteria in the North Pacific Ocean

Biome: root:Environmental:Aquatic:Marine:Oceanic
Equatorial Pacific Ocean Targeted loci environmental

To (i) document vertical distributions of bacterial diversity and community composition, (ii) investigate how these communities vary from one oceanographic region to another, and (iii) test the extent to which bacterial communities of deep subseafloor sediment may originate in the water column, we used 454 pyrosequencing technology and the v4-v6 hypervariable region of the bacterial 16S rRNA gene to examine bacterial community composition (presence/absence and relative abundance) in the water column, near-seafloor sediment (5 cm), and subseafloor sediment at three environmentally distinct Pacific sites: the very high-productivity eastern equatorial upwelling region (EQP1), the moderately high-productivity open-ocean central equatorial upwelling region (EQP8) and the very low-productivity northern gyre (EQP11) (Figure 1).

Biome: root:Environmental:Aquatic:Marine:Oceanic
Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Indian Ocean 2015

The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the Bay of Bengal in Auguest-September 2015 to examine phytoplankton community diversity.

Biome: root:Environmental:Aquatic:Marine
Comparative study in validity of three regions of 18S-rRNA for eukaryote amplicon sequence analyses

In the present study, we performed a detailed investigation of the 18S-rDNA, namely, numbers of registered sequences, frequencies of amplification success, the amplicon sequence variability among three regions containing V1-V3, V4-V5 and V7-V9 regions using in silico PCRs based on public databases, and the identification power by NGS-based environmental surveys of planktonic eukaryote community. Although the number of registered sequences in V4-V5 regions was remarkably higher than other regions, the identification power in NGS-based environmental surveys was lowest in V4-V5 regions due to the lowest sequence variability. The number of registered sequences in V1-V3 region was ca. two times smaller than V7-V9 region, and the sequence variability in V1-V3 region was significantly higher than that in V7-V9 region. Then, the identification power was not significant between these two regions, implying identification power is affected by combination of numbers of registered sequences and the sequence variability. We therefore believe V1-V3 region will be the best one for applying to NGS-based monitoring of planktonic eukaryote community in the near future as the number of sequences deposited increases in public databases.

Biome: root:Environmental:Aquatic:Marine:Coastal
Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans

This study investigated the response of bacterioplankton communities to the polysaccharides chitin, alginate, and agarose using seawater microcosms at four distant locations in the Southern and Atlantic Oceans.

Biome: root:Environmental:Aquatic:Marine
AMF from contaminated and uncontaminated rhizosphere soils Metagenome

The aim of this study was to compare AMF communities from petroleum-contaminated and adjacent uncontaminated soils, and to determine whether willow planting influenced community composition.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Depth dependent (0-5,000 m) and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific.

Archaeal community composition was examined throughout the water column (0-5,000 m) of the subtropical and subarctic western North Pacific Ocean using a pyrosequencing-based analysis of archaeal 16S rRNA gene. Samples were collected on four occasions between 2011 and 2012 to explore seasonal variability in the community composition.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Ocean sediment-basement interface Targeted Locus (Loci)

Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface. Furthermore, the few studies thus far conducted in deep oceanic crust reveal an active microbial community in this habitat. Yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. Are microbial communities in sediments seeded from basement communities, or vice versa? If there is influence from one habitat type on the other, how far does this influence extend, both with vertical distance away from the interface and laterally along the flow path of fluids within basement? We propose to conduct tag pyrosequencing on samples from a spectrum of sediment-basement habitats to identify patterns in microbial community shifts across sediment-basement interfaces. Such comparisons will allow us to evaluate whether microbial groups from one habitat are found in another, and to examine whether members of the ''rare biosphere'' in one habitat come to dominate in another. Analysis of the pyrosequencing data will help us better understand how subsurface microbial communities are established and evolve, in addition to expanding our knowledge of microbial biogeography across sediment-basement interfaces in different oceanic basins.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
uncultured soil ammonia oxidizing bacteria PCR amplicom

This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil ammonia oxidizing functional gene (amoA)

Biome: root:Environmental:Terrestrial:Soil
Chernobyl soils Targeted Locus (Loci)

High throughput pyrosequencing was used to get a comprehensive picture of the phylogenetic diversity of Bacteria and Archae in radionuclides-contaminated and control soils collected in the trench T22 area, within the Chernobyl exclusion zone.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Arctic Ocean

Characterization of bacterial communities from the Arctic Ocean

Biome: root:Environmental:Aquatic:Marine:Oceanic
Hydraulic fracturing fluid-groundwater-soil incubations Targeted Locus (Loci)

Soil-groundwater mixtures were incubated with different levels of hydraulic fracturing fluids to monitor degradation of organic constituents over time

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Uncultured marine eukaryotes Targeted Locus (Loci)

A community study of the large-fraction eukaryotes present in the Beaufort Sea as determined by pyrosequencing of 18S molecules.

Biome: root:Environmental:Aquatic:Marine
L''Atalante sediment - Microbial Metagenome

SSU 16S pyrosequencing project of the microbial metagenome of a DHAB sediment (L''Atalante) from the Eastern Mediterranean.

Biome: root:Environmental:Aquatic:Marine:Sediment
P2IRC 1.3 Soil microbiome as plant phenotype

The study goal is to support crop breeders in identifying microbial communities and characteristics that improve crop yield. The microbial community associated with the roots of canola grown over a three-year period in a Saskatchewan field will be analyzed. DNA extraction and analysis results from the roots and soils will identify specific microbes or communities of microbes connected with the high yielding varieties. In combination with other phenotypic data, unique identifiers of the microbial community will be determined and then tested under controlled experimental conditions to validate their link in improved crop performance.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Soil microbial diversity patterns of a lowland spring environment.

The Po river plain lowland springs comprise unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and had constant use ever since. Our aims were to identify the land use effects on the microbial communities of these soils, seek for associated diversity drivers and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high throughput sequencing of partial 16S rRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon (TOC) and pH were major diversity drivers for Bacteria, while pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights about potential roles of taxa in the organic carbon turnover. Verrucomicrobia, coincided with the higher values of the recalcitrant organic carbon while Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the less enzymatically active and relatively poorer in nutrients soils, may be explained to an extend by niche based theories like the resource heterogeneity hypothesis and Connell''s intermediate disturbance hypothesis. Multiplexed 16S rRNA gene amplicons from soil DNA extracts of samples derived from three soils (each in biological triplicates).

Biome: root:Environmental:Terrestrial:Soil
Sequences obtained from two sponge genera (Hyrtios, Aiolochroia), one zoanthid (Palythoa), and marine sediments. Metagenome

Study of the diversity of bacteria present in sponges and marine sediment, by 16s rRNA gene sequencing

Biome: root:Environmental:Aquatic:Marine:Sediment
Mesocosm mine tailing cores Targeted Locus (Loci)

The objective of this study was to analyze the temporal dynamics of the microbial communities colonizing the rhizosphere of plants growing in compost-amended mine tailings with the goal of linking community structure to ecosystem function. Metalliferous mine tailings, which usually have high acid-generating potentials, are often subject to phytoremediation to prevent the dispersion (by eolian and hydraulic action) of these metal-bearing particles. Assisted phytostabilization is a type of phytoremediation technology in which the mine tailings are amended with compost (as a source of carbon and nutrients, and pH buffer) and then are seeded with a native plant specie that has been specifically selected based on its capacity to grow on the tailings without accumulating elevated levels of toxic metals in the shoot tissues. Therefore, the metal contaminants are immobilized in the soil to minimize the health and environmental risks associated with the dispersion of exposed mine tailings. A major knowledge gap in the understanding of phytostabilization as a viable alternative for the remediation of mine tailing piles is the ecology of the microorganisms that grow in the root-zone of the plants. Little is known of how these microbial communities respond to plant growth and compost amendment, how they may influence the stabilization of the metal contaminants, how they may affect or enhance plant colonization of the tailings, and how their structure may reflect the state of the phytoremediation treatment. To try to answer some of these questions, we conducted a yearlong greenhouse experiment with 3 treatments (in triplicate): (1) tailings only control, (2) tailings amended with 15% compost control, (3) tailings amended with 15% compost and seeded with a shrub (quail-bush; Atriplex lentiformis). During that year, core samples were collected every 3 months to extract metagenomic DNA and analyze the structure of the microbial communities (i.e. phylogenetic and functional structure).

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Marine sediment metagenome raw sequence reads

Marine sediment amplicon study from brine disposal vincinity

Biome: root:Environmental:Aquatic:Marine:Sediment
DD_cyano Targeted loci environmental

To understand the distribution of diverse picocyanobacterial clades and environmental factors regulating their distribution, abundance and genetic diversity was investigated in adjacent waters of Dokdo showing diverse physical properties not only by seasonal variation but also by diverse physical processes.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJEB29127 data set (A causal role of the gut microbiome in schizophrenia).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB29127, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Hindgut:Rectum.

Biome: root:Host-associated:Human:Digestive system:Hindgut:Rectum
coastal sediments Targeted Locus (Loci)

The goal of this project is to study the bacterial communities and hydrocarbon degrading bacterial populations from coastal sediments of Patagonia, as well as their response to oil input. The study has got relevance regarding the bioremediation of cold coastal environments, as hydrocarbon pollution in high latitude marine environments is expected to increase.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Foraminifera 18S rDNA and rRNA diversity for fish farms biomonitoring

Both 18S ribosomal DNA and RNA taxonomic markers were sequenced to investigate the response of benthic foraminiferal communities to environmental gradients related to the presence of salmon fish farms in two Scotland fjords. For both DNA and RNA extractions performed on 45 sediment samples and cDNA synthesis for RNA, we PCR amplified the 37f hypervariable region of the foramnifera using tagged PCR primers prior to library preparation (TruSeq) and MiSeq paired-end sequencing. The combinations of tagged primers are contained in the paried reads and could be used to assign the sequences the their sample of origin.

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

Tracking environmental selection of marine microbial eukaryotes using 18S rRNA genes and 18S rRNA in the Gulf of Maine

Biome: root:Environmental:Aquatic:Marine
A community genomics investigation of fungal adaptation to cold

We sampled soils across the Arctic and have identified the resident fungi using molecular methods in order to ascertain which fungi are able to grow in the coldest climates.

Biome: root:Environmental:Terrestrial:Soil
Semi arid steppe soil Metagenome

We extracted soil DNA and sequenced using 454 pyrosequencing to evaluated soil AM fungal responses on the future climate change.  Arbuscular mycorrhizal fungal DNA was extracted from a semi arid steppe in Inner Mongolia.

Biome: N/A
Bacterial communities in agricultural soils under contrasting agronomic managements and biomes of Argentina

The aim of this study was to compare soil bacterial communities in agricultural lands attempted to soybean production in different regions of Argentina. Intensive and conservative management practices were evaluated in contemporary long-term field experiments carried out in three different locations of the rolling pampas region.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Microbial community structure is affected by cropping sequences and bio-covers under long-term no-tillage

Changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites. Main effects of 4 four different cropping sequences of corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max L.) were rotated in four year phases for 12-yrs at two Tennessee Research and Education Centers in a randomized complete block design with split-block treatments of four winter bio-covers: hairy vetch (Vicia villosa L.), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Using Illumina high-throughput sequencing of 16S rRNA genes, bacterial community composition was determined.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Leaf litter Genome sequencing

Monitoring bacterial community changes during leaf litter degradation of Zea mays in arable soil

Biome: root:Environmental:Terrestrial:Soil
Soil bacterial community in temperate grassland

Anthropogenic disturbance and global climate change are greatly affecting ecosystems worldwide by ways such as widespread nitrogen (N) deposition and changing precipitation regimes. It is predicted that the mean annual precipitation and N deposition in North China will continue to increase in future. Although much of work has been focus on the response of above-ground plant community to presumed climate change, the effects of nitrogen and water addition on the soil microbial community has not yet been systematically surveyed. Given the important role of soil microbial communities in nutrient cycling in terrestrial ecosystem, the effects of nitrogen and water addition and their interaction on soil microbial communities increased our attention. The specific aims of this project are: (1) to analyze the response of soil microbial diversity and community structure to the increase of soil N inputs and soil moisture; (2) to reveal the relationship between the variation of microbial communities and the above-ground plant community. The study sites were located in Duolun county, Inner Mongolia (E 116°17’20”, N 42°2’29”). A field experiment with a constant increase in precipitation and three Nitrogen supply levels was established in 2005 to examine the potential effects of N deposition and changes in precipitation regime on the ecological processes. A split-plot experimental design was employed in this study. The block was divided into two main plots with water treatment (ambient precipitation and water addition). Each main plot was divided into twenty-eight 8 m × 8 m subplots with a 1-m wide buffer zone. Four levels of Nitrogen treatment (N0 (control), N5 (5 g N m-2 yr-1), N10 (10 g N m-2 yr-1), N15 (15 g N m-2 yr-1), each including seven replicates, were randomly assigned to each subplot within main plot. In the middle growing season from June to August, the water addition plots received 15 mm of precipitation weekly by sprinkling irrigation. A total of 180 mm precipitation, approximately 50% of mean annual rainfall, was added yearly during the growing season from 2005 to 2013.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Mediterranean mud volcano flow Targeted loci

Mud volcanoes (MVs) expel mobilized muds, gases, and fluids from the subsurface at convergent margins. These muds and fluids originate from numerous sources and depths that range from methanogenic sediment layers, destabilizing gas hydrate deposits, clay dehydration reactions, and thermogenic hydrocarbon sources–and thus represent a convenient window into the deep biosphere. The proposed sequencing opportunity will address bacterial and archaeal community diversity in recent mud flows of the Venere Mud Volcano and underlying mud volcano sediments to assess how mud flow deposition and subsurface fluids influence microbial community composition and dynamics. We sequenced 16S V4V5 amplicons from bacterial and archaeal communities at varying mud flow depths with contrasting deep fluid chemistries.

Biome: root:Environmental:Terrestrial:Volcanic
Mount Hope Bay bacteria Targeted Locus (Loci)

Coastal marine environments have been impacted by human activity for several centuries, including shoreline alteration, nutrient introduction, sedimentation, toxic compound release, and thermal modification. Mt. Hope Bay, Massachusetts is an ideal site to base a study of human pathogen presence and distribution because it has several important sources of human impact, including sewage disposal sites and the thermal outfall of a power plant within a mile of each other. The Bay has undergone limited monitoring for several different parameters, including fish populations, river runoff, meteorological forcing, tidal cycles and water chemistry as part of the Mt. Hope Bay Natural Laboratory (MHBNL) program, a 5-year interdisciplinary project at the University of Massachusetts Dartmouth School of Marine Science and Technology (SMAST). While phytoplankton and zooplankton communities in the water column have been fairly well monitored, although not at a molecular level, microbial communities remain relatively uncharacterized. This project presents comprehensive (eukaryal, bacterial, archaeal) data from small-subunit ribosomal RNA gene clone libraries and next-generation Illumina amplicon sequencing for samples collected near the thermal plume and underlying sediments of the Brayton Point Power Plant. Not surprising, our findings reveal a highly diverse consortium of the three domains including relatives of sludge bacteria, polyaromatic hydrocarbon-degrading bacteria, and representatives related to the genera Staphylococcus, Streptococcus, and Clostridium. It is clear that even limited knowledge about the overall microbial community composition can lead to important observations about the ecosystem as a whole. Furthermore, understanding whether free-living pathogens participate in relationships with other members of the microbial community will be important in understanding their distributions and persistence.

Biome: root:Environmental:Aquatic:Marine:Coastal