SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Dune soil fungi Metagenome

This study aimed to wholly describe fungal diversity and community composition in a semi-closed coastal sand dune ecosystem, and to relate changes in fungi with variations in soil physiochemistry and shifts in ecosystem function at 8 different stages of succession.

Biome: root:Environmental:Terrestrial:Soil:Sand
Municipal Pensacola Beach Sand Metagenome

This study investigated the successional patterns of functional and taxonomic diversity for over one year after the Deepwater Horizon oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques.

Biome: root:Environmental:Terrestrial:Soil:Sand
Upper-line Targeted Locus (Loci)

Sample taken 1 m before the dune zone and the vegetation

Biome: root:Environmental:Terrestrial:Soil:Sand
Forest Soil Targeted Locus (Loci)

The purpose of this study was to explore the diversity of ammonia-oxidizing microbes (bacteria and archaea) in the soils at Coweeta LTER, a research site in western North Carolina.

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Soil microflora Targeted Locus (Loci)

Tracking the soil microflora components associated with fast- and slow-growing mycelium of summer truffle (Tuber aestivum)

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Soil Samples Targeted Locus (Loci)

The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, USA. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Fungi Metagenome

Biodiversity and climate change in european forests

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Rolainville truffle orchards Metagenome

Soil samples have been collected in a truffle orchard located in the Vosges (France). DNA was extracted and used to decipher the structure of the bacterial communities along truffle maturation.

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Agricultural Soil Targeted Locus (Loci)

Study of change in soil microbial diversity due to different experimental climatic conditions

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
HN

Promoting methanogenesis

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
Paddy soils Metagenome

Ammonia oxidizing archaea and bacteria in Chinese paddy soils from three provinces.

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
Effect of biochar on bacterial community in rice paddy soils

Impacts of biochar soil amendment (BSA) on soil bacterial community have not been well documented. In this study, we present a cross site field experiment on bacterial community changes of rice paddy in three sites (JX in Jiangxi, HN in Hunan and SC in Sichuan provinces) from South China with wheat straw biochar amended in May 2010. Using quantitative real-time PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) combined with tag-encoded amplicon pyrosequencing, changes in bacterial abundance and diversity under BSA at 0, 20 and 40 t ha-1 (C0, C1 and C2, respectively) were assessed with topsoils sampled at rice harvest.

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
Rice paddy soil Metagenome


Biome: root:Environmental:Terrestrial:Soil:Crop
soil bacteria and fungi Targeted loci environmental

This study evaluated differences in community composition of all bacteria and fungi present in woody plant encroached streams and soils versus restored (woody plants removed) streams and soils

Biome: root:Environmental:Terrestrial:Soil
Amplicon-based sequencing of soil fungi from wood preservative test sites

Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array.

Biome: root:Environmental:Terrestrial:Soil
BES pyrosequencing

Pyrosequencing analysis of BES sample

Biome: root:Environmental:Terrestrial:Soil
Bacterial 16S rRNA gene sequencing of Antarctic soil

We analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes located in Holocene raised beach and Tertiary volcanic stratigraphy. This is the first study to provide evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.

Biome: root:Environmental:Terrestrial:Soil
Soil DNA extracted from Robinson Ridge, East Antarctica Raw sequence reads

To investigate the functional potentials of microbial community

Biome: root:Environmental:Terrestrial:Soil
Oklahoma soil 10 year warming Metagenome


Biome: root:Environmental:Terrestrial:Soil
Soil Microbiomes Metagenome

To probe environmental DNA for the presence of biosynthetic gene clusters.

Biome: root:Environmental:Terrestrial:Soil
Evaluation of PGM for gene-targeted studies using nifH

To evaluate PGM as substitution of 454 for microbial ecology study

Biome: root:Environmental:Terrestrial:Soil
Acidic northern peatland Transcriptome or Gene expression

Northern peatlands play an extraordinary role in the global carbon balance. The most extensive type of these ecosystems is represented by Sphagnum-dominated acidic peatlands, which are inhabited by microorganisms whose degradation capabilities remain poorly understood. We attempted to identify microorganisms involved in degradation of cellulose, xylan, and pectin, which are the major components of Sphagnum-derived litter, and chitin, which is derived from exoskeletons of peat-inhabiting arthropods.

Biome: root:Environmental:Terrestrial:Soil
RDX degrading microbial communities from a navy installation site in Virginia

RDX degrading communities were obtained from surface soil samples from a navy installation site in Virginia. Sequences from total genomic DNA extracted from the initial soil, samples treated with glucose, without glucose, with RDX and without RDX were sequenced using amplicon sequencing procedures.

Biome: root:Environmental:Terrestrial:Soil
The Metagenome of acidic soil sample before and after the remediation of bioelectrochemistry

The Metagenome of acidic soil sample before and after the remediation of bioelectrochemistry. Besides the raw soil and control sample, other 4 acidic soil sample were operated in microbial fuel cells under different external resistance (1000, 1000, 100 and 10).

Biome: root:Environmental:Terrestrial:Soil
The samples are: (1) soil - RCM based inoculum, used for fermenting glycerol to 1,3 propanediol and (2) the final fermentation samples from select batches Genome sequencing

Soil based inoculum for glycerol to 13-PD fermentation

Biome: root:Environmental:Terrestrial:Soil
Soil enriched in organic materials Targeted Locus (Loci)

Study of the effects of organic amendments to arbuscular mycorrhizal fungi

Biome: root:Environmental:Terrestrial:Soil
Insights into soil''s environmental quality indicators for amendments made from organic residues

In order to obtain the status of microbial communities and their organization in a soil that had been fertilized with composted organic residues, DNA was extracted from soil samples fifteen days after fertilization

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

Microbial community survey in Heilongjiang China

Biome: root:Environmental:Terrestrial:Soil
Jizan project

Soil microbiology

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

Analyze the soil bacterial communities along elevation gradients of southwestern highlands

Biome: root:Environmental:Terrestrial:Soil
Bacteria Metagenome

To investigate how soil bacteria responsed to warming and precipitation.

Biome: root:Environmental:Terrestrial:Soil
amoA gene sequences from soil Targeted Locus (Loci)

Both climate and pH are key in determining soil archaeal community structure and diversity

Biome: root:Environmental:Terrestrial:Soil
Alpine soil eukaryote Metagenome

Investigate the eukaryote community under different water gradient in alpine ecosystem.

Biome: root:Environmental:Terrestrial:Soil
Alpine soil archaea Metagenome

Investigate the archaea community under different water gradient in alpine ecosystem.

Biome: root:Environmental:Terrestrial:Soil
The Greater Khingan Mountains Metagenome

To investigate post-fire changes in soil AMF community structure and diversity. Our work was aimed at studying the short- and long-term response of the AMF communities, so sampling was performed at sites were fires had burned 1 or 11 years prior and compared to nearby unburned control sites. To achieve the purpose, we want to evaluate (i) how soil AMF communities respond to short- and long-term effect of wildfire, and (ii) which factors affect AMF communities and whether there are thresholds for factors driving AMF communities.

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

Communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment.

Biome: root:Environmental:Terrestrial:Soil
Tundra soil Metagenome

Investigation distribution of soil microbial community

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

Fine-scale spatial structure of belowground communities

Biome: root:Environmental:Terrestrial:Soil
Farmers soil

Amplicon sequence originating from grassland or agricultural soil, incubated in lab for 120 days under constant humidity and temperature.

Biome: root:Environmental:Terrestrial:Soil
Yangzhou University Soil Samples Targeted Locus (Loci)

Yangzhou University Soil Samples

Biome: root:Environmental:Terrestrial:Soil
ECOFINDER LTO soil samples Metagenome

The EU FP7 EcoFINDERS project, represents a large consortium of European partners, which brings together a range of expertise and knowledge of soil biodiversity and functioning. The main aims of the project are to characterise the biodiversity of European soils according to soil types, threats, climatic zones and land uses, and to decipher the links between soil biodiversity, functioning and ecosystem services.

Biome: root:Environmental:Terrestrial:Soil
1) Fungi; 2) Soil; 3) Community Targeted Locus (Loci)

To investigate the affects of prescribed fire intervals on the soil fungal communities.

Biome: root:Environmental:Terrestrial:Soil
Uncultured Antibiotic Resistance Genes from Grassland and Agricultural Soil

Shotgun-cloned metagenomic libraries from 18 soils (9 grassland, 9 agricultural) were each expressed in E. coli and those DNA fragments conferring antibiotic resistance were isolated, sequenced, assembled, and analyzed. Each soil library was selected against a panel of 18 antibiotics.

Biome: root:Environmental:Terrestrial:Soil
Bacteria from soil, sediment and water samples Metagenome

We analyzed the bacterial community composition in the soil, sediment and water environment adjacent to pig feedlots, and determined the potential pathogenic bacteria.

Biome: root:Environmental:Terrestrial:Soil
Qiyang soil Metagenome

16S rRNA Metagenome in soil

Biome: root:Environmental:Terrestrial:Soil
Terranova Bay soil Metagenome

Achievement of a background research through the preliminary study on the terrestrial biodiversity in Victoria Land for the long-term monitoring by climate change and human activity

Biome: root:Environmental:Terrestrial:Soil
Soil bacterial 16S rRNA genes

Patterns in species persistence in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly.

Biome: root:Environmental:Terrestrial:Soil
1-1-start Metagenome

First genome sequencing targeting archaea and bacteria in soil treatment system.  Sample collected from the first sampling layer of Column 1 of Soil Aquifer Treatment system at Day 0.

Biome: root:Environmental:Terrestrial:Soil
Fertilizer management Metagenome

Microbial 16S rRNA gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements

Biome: root:Environmental:Terrestrial:Soil
Bacterial composition of tropical earthworm casts

Tropical soils are often nutrients-depleted in their mineral form, constraining crop growth. Therefore any process leading to the mineralization of N and P trapped into the soil organic matter need to be studied with the hope to constitute a durable agricultural tool in the future. Priming effect (PE) is defined as a stimulation of the soil organic matter mineralization (SOM) by a fresh organic matter amendment (FOM). But this microbially-mediated process is not completely understood. Endogeic earthworms are ecosystem engineers known to influence the dynamic of SOM, by the wakening of soil microbial activities. During a laboratory study we followed the capacity of 3 different worm specimens (Pontoscolex corethrurus, Kynotus parvus and Dichogaster saliens) to stimulate or inhibit a Priming effect generated by a wheat straw amendment.

Biome: root:Environmental:Terrestrial:Soil
A study of microflora of plant growth substrate

The study focuses possibilities of manipulations of microflora of artificial plant growth substrates in order to optimalize and unify their microbiological properties

Biome: root:Environmental:Terrestrial:Soil
Uncultured soil denitrification bacteria Targeted Locus (Loci)

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

Biome: root:Environmental:Terrestrial:Soil
uncultured soil nitrogen-fixing bacteria Targeted Locus (Loci)

This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil nitrogen-fixing functional gene (nifH)

Biome: root:Environmental:Terrestrial:Soil
cbbL-red like:uncultured soil carbon-fixing bacteria Targeted Locus (Loci)

cbbL-red like:This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil carbon-fixing bacteria functional gene (cbbL-red like).

Biome: root:Environmental:Terrestrial:Soil
Uncultured bacteria soil carbon-fixing Targeted Locus (Loci)

This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil carbon-fixing functional gene (cbbL-green like).

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

To investigate the effects of biochar and compost on extracellular electron transfer

Biome: root:Environmental:Terrestrial:Soil
The samples about fungi Targeted Locus (Loci)

The objectives of this study were 1) to reveal the bacterial community compositions in Black soils; 2) to determine which environmental factors are dominating predict the distribution of bacterial community structures; and 3) to compare the difference/similarity of bacterial communities among 26 black soils.

Biome: root:Environmental:Terrestrial:Soil
16S rRNA soil metagenom

Analysis of 16S rRNA soil metagenome in different parts of Russia

Biome: root:Environmental:Terrestrial:Soil
Bacteria Metagenome

Bacterial communities within soils in the Fildes Region

Biome: root:Environmental:Terrestrial:Soil
Bacterial and archaeal communities in mangrove sediments under oil contamination and nitrate stimulation

We want to reveal bacterial shift in mangrove soils under oil contamination and nitrate stimulation

Biome: root:Environmental:Terrestrial:Soil
Depth-resolved soil samples collected across an LNAPL body Metagenome

Advancements in understanding of the microbial ecology in soils containing light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct biogeochemical zones were identified: (I) an aerobic, low-contaminant mass zone at the top of the vadose zone, (II) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone, (III) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone, and (IV) a sulfate-reducing, low-contaminant mass zone below the LNAPL body. Evidence suggested hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zones II and III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, thus linking these genera with in situ hydrocarbon degradation in the LNAPL body.

Biome: root:Environmental:Terrestrial:Soil
Rhizobacterial soil sample

Microbial community diversity of rhizobacterial soil sample

Biome: root:Environmental:Terrestrial:Soil
Soil Genome sequencing

The analysis of bacterial community structure

Biome: root:Environmental:Terrestrial:Soil
Metagenome study of rice samples under various conditions

Microbial diversity of flooded rice soil under various situations

Biome: root:Environmental:Terrestrial:Soil
Soil mesocosm Targeted Locus (Loci)

Evaluation of the dynamics of total, core and accessory taxa in bacterial communities of a soil mesocosms in relation to the treatment of soil with Cd, employing a metagenetic approach on 16S rRNA gene based on Illumina sequencing technology.

Biome: root:Environmental:Terrestrial:Soil
Soil microbial community of soil aggregates of different size in conditions of extreme land use practicies

Investigation of microbial community composition in aggregates of different size is to some extend correlated with the task of studying of microbial population in soil microhabitats (microniches). The unique taxa found only in one of the certain size fractions of structural units may be used in in the further research as indicators of the presence of this faction in soil samples investigated. The unique taxa discovered in samples isolated from such extreme land uses as the permanent fallow (50 years), continuous wheat cropping (50 years) and wild land (15 years of soil remediation under natural vegetation after permanent fallowing) could be used as indicators of proceses of soil disturbance (soil structure loss), soil exhaustion and soil recovering processes

Biome: root:Environmental:Terrestrial:Soil
Soil microbial community Metagenome

Microbial communities structure was studied in 3 soils under different conditions: organic land use, conventional land use and forest as a control. The differencies in microbial community composition will show the biological indicators of transition between forest and agricultural lands.

Biome: root:Environmental:Terrestrial:Soil
Mushroom Farm Soil, AMD, and Iron Mound material Random survey

Evaluation of microbial community response to AMD intrusion

Biome: root:Environmental:Terrestrial:Soil
Drosera intermedia Metagenome

Bacterial communities from bulk soil and rhizosphere of Drosera intermedia plants that were either fed with flies or maintained without flies

Biome: root:Environmental:Terrestrial:Soil
Soil samples from Canadian High Arctic Targeted Locus (Loci)

16s rRNA gene sequences from bacterial communities inhabiting polar soils of the High Arctic

Biome: root:Environmental:Terrestrial:Soil
Soil eukaryotes Genome sequencing

Evaluate soil eukaryotic diversity

Biome: root:Environmental:Terrestrial:Soil
Paddy and uncultivated soil Genome sequencing

Microorganisms involved in the anaerobic oxidation of ammonium coupled to iron(III) reduction

Biome: root:Environmental:Terrestrial:Soil
Soil Random survey

Soil fusarium community

Biome: root:Environmental:Terrestrial:Soil
Shennongjia Mountain Metagenome

To understand the soil microbail community structure and diversity in Shennongjia Mountain.

Biome: root:Environmental:Terrestrial:Soil
Soil environment Metagenome

This project aims to determine the diversity of fungi surrounding individual pine trees in Point Reyes National Seashore, California

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

The variation of microbial communities following the land-use change

Biome: root:Environmental:Terrestrial:Soil
Chinese soil Metagenome

Microbial ecology of Chinese soils

Biome: root:Environmental:Terrestrial:Soil
Metagenome sequencing of Prokaryotic Microbiota from Saline Desert Soil of Little Rann of Kutch, Gujarat, India

Sample was collected from different area of kutch Runn like Farasi, Near Salt Agar, Zinzewaea, Vacheradad. Physical properties: Sample was salty, moist with fine silt, brown in color.

Biome: root:Environmental:Terrestrial:Soil
Cixi.454Reads Targeted Locus (Loci)

Soil samples from a chronosequence of 0-700 years of rice cropping in the Bay of Hangzhou, China by 454 pyrosequencing

Biome: root:Environmental:Terrestrial:Soil
Eukaryotic organisms involved in carbon fluxes in soil food webs depending on carbon from glucose, cellulose, maize leaf and root litter. Targeted Locus (Loci)

Eukaryotic organisms involved in carbon fluxes in soil food webs depending on carbon from glucose, cellulose, maize leaf and root litter.

Biome: root:Environmental:Terrestrial:Soil
Bacterial diversity in arable soil

Bacterial diversity in different depths of arable soil in Germany.

Biome: root:Environmental:Terrestrial:Soil
Food web relevant soil bacterial utilizers of different detritus substrates

Glucose, Cellulose, Maize leaf and root litter are mainly degraded by temporal dynamic specific bacterial populations.

Biome: root:Environmental:Terrestrial:Soil
Soil and water from an agricultural field Targeted Locus (Loci)

Natural soil bacteria selectively transported by seepage water are revealed to resemble root-associated microbiota. Mechanisms of mobilisation and transport appear related to preferential flow. Mobilised bacterial biomass carbon represents only a minor contribution to overall organic carbon flux.  Bacterial 16S rRNA gene pyrotags from depth resolved soil and seepage water samples from a maize field near Gottingen, Germany. Sampled in January 2010.

Biome: root:Environmental:Terrestrial:Soil
Soil 454 sequencing data

To analyze the soil bacterial and eukaryotic community structure and diversity

Biome: root:Environmental:Terrestrial:Soil