SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
CN1E1 Metagenome

From a naphthalene-enriched community (CN1) derived from a polyaromatic hydrocarbon contaminated soil. The soil samples were obtained from a parcel on the northern Iberian Peninsula contiguous to a chemical plant (Lugones, Oviedo, 401833N, 33931W, at an altitude of 300 m).

Biome: root:Environmental:Terrestrial:Soil
Saline desert soil sample Targeted Locus (Loci)

Study of bacterial diversity of rhizospheric and non-rhizospheric soil samples from saline desert of Kutch, Gujarat

Biome: root:Environmental:Terrestrial:Soil
Bacterial diversity in an agricultural soil Metagenome

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work we used barcoded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyse bacterial diversity in a profile (depths: 10 cm, 25 cm, and 45 cm) of a well-characterized field of winter wheat. To ensure that the results obtained closely reflect real-life conditions, taxonomic assignment with the RDP classifier program was carried out with three bootstrap scores: 0, 0.80, and 0.99. We found biomass and bacterial quantity and diversity to decrease greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81% of the most represented OTUs (relative abundance =1%), notably the OTUs Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 cm and 25 cm) and subsoil (45 cm) than between levels in the topsoil. The subsoil also contained more unknown bacteria, 53.96% on the average, than did the topsoil, with 42.06% at 10 cm and 45.59% at 25 cm. Most of these unknown bacteria seem to belong to the taxa Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.

Biome: root:Environmental:Terrestrial:Soil
16S sequences from B. vivipara roots and bulk soil


Biome: root:Environmental:Terrestrial:Soil
Cellar mud Targeted Locus (Loci)

Cellar mud

Biome: root:Environmental:Terrestrial:Soil
Soil microcosms 16S Illumina Paired end reads


Biome: root:Environmental:Terrestrial:Soil
AM fungal DNA from soils in a semiarid steppe Metagenome

To investigate the effects of warming, precipitation and N fertilization on arbuscular mycorrhizal fungal community in a semiarid steppe.   We collected samples from experimental plots (full factorial design of warming, precipitation and N fertilization) and extracted AM fungal DNA. Fungal DNA were sequenced using 454 pyrosequencing. In August 2011, soil samples from a semiarid steppe in Inner Mongolia were collected.

Biome: N/A
Black soil Targeted Locus (Loci)

The objectives of this study were 1) to reveal the bacterial community compositions in Black soils; 2) to determine environmental factors.  Soil samples were collected from 26 farmlands across a wide range of Black soil zone of Northeast China in September 2012. Soil pH varied from 4.56 to 6.57. Soil total C and total N varied from 11.77 to 53.53 gkg-1 and from 0.99 to 4.25 gkg-1, respectively. Soil MBC ranged from 64 to 595 mgkg-1.

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

Microorganisms involved in the iron biogeochemical cycling.  Soil samples were collected from the long-term fertilization experiment site (established in 1990) located in the Taoyuan Agro-ecosystem Research Station (2855N, 11127E), central Hunan Province of China. The paddy soil in this station was developed from quaternary red clay and classified as a waterloggogenic paddy soil.

Biome: root:Environmental:Terrestrial:Soil
Soil bacterial diversity Metagenome

Assess the influence of fire burning on the community structure of soil bacteria community

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

Survey of 16S rRNA genes from undisturbed subsoil adjacent to a surface mined site

Biome: root:Environmental:Terrestrial:Soil
Agricultural soil samples pyrosequencing of nifH gene from soil samples

The aim of this study was to examine the abundance, diversity and structure of diazotroph communities in a gradient of Argentinean agricultural soils, under different agricultural practices, using deep pyrosequencing-based analysis of the nifH gene.

Biome: root:Environmental:Terrestrial:Soil
Soil from rural backyards Targeted Locus (Loci)

In the State of Yucatan, Mexico, there are a number of rural houses where the sewage daily produced by laundry and general washing has for decades been disposed directly on the soil of the backyards. This wastewater contains not only a mixture of several detergents, mainly in powder, but occasionally also bleach, soap, hot water, and even food scraps. It is to be expected that this exert a selective pressure when present in soils, bringing about modifications in the structure of the edaphic bacterial communities. In the present work, bacterial community structures of three samples from detergent-contaminated soils and three from non-contaminated soils were assessed by 16S rRNA pyrosequencing. The results may contribute to better understand how selective pressure imposed by this anthropogenic contamination can modify soil bacterial communities, to plan possible remediation procedures, and to find out how to use the metagenomes of contaminated environments in the search for biotechnological products.

Biome: root:Environmental:Terrestrial:Soil
Contaminated Beach - Tabasco State, Mexico Targeted Locus (Loci)

To introduce options for oil spills remediation by obtaining diesel degrading consortia.  Environmental samples taken from oil contaminated soil located on the coast of Tabasco State in Mexico.

Biome: root:Environmental:Terrestrial:Soil
Agricultural field soil Metagenome

To identify soil bacteria and fungal community assemblages associated with biodegradable mulch films.  Samples collected from Knoxville, TN, Lubbock, TX, and Mount Vernon, WA.

Biome: root:Environmental:Terrestrial:Soil
Whole genome amplification influence on microbial community profiles

This study comprised a systematic evaluation of bias in microbial community profiles induced by whole genome amplification.  Environmental soil sample from Wildekamp near Bennekom (The Netherlands).

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

This project characterised the diversity of bacterial communities associated with 42 vegetation-free soils along a maritime Antarctic latitudinal gradient (60-72oS) using 16S rRNA gene amplicon pyrosequencing. The dataset provides a base-line for future monitoring of maritime Antarctic soil bacterial communities.

Biome: root:Environmental:Terrestrial:Soil
Pig farm & soil Targeted Locus (Loci)

16S amplicon sequencing of pig and farm soil from Wenzhou, China.  GBPM (A1) swine manure 2013-01-04 Wenzhou, China pig farm (adult pig) GSPM (A2) swine manure 2013-01-04 Wenzhou, China pig farm (juvenile pig) ABPM (A3) swine manure 2013-01-04 Wenzhou, China pig farm (adult pig) ASPM (A4) swine manure 2013-01-04 Wenzhou, China pig farm (juvenile pig) GPMS (A7) soil 2013-01-09 Wenzhou, China test field APMS (A8) soil 2013-01-09 Wenzhou, China test field

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

We investigated the soil bacterial community compositions among 26 soil samples collected from black soil zone in NE China by using a high resolution bar-coded pyrosequencing technique. 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.  Soil samples were collected from 26 farmlands across a wide range of Black soil zone of Northeast China in September 2012. Soil pH varied from 4.56 to 6.57. Soil total C and total N varied from 11.77 to 53.53 gkg-1 and from 0.99 to 4.25 gkg-1, respectively. Soil MBC ranged from 64 to 595 mgkg-1.

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

Phosphorus fertilization is an important agricultural practice for improving plant nutrition and achieving high crop yield, due to their effects on soil cycling of organic compounds, soil nutrient dynamics. As the underling mechanisms, soil microorganisms play critical roles in regulating the cycling of carbon, nutrient availability and soil fertility since these organisms regulate many fundamental processes. Thus microbial indicators such as microbial diversity and composition are believed to be more dynamic than based on physical and chemical properties, and may have the potential to serve as early indicators of change in the quality of the soil ecosystem. This study determined the effects of phosphorus fertilization on soil bacterial community structures and corresponding changes in soil quality.  A plot experiment on P management for paddy field was established in April 2005 at the demonstration park of YuHang County Agricultural Research Station (3018''51.84"N, 11954''13.37"E) in ZheJiang, China. The soil samples from a field experiment after 7-year of chemical P fertilization with superphosphate along a gradient of 0 (P-0), 30 (P-30), 60 (P-60), 90 (P-90) kg P ha-1.y-1 , using superphosphate since 2005, in order to evaluate the role of P on the bacterial community structure.

Biome: root:Environmental:Terrestrial:Soil
Rice fields Targeted Locus (Loci)

Genetically modified (GM) crops soil

Biome: root:Environmental:Terrestrial:Soil
Big Brown Mine Targeted Locus (Loci)

16S rRNA short reads from soil DNA sampled in 2009 at Texas, USA

Biome: root:Environmental:Terrestrial:Soil
Wuliangsuhai wetland soil ,Wuliangsuhai sediment ,Wuliangsuhai farmland soil Targeted Locus (Loci)

Bacteria are important drivers for biogeochemical cycles in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. Sediments from Lake Wuliangsuhai and soils from Wuliangsuhai wetland were surveyed to characterize the structure and diversity of its microbial communities using barcoded pyrosequencing based on the 16s rDNA. Investigations of sediment and soil bacterial communities were believed to be able to obtain a better understanding of aquatic and wetland ecosystems. The results of this research identified the relationships they share with their environment; and provide new insights into and add valuable reference for the bacterial communities in eutrophic lakes and wetlands

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

To understanding the relationships between bacterial community structure and environmental variables in Arctic tundra soil.

Biome: root:Environmental:Terrestrial:Soil
1996OB Targeted Locus (Loci)

Survey of 16S rRNA genes associated with surface mining-disturbed overburden (1996)

Biome: root:Environmental:Terrestrial:Soil
Bacterial community structures of soils and anodes of microbial fuel cells

Study the responses of bacterial community structures to bioelectrochemically enhanced remediation of petroleum hydrocarbons contaminated soil

Biome: root:Environmental:Terrestrial:Soil
Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

Despite more than three decades of progress, extraction of high molecular weight (HMW) DNA from soils with high clay or iron oxide cemented clay content has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage in DNA libraries. Several nucleic acid extraction procedures that included liquid N2 grinding and bead milling were compared for preparation of HMW DNA from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions (eg. Na2SO4 and NH4H2PO4) offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides and low in humus. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22  2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46  0.25 g DNA/g clay with the PowerlyzerTM soil DNA system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots based on 16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the PowerlyzerTM soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered. Additionally, some OTUs having more than 100 sequences in libraries prepared from DNA acquired using the PB desorption method were absent in samples extracted using the PowerLyzerTM reagents or prior lysis methods.

Biome: root:Environmental:Terrestrial:Soil
DG Metagenome

Swamp soil diversity.

Biome: root:Environmental:Terrestrial:Soil
RA Metagenome

Swamp soil diversity.

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

Characterization of bacterial community structure from paddy field bulk soil with alfalfa-rice crop rotation.

Biome: root:Environmental:Terrestrial:Soil
Soil fungal communities and their contributions to SOM cycling

Quantifying the contribution of EM mycelia to SOM turnover is of critical importance to carbon models . In this study, we evaluated a system to trap enzymatically active EM hyphae under field conditions. Natural-substrate filled mesh bags, surrounded by a sand barrier were effective at trapping EM hyphae while minimizing colonization by obligate saprotrophic fungi. The generated fungal communities were similar in composition to those in the surrounding fermentation/humus layer at both trophic and higher taxonomic levels. Consequently, this system allowed us to study the contribution of EMF mycelia to soil enzyme activity and to SOM-C cycling.

Biome: root:Environmental:Terrestrial:Soil
Metagenomic analysis of an Arctic soil profile

This is a metagenomic study of the microbial community in an Arctic peat soil profile from a medium-aged drained thaw-lake basin near Barrow, Alaska. Four metagenomic libraries were constructed representing depths of 0-10, 10-20, 20-30 and 30-40 cm. The main goal of this work was to analyze the anaerobic respiratory pathways in this soil, with particular emphasis on microorganisms capable of reducing iron and humic substances in anaerobic respiration.

Biome: root:Environmental:Terrestrial:Soil
Harvard Forest Chronic Nitrogen Addition Soils Targeted Locus (Loci)

Amplicon sequencing of internal transcribed spacers 1 and 2 and large-subunit D2-D3 region of fungi. Sequences derived from the organic soil horizon of a 20+ year nitrogen enrichment experiment in a northeastern US hardwood forest.

Biome: root:Environmental:Terrestrial:Soil
Bacteria 16S rRNA amplicon pyrosequencing

Bacteria / white rot fungus interaction during wood decay.

Biome: root:Environmental:Terrestrial:Soil
Linuron contamination of an on-farm biopurification system

Response of the bacterial community in an on-farm biopurification system to linuron contamination studied in several microcosms.  Soil from an on-farm biopurification system was kept as six microcosms with stable temperature and moisture for 25 days. Three of the six samples were treated with the pesticide linuron (25 mg/g) to select for linuron degrading bacteria and plasmids.

Biome: root:Environmental:Terrestrial:Soil
Soil DNA Soil Bacteria Amplicon Sequencing

Prairie plant associated soil bacteria.

Biome: root:Environmental:Terrestrial:Soil
Rock Varnish Metagenome

Rock Varnish and associated soil from Cima Volcanic Field and Darwin Pass.

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

Bacterial community compositions in different soil samples.

Biome: root:Environmental:Terrestrial:Soil
G1E;G2E;G3E Soil Metagenome

This study presented the eukaryotic diversity of the soil in Grove Mountains, East Antarctica, and provided reference for the investigating of the function of the Antarctic ecosystem.  The Grove Mountains area, located in the interior of East Antarctica, is low in rain and temperature. Soil in this area came into shape slowly and formed cold desert soil. To investigate the microeukaryotic diversity of the cold desert soil from Grove Mountains, three soil samples were collected from the south of Mountain Harding during the 26th Chinese Antarctic scientific expedition. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V4 region of the 18S rRNA gene sequences were analysed, the microeukaryotic diversity of soil from Grove Mountains was generally achieved.

Biome: root:Environmental:Terrestrial:Soil
PAHs contaminated soil Metagenome

We also have applied 454 pyrosequencing to explore 66,507,993 bp of metagenomic sequence data from the 24 soil samples. The purpose of this study was to identify the dynamic changes of microbial community structure in degradation with effective degradation bacteria Kocuria sp. P10 strain.

Biome: N/A
1) Glacier Forefront 2) Fungi and Bacteria Community Targeted Locus (Loci)

Early community assembly of soil microbial communities is an essential process for pedogenesis and development of organic legacies. We examined fungal and bacterial succession along a well-established temperate glacier forefront chronosequence representing ~70 years of deglaciation to determine community assembly. As microbial communities may be heavily structured by establishing vegetation, we included non-vegetated soils as well as soils from underneath four plant species with differing mycorrhizal ecologies (Abies lasiocarpa, ectomycorrhizal; Luetkea pectinata, arbuscular mycorrhizal; Phyllodoce empetriformis, ericoid mycorrhizal; Saxifraga ferruginea, non-mycorrhizal). Our main objectives were to contrast fungal and bacterial successional dynamics and community assembly as well as to decouple the effects of plant establishment and time since deglaciation on microbial trajectories using high throughput sequencing.

Biome: root:Environmental:Terrestrial:Soil
Soil community for preservation Metagenome

Soil was stored at three temperatures over two weeks to determine the most appropriate method for preserving the soil microbiome.  Soil was collected from the mineral soil surface to a depth of ~6 inches underneath a native riparian California bay tree at California Polytechnic State University (N 35 18'' 46.59'''', W 120 39'' 7.26''''). There was substantial organic matter buildup in this soil, but it is serpentinite in nature with low calcium and high magnesium content.

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

Investigation of Methane Emission and Bacterial and Archaeal Communities in Rice Paddy Soil during Rice Cultivation.

Biome: root:Environmental:Terrestrial:Soil
Arable soils under rice-wheat cropping system

Fertilization is a common practice to improve plant nutrient and increase crop production, but it can also affect soil bacterial communities. In addition, soil microbial communities are dynamics in seasonal changes. Therefore, this study focuses on the responses of bacterial communities in arable soils under rice-wheat cropping system to different fertilizer regimes and sampling time.

Biome: root:Environmental:Terrestrial:Soil
Soil sample Metagenome

The study aims to determine factors which determine the diversity and species distribution of fungi (especially ectomycorrhizal fungi) in forest soils.  Pine forest sample - buried mesh bag containing sterile sand and DNA extracted from sand after 2 months burial in forest soil (approx 10 cm depth).

Biome: root:Environmental:Terrestrial:Soil
PCP contaminated soil samples Metagenome

The main objective of the project was to compare the diversity of soil bacterial communities estimated using the Ion Torrent PGM or a new framework based on DGGE profiling.  Two differently textured soils were divided into 4 subsamples. For each soil, three subsamples were contaminated with pentachlorophenol at concentrations of 300, 900 and 3000 mg/kg.

Biome: root:Environmental:Terrestrial:Soil
Old Rifle Site metagenome

Metagenomic DNA from soil and from bottle cultures innoculated with soil form the Old Rifle Uranium Mill Tailing site.

Biome: root:Environmental:Terrestrial:Soil
F1RT Metagenome

Metacellulosomics-driven discovery of bacterial synergism in a soil-derived cellulose-degrading community.

Biome: root:Environmental:Terrestrial:Soil
Soil microbial communities from the Bolivian Altiplano Targeted Locus (Loci)

Characterize the response of soil fungal and bacterial communities to fallow period length and to a common fallow shrub in the Bolivian Highlands called ''thola''.

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

The study aimed to determine how inhibitors would affect the microbial community structure and hydrocarbon-degrading activity within an Arctic soil.  Bulk Arctic soil treated with diesel and various inhibitor combinations.

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

Despite the significant ecological and economical importance of the Cerrado, little is currently known about its biodiversity, especially concerning its soil microbial diversity.A still open question is how different land use systems influence the diversity and structure of microbial communities under the same soil type. In this context, the aim of this work was to analyze and compare the soil bacterial communities from Cerrado under different land use systems using high throughput pyrosequencing of 16S rRNA genes.  The research was performed on soil samples from agricultural and natural areas in the Triangulo Mineiro region in the state of Minas Gerais, Brazil, at 1858 S and 4702 W and 939 m above the sea level. A total of 12 soil samples (three for each environment) were chosen for sampling and were taken from four locations under Natural Forest (mesophilic forest comprised by species of Qualea grandifolia, Bowdichia virgilioides, Pterodon pubescens, Caryocar brasiliense, Vatairea macrocarpa, Astronium fraxinifolium, Eugenia dysenterica, and Hymenaea stigonocarpas), Grassland (used for grassing, comprised by Brachiaria decumbens ~ 20 years old), Sugarcane field (monoculture of sugarcane ~15 years old and annually fertilized with P, K and N) and Coniferous Forest (dense forest of Pinus caribaea var. hondurensis with 32 years old; the soil surface presented a 10 cm layer of litter consisting of needles, cones and woodchipsan area).

Biome: root:Environmental:Terrestrial:Soil
gts.soil.sample Metagenome

Soil fungi in Gutianshan.

Biome: root:Environmental:Terrestrial:Soil
Soil bacterial diversity shifts after digestate and chemical fertiliser treatments

Comparing the effect of digestate and chemical fertiliser on soil bacteria.

Biome: root:Environmental:Terrestrial:Soil
The diversity of culturable soil bacterial communities

Understanding the difference in community composition between culturable and unculturable soil bacteria.

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

Analysis the microbial composition change after co-cultivating with some substrates.  Norway peat soil that has been amended for more than 30 years.

Biome: root:Environmental:Terrestrial:Soil
Microbial community at industrially contaminated site Metagenome

The taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.  The soil sample was collected from the contaminated banks of Khari-cut canal.

Biome: root:Environmental:Terrestrial:Soil
Mars Oasis Metagenome

A random soil sample from Mars Oasis, Antarctica.

Biome: root:Environmental:Terrestrial:Soil