SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Ground-level meiofauna 18S rDNA Targeted Locus (Loci)

Metabarcoding allows eukaryote biodiversity to be measured rapidly, cheaply, comprehensively, repeatedly, and verifiably. Metabarcoding helps to remove the taxonomic impediment, which refers to the great logistical difficulties of describing and identifying species, and thus promises to improve our ability to detect and respond to changes in the natural environment. Now, sampling has become a rate-limiting step in biodiversity measurement, and in an effort to reduce turnaround time, we use arthropod samples from southern China and Vietnam to ask whether soil, leaf litter, and aboveground samples provide similar ecological information. A soil or leaf-litter sample can be collected in minutes, whereas an aboveground sample, such as from Malaise traps or canopy fogging, can require days to set up and run, during which time they are subject to theft, damage, and deliberate contamination. Here we show that while the taxonomic compositions of soil and leaf-litter samples are very different from aboveground samples, both types of samples provide similar ecological information, in terms of ranking sites by species richness and differentiating sites by beta diversity. In fact, leaf-litter samples appear to be as or more powerful than Malaise-trap and canopy-fogging samples at detecting habitat differences. We propose that metabarcoded leaf-litter and soil samples be widely tested as a candidate method for rapid environmental monitoring in terrestrial ecosystems.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Pooled Ectomycorrhizal Root Tips Targeted Locus (Loci)

Soil cores were collected from 72 forest plots (20x40 m) evenly divided into four treatments (elevated pH, elevated P, elevated pH+P, and untreated control) across 2 physiographic regions of Ohio. Each region contained 36 plots within 3 forests. Within each plot, ten cores were sampled 1-m from the base of an adult tree. Cores were sieved to separate roots and soil and root tips that were visually confirmed to be colonized by ectomycorrhizal fungi were pooled into single composite samples for each plot. Genomic DNA was extracted from the pooled root tips from each plot and the primer set ITS1-F/ITS2 was used to amplify the ITS1 region of the rRNA gene. A set of 24 Multiplex Identifiers were used to separate sequence reads into treatment x forest x region combinations and sequencing was completed on the GS-FLX 454 System.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Amplicon pyrosequencing and development of new Real-time specific assays reveal Phytophthora species diversity in Holm Oak in eastern Spain

Oak decline in non calcareus soils in south-western Spain has been associated with Phytophthora cinnamomi for decades. However, other Phytophthora species such as P. quercina and P. psychrophila have been associated with Quercus decline in the eastern part of Spain where calcareous soils are predominant. With the aim of investigating the involvement of Phytophthora spp. in oak decline in eastern Spain, two forests in different geographical areas were selected as sampling sites: the Natural Park Carrascar de la Font Roja (Alicante) and the Natural Park Tinenca de Benifassa (Castellon). Soil samples were analyzed in parallel by isolation using baiting methods and by amplicon massive sequencing.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Fungal ITS2 amlicons Targeted Locus (Loci)

In this project we have used high throughput 454-pyrosequencing of ITS2 amplicons to analyse fungal communities in humus and litter from 26 old-growth boreal forests in central Sweden. The sites represent a gradient in nitrogen availability and pH, as well as different vegetation types with respect to dominant tree (Pinus sylvestris, Picea abies) and understory species.

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

Raw sequence data from fungal amplicons sequenced from soil samples collected in major Pinus biomes across North America.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Degrading lignocellulose Metagenome

Metataxonomic profiling and prediction of functional behaviour of novel lignocellulolytic microbial consortia

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

Evaluate the effect of short rotation of woody biomass on soil microbial community

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Bacterial community composition on leaf litter of F. sylvatica Targeted Locus (Loci)

Identification of bacterial community composition on leaf litter of F. sylvatica by 454 amplicon sequecing of 16S rRNA gene fragments

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Forest soil Metagenome AOA amoA gene library

Compare AOA amoA community composition in forest soils of different pH

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

Assess the relation ship between forest age class, tree species composition and soil related biotic and abiotic parameters on the fungal community composition.  Forest soils collected from three age class forests in a subtropical forest in China.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Soil microcosm Metagenome

Analysis of the microbial diversity influenced by ambient and exceeded N supply in an incubated forest soil.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Bamboo invaded forest soil Metagenome

To better understand the impacts of moso bamboo invasion on the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation and bamboo-invaded transition zone.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Soil Mesocosm Synthetic Targeted Locus

Soil metagenome analysis from a artificial tree experiment analyzing tree species identity and diversity, as well leaf littereffects on soil bacterial communities.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Bankhead National Forest 2012 Metagenome

Bankhead National Forest 2012 Metagenome - Bacterial and Fungal Sequences

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Soil microbe Metagenome

Metagenomic analysis on 16S rDNA

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Leaf litter and underneath soil Targeted Locus (Loci)

Understanding the difference in bacterial community composition between leaf litter and underneath soil, and between tropical and temperate forests.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Sonoran Desert soil Targeted Locus (Loci)

Understand response of ammonia-oxidizing microorganisms to nitrogen fertilization in arid land soils

Biome: root:Environmental:Terrestrial:Soil:Desert
Cold desert Metagenome

Targetted geno-diversity Of lipase genes in cold desert Of Drass (Ladakh, Jammu and Kashmir)

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

Bacterial community data (cDNA; 16S rRNA gene) from desert soil samples (Namib) taken over the course of a 5 day period in April 2013 and representative of the diurnal cycle (morning, midday, night).

Biome: root:Environmental:Terrestrial:Soil:Desert
Metagenomes of Saline Desert,Kutch,Gujarat, India, Project-151, Gujarat Genomics Initiative, GSBTM, DST, Gandhinagar, Gujarat, India

Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India

Biome: root:Environmental:Terrestrial:Soil:Desert
Bacteria and eukaryote in biological soil crusts Metagenome

Microbial communities in BSCs.  The sample was in the topmost 2-3 mm layers of the desert soil.

Biome: root:Environmental:Terrestrial:Soil:Desert
Saline Desert soil of Kutch, Gujarat Targeted Locus (Loci)

The microbial diversity of Kutch desert was analysed to get insight on role of CO2 on survival of microbial community in desert.

Biome: root:Environmental:Terrestrial:Soil:Desert
Saline Desert S1 Metagenome

Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India.  Saline desert soil sample was collected from Desert of Kutch, India.

Biome: root:Environmental:Terrestrial:Soil:Desert
Saline Desert S2 Metagenome

Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India.  Saline desert soil sample was collected from Desert of Kutch, India.

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

Soil and Rhizosphere samples taken from the Sonoran Desert in and around Tucson, Arizona,

Biome: root:Environmental:Terrestrial:Soil:Desert
Antarctic Soil Hypolithic Samples Metagenome

The surface of hyperarid deserts is often paved with quartz rocks. These rocks are colonized by assemblages of photosynthetic microbial communities. Members of these communities, called hypoliths, are expected to represent a significant input source of Carbon and Nitrogen within this desert and other depauperate environs. The development and assembly mechanisms for these communities is yet to be fully understood. Here we aim to investigate hypolith assembly and development patterns.

Biome: root:Environmental:Terrestrial:Soil:Desert
Bacteria 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
Bacteria_NM_soil_plots

The aim of our study was to (1) investigate the diversity of bacterial and fungal communities in a historically contaminated soil from a former coking plant site (Neuves-Maisons, France), (2) assess the impact of plant-assisted attenuation on microbial diversity, (3) characterize the temporal modifications of microbial diversity linked to edaphic parameters.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Fungi_NM_soil_plots

The aim of our study was to (1) investigate the diversity of bacterial and fungal communities in a historically contaminated soil from a former coking plant site (Neuves-Maisons, France), (2) assess the impact of plant-assisted attenuation on microbial diversity, (3) characterize the temporal modifications of microbial diversity linked to edaphic parameters.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Microorganisms responsible for carbon uptake from ethylbenzene and its degradation products

This study aimed at identifying microorganisms that are involved in the carbon uptake from ethylbenzene and its degradation products in soil microcosms. These microcosms were determined by combing stable isotope probing and high throughput sequencing techniques. Briefly total genomic DNA was extracted from microcosms that degraded approximately 80% of the added labeled or unlabeled ethylbenzene and was subject to gradient ultracentrifugation and were divided into fractions for further analysis. Heavy fractions and total genomic DNA samples from all microcosms were sampled. This BioProject contains the illumina sequences generated from the total genomic DNA samples from all microcosms.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Landfill leachate Metagenome

Microbial community structure and function of landfill

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Silver-induced disturbance increases diversity in soil microbial communities and selects for persistent/resistant phenotypes.

Silver-induced microbial selective pressure is becoming increasingly relevant due to the concurrent increase in biomedical uses of silver and its mass commercialisation in antibacterial consumer products. With demonstrated links between environmental resistomes and clinical pathogens it is important to identify microorganisms with the propensity for silver tolerance/resistance. This study investigated the effects of ionic Ag stress on total soil bacterial communities (a potential source of resistant phenotypes) and identified resistant/persistant populations to the near species level. Silver treatments of 50 - 400 mg Ag kg-1 soil were established in five soils. Chemical profiling using Diffusive Gradients in Thin-film devices confirmed that effective Ag selective pressure was operating throughout the 9 month incubation period, albeit with decreasing intensity. X-ray Absorption Near Edge Spectroscopy showed this was due to changes in Ag speciation to less soluble forms such as Ag0 and Ag2S. Real-time quantitative PCR and Illumina MiSeq partial sequencing of the 16S rRNA bacterial gene were used to determine the effects on bacterial diversity and population dynamics, and to identify persistent/resistant populations using both taxonomy-based and operational taxonomic unit approaches. Structural bacterial community changes occurred in all soils. 16S rRNA gene counts and a-diversity were inversely related, with the former showing immediate significant reductions following Ag application which persisted in some soils but recovered in others. These effects were influenced more by exposure time than applied Ag dose. Dominant taxa in Ag-exposed samples included a range of known persister species (mostly gram positive), including metal tolerant bacteria and slow growing Mycobacteria.

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

Changes in soil bacterial populations following incubation with mixtures of hydrocarbons

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Microbial community analysis of aerobic enrichment cultures sustaining nitrification from coal biotransformation

Screening of microbial populations driving the metabolism of carbon from coal and feeding into the nitrification process.

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

Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils

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

Describe bacterial communities inhabiting hydrocarbon-contaminated soils

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Metagenome on soil background with high concentration of arsenic and antimon Genome sequencing

Metagenome sequencing on soil background with high concentration of arsenic and antimony

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Microbial community structure and composition of raw landfill leachate of different ages

Microorganisms play a key role in the degradation of raw leachate generated in sanitary landfills, leading to the breakdown of organic matter and toxic compounds into less hazardous intermediate and end products.  To expand on the knowledge about these contaminated ecosystems, the microbial communities in leachate produced by three landfill cells of a sanitary landfill in Northeast Brazil were analyzed using a high-throughput sequencing approach of the 16S rRNA gene with universal primers.  In the related paper we describe the structure and composition as well as the metabolic function of leachate communities at different stages in the adaptation process to their environment.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Czech Republic Norway Spruce soil fungal hyphae Metagenome

We investigated fungal hyphal ingrowth and community composition in buried meshbags (3, 5, 15, 25 cm depths), amended with apatite, biotite or hornblende (1%), in a series of Norway spruce forests with different nutrient status (varying in K, P, and Mg). We assayed the fungal colonization of mineral amended mesh bags by measuring the ergosterol and performed fungal community analysis with 454 sequencing of the ITS region (ITS1f-ITS4). Bioinformatic analysis was conducted on extracted sequences from the ITS2 region.

Biome: root:Environmental:Terrestrial:Soil:Boreal forest
Sod-podzolic soil Metagenome

Our goal is to analyze seasonal dynamics of prokaryotic microorganisms of non-arable sod-podzolic soils by means of NGS sequencing technologies. The study incorporates metagenomic and metatranscriptomic data.

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

Response of soil fungi to boreal forest fires

Biome: root:Environmental:Terrestrial:Soil:Boreal forest
USS-2

environmental research

Biome: root:Environmental:Terrestrial:Soil:Agricultural
DOW-2

environmental research

Biome: root:Environmental:Terrestrial:Soil:Agricultural
DOS-1

environmental research

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

Investigate changes to soil communities with plant secondary succession

Biome: root:Environmental:Terrestrial:Soil:Agricultural
RDX degrading microbial communities

RDX degrading enrichments were obtained using four different agricultural soils as innocula. The total genomic DNA samples extracted from the communities after two amendments of 20 mg/L of RDX was degraded, was subjected to high throughput amplicon sequencing. Time zero total genomic DNA samples of the agricultural soils were also sequenced.

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

Five Streptomyces isolates and their combination plus a non-inoculated control was inoculated into field for the biocontrol of potato scab disease. Soil samples from each pot were collected pre-planting and in mid-season. the DNA sequences from each soil samples were extracted and amplified in order to understand the construction of soil microbial community during biocontrol and the influences of indigenous microbial community on biocontrol results.

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

Comparing the bacterial community between ancient and modern paddy soil

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

Mid-term abandoned agricultural land (grassland) in Veluwe, the NETHERLANDS

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Metatranscriptomic analyses of plant polymer breakdown in paddy soil

Paddy soil slurries were amended with rice straw and incubated for four weeks at 30C to mimick the early stage of rice straw breakdown. The anaerobic breakdown of rice straw was studied by metatranscriptomics to gain insights into changes in microbial community structure and gene expression. The focus was on methanogen dynamics and analysing glycosyl hydrolase expression.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Soil bacteria Metagenome

The study focused on determining bacterial diversity in soil that has been under (1) continuous no-tillage and (2) continuous plow-tillage for five decades. Soil bacterial diversity under a long-term soil management practice is relevant since it provides clues about the effect of long-term agricultural management practices on soil microbial environment.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Iron plaque of paddy rice root Targeted Locus (Loci)

To explore the divergence of microbial community structure among iron plaque, bulk soil and rihzosphere soil of paddy field

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Total soil fungi Genome sequencing

The aim of the present survey was to relate soil physicochemical parameters and patterns of fungal community composition to different soil management practices: conventional tillage or reduced tillage, retention or removal of crop residues, in an experimental design combining each tillage practice with each crop residue management practice.

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

Bacterial community structures

Biome: root:Environmental:Terrestrial:Soil:Agricultural
a paddy soil chronosequence genome sequencing

In this study, we investigated how bacterial communities might change with respect to soil physicochemical development during 2000-year rice cultivation after reclamation from tidal wetlands, using the soil chronosequence in the Yangtze River Delta, China. This knowledge would provide useful suggestions for sustainable development of paddy ecosystem.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Rice field soils bacterial 16S rRNA genes raw sequence reads

Detect the response of bacterial and archaeal community in rice field soils to rice straw addition under methanogenic conditions

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Genome for paddy soils Genome sequencing

To gain a comprehensive understanding of the impacts of different fertilization regimes on the soil microbial communities, 454 pyrosequencing was used to examine differences in microbial community structures among experimental sites managed for 22 years with different chemical fertilizer treatments.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Bacteria Metagenome

The aim of our survey is to detect patterns in bacterial community composition related to different soil management, consisting in a combination of tillage practice (conventional tillage and reduced tillage) and crop residue management (residue retaining and residue removal.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Arable soil bacteria Metagenome

Manure application well contributes to the disturbance of bacterial communites in arable soil.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Soil and cattle excrements Metagenome

Diversity of bacteria and archaea in cattle impacted soils and cattle excrements

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Microbial community enriched from paddy soil

Depiction of microbial community structure

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

Nitrous oxide reductase sequences obtained by targeted amplification of the nosZ gene from arable soils in field sites throughout Europe.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Scheyern-soil Metagenome

Agricultural soil metagenome

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Agriculture soils Metagenome

A central goal in ecology is to understand the factors that control microbial biodiversity and patterns in spatial distribution. In this project, the effect of limited tillage versus traditional tillage, residue retention versus removal and crop rotation (maize-wheat) versus monoculture (maize) on the bacterial community structure is being investigated.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Arbuscular Mycorrhizal Fungi Metagenome

The goal of this study was to know the communities of arbuscular mycorrhizal fungi in productive fields under different soil agricultural practices

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Soil Metagenome after long-term green manure

To study effect of long-term green manure

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

Improved cultivation

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Soil Carbon Content and Relative Abundance of High Affinity H2-Oxidizing Bacteria Predict Atmospheric H2 Soil Uptake Activity Better than Soil Microbial Community Composition

We examined the microbial community structure based on ribotyping analysis as predictors for atmospheric H2 uptake rate in soil samples collected from different land-use types.

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

The effect of biochar on soil bacterial diversity in Greater Khingan Mountains,Inner Mongolia Autonomous Region, China

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Extremely alkaline saline soil Texcoco Metagenome

It is most likely that the soil of the former lake Texcoco harbors much more novel microbial species with unique characteristics. However, the extent to which new microbial species can be found in this environment has not been determined. In this project, archaeal-specific primers were used combined with 454 pyrosequencing to investigate the archaeal diversity in soils from the former lake Texcoco

Biome: root:Environmental:Terrestrial:Soil:Silt