SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bacterial Diversity of the Cold Desert Soil from Grove Mountains, East Antarctica

This study presented the bacterial diversity of the soil in Grove Mountains, East Antarctica, and provided reference for the investigating of the function of the Antarctic ecosystem.

Biome: root:Environmental:Terrestrial:Soil
Phototrophs Metagenome

454 amplicon pyrosequencing was used to assess bacterial (16S rRNA), fungal (ITS region) and phototroph (23S rRNA genes of plastids) community structure at the soil surface (upper 3mm) of pasture soil following incubation under light (16hr:8hr light:dark cycle) and dark conditions for 80 days.  Phototrophs at Gartenacker soil surface.

Biome: root:Environmental:Terrestrial:Soil
Soil in greenhouse China Metagenome

This research, by means of 454 pyrosequencing, determined the effects of 1,3-D on the bacterial community. The results of this study will evaluate the effects of 1,3-D on the soil bacterial community of greenhouse vegetable industry and offer a theoretical foundation to the use of 1,3-D on greenhouse vegetable industry.  These soil samples were collected in in a commercial field near Fang county, Taian City, Shandong province, China. The soil at the experimental site was a silt loam, composed of 15% sand, 80% silt, and 5% clay, with an organic matter content of 24.8 g kg-1 of soil, pH 7.2, and a soil density of 1.21 g cm-3

Biome: root:Environmental:Terrestrial:Soil
Bacterial community diversity and structure of winter wheat-cultivated soils

Bacterial community diversity and structure of two typical grain food rotations of winter wheat-rice and winter wheat-maize soon after wheat harvested are studied. It will help us have a knowledge of sustainable agriculture systems.  In this study, soil samples were collected soon after winter wheat harvest from two typical rotation systems, i. e. winter wheat-rice located in Changshu (CS), Jintan (JT), and Zhangjiagang (ZJG), Jiangsu province and winter wheat-maize located in Dezhou (DZ), Shandong province, and in Quzhou (QZ), Hebei province in China.

Biome: root:Environmental:Terrestrial:Soil
Peat layer 16S amplicon

Peat-accumulating ecosystems playing a key role in the global carbon and water budget.  Surface and subsurface peat layers of a northen wetland.

Biome: root:Environmental:Terrestrial:Soil
Soil aquifer treatment site soil samples and simulated conditions Metagenome

Effect of initial concentration of pharmaceuticals and personal care products on their removal in laboratory-scale biofilm columns.  Soil samples taken from soil aquifer treatment site over wetting cycle and simulated soil samples from laboratory columns.

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

To investigated the bacterial and archaeal diversity in the rice paddy soils which have been fertilized for 23 years.

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

Analysis of the taxonomic composition of soil microbiome for the microbiological mapping of the soil types in order to improve agronomic practices.  16S rRNA gene pyrosequencing from the various soil types in Russia.

Biome: root:Environmental:Terrestrial:Soil
Permafrost soil along CRCOP Metagenome

Bacterial biodiversity was investigated by 454 pyrosequencing of 12 soil samples from 4 different permafrost sites along the China-Russia Crude Oil Pipeline, in order to reveal the background communities for assessing the impact of accidental oil spills on intrinsic bacterial consortia.

Biome: root:Environmental:Terrestrial:Soil
Soil microbial diversity of 106 samples Metagenome

These data contain the information about the response of soil bacterial diversity and composition to multi-factorial environmental changes, including increased precipitation, rising temperature, adding nitrogen, adding phosphorus, removing plant functional groups, grazing, and some of their combination. Specifically, C8,C10,C12,C32 and C33 represent the treatment of removing no plant functional group; C5,C6,C9,C11,C13,C14,C21,C22,C23,C24,C25,C28,C29,C39 and C40 represent the treatment of removing one plant functional group; C1,C2,C4,C7,C17,C18,C19,C20,C26,C3,C30,C34,C35,C36 and C38 represent the treatment of removing two plant functional groups; and C15,C16,C27,C31,C37 represent the treatment of removing three plant functional groups. Meanwhile, D16,D23,D32,D40,D47,D51 and D64 represent the control; D18,D19,D46,D55,D60 and D9 represent the treatment of warming; D22,D36,D38,D41,D42,D56 and D57 represent the treatment of watering; D15,D31,D37,D39,D4 and D50 represent the treatment of simultaneous warming and watering; D21,D26,D58 and D63 represent the treatment of adding phosphorus; D30,D34,D49 and D65 represent the treatment of adding nitrogen; D14,D35,D45 and D5 represent the treatment of simultaneous adding N and watering; D17,D48,D54 and D6 represent the treatment of simultaneous adding N and P; D25,D62,D66 and D8 represent the treatment of grazing; D11,D2,D43 and D59 represent the treatment of simultaneous grazing and watering; D10,D29,D3 and D44 represent the treatment of simultaneous grazing and adding P; D27,D28,D33 and D7 represent the treatment of simultaneous grazing and adding N; D1,D12,D20 and D52 represent the treatment of simultaneous grazing and adding N and watering; D13,D24,D53 and D61 represent the treatment of simultaneous grazing and adding N and P.

Biome: root:Environmental:Terrestrial:Soil
An Evaluation of the Impact of Multi-walled Carbon Nanotubes on Soil Microbial Community Structure and Functional Diversity

The goal of this project was to evaluate the effects of multiwalled carbon nanotubes on microbial community in soil (functionality as well as community composition) at different exposure concentration.

Biome: root:Environmental:Terrestrial:Soil
Mock and soil DNA Targeted Locus (Loci)

Study on the effects of the type of polymerase and PCR cycle number on the accuracy of pyrosequencing analysis of bacterial community.

Biome: root:Environmental:Terrestrial:Soil
Organic Farm Targeted Locus

16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing based on soil surface samples collected from the first certified organic farm (Tune Farm) in Alabama.

Biome: root:Environmental:Terrestrial:Soil
PAMPA Dataset: Argentinean agricultural pampean soils Metagenome

Soil microbial communities are among the most diverse and complex environments in the world. Our information about the identity and metabolic capabilities of terrestrial microbes is still scarce. Moreover, although microorganisms in soil are essential for nitrogen, carbon, phosphorous and sulfur cycling as well as plant growth and crop production, only a few microbial species involved in these processes have been described in detail. The future years will face the challenge of increasing agricultural yields conserving soil microbial communities and soil quality. To do so, a better comprehension of micro-ecosystem functioning and microbial description will be needed. As a first modest approach towards the understanding of soil microbial communities and how land use affects them, we have generated a metagenomic dataset obtained by high throughput sequencing of samples from Argentinean Pampas. Three different geographic regions, three different types of land uses and two soil types (bulk and rhizospheric) were analyzed using whole genome shotgun (WGS) and amplicon sequencing. A total of 19 Mi (7.7 Gb) WGS reads and over 1 Mi 16 rRNA pyrotags were generated. Our preliminary results suggest that soil microbial communities are different at both, taxonomic and metabolic level, on each type of tillage system and geographic region in bulk soils. Rhizospheric microbial communities resulted markedly different from those in bulk soils and less sensitive to the type of tillage system. This dataset is the first soil metagenomic study in Argentina and one of the few available in the world. This should be considered as a kick-start for future efforts towards a better comprehension of soil microbial communities in agricultural systems in the Argentinean region and a useful comparison dataset for other regions in the world.

Biome: root:Environmental:Terrestrial:Soil
Bacterial 16S rRNA genes from heavy-metal contaminted soils Targeted Locus (Loci)

Analysis of bacterial diversity in heavy metal-contaminated soils.

Biome: root:Environmental:Terrestrial:Soil
Biochar-amended soil Targeted loci environmental

To evaluate the effect of biochar-mineral complexes on organic soil microbial communities.

Biome: root:Environmental:Terrestrial:Soil
Soil from Cuatro Cienegas Basin, Coahuila, Mexico Targeted Locus (Loci)

The purpose of this study was to follow microbial succession following sterilization of soil plots in arid and humid locations within the Cuatro Cienegas Basin, a desert oasis.

Biome: root:Environmental:Terrestrial:Soil
Active ammonia oxidizers in an acid soil are phylogenetically closely related to neutrophilic Nitrososphaera viennensis

All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular survey also indicates broad existence of Nitrososphaera-like phylotype in acid soil, but its ecological role is poorly understood. In this study, we present molecular evidences for chemolithoautotrophic growth of the Nitrososphaera-like AOA in an acid soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by significant increase in abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of buoyant density of DNA gradient following ultracentrification of the total DNA extracted from SIP microcosms indicated substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the heavy DNA fractions suggested that archaeal and nitrite-oxidizing bacterial communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting chemolithoautotrophic lifestyle. Sequencing analysis of both amoA and 16S rRNA genes revealed that the 13C-labeled AOA were phylogenetically closely related to neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptative growth of Nitrososphaera-like AOA in acid soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

Effects of functionalized multi-walled carbon nanotubes on soil bacterial community composition.

Biome: root:Environmental:Terrestrial:Soil
Sulfidic cave snottites Metagenome

Snottites are extremely acidic (pH 0-2) biofilms that form on the walls and ceilings of H2S-rich caves. We investigated the community composition, metabolic potential, and biogeochemistry of these biofilms using metagenomics in combination with full-cycle rRNA and other methods.

Biome: root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
Targeted loci sequencing of anaerobic benzene-degrading enrichment cultures

This project aims to characterize the microbial community of anaerobic benzene-degrading cultures originating from different subsurface environments. In this project, we used 454-based DNA amplicon sequencing targeting v6-v8 region of 16S rRNA genes.

Biome: root:Environmental:Terrestrial:Deep subsurface
Hot springs Metagenome

Investigation of microbial diversity

Biome: root:Environmental:Aquatic:Thermal springs:Sediment
Cave sediment Metagenome

Bacterial diversity in Farpuk cave, Mizoram

Biome: root:Environmental:Aquatic:Sediment
microbial community diversities of Tuosu Lake

Detecting the bacterial, archaeal and fungal population diversities in Tuosu Lake

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

horizontal sediment samples in different seasons from Dianchi Lake and Erhai Lake

Biome: root:Environmental:Aquatic:Sediment
16S sequencing of environmental samples to test the impact of sediment source

The Broad Institute sequenced environmental samples to tests the impact of sediment source, supplemental cellulose source, and depth within Winogradsky columns, on microbial community structure. The study was conducted, in part, within introductory microbiology courses at Vassar College (Poughkeepsie, NY) and Williams College (Williamstown, MA). Sequencing was conducted at the Broad Institute (Cambridge, MA). Winogradsky columns were created from sediment collected near the edge of two small ponds (under approximately 15-30 cm of water) in late October 2008. Ponds were located near the campus of Williams College in Williamstown, Massachusetts: Buxton Pond (N 42.70o (42 o 42 15)  W 73.2114 o (73 o 12 41) and Ephs Pond (N 42.7201o (42 o 43 12)  W 73.1975 o (73 o 11 51).

Biome: root:Environmental:Aquatic:Sediment
MeHg Coal Ash

Mercury (Hg) associated with coal ash is an environmental concern, particularly if the release of coal ash to the environment is associated with the conversion of Hg to methylmercury (MeHg), a bioaccumulative form of Hg that is produced by anaerobic microorganisms. In this study, sediment slurry microcosm experiments were performed to understand how spilled coal ash might influence MeHg production in anaerobic sediments of an aquatic ecosystem. Two coal ash types were used: (1) a weathered coal ash; and (2) a freshly collected, unweathered fly ash that was relatively enriched in sulfate and Hg compared to the weathered ash. These ash samples were added to anaerobic sediment slurries constructed with a relatively pristine sediment (containing 0.03 mg kg-1 Hg) and a Hg-contaminated sediment (containing 0.29 mg kg-1 Hg). 16S amplicon sequencing of microbial communities in the slurries was done for each microcosm.

Biome: root:Environmental:Aquatic:Sediment
Lake Washington sediment enrichments

In this study, we addressed the role that provided nitrogen plays in determining the composition of methane-consuming communities and the methane oxidation potential in a well-studied model system. We applied a multi-phase approach combining microcosm enrichments and pure culture studies with methane oxidation potential measurements and high throughput sequencing. We focused on incubation conditions with a limited O2 availability as observed in the natural environment. 16S rRNA gene profiling showed that with N2 as the only available nitrogen source, communities were dominated by Methylomonas species as the major methane-oxidizing bacteria (MOB). In the presence of added nitrate however, Methylobacter species were the dominant MOB. Pure culture studies of Methylomonas and Methylobacter isolated from the same environment and incubated in the same way confirmed that the growth of a Methylomonas strain was not significantly affected when N2 was the only provided nitrogen source, while growth of a Methylobacter strain was negatively impacted. By further exposing long-term methane fed microbial communities to different nitrogen sources, intraspecific dynamics of non-methanotrophic community members were observed, suggesting nitrate as an additional selective factor for co-occurring species. Our results show that provided nitrogen source is an important factor determining specific responses of individual community members and consequently affecting community composition and overall methane consumption.

Biome: root:Environmental:Aquatic:Sediment
Fluctuating redox regimes raw sequence reads

Evaluate the changes in the active microbial community due to fluctuating, stable oxic and stable anoxic redox conditions.

Biome: root:Environmental:Aquatic:Sediment
Sediment saline lake Grevelingen (Netherlands) Raw sequence reads

Microbial diversity in sediment of the saline lake Grevelingen (Netherlands)

Biome: root:Environmental:Aquatic:Sediment
Old Rifle sediment Raw sequence reads

A systematic column study compared the interactive effects of acetate amendment, sediment geochemistry, and bacterial community composition on in-situ bioremediation of U(VI) using sediments from the subsurface at the U.S. Department of Energys Integrated Field Research Challenge site in Rifle, Colorado that were either contaminated or non-contaminated by a uranium plume.

Biome: root:Environmental:Aquatic:Sediment
Bacterial biogeography of a High Arctic ice cap

This study investigates the roles of dispersal, environmental and biotic filtration in bacterial assemblies, in order to understand the environmental influences in cryoconite ecosystems. Foxfonna dome is used as a model ecosystem to observe the bacterial biogeography of an ice cap.

Biome: root:Environmental:Aquatic:Sediment
Transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)

In the Zambales ophiolite range, terrestrial fluid seeps host diverse microbial communities, which may be supported by hydrogen gas generated via serpentinization. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. These data provide context for future serpentinizing seep ecosystem studies, particularly in tropical biomes.

Biome: root:Environmental:Aquatic:Sediment
Sediment bacterial diversity

This study investigated the effects of salmonid aquaculture on microbial diversity and community composition of sediments in Chiloe, southern Chile using Roche 454 GS-FLX of the 16S ribosomal RNA gene. Bacterial diversity was found to be significantly lower in aquaculture sites than in reference sites. Bacterial communities were found to differ significantly between reference and aquaculture sites, but OTU richness was not significantly different between sites. The bacterial groups significantly enriched in aquaculture sites were genera belonging to Bacteroidetes (Flavobacteria) and Gammaproteobacteria, which play key roles in organic matter mineralization and sulfur oxidation. These findings show that current practices related to Chilean salmonid aquaculture alter the structure and functionality of marine microbial communities in sediments and suggest major changes in the biogeochemical processes.

Biome: root:Environmental:Aquatic:Sediment
Sewer sediments Targeted loci environmental

16S rRNA gene metagenomic study of sewer sediments

Biome: root:Environmental:Aquatic:Sediment
Boreal lake sediment 16S rRNA gene amplicon (454-pyrosequencing) raw sequence reads

Boreal lake sediment 16S rRNA gene amplicons

Biome: root:Environmental:Aquatic:Sediment
Antimony contaminated sediments Raw sequence reads

Water and surface sediments were collected from six sites with different extent of Sb contamination along Chahe watershed and were analyzed for geochemistry as well as bacterial diversity.

Biome: root:Environmental:Aquatic:Sediment
Sippewissett Salt Marsh tide pool sediment Targeted Locus (Loci)

Bacterial community phylogenetic study in sediments of salt marsh

Biome: root:Environmental:Aquatic:Sediment
KB34 Transcriptome or Gene expression

Eubacterial and archaeal community identification in historically contaminated subsurface sediment and community shift during PHC degradation under given experimental conditions.  Historically contaminated subsurface sediment was used to monitor hydrocarbon degradation behavoir under sulphate reducing and methanogenic conditions over 450 days. Total RNA was isolated from experimental sets and reverse-transcribed to cDNAs. Phylogenetic marker gene 16S rDNA was amplified with eubacterial and archaeal universal primers and amplicons were sequenced on Roche 454 sequencing platform.

Biome: root:Environmental:Aquatic:Sediment
Salt marshes sediment microhabitats Metagenome

In the present study, microbial communities of bulk and rhizosphere sediments were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of bulk sediment and two plant species inhabiting salt marsh systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences after demultiplexing thus without a chimera check and other quality filtering. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.

Biome: root:Environmental:Aquatic:Sediment
Bacterial communities from Thrombolites of Lake Sarmiento

The aim of this study was to examine the bacterial diversity of field (lived) versus cultured (kept in an aquarium system) thrombolites from Sarmineto Lake by sequencing of the V4 hypervariable region of the 16S rRNA gene. We attempt to reveal the chemical composition (before and after culturing) of our samples and to compare the bacterial populations founded with those from worldwide sites where microbialites thrive, in order to discern bacterial communities drivers within similar ecosystems.

Biome: root:Environmental:Aquatic:Sediment
zooplankton environmental sample Metagenome

COI sequences of Zooplankton in Lake Tai Metagenome

Biome: root:Environmental:Aquatic:Sediment
Biogeography of subsurface prokaryotic communities along with sediment deposition of sediments

454 pyrosequencing of 16S rRNA gene amplicons were used to investigate the geological distribution of bacteria and archaea along with salinity.

Biome: root:Environmental:Aquatic:Sediment
Saltern of Margherita di Savoia Metagenome

We analyzed the prokaryotic communities of the Salterns of Margherita di Savoia (Italy).

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Saltern microbial community diversity

Microbial diversity analysis

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Metagenomics Cabo Rojo Salterns

Culture independent study of microbial communities in hypersaline environments in a tropical solar saltern in Cabo Rojo, Puerto Rico. This project aims to determine the diversity present using direct 16S rRNA amplification. A different diversity is expected due to the stable conditions year round which in turn may lead to identification of new species.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Protistan plankton diversity along salt gradient

High-throughput pyro-sequencing was used to investigate protistan diversity in solar saltern ponds

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
solar evaporation pond sample Metagenome

metagenomic data of solar evaporation pond of ramnagar, west bengal, india.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Saltern bacteroidetes

Uncultured bacteroidetes were directly recovered from the solar saltern CR30 (Santa Pola, Alicante, Spain) by using fluorescence activated cell sorting and then single cell were lysed and their genomes amplified by multiple displacement amplification. Finally, genomes were sequenced by Illumina technology.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond