SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial eukaryote 454 Roche sequencing in estuarine ecosystems

Using 454 Roche sequencing of the 18S nSSU taxonomy marker, we investigate which of the focal natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of estuarine ecosystems. The data cover two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Pearl River Estuary sediments Targeted Locus (Loci)

Archaea are widespread and play an important role in the global carbon and nitrogen cycles. However, we still have limited knowledge about how the function of Archaea in varying habitats. The goal of this study was to examine the change in community structure of Archaea in the sediments collected from the lower Pearl River, its estuary, and coastal South China Sea in order to evaluate how archaeal ecological function changes along the salinity gradient. Pyrosequencing of the 16S rRNA gene of Archaea was performed on sediment samples from Feilaixia Dam to Wanshan islands, which have a salinity range of 0.11 to > 31.27. Methanogens like Methanoregula, Methanosaeta, Methanosarcina and ammonia-oxidizing Archaea like Nitrososphaera were abundant in freshwater sediments of the Pearl River whereas Methanococcoides and Nitrosopumilus were abundant in the estuary and coastal South China Sea. This study provides the initial observation of the changing archaeal community structure from the lower Pearl River, its estuary and coastal South China Sea, which will aid the understanding of ecological functions of Archaea in the dynamic continental margins such as the South China Sea.

Biome: root:Environmental:Aquatic:Estuary:Sediment
PREsediment Targeted Locus (Loci)

Microbial community of sediment of Pearl estuary

Biome: root:Environmental:Aquatic:Estuary:Sediment
The effect of salinity in prokaryotic communities in an estuary

The goal of this project is to understand the effect of a salinity gradient in an estuary on prokaryotic communities and nitrifying communities

Biome: root:Environmental:Aquatic:Estuary:Sediment
Effects of Fecal Input, Environmental Conditions, and Environmental Sources on Enterococci Concentrations in an Estuarine Ecosystem

To determine major factors influencing enterococci concentrations seen in an estuary and marine beach setting. More specifically delineating fecal input, environmental conditions and environmental reservoirs to determine their combined impact on enterococci concentrations.

Biome: root:Environmental:Aquatic:Estuary:Sediment
the diversity of anammox bacteria in the subterranean estuary

The microbial diversity, distribution pattern of anammox in the subterranean estuary

Biome: root:Environmental:Aquatic:Estuary
eDNA barcoding of protists for environmental monitoring of aquafarming activities

Goal of the study is the evaluation of protistan eDNA meta barcodes from environmental samples as indicators for environmental quality. The impact includes the implementation of protistan eDNA barcoding in routine environmental monitoring programs

Biome: root:Environmental:Aquatic:Aquaculture
Seawater metagenome Targeted loci environmental

Red conger eel (Genypterus chilensis, Guichenot) is a native Chilean species whose meat is characterized by high gastronomic demand and is now part of the Chilean aquaculture diversification program. Two disease outbreaks derived from its intensified aquaculture farming have been reported and were associated with Vibrio spp. and Tenacibaculum spp. However, the role of individual species is not clear because there is a lack of information about the bacterial community composition associated with the rearing environment of healthy specimens of this fish species. This study examined the microbial community in the seawater of a G. chilensis aquaculture facility using both culture-based methods and 16S rRNA amplicon sequencing of the V4V5 region using Illumina MiSeq.

Biome: root:Environmental:Aquatic:Aquaculture
Tyrolerfjord-Young Sound 16S raw sequence reads

V1-V2 region of 16S rRNA genes sequenced using Illumina; samples were collected from three rivers and in the fjord of the Tyrolerfjord-Young Sound system.

Biome: root:Environmental:Aquatic
Eukaryotic protists Metagenome

Spatial differences in beta diversity between the open ocean, outer shelf, Inner shelf and estuarine waters experiencing different hydrography and biogeochemistry reflect diverse communities of heterotrophic protists. Gradients in Chlorophyll a, temperature, salinity, nitrate, nitrite and dissolved oxygen may serve as barriers to the distribution of heterotrophic protists, enabling selection and diversification of distinctive communities. The present study provides the base line information that can allow comparison of diversity metrics with world ocean sites. This work examines spatial changes in protist communities associated with various low oxygen sites.

Biome: root:Environmental:Aquatic
Thermophilic endospores in temperate sediments

Sediment heating experiments were performed with freshwater, brackish and marine sediments to investigate the dispersal of microorganisms in aquatic environments

Biome: root:Environmental:Aquatic
Natural seawater bacterial community in exopolysaccharides utilization

We report the microbial EPS degradation in incubation experiments with seawater from estuarine and open ocean sites (surface and deep water), shifts in microbial community structure during the incubation were investigated. Microbial genomic DNA was extracted from the polycarbonate membranes (microbial cells filtered) and the 16S rRNA gene sequences were amplified by PCR. To understand the changes in the bacterial community structure during the early stage of the incubations, we classified the OTUs based on their phylogenetic affiliations and determined their relative proportions on the total number of sequencing reads.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Fungal communities across four coastal marine habitats in North Carolina, USA

Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbial diversity and skin mucosal microbiota in farmed Atlantic salmon with ulcerative disorders, raw sequence reads

The Norwegian aquaculture of Atlantic salmon Salmo salar is hampered by ulcerative disorders associated with bacterial infections. Studying the composition of microbial communities on skin mucus, and how the microbiota is structured in ulcers will enhance our understanding of ulcer etiology. To achieve this we used seawater farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and at the end of summer (September), in addition to skin-mucus of healthy individuals. In order to assess microbiota associated to the host and to get a better insight into the environmental ecology we additionally sampled the seawater column and sediment layer underneath the farm facility in addition to the distal intestine of Atlantic salmon.

Biome: root:Environmental:Aquatic:Aquaculture
Microbial Diversity in the Southwest Atlantic Ocean and Patagonian Freshwater Bodies

The Southwest Atlantic Ocean (SAO) has one of the largest and most productive continental shelves of the World, notwithstanding which microbiological studies of this region are rather scarce. Likewise, the majority of Continental Patagonian (CP) lakes, rivers and other water bodies remain as pristine as microbiologically unstudied. This project constitutes an initiative aimed to contribute to surveying, systematizing and understanding the dynamics (i.e. ecology and evolution) of microbial communities from this region.

Biome: root:Environmental:Aquatic:Freshwater:Pond
SJP and SJUP Metagenome

SJP- Uranium polluted sediment sample collected from Cauvery bank of Kokarayanpettai, Erode District. SJUP- Unpolluted sample collected from agriculture field of Bhavani, Erode District.

Biome: root:Environmental:Terrestrial:Soil:Uranium contaminated
uncultured prokaryote Metagenome

In the present study, microbial communities ofsponges, Sediments and Seawater inhabitingcoral reef ecosystems were investigated usingbarcoded pyrosequencing of 16S rRNA geneamplicons. Our main goals were to compare thebacterial and archaeal richness and composition ofsponge species, sediment and seawaterinhabiting coral reef systems. FLX 454 titanium pyrosequencing study.

Biome: root:Environmental:Aquatic:Marine
Zooplankton microbiome of the Amazon River Plume and western trophic North Atlantic

The goal of this study was to investigate if mesozooplankton grazers in the Amazon River plume-influenced western trophic North Atlantic directly grazed upon diazotrophic organisms.

Biome: root:Environmental:Aquatic:Marine
microbial community composition of marine water and sediment

To study the diversity and composition of water and sediment microbial community in seaweed cultivation zone and natural sea zone.

Biome: root:Environmental:Aquatic:Marine:Coastal
Dehalococcoides-containing environmental samples and enrichment cultures Metagenome

The organohalide respiring bacteria, Dehalococcoides mccartyi, are pertinent to bioremediation of perchloroethene (PCE) and trichloroethene (TCE), due to their unique metabolic capability to transform chlorinated ethenes to the non-toxic, ethene. Despite their widespread environmental distribution, biostimulation of Dehalococcoides in soil/sediment microcosm studies and during in situ bioremediation has failed to consistently promote reductive dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), commonly attributing this observation to the lack of strains with cis-DCE and vinyl chloride-reducing abilities. Consistent with this observation, in our study, microcosms established with garden soil and mangrove sediment stalled at cis-DCE, even after an extended incubation (200 days) and multiple biostimulation events. Only microcosms containing PCE-contaminated groundwater sediment produced ethene as the end-reduced product. Transfers from cis-DCE stalled microcosms to fresh medium in the absence of soil or sediment, however, yielded complete dechlorination of TCE to ethene, thus, unveiling the true biological potential of the endogenous Dehalococcoides. We hypothesized that biostimulation of Dehalococcoides in our cis-DCE-stalled microcosms was impeded by soil or sediment components serving as terminal electron acceptors for growth of microbes competing with Dehalococcoides for electron donor (H2). Therefore, dilution of the soil/sediment and competing microorganisms fostered the growth of Dehalococcoides and the production of ethene in the microcosm transfers. Our findings support this hypothesis through several lines of evidence. We found that i) Proteobacteria classes which dominated soil/sediment microbial communities became undetectable in the enrichment cultures, ii) the enrichment cultures developed contained up to 109 Dehalococcoides mccartyi cells mL-1 and achieved close to dechlorination of 0.5 mmol L-1 TCE to >80% ethene in 1.7 days, iii) methanogenesis drastically decreased in the enrichment cultures, and iv) garden soil and mangrove sediment microcosms bioaugmented with their respective enrichment cultures produced ethene. Our results provide an alternate explanation to unsuccessful microcosm experiments, providing a new perspective from which to better understand contaminated site assessments and to improve the bioremediation process.

Biome: root:Environmental
Bacterial, IncP-1 and merA diversity in soil and wastewater

The diversity of bacterial 16S rRNA gene, IncP-1 replication (trfA) gene and mercuric reductase (merA) gene in two different soils (forest soil and copper, chrome and arsenic contaminated soil) and wastewater studied by amplicon pyrosequencing. Three replicates were collected from each location.

Biome: root:Environmental:Terrestrial:Soil
wastewater Metagenome

Investigating the prevalence of antibiotic resistance genes and heavy metal resistance genes along with bacterial community in wastewater treatment plant

Biome: root:Engineered:Wastewater:Water and sludge
Sand sample from sand bioreactor treating high salt turkey processing wastewater

Sand samples were taken from sand bioreactors treating turkey processing wastewater with added salt from 6 g/L NaCl to 35 g/L NaCl.

Biome: root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
Saltwater aquarium tank mesocosm vertebrate 12S ribosomal locus

A 4.5-million liter aquarium tank was used as a mesocosm to test whether environmental DNA can be used to reconstruct the known vertebrate community within the tank. This tank is part of a flow through system circulating water from Monterey Bay, CA. Water samples were collected and probed for a mitochondrial DNA locus (12S ribosomal gene) that is conserved across vertebrates.

Biome: root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
Altavista VA wastewater lagoon sediment microorganism Raw sequence reads

The main goal of this study is to investigate the microbial communities in sediments from a wastewater lagoon with polychlorinated biphenyl (PCB) contamination. Our study helped better understand the effect of PCB contamination on microbial communities and in situ microbial PCB degrading potential.

Biome: root:Engineered:Wastewater:Industrial wastewater
Identification of filamentous Chloroflexi morphotypes in Activated sludge plants

This study reports the identification of the Eikelboom morphotypes type 0041 and type 0675. Because these morphotypes differ only in their filament diameters, they are often considered together in surveys based on microscopic identifications. Here we show that they are phylogenetically distinct, and so should be viewed no longer as morphological variants of a single population. Amplicon sequencing data of Australian EBPR plant biomass containing types 0041 and 0675 was utilized to achieve this. Roche 454 amplicon data generated by the Australian Genome Research Facility (AGRF) V1-V3 region of the 16S rRNA gene. Analysis and FISH probes designed against several of these amplicon sequences indicated that these two morphotypes were members of the phylum Chloroflexi. Subsequent surveys of full-scale plant biomass samples showed these two filaments were common in these systems. However, considerable further diversity appears to exist and therefore should be a subject of further research.

Biome: root:Engineered:Wastewater:Activated Sludge
Shotgun sequencing on multiple activated sludge samples

We performed massive shotgun-sequencing on activated sludge samples from four full-scale industrial and two municipal wastewater treatment plants, each sampled at two different times and with two technical replicates, to determine the functional potential of sludge metagenomes.

Biome: root:Engineered:Wastewater:Activated Sludge
Bacterial survey in industrial activated sludge through 454 pyrosequencing

We performed 16S-rRNA gene pyrosequencing on activated sludge of different industrial wastewater treatment plants.

Biome: root:Engineered:Wastewater:Activated Sludge
Activated sludge Metagenome

In order to control biofilm formation in wastewater treatment

Biome: root:Engineered:Wastewater:Activated Sludge
Sewage sediments Targeted Locus (Loci)

This study reflects on the relationship between microbial groups and sewage operation environments.

Biome: root:Engineered:Wastewater
Shanghai Laogang landfill leachate

investigate the bacterial and archael community composition in landfill and assess the variation of the bacterial and archael compositions in refuse decomposition process.

Biome: root:Engineered:Wastewater
Microbial Community Structure of a Pilot Scale Thermophilic Anaerobic Digester Treating Poultry Litter

16s rRNA bacterial survey of anaerobic digester

Biome: root:Engineered:Solid waste:Composting:Bioreactor
CPM-2

environmental investigation

Biome: root:Engineered:Solid waste:Composting
FPM-1

environmental investigation

Biome: root:Engineered:Solid waste:Composting
FPM-2

environmental research

Biome: root:Engineered:Solid waste:Composting
DSW-1

environmental research

Biome: root:Engineered:Solid waste:Composting
compost Metagenome

the metagenome of wheat straw compost

Biome: root:Engineered:Solid waste:Composting
Persistence or attenuation of antibiotic resistance genes during full-scale swine manure vermicomposting via housefly larvae (Musca domestica)

The widespread use of antibiotics in the swine industry has the potential to exert selective pressure for antibiotic resistance genes (ARGs) in both swine-associated microbiota and the bacterial communities in associated environments, posing a potential threat to public health. Full-scale vermicomposting utilizes housefly larvae (Musca domestica) to remove water and aid decomposition of swine manure. Here we determined the prevalence and persistence of ARGs in larvae-associated bacterial communities undergoing ecological succession. The concentrations of four classes of antibiotics, comprising 17 different compounds, and the abundance of their corresponding ARGs, were assessed. Most tetracyclines and sulfadiazine compounds were significantly (p< 0.05) attenuated, while quinolones showed no degradation and were the dominant antibiotics detected in unprocessed manure. Correspondingly, genes encoding tetracycline resistance (tetM, tetO, tetQ, and tetW) were depleted over the course of the study, while two quinolone resistance genes (qnrA and qnrS) were persistent. Interestingly, while sulfonamide was barely detected in late stages of vermicomposting, 2genes encoding sulfonamide resistance (sul1 and sul2) were shown to increase in abundance. While no significant difference in phylum-level bacterial community structure was observed, diversity and species richness did significantly decrease as a result of an increase in abundance of certain taxa, e.g. the relative abundance of a Flavobacteriaceae genus increased 100x, probably representing an excreted intracellular larval symbiont. The persistence of qnrA and qnrS maybe closely related an increase in the relative abundance of certain genera, which responded to shifts in the physicochemical characteristics of the manure (water content, total nitrogen, temperature and pH). The observed sustained bacterial sulfonamide resistance in manure should be a major concern as treated manure is applied to farmland as fertilizer.

Biome: root:Engineered:Solid waste:Composting
Bacterial community in the solid and liquid wastes of Mizoram, India


Biome: root:Engineered:Solid waste
Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

The goal of this work is to develop and test synthetic 16S rRNA gene spike-in standards for use in high-throughput 16S rRNA gene amplicon sequencing experiments. The newly developed spike-in standards were tested using mock community mixtures and environmental microbiome samples.

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Synthetic marine metagenome high-throughput sequencing

Study the bacterial community structure and discuss the environmental relatedness.  Collected from seawater and sediment from the ECS.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
5 bacterial species mock community genome sequencing

Sequencing a mock community consisting of T. roseus DSM 18391, C. akajimensis DSM 45221, P. stutzeri DSM 4166, P. inhibens DSM17395, and G. obscurus DSM 43160 for a comparative analysis of multiple displacement amplification performed in standard bulk reactions or in emulsions. Samples also include unamplified controls and no template negative controls.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Quantifying Bias in 16S rRNA Experiments due to DNA Extraction, PCR Amplification, and Sequencing and Classification

The goals of this project are to quantify and characterize bias in 16S rRNA Studies due to a particular choice of DNA extraction, PCR amplification, and sequencing and taxonomic classification protocols. Labs will make choices in protocol based on the environment of interest, but bias will always remain. This experiment is designed to quantify the differences between actual and observed community compositions when equal numbers of 1) cells, 2) DNA, and 3) PCR product are blended. By comparing the results of the experiments, one can quantify the contribution to bias of each step. Also, one can build models to predict true community composition based on the observed community composition.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Synthetic microbial community partial 16S rRNA amplicons and metagenomes from synthetic microbial community

Next generation sequencing has dramatically changed the landscape of microbial ecology, large scale and in depth diversity studies being now widely accessible. Determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community diversity but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community, but all tested primers lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Study of bacterial communities in microcosms amended with brown algae

Marine minimum medium was amended with brown algal biomass and antibiotics (kanamycin and streptomycin), and inoculated with a WT or alyA1-deficient strain of Z. galactanivorans. Bacterial communities were characterized by Miseq 16S rRNA-gene sequencing.

Biome: root:Engineered:Lab enrichment:Defined media:Marine media
Uncultured Environmental Isolate Targeted loci environmental

Safe disposal of nuclear waste necessitates a thorough understanding of the role microorganisms play on the fate of the waste materials over time. In this study we conducted enrichment experiments to assess the potential for plasticised PVC, commonly used in the nuclear industry, to fuel nitrate reduction by a high pH-adapted microbial community at pH 10. Non-plasticised PVC powder served as an additive-free control, and samples of both materials were gamma irradiated (1 MGy) under hyperalkaline conditions, representative of conditioned nuclear waste, to assess the effect of irradiation on bioavailability.

Biome: root:Engineered:Lab enrichment