SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Marine DNA/RNA samples from Western English Channel site L4

Marine DNA/RNA samples from Western English Channel site L4.   The seasonal structure of microbial communities in the Western English Channel - 2007   Here we present a multi-omic study of the Bacterial and Archaeal diversity found at the L4 long-term marine observatory.  We have previously generated a six year time series from L4 that showed that the bacterial community shows strong seasonal structuring and diversity peaks every year on the winter solstice.  Here we further confirm this pattern by extending this study to include genes and transcripts generated for eight additional time points in 2008.  This data includes further 16S datasets as well as eight metagenomes (1.2GB) and eight metatranscriptomes (157MB).  These time points cover three seasons (Jan, April and August) and include day and night (diel) samples.  In addition, the August samples (4) include 4 consecutive samplings within 24 hours at six hour intervals.  Using these data we test whether Archaea also show the same observed seasonal patterns and whether these patterns hold true at the gene (functional) level.   Analysis of this combined data set allows five main conclusions to be drawn.  First, Archaea show evidence of following the same seasonal patterns as Bacteria, but have ~6% the richness.  Second, for both Bacteria and Archaea, we confirm that higher 16S diversity reflects higher diversity at the gene-level (including expressed genes) and this diversity also peaks at the winter solstice. Third, interestingly, detectable diversity appears to be higher at night, and this is of special potential relevance as there is more diversity in winter when nights are longer.  Fourth, despite the diversity of these communities, night and day samples taken using Lagrangian (drift) sampling were successful in isolating the same community suggesting communities are more structured than is commonly believed. Finally, this data, as expected, contains a large proportion of orphan genes without known homologues.  When compared to the housekeeping genes identified through SEED subsystem classification, these unknown genes appear to be driving the differences between samples across seasons.  This underscores the importance of determining the functions of more of these sequences in the future.   In summary, this study further confirms the strong seasonal patterns characterizing both the bacterial and archaeal communities at this important marine site.  The finding that, despite the huge diversity of these communities, there are evident signs of predictable patterns and detectable stability over time provides compelling evidence that renewed efforts should

Biome: root:Environmental:Aquatic:Marine
Elevated CO2 induces a bloom of microphytobenthos

The geological storage of carbon dioxide (CO2), captured from large industries and power plants, is expected to be an important component of future carbon emissions mitigation globally. Alongside the need to understand the impacts of a CO2 leak on the marine environment, there is an urgent need to develop monitoring protocols for leakage detection. In the present study, sediment cores were exposed to seawater acidified using CO2 to five different pH levels (8.0, 7.5, 7.0, 6.5 and 6) for a period of 10 weeks. A pink microphytobenthos mat containing Spirulina sp. and diatoms appeared on top of sediment exposed to pH 7.0 and 7.5 after five weeks, peaked at eight weeks and was still present in small patches within the pH 7.0 cores after 10 weeks. Quantitative PCR measurements of the abundance of cyanobacterial 16S rRNA also indicated an increase to the abundance of cyanobacterial or chloroplast 16S rRNA within the pH 7.0 treatments after 10 weeks incubation. Detailed comparisons of the microbial communities with the pH 7.0, 7.5 and 8 treatments revealed a shift in community composition within the pH 7.0 cores: an increase in abundance of sequence most closely related to Spirulina sp. and the diatom Navicula sp., and a corresponding decrease to the abundance of Alphaproteobacteria, specifically of the family Rhodospirillales, the Crenarchaeota Class Marine Group I and the Planctomycetes Class OM190. Monitoring for blooms of microphytobenthos may prove useful as an indicator of a CO2 leak from injection pipeline failure in coastal areas.

Biome: root:Environmental:Aquatic:Marine:Sediment
Whale fall

Deep-sea whale falls create sulfidic habitats of which microbial structure is poorly evaluated. We sampled the sediment in the whale fall area and targeted the V9 of the 18S SSU to determine the protistan community.

Biome: root:Environmental:Aquatic:Marine:Sediment
Baltic Expression Project

cDNA  samples were pyrosequenced using 16S rRNA primers. Samples from which cDNA was obtained were surface marine sediment samples from the Bothnian Bay (Baltic Sea) and Skagerrak (North Sea).

Biome: root:Environmental:Aquatic:Marine:Sediment
Gulf of Mexico Alkane Reactors Metagenome

Pyrosequencing of Gulf of Mexico sediments from anaerobic batch reactors with short-chain alkanes.

Biome: root:Environmental:Aquatic:Marine:Sediment
Depth profile of ancient sediments

Recruitment of bacteria from the different depth of sediments

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
marine metagenome Targeted Locus (Loci)

This project investigated the production of different classes of iron-binding ligands, iron concentrations, macronutrient concentrations, and phytoplankton and bacterioplankton assemblage composition in iron amended microcosm incubations conducted in oligotrophic waters collected off the Southern California Bight.

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_LCR

The LACAr cooperative project: microbial diversity in coastal systems along a latitudinal gradient from South Atlantic to the Caribbean.

Biome: root:Environmental:Aquatic:Marine
Composition and structure of soil fungal community in Inner Mongolian steppe

Fungi serve important roles in terrestrial ecosystem. However, its geographic distribution and driving factors shaping fungal community structure remain elusive. In this study, we utilized Illumina Miseq sequencing technique for the nuclear ribosomal internal transcribed spacer 2 (ITS2) region to investigate soil fungal distribution along a 360-km transect in Inner Mongolian steppe.

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

The goal of this study was to assess the spatial distribution of soil bacteria in an agricultural context. We compared soil bacterial communities in corn and switchgrass cropping systems across a topographic gradient and two years. In addition, we quantified scale-specific spatial patterning of soil bacterial communities. Because of their important role in biogeochemical cycling, understanding spatial patterning of microbial communities is important for our ability to model carbon and nitrogen cycling.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Polymetallic nodule field Targeted loci environmental

Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1 claim area within the Clarion-Clipperton fracture zone in the Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic
ADDOMEx

Here we describe microbial community dynamics in the GOMOO mesocosm experiment. Using 16S rRNA gene sequencing of filtered water samples collected every 12 hours from the mesocosm treatments, we characterized community membership and structure to determine how the mesocosm communities responded to the water accomdated fraction of oil with and without the dispersant Corexit.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
Changes in the bacterial communities of subtropical soils from Argentina with different land uses.

The goal of this study was to analyze the modifications in the structure of the bacterial communities from Argentinean subtropical soils caused by changes in land use. The samples included soils from undisturbed forests and from sites that were deforested between 100 and 5 years ago and used for soybean or sugar cane cultivation. The changes in community structure were evaluated by 454 GS FLX high throughput sequencing of the 16S rRNA gene.

Biome: root:Environmental:Terrestrial:Soil
Evaluation of molecular techniques in characterization of deep terrestrial biosphere

Depending to the methods used for characterization of uncultured microbial communities from environmental samples, the results may differ profoundly. Here we have employed three different molecular community screening tools (DGGE, cloning, NGS) and compared their performance for revealing the microbial community profiles in groundwater samples. DGGE is a quick method for community profiling, but may leave many of the microbial groups present undetected. Cloning libraries generally perform better than DGGE, but is labor-intensive and cost ineffective, and may also suffer from incompatibility between insert and transformation host. The NGS method performed best and gave the most complete picture of the uncultured microbial community, but the drawback of this method is the shortness of the sequence reads obtained. In this paper we discuss the pros and cons of these methosd in environmental microbiology.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Biological rejuvenation of iron oxides in bioturbated marine sediments

This project seeked to understand the distribution of iron-oxidizing Zetaproteobacteria in coastal marine sediments, which could allude to their importance to the Fe cycle in these systems.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
San Diego Seagrass

For a comparative analysis of microbial community structure between sites with and without seagrass in and outside of San Diego Bay.

Biome: root:Host-associated:Plants
PCB-contaminated sediment Genome sequencing

Extracellular organic matter (EOM) from Micrococcus luteus was used to enhance biphenyl biodegradation. The effect of the EOM on the composition of bacterial community was investigated by Illumina high-throughput sequencing.

Biome: root:Environmental:Aquatic:Marine:Sediment
L''Atalante sediment - Extracellular Metagenome

SSU 16S pyrosequencing project of the extracellular DNA metagenome of a DHAB sediment (L''Atalante) from the Eastern Mediterranean.

Biome: root:Environmental:Aquatic:Marine:Sediment
Plastisphere Targeted Locus (Loci)

Plastic marine debris is a recent introduction to marine ecosystems resulting from the widespread use of polymers in consumer goods after World War II. The current global annual production of plastic is 245 million tonnes or 35 kg of plastic for each of the 7 billion humans on the planet, rivaling the combined biomass of all humans. Drifter buoys and physical oceanographic models demonstrate that surface particles passively migrate from the coastline to the central gyres in less than 60 days, illustrating how quickly human-generated debris can impact the ‘pristine’ gyre interiors, more than 1000 km from land. Plastic debris has been implicated as a vector for transportation of harmful algal species and persistent organic pollutants, and provides a substrate for microbes that moves between environments and lasts much longer than most natural floating substrates. Despite increases in plastic production no significant trend in plastic accumulation has been observed since 1985. Physical shearing and photodegradation are known mechanisms of plastic degradation, but microbial degradation has also been implicated. Unpublished data from our laboratories employing pyrotag amplicon sequencing targeting bacterial and eukaryotic small subunit ribosomal RNA gene sequences, together with Scanning Electron Microscopy (SEM) data are consistent with the notion that plastic debris harbors a unique association of microbes including members capable of degrading plastic. The term ‘Plastisphere’ describes this unique microbial community attached to and surrounding marine plastic debris and distinct from microbes in the surrounding seawater and on natural substrates such as macroalgae. This proposal will: (1) characterize diversity through amplicon sequencing and comparative -omics combined with SEM and confocal microscopy to investigate the microbial composition of the Plastisphere; (2) describe function of the Plastisphere taking a cultivation-independent environmental DNA gene expression approach, as well as a cultivation-based approach to interrogate environmental clones and microbial isolates for the ability to degrade hydrocarbons; and (3) determine key biological factors that control the fate of plastic debris in the upper water column.

Biome: root:Environmental:Aquatic:Marine
EFFECT OF POSTNATAL LOW-DOSE EXPOSURE TO ENVIRONMENTAL CHEMICALS ON THE GUT MICROBIOME IN A RODENT MODEL

Using the Sprague-Dawley rat model, three chemicals that are widely used in personal care products, i.e. diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) and their mixture (MIX), were administered at doses comparable to human exposure from birth through adulthood. The fecal samples were collected at two time points, i.e. postnatal day (PND) 62 (adolescence) and PND 181 (adulthood).  The gut microbiome was profiled by 16S rRNA gene sequencing followed by taxonomic assignment and diversity analysis.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB54966 data set (Papua New Guinean oral metagenomes).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB54966, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Human:Digestive system:Oral
EMG produced TPA metagenomics assembly of PRJNA779415 data set (Vaginal microbiome of reproductive age mother daughter pairs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA779415, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJEB37382 data set (Assessment of different methods for library preparation of human vaginal samples).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37382, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJEB51898 data set (Vaginal metagenome dataset of 47 healthy women).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB51898, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJNA669294 data set (Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA669294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJNA760651 data set (Exploring the possible link between the gut microbiome and fat deposition in pigs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA760651, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA741980 data set (Comparison of viromes and microbiomes of 14 pig fecal samples).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741980, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA793167 data set (Healthy and diarrhea piglets feces microbiota analysis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA793167, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJEB19642 data set (Metagenomic analysis of gut microbiota in sows and piglets (EBI)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19642, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJEB15296 data set (Structure and function of the fecal microbiota in diarrhoeic neonatal piglets).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15296, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA389749 data set (Caecal Metagenome of Pigs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389749, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
EMG produced TPA metagenomics assembly of PRJNA757683 data set (Apical Periodontitis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757683, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA380727 data set (human saliva metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA380727, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA470402 data set (human saliva metagenome Raw reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA470402, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA791464 data set (Oral saliva microorganisms in 3-year-old children with different caries risk).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA791464, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJDB10606 data set (Shotgun metagenome sequencing of saliva microbiome of MRONJ patients using HiSeq).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB10606, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA762218 data set (Salivary Microbiome in Adenoid Cystic Carcinoma).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA762218, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
18S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2018

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2018 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).

Biome: root:Environmental:Aquatic:Marine
18S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2019

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2019 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).

Biome: root:Environmental:Aquatic:Marine
Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

Analysis of 18S DNA in Tara Oceans Polar Circle Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The DNA was extracted and amplified by PCR.

Biome: root:Environmental:Aquatic:Marine
16S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2018

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2018 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).

Biome: root:Environmental:Aquatic:Marine