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MGYS00006667
|
EMG produced TPA metagenomics assembly of PRJNA434147 data set (Delta Smelt gut content study).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA434147, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.
|
root:Host-associated:Fish:Digestive system
|
MGYS00006664
|
EMG produced TPA metagenomics assembly of PRJEB30661 data set (TO INVESTIGATE THE MICROBIAL COMMUNITY ASSOCIATED WITH FISH GUT).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30661, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.
|
root:Host-associated:Fish:Digestive system
|
MGYS00006665
|
EMG produced TPA metagenomics assembly of PRJNA433811 data set (shotgun metagenome sequencing salmo salar gut microbiota).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA433811, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.
|
root:Host-associated:Fish:Digestive system
|
MGYS00006663
|
EMG produced TPA metagenomics assembly of PRJNA506751 data set (Puffer fish gut Metagenome).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA506751, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.
|
root:Host-associated:Fish:Digestive system
|
MGYS00002675
|
EMG produced TPA metagenomics assembly of the Oral microbiome Metagenome (human oral metagenome) data set.
|
The human oral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA255922. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.
|
root:Host-associated:Human:Digestive system:Oral
|
MGYS00006028
|
Bio-GO-SHIP: Global marine 'omics studies of repeat hydrography transects
|
The Global Ocean Shipboard Hydrographic Investigations Program (GO-SHIP) is a ship-based global survey of ocean hydrographic sections, which are repeatedly measured on a decadal time scale. The program covers a suite of physical (light, heat, currents, water column structure, etc.) and chemical (nutrients, oxygen, dissolved organic and inorganic carbon, pH, etc.) state variables over the full ocean water column, and in areas of the ocean inaccessible to other platforms. The principal scientific objectives for GO-SHIP are: (1) understanding and documenting the large-scale ocean water property distributions, their changes, and drivers of those changes, and (2) addressing questions of how a future ocean will increase in dissolved inorganic carbon, become more acidified and more stratified, and experience changes in circulation and ventilation processes due to global warming and altered water cycle.The vision of the biological GO-SHIP initiative, or "Bio-GO-SHIP," is to develop a deep understanding of the link between the physio-chemical environment and global ocean plankton diversity, abundance, and biogeochemical roles in the context of a changing ocean. This will be achieved through systematic, high-quality, and calibrated sampling of marine 'omics products.In this BioProject, we aim to provide a singular resource for Bio-GO-SHIP 'omics datasets. We also provide appropriate metadata such that the 'omics data may be linked to the broad range of state variables measured by GO-SHIP and associated oceanographic transects.
|
root:Environmental:Aquatic:Marine
|
MGYS00005851
|
metabarcoding of eDNAbyss sediment samples
|
Sediments were collected using multicore sampler, or simple cores when a submarine or a remote operated vehicle (ROV) were present. The cores were collected and sliced according to sediment depth and using a standardized scheme. Slices were preserved and treated individually. When hard substrate was collected, the gear ELFES designed on purpose to scratch and collect the surface of substrate, or bulk samples were retained after sieving communities. Nucleic acids (DNA or RNA) were extracted and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00006281
|
Metagenomes from an Argentine salt flat
|
Analysis of assembled metagenomes from an Argentine salt flat
|
root:Environmental:Terrestrial:Soil
|
MGYS00006069
|
EMG produced TPA metagenomics assembly of PRJEB11419 data set (American Gut Project).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human.
|
root:Host-associated:Human
|
MGYS00006006
|
Extensive microbial novelty in the Hadza and Nepali gut microbiome reveals how lifestyle impacts composition and function
|
The gut microbiome has been identified as a key to immune and metabolic health, especially in industrialized populations. Non-industrialized individuals harbor more diverse microbiomes and distinct bacterial lineages, but systemic under-sampling has hindered insight into the extent and functional consequences of these differences. Here, we performed ultra-deep metagenomic sequencing and laboratory strain isolation on fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophage, and eukaryotes, and find that 43% are novel upon aggregating with existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, and high-resolution strain tracking reveal dynamics in the hunter-gatherer gut microbiome that are distinct from industrialized populations. Industrialized versus Hadza gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. We use phylogenomics to reveal that global spread of the spirochaete Treponema succinifaciens parallels historic human migration prior to its extinction in industrialized populations. When combined with a detailed definition of gut-resident strains that are vanishing in industrialized populations, our data demonstrate extensive perturbation in many facets of the gut microbiome brought on by the industrialized lifestyle.
|
root:Host-associated:Human:Digestive system
|
MGYS00002061
|
EMG produced TPA metagenomics assembly of the Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn''s disease (human gut metagenome) data set
|
The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA321058. This project includes samples from the following biomes : Human gut.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000633
|
Microbial composition of samples from infant gut
|
The microbial composition of the gut likely contributes to a wide-range of health and disease states including intestinal inflammation, atopic disease, and possibly diseases of adulthood, such as heart disease and obesity. The early establishment of the gut microflora is suspected to have a particularly profound impact protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. In contrast to the large-scale efforts of the Human Microbiome Project to characterize the microbial flora of healthy adults, relatively little has been accomplished to characterize the early establishment of the microbiota in infants. The administration of antibiotics to infants has the capacity to profoundly affect the early acquisition, establishment, and natural maturation of commensal microflora. Prematurity is another major factor that is thought to influence 'normal' gut microbial composition in early life. A high number of pre-term infants receive antibiotic therapy prophylactically; the immediate and long-term effects of antibiotic treatment on infant and later health outcomes are unknown. We hypothesize that gestational age influences the ability to support 'normal' gut microbiota, and that antibiotic administration in the first few weeks of life can alter or delay the development of a 'normal' microbiota and may lead to adverse health outcomes. If we hope to promote the healthy establishment of early gut colonization and thereby improve health outcomes, we need to establish what 'normal' colonization looks like across gestational ages and apply this knowledge as a benchmark to understand the impact of antibiotic treatment in early postnatal life. In this project, we propose to examine the microbiome in four cohorts ranging from extremely preterm to term, with birth weights appropriate for gestational age: Group 1) 23 to 27 weeks and extremely low birth weight [ELBW, <1000 grams]; Group 2) 28 to 32 weeks and very low birth weight [VLBW, >1000 to <1500 grams]; Group 3) 33 to 36 weeks and low birth weight [LBW, >1500 to <2500 grams]; and Group 4) term (37 to 42 weeks) and normal [>2500 to <4000 gram] birth weight. The infant gut microbiome will be assessed longitudinally in study infants from the first postnatal week to 18 months of age, and will include untreated and antibiotic-treated infants.
|
root:Host-associated:Human:Digestive system:Large intestine
|
MGYS00002529
|
Dark ocean microbial diversity
|
The goal of the study is to assess the diversity of bacteria and archaea in the water masses of the open ocean.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00001036
|
16S rRNA gene sequences from temperate soils Targeted Locus (Loci)
|
Both climate and pH are key in determining soil archaeal community structure and diversity
|
root:Environmental:Terrestrial:Soil
|
MGYS00004597
|
Peru margin subsurface
|
Investigation of the microbial diversity in subsurface sediments of Peru margin
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00002238
|
Oral microbial changes in ASD children
|
This project depicts the characteristics of oral microbiome in autistic children.
|
root:Host-associated:Human:Digestive system:Oral
|
MGYS00000716
|
structural analysis of microbial community for feild soil and compost made from coffee lees
|
Our final end is to change organic agriculture to matter production system based on scientific basis by stationary measurement of soil microbial community.This year,We analyze bacteria and fungi community at feild soil fertilized by compost made from coffee lees.We also analyze compost made from coffee lees.
|
root:Environmental:Terrestrial:Soil
|
MGYS00001656
|
Universal metabarcoding of pico- mesoplankton reveals seasonal dynamics and a bacterial bloom
|
Most studies of biodiversity focus on either macroscopic or microbial communities, with little or no simultaneous study of eukaryotes and prokaryotes. We tested whether a universal metabarcoding approach could be used to study the total diversity and temporal dynamics of aquatic pico- to mesoplankton communities in a shallow temperate lake. The approach revealed significant changes in the relative abundance of eukaryotic and prokaryotic plankton communities over a period of three months. These patterns, based on sequencing reads, fit with counts using traditional methods. We also witnessed the bloom of a conditionally rare bacterial taxon belonging to Arcicella, a genus that has been largely overlooked in freshwaters. Our data demonstrate the potential of universal metabarcoding as a complement to traditional studies of plankton communities, and for long-term monitoring across a broad range of organisms.
|
root:Environmental:Aquatic:Freshwater:Lake
|
MGYS00002810
|
peptide incubation in GOM C6 seawater bacteria Metagenome
|
Study bacteria community changes in the peptide decomposition in different seawater
|
root:Environmental:Aquatic:Marine
|
MGYS00002567
|
Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea
|
The Red Sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north to south axis. It is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. In this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16S rRNA genes of bacteria in surface water samples collected from the northeastern half of this water body. A combined total of 1,855 operational taxonomic units (OTUs) were recovered as free-living and particle-attached bacterioplankton. Here, a few major OTUs affiliated with Cyanobacteria and Proteobacteria accounted for ~93% of all sequences whereas a tail of “rare” OTUs represented most of the diversity. OTUs allied to Surface 1a/b SAR11 clades and Prochlorococcus related to the high light-adapted (HL2) ecotype were the most widespread and predominant sequence types. Interestingly, the frequency of taxa that are typically found in the upper mesopelagic zone was significantly elevated in the northern transects compared to those in the central, presumably as a direct effect of deep convective mixing in the Gulf of Aqaba and waters exchange with the northern Red. Although temperature was the best predictor of species richness across all major lineages, both spatial and environmental distances correlated strongly with genetic distances. Our results suggest that the bacterial diversity of the Red Sea is as high as in other tropical seas and provide evidence for fundamental differences in the biogeography of pelagic communities between the northern and central regions.
|
root:Environmental:Aquatic:Marine:Pelagic
|
MGYS00000710
|
Alwernia Metagenome
|
Pyrosequencing of V3-V4 16S rRNA gene fragments amplified from metagenomic DNA isolated from heavy metals-contaminated soils collected near chromium green-producing facility in Alwernia, Poland. Two samples of soils from Alwernia, Poland, collected at the vicinity of chromium green-producing factory.
|
root:Environmental:Terrestrial:Soil
|
MGYS00003004
|
Submarine Ligurian Canyons Water Prokaryotic and Protist Communities
|
Planktonic prokaryote communities in a submarine canyon system in the Ligurian Sea (NW Mediterranean)
|
root:Environmental:Aquatic:Marine
|
MGYS00004596
|
Marine sediment in Arctic Raw sequence reads
|
This study assessed the diversity and distribution of fungal communities associated with marine sediments in Arctic.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00002552
|
North Pacific Subtropical Gyre Microbial Community
|
16S amplicon libraries were collected as a portion of the Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns, also known as Prochlorococcus of Warming Ocean Waters (POWOW) Cruise series. The samples were collected in January 2013 (KM1301) and July 2013 (KM1312) in the Eastern North Pacific Ocean. The goal of this project was to characterize ecosystem scale changes associated with shifts in temperature.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00003089
|
Marine metagenome ICM_JRV
|
Microeukaryote diversity in the Gulf of Maine: Under-explored microbial diversity in a well-studied coastal marine ecosystem.
|
root:Environmental:Aquatic:Marine:Coastal
|
MGYS00003115
|
Diversity and structure of benthic bacterial community from South-Eastern Pacific Ocean, Targeted Locus (Loci)
|
Assessing diversity and structure of sediment microbial communities under the influence of the oxygen minimum zone of an Eastern Boundary Current ecosystem: the Humboldt marine ecosystem
|
root:Environmental:Aquatic:Marine:Oceanic:Benthic
|
MGYS00006562
|
EMG produced TPA metagenomics assembly of PRJEB54673 data set (Paediatric Oral Microbiome).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB54673, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.
|
root:Host-associated:Human:Digestive system:Oral
|
MGYS00006660
|
Picoplankton 16S rRNA gene sequences (DNA and RNA) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition
|
The study here includes 182 samples (91 DNA and 91 RNA) of the 16S from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.
|
root:Environmental:Aquatic:Marine
|
MGYS00006659
|
Amplicon 18S rRNA Illumina TAGs from Malaspina Bathypelagic samples
|
Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the 18S rRNA gene
using primers XXXXX and XXXX. Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
eukaryotic diversity from bathypelagic samples and describe its
biogeography.
|
root:Environmental:Aquatic:Marine
|
MGYS00006658
|
Amplicon 16S rRNA Illumina TAGs from Malaspina Bathypelagic samples
|
Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the V4 and V5 hypervariable regions of the 16S rRNA gene
using primers 515F-Y (5’-GTGYCAGCMGCCGCGGTAA-3’) and 926R
(5′-CCGYCAATTYMTTTRAGTTT-3′). Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
bacterial diversity from bathypelagic samples and describe its
biogeography.
|
root:Environmental:Aquatic:Marine
|
MGYS00002392
|
Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.
|
Analysis of 18S DNA in Tara Oceans 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.
|
root:Environmental:Aquatic:Marine
|
MGYS00004011
|
Microbial communities of methane seeps in shallow, porous sands off Elba
|
The methane cold seeps near Pomonte (Elba) are unique ecosystems situated in very shallow and porous coastal sands. We investigated the influence on hydrodynamics on microbial community structure and function. Understanding these ecosystems is important to estimate their role in carbon cycling and their emission of methane to the atmosphere.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00000988
|
Global fungal diversity
|
This is a global dataset of unprecedented scope to disentangle the relative roles of climatic, edaphic, floristic, and spatial variables governing global-scale patterns of soil fungal diversity. We also address key macro-ecological phenomena such as latitudinal gradients of diversity and Rapoport’s rule (expansion of species’ latitudinal range with increasing latitude) as well as cross-biome and cross-continental biogeographic relationships in multiple phylogenetic and functional groups of fungi.
|
root:Environmental:Terrestrial:Soil
|
MGYS00001509
|
Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea
|
Microscopic plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. Next Generation Sequencing (NGS) of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but also novel groups to the Baltic were observed, such as relatives to the coccolithophore Emiliana huxleyi in the northern Baltic Sea. The deep sequencing also enabled accurate enumeration of highly resolved (> 99% identity) operational taxonomic units, which revealed contrasting distribution profiles among closely related populations, reflecting niche partitioning into ecotypes. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.
|
root:Environmental:Aquatic:Marine
|
MGYS00004228
|
marine sediment metagenome Genome sequencing and assembly
|
To share species we detected in the South China Sea
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00003016
|
Distinctive community structure and high diversity in particle-associated prokaryotes in tropical and subtropical Pacific Ocean surface seawater
|
The specific aim of this project was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the tropical and subtropical Pacific Ocean.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00003989
|
Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the Western Antarctic Peninsula
|
The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and materials flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters compared to lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We characterized bacterial, archaeal, and eukaryotic community diversity and composition from two depths (near surface and below the euphotic zone) at four sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern ones but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents but did vary with depth. Archaea were virtually absent in summer surface waters but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of “winter water” below the euphotic zone. Inter-domain heterotroph-phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in microbial communities may be assessed.
|
root:Environmental:Aquatic:Marine
|
MGYS00004213
|
Abalone seed nursing ecosystem Metagenome
|
In this study, using abalone seed nursing pond as a model system, we separately collected the time-series samples of three
|
root:Environmental:Aquatic:Marine
|
MGYS00001536
|
Habitat diversity and ecosystem multifunctionality - the importance of direct and indirect effects
|
Ecosystems worldwide are facing habitat homogenization due to human activities. While it is commonly proposed that such homogenization can have negative repercussions for ecosystem functioning, this remains to be explicitly studied. Here, we expand on the framework for the functional consequences of biodiversity loss, by scaling up from the level of species to the level of entire habitats. Just as species diversity generally begets ecosystem functioning through positive interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and by the exchange of material and energy. We show that experimental ecosystems constituted by a diversity of habitats have higher levels of multiple ecosystem functions compared to ecosystems with low habitat diversity. The effect of habitat diversity on multifunctionality varied with season; it was direct in summer, indirect via changes in species diversity in autumn, whereas there was no effect in spring. We propose that jointly considering habitat and species diversity will prove valuable for both research and environmental management.
|
root:Environmental:Aquatic:Marine:Coastal:Sediment
|
MGYS00000818
|
Hydrocarbon polluted soil Targeted Locus (Loci)
|
The aim of the study was to determine the microbial diversity in soil from a landfarming site amended with hydrocarbon contaminants. To determine the microbial diversity amplicon pyrosequencing was used of different regions of the 16S rRNA gene.
|
root:Environmental:Terrestrial:Soil
|
MGYS00004112
|
Marine metagenome ICM_CNE
|
Temporal Dynamics of Coastal Bacterioplankton
|
root:Environmental:Aquatic:Marine
|
MGYS00001476
|
Comparison of limnic and marine particle-associated microbial communities
|
Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in-situ hybridization with rRNA-targeted probes and tag pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles, defined operationally by a diameter of >5 and >10 μm, respectively. Samples were obtained from Lake Stechlin and Grosse Fuchskuhle, the Adriatic Sea and the North Sea. On average, particle abundance was higher in limnic (1×107 L-1) than in marine systems. Whereas limnic particles were smaller in size (average areas of 471 vs. 2050 μm2), they were more densely colonized compared to marine ones (average bacterial densities of 7.3 vs. 3.6 cells per 100 μm2). Therefore, particle-associated (PA) bacteria accounted on average for a larger fraction of total bacteria in limnic (15%) than in marine environments (4%). Unlike previously suggested limnic PA bacteria harbored beyond Alphaproteobacteria and Betaproteobacteria sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. PA bacteria were in 2/3 of the cases more diverse than free-living (FL) bacteria. Accordingly, we propose a new index to characterize particle colonization based on the PA/FL Chao1 diversity index ratio. Large heterogeneities in individual particle colonization could be shown. However, high-throughput sequencing revealed significant overlap between PA and FL communities and thus highlights an underestimated connectivity between these fractions. Overall, despite seemingly similar ecological niches our study found large differences between limnic and marine PA communities.
|
root:Environmental:Aquatic:Marine
|
MGYS00002546
|
Pelagic Gulf of Mexico Targeted loci environmental
|
Methane and microbial dynamics in the Gulf of Mexico water column
|
root:Environmental:Aquatic:Marine:Pelagic
|
MGYS00002584
|
Marine Sediment from the Berkeley Bay Targeted Locus (Loci)
|
Community analysis (16S) of a marine samples enriched with perchlorate
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00001658
|
Vertical organization of freshwater sediment microbial communities: implications for microbial activities and burial processes
|
Microbial activity in lake sediments plays a key role in the cycling of nutrients and organic matter that continuously sink from water columns. As organic matter accumulates at the sediment surface, upper sediment layers become buried, resulting in a decrease in microbial activity and cell turnover rate with increasing depth. To better understand the structure of freshwater sediment communities and how the burial processes influence it, we quantified the distribution of a broad range of environmental parameters and the community structure of microbial archaea, bacteria, and eukaryotes in the sediments of a clear, temperate lake. Our findings suggest that the two uppermost horizons of the sediment community, which cover approximately the last 70 years, are characterized by a high taxa replacement influenced by “present” environmental parameters. Richness effects became increasingly important in the lowest studied horizon (14-30 cm, age 70-150 a) and could be readily explained by conservative “past” environmental parameters. The lowest horizon is also characterized by a switch in dominance toward archaea, as has been found in marine sediments. Our pioneering study shows that the freshwater lake's community structure, taxa, and vertical arrangement share many features previously observed for marine sediments.
|
root:Environmental:Aquatic:Freshwater:Lake
|
MGYS00002775
|
Amundsen Gulf Overwintering Eukaryote Community
|
Year-long time series of eukaryote community in Amundsen Gulf, Arctic Ocean
|
root:Environmental:Aquatic:Marine
|
MGYS00004496
|
Enrichment of abundant sedimentary Bathyarchaeota demonstrating organoautotrophic metabolic capabilities
|
metabolic capabilities of Bathyarchaeota
|
root:Environmental:Aquatic:Marine
|
MGYS00004176
|
Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels.
|
Methods evaluation for sample collection and nucleic acid extraction from multiple trophic levels simultaneously (i.e. bacteria, phytoplankton, zooplankton, vertebrates). Specifically, filter types and DNA extraction kits were evaluated for producing Illumina MiSeq reads for 12S, 16S and 18S amplicons from water samples collected in Monterey Bay California.
|
root:Environmental:Aquatic:Marine
|
MGYS00003006
|
A study on microbial functional groups producing a climate related gas in the ocean
|
Dimethylsulfoniopropionate (DMSP), the precursor of dimethyl sulfide (DMS), is mainly produced by marine phytoplankton, and is one of the most important sulfur and carbon sources for marine bacteria. To reveal the abundance and distribution of bacterial DMSP-degrading genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we performed deep sequencing of environmental DNA obtained from DMS hotspot samples in the Pacific Ocean.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00004160
|
uncultured bacterium Targeted Locus (Loci)
|
The bacterial community at 2,000-m depth was studied over one-year survey in 2011 at the ANTARES site (Northwestern Mediterranean Sea). The most active member were analysed in October and May through ribosomal diversity.
|
root:Environmental:Aquatic:Marine
|
MGYS00001224
|
TRIF signalling drives homeostatic intestinal epithelial antimicrobial peptide expression
|
Recent results indicate a significant contribution of innate immune signalling to maintain mucosal homeostasis but the precise underlying signal transduction pathways are ill-defined. By comparative analysis of intestinal epithelial cells isolated from conventionally raised and germ-free mice as well as animals deficient in the adaptor molecules MyD88 and TRIF, the Toll-like receptors (TLR) 3 and 4, as well as the type I and III interferon (IFN) receptors, we demonstrate significant TLR-mediated signalling under homeostatic conditions. Surprisingly, homeostatic expression of Reg3γ and Paneth cell enteric antimicrobial peptides critically relied on TRIF and in part TLR3 but was independent of IFN receptor signalling. Reduced antimicrobial peptide expression was associated with signicantly lower numbers of Paneth cells and a reduced Paneth cell maturation and differentiation factor expression in TRIF mutant compared to wildtype epithelium. This phenotype was not transferred to TRIF sufficient germ-free animals during cohousing. Low antimicrobial peptide expression in TRIF deficient mice caused reduced immediate killing of orally administered bacteria but was not associated with significant alterations in the overall composition of the enteric microbiota. The phenotype was rapidly restored in a TRIF-independent fashion after transient epithelial damage. Our results identify TRIF signalling as truly homeostatic pathway to maintain intestinal epithelial barrier function revealing fundamental differences in the innate immune signalling between mucosal homeostasis and tissue repair.
|
root:Host-associated:Mammals:Digestive system:Large intestine
|
MGYS00002510
|
Hatteras return: Oligotrich and choreotrich ciliates diversity at small scales
|
Hatteras return: diversity and community composition of Oligotrich and choreotrich ciliates at small scales (1-3 km) off the New England coast
|
root:Environmental:Aquatic:Marine
|
MGYS00004565
|
Coral metagenome ICM_CCB
|
Exploring the microbial diversity and testing co-evolutionary hypotheses in Caribbean coral species using a 454-tag sequencing approach.
|
root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
|
MGYS00005716
|
Metabarcoding of eDNAbyss water samples
|
Water from different depths was prefiltered in situ using Salsa pump or collected in CTD bottled before being filtered onboard to retain small cell sizes or nucleic acids (DNA/RNA). Nucleic acids were extracted from filters and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).
|
root:Environmental:Aquatic:Marine
|
MGYS00004038
|
Uncultured Microbial Consortia in Industrialized Sites on Egypt''s Red Sea Coast Targeted loci environmental
|
Egypt''s Red Sea Coast: Phylogenetic Analysis of Uncultured Microbial Consortia in Industrialized Sites
|
root:Environmental:Aquatic:Marine:Coastal:Sediment
|
MGYS00004190
|
Oxic sediment - Microbial Metagenome
|
SSU 16S pyrosequencing project of the microbial metagenome of an oxic deep-sea sediment from the Eastern Mediterranean.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00004320
|
Sediment bacterial 16S in Hachiro polder.
|
Sediment bacterial 16S ribosomal RNA gene from surface to depth 30 m at hot spots of high concentration phosphate water springs in Hachiro polder.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00005115
|
Microbes in drinking water and biofilms (18S rDNA amplicon study)
|
18S rDNA amplicon study of bulk water and shower hose biofilm samples. Cold water samples were collected from the water outlet of a drinking water treatment plant and from the water inlet of two neighboring buildings, warm water samples (ca 37 degrees C) were taken from showers within the two buildings: one building with a copper-silver-ionization-system to disinfect the water, the other building without such a system. Biofilms were taken from shower hoses within the two buildings. For further experimental details see: Stüken et al. 2018. Environ Sci Technol.;52(6):3354-3364. doi: 10.1021/acs.est.7b0596318S rDNA amplicons were generated with forward primer 1391F (GTA CAC ACC GCC CGTC) and reverse primer 1510R (CCT TCY GCA GGT TCA CCT AC). AdapterRemoval ver 2.3.0 and cutadapt vers. 1.18. were used to prepare samples for sequence submission (removal of remaining Illumina adapters, demultiplexing, removal of heterogeneity spacers, primers, low quality bases and sequences < 50 bp lengths).
|
root:Environmental:Aquatic:Freshwater
|
MGYS00002605
|
Mariana and Kermadec Trench sediment 16S rRNA gene sequencing
|
This project studies the microbial communities within the Mariana and Kermadec trenches as a function of trench, sediment, and water depth using 16S rRNA gene sequencing.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00003015
|
Protists tag sequencing of 18S rRNA HV 9
|
First comprehensive description of protist community diversity in meso- bathypelagic regions of the Ross Sea (Antarctica)
|
root:Environmental:Aquatic:Marine
|
MGYS00003118
|
Diversity and abundance of Bathyarchaeota (MCG) in South China Sea sediments and the implication of its ecological roles
|
understand the niche separation and adaptation of different bathyarchaeotal subgroups.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00002818
|
Seawater Targeted Locus (Loci)
|
We applied culture-independent, high throughput pyrosequencing to characterize the microbial communities associated with coastal seawater adjacent to populated Broward County, FL. These waters flow over adjacent coral reefs, which help compose the Florida reef tract, and also close to recreational beaches. In partnership with the NOAA FACE program to survey water quality, 38 total nearshore seawater samples were collected and characterized for bacterial populations from 6 distinct coastal locales - the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and associated reef waters over the course of one year. More than 227,000 quality checked 16S rRNA V4 amplicon sequences were generated for longitudinal taxonomic profiles of marine bacteria and archaea. From these sequences, 4447 unique OTUs were found and there was a mean OTU count of 5986.816 across all site. Sequences were found to vary significantly due to seasonal effects and by site, but depth showed no significant correlation. Abundant microbial taxa across all samples included Synechococcus, Pelagibacteraceae, Bacteroidetes, and various Proteobacteria. Inlet-based communities significantly differed from outfall and reef communities, with a relative increase in Rhodobacteraceae and Cryomorphaceae, and depletion of SAR406 sequences. Unifrac analysis confirmed significant differences in the inlet populations relative to reef and outfall microbial communities. However, based on alpha diversity measurements, the outfalls sites showed the most diversity with the occurrence of Thiotrichales, Alteromonadales, and the archaean Thermoplasmata. This study also found increased levels of Firmicutes, Chloroflexi, and sludge associated bacterial OTUs such as SBR1093 at the outfall and reef sites.
|
root:Environmental:Aquatic:Marine:Coastal
|
MGYS00001560
|
THERMOPHILIC HYDROGEN PRODUCTION IN ACIDOGENIC PACKED BED REACTOR (APBR) FED WITH SUGARCANE VINASSE: PERFORMANCE DURING LONG-TERM OPERATION
|
This study aimed to evaluate the long-term operation of an up-flow anaerobic packed bed reactor (APBR) filled with low-density of polyethylene (LDP) and applied to thermophilic hydrogen production using sugarcane vinasse as substrate. The APBR was operated at organic loading rate (OLR) of 84.2 kg-COD.m-3.d-1, value determined in earlier study. The maximum values of hydrogen production and yield were 5,252.6 mL-H2.d-1 and 3.7 mol-H2.mol-1total carbohydrates, respectively. However, as the OLR applied was constant, the values of specific organic load rate (sOLR) decreased throughout operation from values from 1.38 to 0.72 g-Total carbohydrates.g-VS-1.h-1, thus, interfering negatively on hydrogen production. sOLR values around 1.22 g-Total carbohydrates.g-VS-1.h-1 indicated optimal conditions for hydrogen production. The microbial community was study by 454-pyrosequencing analysis. Organisms belonging to genera Caloramotor, Clostridium, Thermoanaerobacterium, Thermohydrogenium, Caldanaerobius and Megasphaera were detected in samples taken from reactor at days 30 and 60 of operation, suggesting a role in the hydrogen production.
|
root:Engineered:Bioreactor:Continuous culture
|
MGYS00002702
|
Metagenomic sequence from soil bacteria
|
This data contains metagenomic 16S rDNA sequence of soil bacteria. 16S rDNA sequence was amplified according to illumina protocol. The aim of this project is to analyze bacterial flora.
|
root:Environmental:Terrestrial:Soil
|
MGYS00004050
|
Prince Edward Island marine metgenome Raw sequence reads
|
Marine and terrestrial ecosystems of the Prince Edward islands (PEIs) are reciprocally connected and any changes in the community composition of one ecosystem will directly influence the other. In the present study, we investigated the pelagic marine microbial community structure (Bacteria, Phytoplankton and Archaea) and dynamics in the PEIs inshore coastline by high throughput sequencing technologies (pyrosequencing). The study revealed temporal shifts in the bacterial community composition during the period of 2012 to 2015.
|
root:Environmental:Aquatic:Marine:Pelagic
|
MGYS00002122
|
PETROMAKS E#12
|
The aim of the study was to asses biodegradation efficiency of dispersed oil of two Norwegian seawater sources. One source of seawater used in the study was local (Trondheimsfjord), while the other source was Svalbard seawater (Van Mijenfjord). The biodegradation experiment was conducted at 0-2C over the period of 64 days.
|
root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
|
MGYS00004276
|
Environmental Foraminifera Raw sequence reads
|
Paleotsunami deposits are primary source of information on past big tsunami events and thereby are critical for earthquake and tsunami hazard assessment. They usually form sandy layers preserved in coastal sediments that may contain indicators of marine origin such as foraminifera microfossils and the geochemical signal of saltwater. Environmental DNA sequencing of marine species targets in a series of up to about 2000 years old sandy paleotsunami deposits is promising to detect ancient tsunami events even in the absence of microfossil and sedimentological evidence.The DNA content of 10 environmental coastal sediment samples was extacted from paleotsunami deposit and peat layers of a core and additional peat and beach sand surface samples taken from a wetland on eastern Hokkaido Island (Japan) facing the Kuril Trench subduction zone generating frequent large tsunamigenic earthquakes. The 37f hypervariable region of the foraminiferal SSU rDNA was PCR amplified and PCR products were pooled in one library for Illumiona MiSeq sequence and diversity analyses.
|
root:Environmental:Aquatic:Marine:Coastal:Sediment
|
MGYS00002583
|
Microbial community in marine sediments
|
16S rRNA amplicon sequencing on the Eastern South Pacific Ocean sediments
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00004129
|
Microbial diversity in shallow water hydrothermal sediments of Gueishan Island, Taiwan
|
To better understand the benthic ecosystem near vents off Gueishan Island, we examined the microbial communities across the three domains of life in sediments collected at different distances from the vent area using small-subunit ribosomal RNA pyrosequencing.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00004594
|
Arctic water Metagenome
|
Diversity and distribution of aquatic fungal communities in the Ny-Ålesund Region, Svalbard, High Arctic
|
root:Environmental:Aquatic:Marine
|
MGYS00003086
|
Marine metagenome ICM_VAG
|
Community Structure Of Benthic Bacteria In Upwelling Ecosystem.
|
root:Environmental:Aquatic:Marine:Oceanic:Benthic
|
MGYS00005267
|
characterizing the gut communitties of twins discordant for obesity in gnotobiotic mice
|
International efforts to characterize the human microbiome in health and disease are producing massive amounts of data about organismal and gene content in our body habitat -associated microbial communities. A challenge is to complement these efforts with a preclinical research pipeline that tests the degree to which a person's physiologic or pathological phenotype can be ascribed to their microbiome and that offers an opportunity to evaluate potential strategies for microbiome-based therapeutics. Here we illustrate such a pre-clinical pipeline by transplanting previously frozen, uncultured fecal microbiota samples from four sets of adult female mono- and dizygotic twins discordant for obesity into groups of adult germ-free C57Bl/6J mice fed a low-fat, plant polysaccharide-rich diet. Capture of a human donor's microbiota in recipient mice is highly reproducible within and between experiments. The increased adiposity phenotype of obese co-twins is transmissible not only with the intact uncultured fecal communities, but with bacterial culture collections generated from these fecal samples. Co-housing mice five days after they received transplants of culture collections from the obese or lean member of a discordant twin pair ameliorated the increased adiposity phenotype that normally develops in recipients of the obese donor's culture collection, while having no effect on the adiposity phenotype of recipients of the lean co-twin's culture collection. These results correlate with taxonomic and metabolic changes in co-housed mice harboring the obese co-twin's culture collection. Our results demonstrate a way to perform pre-clinical studies of microbiome-associated human phenotypes, including methods for identifying, producing and testing candidate probiotic species as therapeutic or preventative agents.
|
root:Host-associated:Mammals:Digestive system:Fecal
|
MGYS00006651
|
EMG produced TPA metagenomics assembly of PRJEB52139 data set (HoloFood Chicken Caecum Metatranscriptome).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52139, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.
|
root:Host-associated:Birds:Digestive system:Ceca
|
MGYS00005155
|
Bacerial and archaeal diversity in Central Park
|
Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of aboveground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here we present an assessment of soil biodiversity and biogeographical patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system can harbor large amounts of undescribed soil biodiversity. Despite high variability across the Park, belowground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographical patterns. Further, Central Park soils harbored nearly as many distinct soil microbial taxa and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents. Our data therefore suggest that the dominant factors controlling soil biodiversity differ markedly to those controlling aboveground plant and animal diversity.
|
root:Environmental:Terrestrial:Soil
|
MGYS00005045
|
Exploring Fronts With Multiple Robots – Schmidt Ocean Institute Cruise to the Pacific Ocean in 2018
|
Samples were obtained during the Schmidt Ocean Institute cruise "Exploring Fronts With Mutiple Robots" to the Pacific Ocean in 2018 (https://schmidtocean.org/cruise/exploring_fronts_with_multiple_aerial-surface-underwater-vehicles/). Water samples for microplankton analysis were collected using a multi water sampler (rosette) from the research vessel "Falkor" and concentrated on board in a 0.2 μm Sterivex filter. This expedition target the Subtropical Front, located approximately 1,000 nautical miles off the coast of Southern California. The study includes samples from: (i) amplicon sequencing after 18S amplification by PCR using TAReuk454FWD1/ TAReukREV3_modified primer set and (ii) amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Libraries were constructed according to Illumina Library protocol.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00005318
|
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny
|
Scleractinian corals’ microbial symbionts influence host health, yet how these coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that corals exhibit anatomical compartmentalization of the microbiome such that the coral surface mucus layer, tissue, and skeleton microbiomes show distinct modern microbial ecology and evolutionary assembly. In corals, these compartments differ greatly in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflects coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.
|
root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
|
MGYS00005154
|
Human gut microbiome viewed across age and geography
|
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.
|
root:Host-associated:Human:Digestive system:Large intestine
|
MGYS00005092
|
Characterization of bacterial communities in soil under no-tillage practices with contrasting fertilization strategies
|
Long term experiment in Argentina.
|
root:Environmental:Terrestrial:Soil:Agricultural
|
MGYS00000889
|
16S rRNA gene-based analysis of soil prokaryotic communities inhabiting fields of the Mezquital Valley, Mexico
|
Central objective of this study is to analyze the diversity and composition of prokaryotic communities present in fields of the Mezquital Valley, Mexico.
|
root:Environmental:Terrestrial:Soil:Agricultural
|
MGYS00000880
|
Natural saline soil, Sicily (Italy) Targeted Locus (Loci)
|
16S rRNA analysis to inspect distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH
|
root:Environmental:Terrestrial:Soil
|
MGYS00002838
|
Northern Gulf of Mexico Hypoxia can Alter Sediment Communities of Nitrifying Archaea
|
The sediments were obtained from station Z02 located at the 20 m isobath south of Terrebonne Bay in the northern Gulf of Mexico (latitude 28.875oN; longitude 90.428oW). The cores were collected in April and September 2006.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00000814
|
Forest Soil Metagenome - Eucalyptus urograndis and Acacia mangium
|
Forest soil under three different compositions: 1 - Eucalyptus urograndis monoculture 2 - Acacia mangium monoculture 3 - Mixed plantation
|
root:Environmental:Terrestrial:Soil
|
MGYS00004215
|
22V-SMAR-TVG10 Targeted Locus (Loci)
|
Bacterial Diversity of Deep-sea Environment
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00004006
|
Ocean Targeted Locus (Loci)
|
The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and co-variance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. Based on 16S rRNA gene sequencing we identified two new clades of Synechococcus, EPC1 and EPC2, and delineated an interannual pattern in a dynamic transition zone where upwelled and eastern boundary current waters mix. In years when more oligotrophic water intrudes further inshore Prochlorococcus HLI and LLI are more abundant, while under stronger upwelling Synechococcus I and IV dominate. However, contributions of some cyanobacterial clades are proportionally relatively constant, e.g., Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than reported. The phylogenetic precision of our analytical approach and depth of barcoded pyrosequencing also allowed us to detect clades at low abundance in unexpected places. For example, Prochlorococcus at the coast, and sequences related to freshwater Cyanobium spp. in the open ocean, although it remains unclear whether these come from resident or advected cells. Our study enhances understanding of cyanobacterial distributions by applying state-of-the-art phylogenetic analysis tools to an ecologically important eastern boundary system.
|
root:Environmental:Aquatic:Marine
|
MGYS00006551
|
EMG produced TPA metagenomics assembly of PRJEB62473 data set (The INTEGRATE project).
|
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB62473, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00002649
|
ADDOMEx Tier 3 Experiments: Mesocosm Si with Gulf of Mexico coastal waters
|
Here we describe microbial community dynamics in the Mesocosm-Si experiment. Using 16S rRNA gene sequencing of filtered water samples collected every 24 hours from the mesocosm treatments, we characterized community membership and structure to determine how the mesocosm communities responded to a passively dosed (via silicone tubing) water accomdated fraction of oil.
|
root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
|
MGYS00000938
|
Complex Heteropolysaccharide Enriched Soils Targeted Locus (Loci)
|
Stable-isotope-probing of two soils using two complex heteropolysaccharides as a substrate.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000879
|
Otumba arable soil Metagenome
|
Soil microbial biomass has been determined since the mid 1970’s by the chloroform fumigation incubation technique as proposed by Jenkinson and Powlson (1976). The microbial biomass C can be determined by subtracting the CO2 emitted from an unfumigated soil (mineralization of soil organic matter) from that emitted from a chloroform fumigated inoculated soil (mineralization of soil organic matter and killed soil microorganisms) and dividing the difference by a proportionality factor (kC 1⁄4 0.45). The question remained which microorganisms recolonized a fumigated soil. An arable soil was fumigated for one day with ethanol-free chloroform or left unfumigated and incubated aerobically after removal of the chloroform for 10 days. The bacterial population structures were determined in the fumigated and unfumigated soil after 0, 1, 5 and 10 days by means of 454 pyrosequencing of the 16S rRNA gene.
|
root:Environmental:Terrestrial:Soil:Agricultural
|
MGYS00001010
|
Haerbin black soil Genome sequencing
|
Black soil different fertilizer
|
root:Environmental:Terrestrial:Soil
|
MGYS00003931
|
Plasma soil pretreatment trail
|
Plasma is the fourth state of matter and it can be generated by coupling sufficient quantities of energy to a gas to induce ionization. Plasma treatment is known for its antimicrobial properties by generating agents such as reactive oxygen and nitrogen species to kill and reduce proliferation of various microorganisms. Here, we examine an effect of plasma exposure on soil samples. Various exposure times and plasma properties were tested. Microbial communities of soil samples were examined by sequencing ribosomal 16S gene and comparing abundance of different microbial groups in treated and non-treated samples.
|
root:Environmental:Terrestrial:Soil:Agricultural
|
MGYS00002522
|
Standard filtration practices significantly distort planktonic microbial diversity estimates
|
Filtration is the standard method for isolating planktonic microbial biomass for analysis. It is unclear how the taxonomic composition of biomass on a filter changes as a function of filtered water volume, potentially due to filter clogging. Using seawater from a marine oxygen minimum zone, we conducted experiments to quantify the 16S rRNA gene composition of biomass on a prefilter (GF/A, 1.6 um pore size) and a downstream collection filter (Sterivex, 0.2 um) over a range of typical collection volumes, from 50 to 5000 ml. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences affiliated with Vibrionales decreased from ~40-60% of the prefilter datasets at low volumes (50-500 ml) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Taxa shown previously to be associated with marine particles, including diverse members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with filter volume (4 to 27-fold). Metrics of taxon richness (97% sequence clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise serious concerns for studies using filter fractionation to separate biomass for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
|
root:Environmental:Aquatic:Marine
|
MGYS00000652
|
Bacterial diversity in agricultural soils
|
Barcoded amplicon sequencing targeting V4 regions of 16S gene from uncultured soil bacteria.
|
root:Environmental:Terrestrial:Soil
|
MGYS00004566
|
Marine metagenome ICM_BSP
|
Seasonal dynamics of bacterioplankton communities in the Baltic Sea Proper.
|
root:Environmental:Aquatic:Marine
|
MGYS00004567
|
Marine metagenome ICM_ABR
|
Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean.
|
root:Environmental:Aquatic:Marine
|
MGYS00004046
|
Prokaryotic community structure in the deep Southwest Indian Ocean with an emphasis on actinobacteria Targeted Locus (Loci)
|
Knowledge about the biodiversity extent and biogeography of deep-sea microorganisms is far from adequate. Due to its remote location, the related investigations of the Southwest Indian Ocean (SWIR) remaine extremely difficult and the microbial diversity at the SWIR has rarely been studied. Only two studies got limited numbers of 16S rRNA gene sequences, and much more in-depth sequencing efforts to evaluate the abundance and diversity of prokaryotes at the SWIR are still needed. In this study, pyrosequencing was used to investigate the community structure and biogeography of prokaryotes, especially actinobacteria, in the deep SWIR. It also identified the factors in contributing to the distribution of the prokaryotes and actinobacteria, the historical contingencies, contemporary environmental factors, or both? The results would provide further insights on the prokaryotic, especially actinobacterial community structure at the SWIR and help to understand the underling mechanisms of the microbial distribution in the deep ocean. To our knowledge, this is the first report on the biodiversity and biogeography of actinobacteria at the SWIR.
|
root:Environmental:Aquatic:Marine:Oceanic:Sediment
|
MGYS00005171
|
Soil bacterial diversity is associated with human population density in urban greenspaces
|
Urban greenspaces form a vital part of the urban ecosystem and provide an extensive array of ecosystem services, including pollutant degradation, water management, carbon maintenance, and nutrient cycling. However, while the soil microbiota in these ecosystems are essential to these services they remain under-characterized. Here we aimed to determine whether turf grass soil bacterial communities were associated with human population density across a range of greenspaces in parks, streets, and residential areas across a major urban area. Results showed that bacterial diversity was significantly positively correlated with population density within the immediate vicinity of the sampled areas; and species diversity was greater in park and street soils, when compared with residential zones. Population density and greenspace type (park vs street vs residential area) also associated with the composition and structure of the bacterial community. Edaphic properties, including pH, moisture and texture, were also significantly correlated with microbial composition and structure. Co-occurrence network analysis revealed that microbial guilds in urban soils were well connected. Soil moisture and texture together with population density and greenspace type showed strong correlations with several network topological features including assortativity degree, edge density, average path, average betweenness and closeness. These results indicate that changes in urban demographics, as well as the changes in land-use may influence the diversity and structure of urban soil microbial communities. As urbanization is rapidly growing across the planet, understanding the consequences of different urban zoning on soil microbiota represents an unmet need.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000770
|
Colonization patterns of soil microbial communities in the Atacama Desert
|
The Atacama Desert is one of the driest deserts in the world and its soil characterized by extremely low moisture, organic carbon content, and oxidizing conditions has been considered to be at the dry limit for life. We collected soil samples from 3 geographic locations in the hyper-arid zone of the Atacama Desert, and from 3 locations along a North-South transect of increasing rainfall, to identify what factors might shape the diversity of its soil microbiome. Analyses of non-culture based, high throughput DNA sequence data revealed that communities from the 6 geographic locations were structurally and phylogenetically distinct (ANOVA test for observed OTU0.03, p<0.001; UniFrac distances) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes, the phylum that comprises most sporulating bacteria, indicated that most bacteria in the soil were in the form of vegetative cells. No archaea were found in an of the soil samples. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities diversity metrics (least square linear regression for observed OTU0.03 and air RH and soil conductivity, p<0.001; UniFrac PCoA spearman’s correlation for air RH and soil conductivity, p<0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples with increased rates in soils from the southern locations. These findings suggest that over geological time, and due to rare rain events, physicochemical factors potentially played a major role in selecting microorganisms that are most adapted to extreme desiccating conditions.
|
root:Environmental:Terrestrial:Soil:Desert
|
MGYS00004116
|
Archaeal diversity of surface seawater (A3,A5,G3,G5) Targeted Locus (Loci)
|
To investigate the archaeal diversity of sea water from Greatwall cove and Ardley cove, Fildes Peninsula, four surface water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013.
|
root:Environmental:Aquatic:Marine
|
MGYS00001724
|
16S amplicon based soil and leaf microbiome survey in Hungarian vineyards
|
Seven Hungarian wine regions have been sampled for leaf and 20cm deep soil samples from the same plants. All vineyards are of different soil types and grape cultivars. Total DNA has been extracted and 16S amplicon sequencing has been applied to the samples.
|
root:Host-associated:Plants
|
MGYS00002807
|
Southern Ocean
|
Southern Ocean bacterioplankton community
|
root:Environmental:Aquatic:Marine:Oceanic
|
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