SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
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.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
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.

Biome: root:Environmental:Terrestrial:Soil
Marine metagenome ICM_CNE

Temporal Dynamics of Coastal Bacterioplankton

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
Pelagic Gulf of Mexico Targeted loci environmental

Methane and microbial dynamics in the Gulf of Mexico water column

Biome: root:Environmental:Aquatic:Marine:Pelagic
Marine Sediment from the Berkeley Bay Targeted Locus (Loci)

Community analysis (16S) of a marine samples enriched with perchlorate

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Amundsen Gulf Overwintering Eukaryote Community

Year-long time series of eukaryote community in Amundsen Gulf, Arctic Ocean

Biome: root:Environmental:Aquatic:Marine
Enrichment of abundant sedimentary Bathyarchaeota demonstrating organoautotrophic metabolic capabilities

metabolic capabilities of Bathyarchaeota

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine:Oceanic
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
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

Biome: root:Environmental:Aquatic:Marine
Coral metagenome ICM_CCB

Exploring the microbial diversity and testing co-evolutionary hypotheses in Caribbean coral species using a 454-tag sequencing approach.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
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).

Biome: root:Environmental:Aquatic:Marine
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

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Oxic sediment - Microbial Metagenome

SSU 16S pyrosequencing project of the microbial metagenome of an oxic deep-sea sediment from the Eastern Mediterranean.

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Environmental:Aquatic:Marine:Sediment
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).

Biome: root:Environmental:Aquatic:Freshwater
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.

Biome: root:Environmental:Aquatic:Marine:Sediment
Protists tag sequencing of 18S rRNA HV 9

First comprehensive description of protist community diversity in meso- bathypelagic regions of the Ross Sea (Antarctica)

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Environmental:Aquatic:Marine:Coastal
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.

Biome: root:Engineered:Bioreactor:Continuous culture
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Aquatic:Marine:Pelagic
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.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
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.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial community in marine sediments

16S rRNA amplicon sequencing on the Eastern South Pacific Ocean sediments

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Environmental:Aquatic:Marine:Sediment
Arctic water Metagenome

Diversity and distribution of aquatic fungal communities in the Ny-Ålesund Region, Svalbard, High Arctic

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_VAG

Community Structure Of Benthic Bacteria In Upwelling Ecosystem.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
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.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
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.

Biome: root:Host-associated:Birds:Digestive system:Ceca
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Aquatic:Marine:Oceanic