SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
16S data describing Antarctic benthic sediment

Here, we collected twenty-four sediments samples over a 5,500 km transect of western Antarctica that spans the Ross Sea up to the Weddle Sea.  Diversity data from all three domains of life were collected via next-generation DNA sequencing and numerous geochemical and nutrient data were also collected, which greatly contributes to the existing understanding of benthic Antarctic sediments communities.

Biome: root:Environmental:Aquatic:Marine:Sediment
Diversity of bacterioneuston and bacterioplankton in coastal waters of Misaki, Japan

Deep sequencing of environmental DNA from surface microlayer obtained using polycarbonate membrane (depth= 33 micrometer), glass plate (depth=42 micrometer) and drum sampler (depth=35 micrometer). The bacterial communities obtained using these three surface microlayer samplers were compared to control underlying water obtained from the depth of 20 cm.

Biome: root:Environmental:Aquatic:Marine:Coastal
Life in a toxic environment

Monitoring of microbial groups along redox gradients in different marine environments.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Metagenome analysis of picoeukaryotes from surface seawater

Surface seawater was collected at two sampling sites in Sendai Bay (C5: 141.083W, 37.976N; C12: 141.317W, 37.974N), Miyagi, Japan on October 7 and December 1 in 2013. Suspended particles were concentrated to 100 fold and divided into two subsamples: (1) mixied with DMSO(5%) and frozen to sore in liquid nitrogen, (2) kept non-frozen. Picophytoplankton cells were sorted by flow cytometry. The genomic DNA was extracted and amplified by whole genome amplification. Partial 18S rRNA gene of the eukaryotes was amplified and sequenced using GS junior.

Biome: root:Environmental:Aquatic:Marine
Xylophaga in situ Eclusion Experiment

We tested the effect of the presence of Xylophaga sp. on the microbial community and on the hydrogen sulfide concentration during a 85 days experiment at 500m deep. We validate the ability of wood falls microbial community to produce a significant amount of hydrogen sulfide in the absence of Xylophaga sp. during the first months of wood falls colonization

Biome: root:Environmental:Aquatic:Marine
Arctic first-year drift ice and under-ice water bacterial communities

Arctic first-year drift ice and under-ice water bacterial communities (16S rRNA gene) were studied with Illumina MiSeq.

Biome: root:Environmental:Aquatic:Marine
Atlantic salmon microbiota

Atlantic salmon skin mucus and surrounding water have been sampled at production facilities both in freshwater and after transfer to seawater. Extracted DNA is sequenced using barcoded 16S primers using PacBio SCC.

Biome: root:Environmental:Aquatic
Multimodal assessment of flax dew-retting and functional impact on short fiber polymer composites

We have undertaken a dynamic analysis of flax retting combining chemical, spectroscopic, microscopic and targeted-metagenomics characterizations of flax straw collected in the field at different periods after harvest.

Biome: root:Host-associated:Plants
Preliminary analysis into the metagenome of the marine fire sponge, Tedania ignis, using assembly independent methods

Tedania ignis, or the mangrove fire sponge is a common species throughout the Caribbean and south Florida. It is well known for the intense burning sensation upon contact with skin. The microbiome of T. ignis was recently sequenced as part of the Sponge Microbiome project, but not much is known of the functional potential of these microbial communities, or the taxonomic domain make-up of this species. Metabolites from T. ignis have been found to have potent anti-cancer properties, but the producing symbiont or symbionts have not been determined. In this study, we show the domain makeup of this species, the functional potential of the sponge, and the taxonomic makeup from assembly-free metagenomes.

Biome: root:Host-associated:Porifera
Coastal eutrophication controls the bacterial community composition in different reef habitats of the Spermonde Archipelago, Indonesia.

Coastal eutrophication is a key driver of shifts in bacterial communities, but related knowledge is very scarce. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do bacterial communities respond to changes in water quality along a spatial gradient? (2) Which water quality parameters influence the  bacterial community composition? (3) Are there bacteria community differences between the different investigated microbial habitats? For this purpose a range of key water parameters were measured at 8 stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM) and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other 7 sites. Shifts in the bacterial communities were specific to each sampled habitat. In the water column, the relative abundance of Gammaproteobacteria increased with distance from Makassar, while that of Alphaproteobacteria decreased.In the sediments, there was a pronounced dominance of Gammaproteobacteria at the inshore site, which decreased along the gradient. There was no gradual shift in bacterial classes for samples obtained from the Fungia mucus. We observed a strong positive correlation between Bacteroidia, Chlamydiia and Acidobacteria_Gp6 and chlorophyll a, TEP and SPM. Deinocooci, Verrumicrobiae and Alphaproteobacteria were, on the other hand, positively correlated to DOC concentrations. In addition, we observed very distinct communities between the investigated habitats. Our data shows strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, this led to a much higher prevalence of potentially pathogenic bacteria at the chronically impacted site closest to Makassar.

Biome: root:Environmental:Aquatic:Marine
Interkingdom signaling: Modulation of bacterial colonization by quorum sensing interference of Aurelia aurita

Host-derived interference with bacterial communication (quorum quenching, QQ) to modulate microbial colonization of the moon jellyfish Aurelia aurita.

Biome: root:Host-associated:Cnidaria
Variations in prokaryotic community assembly and predicted metabolic potential of surface sediments with geography in the coastal northern Zhejiang, East China Sea

The coastal marine area of northern Zhejiang (East China Sea) is important to regional development in the southeast of China. Marine sediment prokaryotes play crucial roles in regional biogeochemical cycling. However, the sediment prokaryotic community assembly and metabolic potential in this ecosystem had not been revealed on an extended spatial scale. We collected surface sediment samples across sixe typical zones (Yushan, Xiangshan Harbor, Hangzhou Bay, eastern Zhoushan Islands, eastern Xiangshan, and Sanmen Bay) of this area and combine 16S rRNA gene sequencing, community-level metabolic reconstruction, and sediment physicochemical measurement to investigate the variations in taxonomic composition and metabolic gene family composition with geography and related environmental conditions. Geographic distance effect won the arm-race in shaping beta-diversity pattern with the major environmental drivers such as oil, temperature, texture, sulfide, and water depth, but left larger proportion of unexplained variation, suggesting the effects of unmeasured factors and stochastic process. We found discriminant assemblages across the zones, suggesting some provincial distributions of prokaryotes. On the other hand, the predicted metabolic potential structure slightly but significantly shifts with geography. The key roles of sulfide and oil in shaping metabolic potential structure suggested the importance of sulfur (S) metabolism in biogeochemical cycling here. Particularly, we found that sulfate reduction was the dominant pathway in S-metabolism in the Yushan sediments as indicated by the evidences from taxonomic composition, predicted enzyme-level gene, and metabolic product. This study provides the first insight into the regional turnover of sediment prokaryotic diversity and metabolic potential in this ecosystem.

Biome: root:Environmental:Aquatic:Marine:Sediment
Cascading influence of inorganic nitrogen sources on DOM production composition lability and microbial community structure in the open ocean

We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on DOM and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 L polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation DOM production DOM composition and microbial community structure responses over 1 week relative to controls

Biome: root:Environmental:Aquatic:Marine:Oceanic
Dissolved compounds excreted by copepods reshape the diversity and the activity of marine bacterioplankton community

Copepods are important suppliers of bioreactive compounds for marine bacteria through fecal pellet production, sloppy feeding and excretion. However, the interaction between copepods and bacteria is poorly understood in the marine environment. Herein, we investigated the nitrogen and phosphorus compounds excreted by copepods fed by two size fractions of natural food (<20 µm and 20-150 µm) in the upwelling zone of central south of Chile in late summer and spring. We then assessed the biogeochemical response of the bacterial community and their structure, in terms of total and active cells, to the addition of these dissolved compounds. Results revealed that copepods actively excreted nitrogen and phosphorus compounds, mainly in the form of ammonium and dissolved organic phosphorus (DOP), reaching excretion rates up to 2.6 µmol L-1 h-1 and 0.05 µmol L-1 h-1, respectively, in spring. The high accumulation of excreted nitrogen and phosphorus was associated in both periods with the 20-150 µm size fraction of food, which coincided with the main food item available for copepods in the field. Variation in the abundance (contribution to total bacterial sequences) of bacteria taxa was characterized by a decrease of Bacteroidetes and Cyanobacteria, and an increase of Proteobacteria, mainly Alphaproteobacteria and Gammaproteobacteria depending on treatment. Some orders, such as Flavobacteriales presented a rapid response to the products excreted by copepods, increasing their abundance between 3 to 10% in the first four hours of the experiment evolution. Moreover, the specific bacterial activity (16S rRNA: rDNA) suggested a differential response associated with the two size fractions of food provided to copepods, Alphaproteobacteria was stimulated in the treatment enrichment with excretion products by copepods fed with <20 µm size fraction, but inhibited at the 20-150 µm size fraction in March. In December, Alphaproteobacteria was active in both treatments, but in the treatment enriched with excretion products by copepods fed with <20 µm size fraction was higher than the treatment enriched with excretion products by copepods fed with 20-150 µm size fraction. Our findings indicate that the different size fractions of food provided to copepods have an impact on the main products excreted by copepods and showed that bacterial community can respond in a short period of time (<4 h) to excreted organic and inorganic substrates.

Biome: root:Environmental:Aquatic:Marine
Limited influence of primary treated sewage waters on bacterial abundance, production and community composition in coastal seawaters

The response of bacteria in terms of abundance, production and community structure to changes induced by the discharge of primary treated sewage waters was investigated combining microbiological, chemical and molecular tools. The primary treatment did not affect substantially the bacterial community structure in wastewaters and did not reduce the concentrations of fecal indicators. The spatial distribution of the sewage plume was governed by vertical stratification and currents. Bacterial abundance and production in the sea receiving waste waters depended predominantly on environmental conditions. In the waters with the highest concentration of fecal pollution indicators the bacterial community was characterized by allochthonous bacteria belonging to Epsilonproteobacteria, Firmicutes, Gammaproteobacteria and Bacteroidetes. The latter two taxa were also present in unpolluted waters but had a different structure, typical for oligotrophic environments. Although the impact of primary treated sewage waters was limited, a sanitary risk persisted due to the relevant presence of potentially pathogenic bacteria.

Biome: root:Environmental:Aquatic:Marine:Coastal
Metagenomic community analysis of marine zooplankton using two plankton nets

Metagenomic analysis was conducted to evaluate effects of plankton nets on marine zooplankton community. Zooplankton samples were collected in the coastal water off Japan, using two types of plankton nets.  PCR was performed to amplify 18S V7-V9 regions, and the 454-pyrosequencing run was carried out .

Biome: root:Environmental:Aquatic:Marine:Coastal
Latitudinal diversity patterns of pelagic copepods in the Pacific using metagenetic analysis

Latitudinal diversity patterns of pelagic copepods in the Pacific were investigated from 40?S to 68?N along 170?W using metagenetic analysis of nuclear large subunit ribosomal DNA.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Seasonal and spatial diversity of bacterial communities in marine sediments of Ningbo Xiangshan Coastal Ocean

With the rapid development of social economy, East China Sea has suffered from excess nutrient emissions, organic pollutants and heavy metals, and formed a complex marine ecological environment in the past decades. The bacterial biogeographic pattern in marine sediments can reflect the time variation and biological processes of the local ecological environment quickly and accurately. In this study, we collected sediment samples of the two seasons of winter and summer in coastal area of East China Sea at 7 stations from the near to the distant for investigating bacterial community with 16S rRNA gene high-throughput sequencing.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Metagenomics of soil

Analysis of the microbial communities of different soils

Biome: root:Environmental:Terrestrial:Soil
Effect of genetics and environment on gut bacteria in Anopheles and Aedes mosquitoes.

The aim was to investigate the effect of genetics and environment on gut bacteria in adult Anopheles and Aedes mosquito. The mosquitoes were both co-reared and reared separately. Larval water, sugar feeding source and adult mosquito-guts were analysed for bacteria.

Biome: root:Engineered:Lab enrichment:Defined media
Microbial community structure and dynamics in the oxygen minimum zone of the Northeast subarctic Pacific Ocean

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Biome: root:Environmental:Aquatic:Marine:Oceanic
Microbiome of St. Lawrence estuary sediments

The myxobacteria are a widely dispersed group of Gram-negative bacteria known for their elaborate fruiting bodies. Principally soil bacteria, they are key players in the breakdown and processing of organic compounds in terrestrial soils, acting as both primary cellulose degraders and bacterial predators. While easily cultivated from soil, isolation of myxobacteria from lakes, rivers and oceans is rare, and for many years it was thought that myxobacteria were incapable of surviving in aquatic environments. We recently conducted a metagenomics analysis of several sites in the Gulf of St. Lawrence, examining the bacteria found free-living in the water column and attached to suspended marine sediment. While sequences corresponding to myxobacteria were not prevalent in the water column, they were widely dispersed in the sediments, forming up to 3-4 % of the active bacterial community in some cases. To determine the role of myxobacteria in the St. Lawrence estuary ecosystem, and to isolate any therapeutically relevant natural products that they may produce, we will pinpoint samples rich in myxobacteria via metagenomics. This will allow us to see how myxobacterial species prevalence changes as we move from freshwater to saltwater sediments.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Dynamics of bacterial communities mediating the treatment of an as-rich acid mine drainage in a field-scale pilot

Passive treatment based on iron biological oxidation is a promising strategy for As-rich acid mine drainage (AMD) remediation. The present study aimed at the characterization of the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biogenic precipitate. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure similar to the natural ecosystem developing in situ in the AMD. Diverse FeOB populations largely dominated the bioreactor including: Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum,… Notable shifts were observed in the distribution of these populations inside the bioreactor. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the presence of Thiomonas related bacteria. The spatio-temporal dynamics of the whole communities were tightly linked to variations in the physico-chemistry of the AMD water transiting inside the bioreactor. The main parameters that proved to exert a control on the bacterial communities potentially involved in the water treatment process were: DO, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. The ubiquity and the physiological diversity of the bacteria identified (including the genus of biotechnological relevance Ferrovum) suggested that this treatment system could be easily adapted to the treatment of AMD with a large range of physico-chemical characteristics.

Biome: root:Engineered:Wastewater:Industrial wastewater:Mine water
VETII samples

The samples relate to the Danish VETII project regarding the relationship between antimicrobial usage in finishing pigs and antimicrobial resistance in their gut microbiome. Five different sub-projects are included; 1. Pilot project containing 10 farms (P), 2. Observational project containing 83 farms, 3. Rearing time related longitudinal study in 6 of the 83 farms, thus both weaners (W) and finishing pigs were sampled in those farms. 4. 2x2 split (A,B) sampling project in 4 of the 83 farms, and 5. Production cycle longitudinal study in 52 of the 83 farms, thus the second sampling was performed two finishing pig production cycles after the first sampling. Sampling took place from Marts 2014 to July 2016. Each faeces sample from a farm consists of 30 individual pig faeces samples pooled into one.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Anaerobic digestion of phenol rich influent

Aims of this study were (1) to investigate the phenol-degrading anaerobic population in operationally identical reactors in order to identify key players involved in phenol degradation and resistance in AD reactors and (2) to determine the impact of the inoculum in shaping the structure of the phenol-degrading community. It was tested whether different starting communities, adapted to different phenolic compounds, were as effective in treating a mixture of dairy and phenolic wastewater.Four different inocula were studied in triplicate lab-scale reactors run over a period of 180 to 265 days. The reactors were operated at mesophilic conditions with a mixture of a synthetic dairy and phenol wastewater.

Biome: root:Engineered:Bioremediation:Persistent organic pollutants (POP)
Airway metagenome of children in Kilifi, Kenya

Naso- and oropharyngeal samples were collected from children with different manifestations of respiratory infection as well as from well controls. Upper airway microbiota were characterised by sequencing the V3/V4 hypervariable region of the bacterial 16S rRNA gene on the Illumina MiSeq platform.

Biome: root:Host-associated:Human:Respiratory system
Microbial induced mineral precipitations caused by nitrate treatment for souring control during microbial enhanced oil recovery (MEOR)

Microbiologically active environments, like oil reservoirs, can suffer different a range of problems due to the presence of sulfate-reducing microorganisms. These includeing, but are not limited to: H2S formation, souring and corrosion caused mainly by sulfate-reducing microorganisms. To prevent biogenic sulfate reduction, nitrate can be used as an environmentally friendly alternative to biocides. However, side effects of nitrate injection are sometimes observed but not well understood. In our study, we used original water from an onshore reservoir, where a microbial enhanced oil recovery (MEOR) application is planned, and investigated the effects of nitrate addition on H2S generation, mineral precipitation and microbiology. We observed that nitrate did inhibit H2S formation in most, but not all cases while available in the medium. During nitrate reduction, iron and calcite minerals precipitated over short- and long-term (10 or 160 days) incubations. This was caused by a nitrate-reducing group of bacteria belonging to the family Deferribacteraceae. Using dynamic sandpack setups and numerical modeling approaches with the simulator TOUGHREACT, we observed significant reduction in permeabilities (~44x) suggesting injectivity issues over time in case nitrate is continuously added to the reservoir. Our study shows that nitrate-dependent processes, which were described separately for pure-cultures before, are also valid for natural mixed communities present in oil fields and underlines the complex interplay of microbial metabolisms associated with those communities.

Biome: root:Environmental:Terrestrial:Oil reservoir
Commensal viruses maintain intraepithelial T cells via non-canonical RIG-I signaling

Much attention has been focused on the role of commensal bacteria in health and disease, but the role of commensal viruses is understudied. Metagenomic analysis shows that the intestine of humans and animals harbors various commensal viruses and the dysbiosis is often associated with intestinal infection and inflammatory diseases, but the role and mechanism of commensal viruses in the homeostasis of intestinal immune system remain unexplored. Here, we show that commensal viruses are essential for the homeostasis of intestinal intraepithelial lymphocytes (IELs). The cytosolic viral RNA sensing receptor RIG-I in antigen presenting cells can recognize commensal viruses and maintain IELs via an interferon-independent, but MAVS-IRF1-IL-15 axis dependent manner. Notably, the recovery of IELs restores the colitis susceptibility of commensal viruses-depleted mice to dextran sulfate sodium. Collectively, our results indicate that commensal viruses can support the homeostasis of IELs and regulate mucosal immunity via non-canonical RIG-I signaling.

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