SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
VARIATIONS IN MICROBIAL COMMUNITY COMPOSITION IN DEEP SUBSURFACE PIEZOMETER INSTALLATIONS

The Boom Clay layer is presently investigated as a potential host rock for geodisposal of nuclear waste in Belgium. The HADES underground research facility (EIG Euridice c/o SCK?CEN), located at 230 m depth under the site of SCK?CEN (Mol, Belgium), provides access to this clay layer for in situ geological, geochemical and geomicrobiological testing.  In order to predict how microbiology will affect the biogeochemical processes in a disposal scenario, the resident microbial communities of Boom Clay and the man-made structures within this clay are being characterised.    \tIn this study, water samples were collected from Boom Clay via various existing HADES piezometers. Microbial cells from these samples were concentrated on a 0.45 ?m filter membrane, followed by DNA extraction, PCR amplification of the V1-V3 region of bacterial 16S rDNA, automated sequencing and an in-house developed bio-informatics pipeline. The aim was to assess differences or shared features of the microbial communities residing in piezometer boreholes, supplementary to the previous screening of a single, vertical piezometer [1],  and to correlate variations to geochemical analyses.  While the boreholes of two piezometers seem highly enriched in one family of Betaproteobacteria (Rhodocyclaceae), the other piezometers seem to balance dominance between members of the Chloroflexi, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chlorobi, although in different ratios and with variations in overall diversity. Along the five piezometers, bacterial communities of the filters within one piezometer seem more similar to each other compared to those in other piezometers, despite a variety of filter materials or Boom Clay layers sampled within one piezometer.   \tThe observed variability in bacterial community composition suggests enrichment of certain members of the community according to the engineering properties of the piezometer installation. Although such locally enriched microbial community might not be representative for the total (engineered) clay environment, it shows that technical installations (such as piezometers) can introduce and promote local variations in the  otherwise oligotrophic clay environment and the associated bioprocesses.   \tFurther studies of other piezometers and of clay samples are needed, to pinpoint the source bacterial community underlying in situ enrichment, to unravel the mechanism that shapes such microbial community in different repository conditions and to outline the relevance of the (dominant) microbial classes in defining borehole water (and gas) chemistry.  [1]\tWouters K, Moors H, Boven P & Leys N (2013) Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water. FEMS Microbiol Ecol. 86: 458-473.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
Calcium induced alteration of gut microbiome in a murine model of colon cancer

Calcium supplementation correlated with distinctly segregating gut microbial communities as defined by 16S rRNA gene sequencing from both fecal and cecal samples

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
Metagenomic analysis of infant stool sample

Stool sample from a premature human infant (UC1).  This study used metagenomic methods (community genomic analysis and sequencing of amplified 16S rRNA genes) to document microbial colonization of the gut of a premature infant born at 28 weeks gestation. Analysis of 16S rRNA gene sequences collected approximately daily revealed three compositional phases during colonization. We reconstructed genomes of the dominant organisms and intensively curated population genomic datasets from the third phase. In the third phase, the communities were dominated by a nearly clonal Serratia population, two Citrobacter strains sharing >99% nucleotide identity, and contained a lower abundance Enterococcus population, multiple plasmids and bacteriophage. The relative abundance of the Citrobacter strains changed significantly over time. Modeling of Citrobacter strain abundances suggests differences in growth rates and/or host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomic profiling of bacterial communities associated with Tyrian Purple production in a marine gastropod

Dicathais orbita is a marine mollusc well known for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the full diversity of bacteria associated with the Tyrian purple producing hypobranchial gland and to identify bacteria specifically associated with the purple producing gland by comparing with the foot tissues using a high-throughput sequencing approach. The total genomic DNA was extracted from the hypobranchial gland and foot of D. orbita for high-throughput sequencing targeting the variable region V1-V3 of 16S rRNA bacterial gene. 16S rRNA bacterial sequences were processed by using combinations of QIIME and MEGAN software. The metagenome analysis revealed highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The most dominant bacteria phylum in the metagenome data set was Proteobacteria followed by Tenericutes, Spirochaetes and Bacteroidetes. Our result has also provided that larger numbers of bacterial taxa were present in the foot than the hypobranchial gland of D. orbita. This study also revealed the high abundance of Vibrio spp. in the Tyrian purple producing gland of a muricid mollusc. It also reports the presence of unique bacterial communities which shows indole production, bromoperoxidase and brominated secondary metabolites in the biosynthetic gland. This study reveals the full diversity of bacteria associated with the Tyrian purple producing gland of a marine muricids and also helped in establishing the potential role of bacteria in the biosynthesis of Tyrian purple.

Biome: root:Host-associated:Mollusca:Digestive system:Glands
16S rRNA genes from benthic Antarctic sediments

We sampled surface sediment from 24 sites across a 5,500 km region of western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities (16S and 18S rRNA) and sediment geochemistry.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Metagenomic study on the Iron-containing microbial mats of the Jan Mayen hydrothermal vent fields

Five iron mat communities were sampled with a hydraulic biosyringe suction pump in the Jan Mayen hydrothermal vent fields (71?N 6?W). The sampling method led to two phases; a solid bottom fraction (raw, R) and a liquid (top, T) part, that were both sampled separately. Two different hydrothermal conditions were considered; high-flux hydrothermal venting (warm, W) as opposed to diffuse fluid flows (cold, C).

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge

Deep-sea hydrothermal sediments are known to support remarkably diverse microbial consortia. Culture-independent sequence-based technologies have extensively been used to disclose the associated microbial diversity as most of the microorganisms inhabiting these ecosystems remain uncultured.  Here we provide the first description of the microbial community diversity found on sediments from Menez Gwen vent system. We compared hydrothermally influenced sediments, retrieved from an active vent chimney at 812 m depth, with non-hydrothermally influenced sediments, from a 1400 m depth bathyal plain. Considering the enriched methane and sulfur composition of Menez Gwen vent fluids, and the sediments physicochemical properties in each sampled area, we hypothesized that the site-associated microbes would be different. To address this question, taxonomic profiles of bacterial, archaeal and micro-eukaryotic representatives were studied by rRNA gene tag pyrosequencing. Communities were shown to be significantly different and segregated by sediment geographical area. Specific mesophilic, thermophilic and hyperthermophilic archaeal (e.g., Archaeoglobus, ANME-1) and bacterial (e.g., Caldithrix, Thermodesulfobacteria) taxa were highly abundant near the vent chimney. In contrast, bathyal-associated members affiliated to more ubiquitous phylogroups from deep-ocean sediments (e.g., Thaumarchaeota MGI, Gamma- and Alphaproteobacteria).\nThis study provides a broader picture of the biological diversity and microbial biogeography, and represents a preliminary approach to the microbial ecology associated with the deep-sea sediments from the Menez Gwen hydrothermal vent field.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
Growth and activity of ANME clades with different sulfate and sulfide concentrations in presence of methane

Extensive geochemical data showed that significant methane oxidation activity exists in marine sediments. The organisms responsible for this activity are anaerobic methane-oxidizing archaea (ANME) that occur in consortia with sulfate-reducing bacteria. A distinct zonation of different clades of ANME (ANME-1, ANME-2a/b and ANME-2c) exists in marine sediments, which could be related to the localized concentrations of methane, sulfate and sulfide. In order to test this hypothesis we performed long-term incubation of marine sediments under defined conditions with methane as a headspace gas: low or high sulfate (?4 and ?21 mM, respectively) in combination with low or high sulfide (?0.1 and ?4 mM, respectively) concentrations. Control incubations were also performed, with only methane, high sulfate or high sulfide. Methane oxidation was monitored and growth of subtypes ANME-1, ANME-2a/b, and ANME-2c assessed using qPCR analysis. A preliminary archaeal community analysis was performed to gain insight into the ecological and taxonomic diversity. Almost all of the incubations with methane had methane oxidation activity, with the exception of the incubations with combined low sulfate and high sulfide concentrations. Sulfide inhibition occurred only with low sulfate concentrations, which could be due to the lower Gibbs free energy available as well as sulfide toxicity. ANME-2a/b appear to mainly grow in incubations which had high sulfate levels and methane oxidation activity, whereas ANME-1 did not show this distinction. ANME-2c only grew in incubations with only sulfate addition. These findings are consistent with previously published in situ profiling analysis of ANME subclusters in different marine sediments. Interestingly, since all ANME subtypes also grew in incubations with only methane or sulfate addition, ANME may also be able to perform anaerobic methane oxidation under substrate limited conditions or alternatively perform additional metabolic processes.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
Microbial community composition in acidic and pH neutral sediments from two hypersaline lakes in Western Australia

Hypersaline environments, especially salt lakes, are extreme habitats for microbial life. The water bodies and sediments of salt lakes in Western Australia show a wide range of geochemical conditions. However, little is known about the composition and potential functions of the native microbial communities in these ecosystems. Here we compared microbial communities in the sediments of two salt lakes in Western Australia, slightly acidic Lake Orr and slightly alkaline Lake Strawbridge. Community composition was determined by 454 pyrosequencing of bacterial and archaeal 16S rRNA genes. The diversity and richness within the slightly acidic sediments of Lake Orr were lower compared to the pH neutral to alkaline sediments of Lake Strawbridge. Furthermore both salt lakes strongly differed regarding their geochemistry and microbial community composition. The archaeal community in both lakes was dominated by the Halobacteriacea, whereas Proteobacteria, Firmicutes and Bacteroidetes dominated the bacterial community. Inferred from the 16S rRNA gene based microbial community composition we found a high metabolic diversity including heterotrophic organisms, phototrophs, methanogens, fermenters, autotrophic organisms, sulfate reducers, sulfur oxidizers and metal reducers. The high phylogenetic and metabolic diversity in the salt lakes suggests that hypersaline lakes are important ecosystems with an active contribution to various biogeochemical element cycles.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
Sources and dynamics of microbial communities in cryoconite on an Alpine glacier

Cryoconite holes, i.e. small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Ecology of cryoconite holes in polar regions has been widely investigated, while that of cryoconite holes on mountain glaciers has been neglected. In this study we investigated the temporal dynamics of the microbial communities in cryoconite holes on the Forni Glacier (Italian Alps) along the ablation season and the contribution of eolian transport from periglacial environments to the microbial communities of cryoconite holes. We used Next-Generation Sequencing to assess the structure of bacterial communities, and estimated also photosynthesis and respiration rates of cryoconite holes with field measurements. We found a seasonal succession of bacterial communities, with autotrophic populations dominating communities after snow melting, and heterotrophic populations increasing in abundance later in the season. However, communities in cryoconite holes were mainly heterotrophic. Surprisingly, we also observed similarity between communities in cryoconite holes within few tens of meters to one another. Conversely, none of the periglacial environments we investigated (moraines, proglacial plain, and the debris of probable endoglacial origin) hosted bacterial communities similar to those found in the cryoconite holes in any season. Hence, periglacial environments seem not to be the source of bacteria living in the cryoconite, but may provide inputs of organic matter to cryoconite necessary to sustain the heterotrophic communities of cryoconite holes even without affecting the structure of their microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Metatranscriptome sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.

Metatranscriptome sequencing from  different depths to retain small cell size (Bacteria Organisms). The RNA was extracted and submitted to high throughput sequencing.

Biome: root:Environmental:Aquatic:Marine
The oral metagenome in health and disease

The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an over-representation of several functional categories, like genes for antimicrobial peptides and quorum sensing. In addition, they did not have mutans streptococci but displayed high recruitment of other species. Several isolates belonging to these dominant bacteria in healthy individuals were cultured and shown to inhibit the growth of cariogenic bacteria, suggesting the use of these commensal bacterial strains as probiotics to promote oral health and prevent dental caries.

Biome: root:Host-associated:Human:Digestive system:Oral
Bacterial diversity of polluted surface sediments in northern Adriatic Sea determined by pyrosequencing

Samples were collected from surface sea sediments at seven sites in the northern Adriatic Sea; there were six sites in proximity of industrial complexes and one from a tourist site (recreational beach). The samples were assayed for alkanes and polycyclic aromatic hydrocarbons. The composition of the hydrocarbon samples suggested that industrial pollution was present in most cases. A sample from one site was also grown aerobically under crude oil enrichment in order to evaluate the response of indigenous bacterial populations to crude oil exposure. Analysis of 16S rRNA gene sequences showed varying microbial biodiversity depending on the level of pollution - ranging from low (200 detected genera) to high biodiversity (1000+ genera), with lowest biodiversity observed in polluted samples. This showed a considerable biodiversity in all the sediment samples, which was severely restricted after selection on crude oil. Phylogenetic analysis of putative alkB genes showed a high evolutionary diversity of the enzymes in the samples and suggested considerable potential for bioremediation and bioprospecting. We present the first systematic analysis of bacterial communities from sediments of northern Adriatic sea that will provide a baseline assessment that may serve as a reference point for the eco - system changes and hydrocarbon degrading potential - a potential that could soon gain importance due to plans for oil exploitation in the area.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Capturing early changes in the marine bacterial community as a result of crude oil pollution in a mesocosm experiment

Shifts in marine bacterial communities resulting from crude oil contamination were characterized by 16S rDNA PCR ? DGGE and 454 high-throughput sequencing with the aims to 1) reveal short-term changes in the structure of the marine bacterial community 2) identify the blooming bacteria resulting from oil occurrence by DNA analysis. A longer-term vision of this study is to use a selection of bacterial genes markers in combination with monitoring technology to sense and warn for oil contamination. Here, we present results obtained from seawater incubations with North Sea oil in absence (O) or presence (OD) of dispersant, carried out at low temperature (4 ?C) and in the presence of zooplankton. Despite the dispersant treatment, chemistry in O and OD was very similar possibly due to the setup with low mixing energy. Both O and OD treatments induced rapid (1 day) re-arrangement of bacterial community and enrichment of Pseudoalteromonas, Pseudomonas, Glaciecola, known as biosurfactant producers, as well as bacteria assigned to Sulfitobacter, Piscirickettsiaceae (Marine Methylotrophic Group 3), Neptunomonas and Vibrio. Pseudofulvibacter genus was enriched by oil in the treatment without dispersant. The oil- contaminated seawater contained bacterial genera of Polaribacter and Marinomonas identical in 98 -99 % to those found in the North Sea crude oil itself. This suggests that bacteria blooming in oil-contaminated seawater can also stem from the bacterial community in oil itself and contribute to the structural community shift observed.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Novel subsurface lineages dominate fumarolic microbial communities at Tramway Ridge, Mt. Erebus, Antarctica

Using 16S rRNA gene amplicons and whole genome shotgun sequencing, we identified and enumerated members of the subsurface-associated microbial community in the high-elevation fumarolic sediments of Tramway Ridge.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Investigation of the protein synthesis potential in bacterial communities from Landsort Deep sediment

Numerous investigations of microbial communities using  sequencing of total DNA have revealed an extensive diversity of microbial taxa in an array of different environments. Community analysis based on total DNA solely, however, does not reveal whether community members are alive (i.e. in a growing, active, dormant state) or dead. This dilemma is of particular concern at the seafloor of the Baltic Sea?s deepest point, the Landsort Deep, where the anoxic bottom sediment is below half a kilometer of highly stratified water column with distinct differences in community structure and functions at different depths. Our previous metagenomics results showed that these anoxic sediments hold a taxonomically diverse community rich in functional capacities, but whether the diversity reflected living organisms was not evident. In this study, we sought to provide improved insight into the physiological state of the Landsort Deep sediment bacterial community members through complementary sequencing of 16S rDNA amplicons, total DNA and total RNA. Ratios of 16S rRNA OTUs in total RNA and rDNA amplicons were used to estimate protein synthesis potential among the sediment community members. Results show surprisingly high protein synthesis potential for sediment Cyanobacteria that are abundant seasonally in surface water. Furthermore, Mycobacteria, which are comparatively abundant in the Landsort Deep sediment metagenome to that of other marine sediment metagenomes, show levels of protein synthesis potential indicating they are alive and contribute to the sediment community functioning. In conclusion, our approach provides a new window of insight into the complexities of sediment microbial communities, and highlights both expected and unexpected members of the living community in the anoxic sediment of Landsort Deep.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Metagenomics of magnetotactic bacteria from Dianchi Lake

We used metagenomics to probe the community structure, magnetosome biomineralization mechanisms and potential ecological roles of magnetotactic bacteria from Dianchi Lake in southwestern China.

Biome: root:Environmental:Aquatic:Freshwater:Lake