SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Funtonal metagenomic of salt resistance

Hypersaline environments are considered some of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes involved in salt resistance from the microbial communities of brines and the rhizosphere of the halophyte Arthrocnemum from the Es Trenc saltern (Mallorca, Spain). The bacterial and archaeal diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of microbial communities that are typical in such environments. Metagenomic libraries were constructed with DNA from brine and rhizosphere samples, they were transferred to the osmosensitive strain Escherichia coli MKH13, and screened for salt-resistant clones. As a result, a total of eleven genes that confer salt resistance were identified, some of which encode for well known proteins previously related to osmoadaptation as a glycerol and a proton pump, whereas other genes encode for proteins not previously related to this function as RNA and DNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and interestingly, three of them exhibited also salt resistance in this bacterium, broadening the spectrum of bacterial species where these genes can operate. This is the first report of salt resistance genes recovered from different metagenomes of a hypersaline environment, which will help to further elucidate novel molecular mechanisms of salt resistance.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Cellar age related dynamics of prokaryotic community in pit muds

Microbes in pit mud (PM) play key roles in the liquor quality. We investigated prokaryotic community structure and diversity in PM samples with different cellar ages (1, 10, 25 and 50 years) using 454 pyrosequencing technique based on 16S rRNA gene. We selected 5 fermentation pits for each cellar age. Samples were collected from upper, middle and lower part locations as replicate samples for every pit.

Biome: root:Engineered:Food production:Fermented beverages
Taxonomic composition of microbial communities in coastal Arctic sediments

The taxonomic composition of microbial communities was examined in two sediment cores taken off the coast of Alaska in the Beaufort Sea in 2009.  One of the cores (PC10) had low methane concentrations while the deep depths of the other core (PC12) had high concentrations.  To examine community composition, variable regions V6-V8 of 16S rRNA genes were amplified using primers 926F and 1392R and the products were sequenced by pyrosequencing.  The analyses indicated that bacteria made up >95% of all sequences while eukaryotes contributed about 3% of the total. Less than 1% of all sequences could be assigned to archaea.  Archaea were relatively more abundant in the methane-rich core than in the methane-poor core.  Deltaproteobacteria were most abundant in the surface layer of both cores, then decrease in relative abundance as depth increased.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
A diverse and metabolically active microbial community persists in deep subsurface clay borehole water

The Boom Clay layer in Belgium is investigated in the context of subsurface nuclear waste storage, making use of the underground laboratory HADES. The HADES facility offers a rather unique access to a subsurface microbial community, in an environment of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a subsurface clay microbial community, residing in Boom Clay borehole water. Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community is disclosed. Despite the low energy environment, the microscopy and molecular analyses show a surprisingly large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among different samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, when using the appropriate media, a considerably large fraction of this community is found cultivable, active in situ and matching the metagenomic data. In conclusion, this study shows the possibility of a microbial community of relative complexity to actively persist in subsurface Boom Clay.

Biome: root:Environmental:Aquatic:Marine:Sediment
Targeted analyses of Dehalococcoidetes (phylum Chloroflexi) diversity and community structures in marine subsurface sediments.

Bacteria of the class Dehalococcoidetes (phylum Chloroflexi) are widely distributed in the subsurface and are especially prevalent in the deep marine subsurface. Nevertheless, little is known about the specific distributions of DEH, the extent of DEH diversity and the variability of DEH sub-group distributions at different sites and depths. Therefore, this study specifically examined the distribution and diversity of DEH through depths of various marine sediment cores by 454 pyrosequencing using newly designed 16S rRNA gene targeting primers to generate amplicons for sequencing. The data reveals Dehalococcoidetes diversity is more pronounced than previously recognized, and that distributions of Dehalococcoidetes changes through depths of marine sediments, suggesting varied metabolic properties in different sub-groups within this clade.

Biome: root:Environmental:Aquatic:Marine:Sediment
A combined massive parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities

A combined massive parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities

Biome: root:Engineered:Bioremediation
Microbial community in on-site tsunami sediment caused by the Great East Japan Earthquake

In this project, we investigated microbial communities in the tsunami sediment at Dec. 2011, Mar. 2012 and Oct. 2013 to clarify time-course change of microbial communities and compare those in the surface (0-2 mm indepth) and core (20-40 mm in depth) sediment.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial community structure or iron oxyhydroxides rich mound in Satsuma Iwo-jima, Japan

Iron oxyhydroxides rich mounds are observed at the bottom of Nagahama bay where iron and silica rich thermal fluid is discharged. The microbial community structure was investigated using V4 region of 16S rRNA gene.

Biome: root:Environmental:Aquatic:Marine:Sediment
Pelagic Sediment Metagenome

Deep sea water sludge of about 1000 m depth was collected from Andaman Sea.

Biome: root:Environmental:Aquatic:Marine:Sediment
How much do we know about marine metazoan biodiversity? Recent disclosures using second generation sequencing.

In response to contemporary threats to biodiversity, accurate and objective methods of species or operational taxonomic unit (OTU) assessment are fundamental to our understanding of mechanistic links among ecosystem components and resilience. Second generation sequencing approaches have been especially insightful for biodiversity analyses of the microbial biosphere, but to date, such approaches have not been used to study Metazoan phyla. Here, we utilize second generation sequencing for interpreting the relative richness of multiple metazoan phyla inhabiting the marine benthos. We identify (a.) comparative and substantial levels of unrecorded richness, that refute currently accepted paradigms of phylum rank abundance, (b.) ecosystem-level community composition at fine level spatial hierarchical scales and (c.) sequences derived from putative metazoan taxa that bear little genetic resemblance to any phylum that has been sequenced previously. These findings suggest that such techniques will provide a valuable addition to the exploratory tool-box for rapidly and simultaneously documenting the identity, composition and potential function of hitherto intractable, but ecologically important, communities.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Time course change of microbial community in tsunami sediment caused by the Great East Japan Earthquake

In this project, we investigated microbial communities in the tsunami sediment collected on Nov. 2012 and incubated under atmosphere in laboratory to clarify time-course change of microbial communities and compare those in the surface (0-2 mm in depth) and core (12-16 mm in depth) sediment.

Biome: root:Environmental:Aquatic:Sediment
Organic matter from melting Arctic sea ice triggers bacterioplankton activity and diversity

As Arctic multiyear ice is being replaced with first-year sea ice, a key question pertains to the cycling and fate of the increasingly dominant first-year ice carbon upon its release into the water column during melt. In this study, we experimentally tested the hypothesis that changes in sea ice dissolved organic matter (DOM) fractions affect the response of under-ice microbial communities and, as a corollary, the cycling of sea ice carbon in surface waters.Size-fractionated DOM fractions were isolated from first-year ice, producing three pools of dissolved organic carbon comprising the full DOM spectrum, large exopolymeric substances (EPS > 100 KDa molecular weight), and small EPS (< 100 KDa and > 10 KDa molecular weight). Enrichment experiments with these fractions revealed, over a 216 h period, significant and contrasting changes in prokaryotic abundance and production, substrate utilization rates, and microbial diversity between enrichments. The different DOM fractions differed in terms of molecular composition, elemental ratios and carbohydrate contribution, with the full DOM spectrum showing the highest proportion of carbohydrates and highest number of low-molecular weight unique compounds. Despite an abundance of low-molecular weight compounds in the DOM enrichment, the EPS fractions induced the strongest and fastest response of underice microbial communities, with highest growth rates and substrate utilization for the small EPS fraction. Shifts in microbial diversity were also observed over the course of the experiment, resulting in different community composition between enrichments. Notably, the EPS and DOM enrichments led to a dominance of Colwellia and Psychromonas, respectively.The results support our hypothesis, showing the fundamental role of the composition of the sea ice dissolved organic matter (DOM) pool and its dual impact, through changes in microbial diversity and substrate utilization, on organic matter cycling at the sea-ice interface. These findings have far-reaching consequences in terms of the cycling and export of sea ice associated carbon in the climatically-impacted Arctic and its role in global biogeochemical cycles.

Biome: root:Environmental:Aquatic:Marine
Microbial processes in iron-rich sediments of Lake Towuti, Indonesia: Disentangling the methane and iron cycles

Lake Towuti is a ferruginous basin with anoxic conditions below 130 m water depth. Due to these special settings, the lake is ideal to study early diagenesis in iron-rich sediments such as those that generated ancient iron formations during the Archean and Proterozoic. We investigated microbial populations present in the sediments, their role in iron cycle and any cryptic link to other elements. For this purpose, we worked on samples from short cores that were retrieved from Lake Towuti by our scientific team from the German Research Centre for Geosciences (Potsdam, Germany) and the University of British Columbia (Vancouver, Canada). This project was supported by the ICDP priority program of the Deutsche Forschungsgemeinschaft through grants to Jens Kallmeyer (KA 2293/8-1) and Aurèle Vuillemin (VU 94/1-1); the Swiss National Science Foundation (grant no. P2GEP2_148621 to Aurèle Vuillemin); the German Research Centre for Geosciences through an expedition grant to Jens Kallmeyer and Dirk Wagner; and an Natural Sciences and Engineering Research Council of Canada Discovery grant (no. 0487) to Sean A. Crowe.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Active microbial eukaryotes amidst a marine subsurface RNA paleome

During the first RNA-based survey of subsurface eukaryotes in a globally distributed sample collection, we detected metazoan, plant, and diatom rRNA signatures in sediments up to 2.7 million years old. The recovery of RNA from those taxa is consistent with burial in sub-seafloor environments during sedimentation, and subsequent preservation of those nucleic acids.  Extensive controls indicate that the recovered RNA does not derive from seawater or aerosol contaminants, supporting the authenticity of an RNA-based subsurface eukaryotic paleome. This paleome has the potential to inform our understanding of environmental conditions at the time of deposition. Within this same dataset, a high diversity of fungi in ocean sediments was found up to 48 meters below seafloor (mbsf) exhibiting statistically significant correlations with total organic carbon  (TOC), sulfide, and dissolved inorganic carbon (DIC). We interpret these correlations, together with the uniqueness of fungal profiles in the subsurface, and microscopic observations of filamentous fungi, yeasts, and spores as indicators of subsurface fungal activity

Biome: root:Environmental:Aquatic:Marine:Sediment
Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterised by strong thermo-halo stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S ribosomal RNA genes (rRNA genes) revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were the features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces were significantly higher in cell count, compared with the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we move from the Alphaproteobacteria-dominated deep-sea to the Planctomycetacia or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. The archaeal marine group I was dominant in the deep-sea water and interfaces; whilst several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II; despite the near-identical populations in the overlaying deep-sea waters. The lowest convective layers harboured interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

Biome: root:Environmental:Aquatic:Marine
Microbial communities in sponge samples from Gulf of Mexico

454 pyrosequencing of v5 v6 regions of 16s rRNA genes

Biome: root:Host-associated:Porifera
Pronounced Seasonal Dynamics of Freshwater Chitinase Genes

Chitinase and 16S ribosomal RNA genes from Lake Erken derived from a seasonal survey.

Biome: root:Environmental:Aquatic:Freshwater:Lake
16S rRNA gene pyrosequencing and clone library revealed highly diverse microbial communities in natural marine biofilms

Microbial communities in biofilms have been suggested to mediate a wide spectrum of ecological functions. However, the underlying mechanism of most of the mediations is still unresolved mainly because of the uncertainty in characterizing members in the communities using existing 16S rRNA gene-based molecular methods. In this study, a newly developed method – barcoded 16S rRNA gene pyrosequencing – was employed to provide a detailed characterization of the bacterial communities in intertidal and subtidal marine biofilms developed in two seasons. This method has high sensitivity to detect low-abundance taxa and is able to generate a large amount of highly reliable data in a very short period of time. Our results revealed highly diverse biofilm bacterial communities varied with season and tidal level. Over 6,000 OTUs with species estimates of up to 15,000 were recovered in a biofilm sample, which is by far the highest record in sub-tropical marine biofilms and is much greater than biofilms developed in certain natural habitats. Nineteen phyla were found in the biofilm samples, for which Cyanobacteria and Proteobacteria were the most abundant phylum dominating the intertidal and subtidal biofilms, respectively. Apart from these two phyla, Actinobacteria, Bacteroidetes, and Planctomycetes were found to be the major groups recovered in both intertidal and subtidal biofilms, yet their relative abundance varied among samples. Full-length 16S rRNA gene clone library was constructed for the 4 biofilm samples and showed similar results with pyrosequencing. The relationship of bacterial community and settlement of larvae of a marine invertebrate is discussed.

Biome: root:Environmental:Aquatic:Marine
Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to deeply investigate the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri, and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1,000 microbial OTUs and an estimate of up to 2,000 species. Altogether 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding seawater and 4 of which were recorded in sponges for the first time. Up to 100 OTUs with an estimate of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest diversity ever recorded for sponges. A non-negligible proportion of unclassified reads in sponges may represent the presence of novel species. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations although they varied to certain degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned into one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently diverged from those in the surrounding seawater. Our results suggested the Red Sea sponges possess highly sponge-species specific microbial communities which are resistant to environmental influence. Although sponges have been regarded as microbial fermenters with a huge microbial diversity being reported among the animal kingdom, much of their microbial diversity remains to be explored.

Biome: root:Environmental:Aquatic:Marine
Characterization of Microbial Community Structure and Population Dynamics of Tetrachloroethene-Dechlorinating Tidal Mudflat Communities using a Multipronged Approach

A multipronged approach comprising microcosm studies, Titanium pyrosequencing, 16S rRNA gene clone libraries, and dechlorinator-targeted quantitative real-time PCR (qPCR) characterized reductive dechlorinating activities and populations in tidal flat sediments collected from South Korea's central west coast near Kangwha.

Biome: root:Environmental:Aquatic:Marine:Sediment
Marine metagenome ICM_DOF

454 Tagging of Deep Ocean Flux Material.

Biome: root:Environmental:Aquatic:Marine
Archaeal diversity of Loki's Castle black smokers at the Arctic Mid-Ocean Ridge

Hydrothermal vent systems harbor rich microbial communities ranging from aerobic  mesophiles to anaerobic hyperthermophiles. Among these, members of the archaeal domain  dominate the microbial communities in such extreme environments, partly because of their  temperature- and mechanically-resistant membrane lipids. In this study, we use geochemical  and molecular microbiological methods to investigate the abundance and diversity of archaea  in black smoker chimneys from the newly discovered Loki's Castle hydrothermal vent field  on the Arctic Mid-Ocean Ridge (AMOR) with vent fluid temperatures of 317°C and pH of  5.5. Archaeal glycerol dialkyl glycerol tetraether lipids (GDGTs) with 0 to 4 cyclopentane  moieties were dominant in all sulfide samples and are most likely derived from both  (hyper)thermophilic Euryarchaeota and Crenarchaeota, which are presumably involved in  sulfur and iron reduction, as well as methanogenesis. GDGTs with an additional covalent  bond between the isoprenoid hydrocarbon chains, so-called H-shaped GDGTs and also  containing 0 to 4 cyclopentane rings, were present with similar abundances. These lipids are  not often reported, but may be derived from sulfur-reducing members of the  Thermococcaceae. Crenarchaeol has been detected in samples derived from the chimney  exterior indicating the presence of Thaumarchaeota, involved in ammonia-oxidation (AOA)  at lower ambient temperatures. Our observations based on 16S rDNA-based taxonomy and  biomarker lipid analysis provide insight into microbial communities thriving within the  porous sulfide structures of an active deep-sea hydrothermal vent, where microbial cycling of  sulfur, hydrogen and methane predominantly by archaea may be the prevailing  biogeochemical processes.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Black smokers
Marine microbial eukaryote community analysis in Korea

To investigate marine microbial euakryote community in Korea, we used the pyrosequencing technology.

Biome: root:Environmental:Aquatic:Marine
Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water columns overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (20 m and 50 m) and deeper layers (200 m and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations, which are 7.4 km apart. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. Our results indicate that the microbial communities sampled in this study are different from those identified in water columns in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.

Biome: root:Environmental:Aquatic:Marine