SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bioelectrochemical toluene degradation in marine environments

Accidental oil spills can lead to considerable release of toxic petroleum hydrocarbons in marine environments. Due to their recalcitrance under anoxic conditions in the sediment, oxidative bioremediation strategies have been developed. Here we investigated an alternative strategy to remove monoaromatic hydrocarbons from marine environments by stimulating the biodegradation with an electrode as solid electron acceptor. Using toluene as a model compound, degradation was accomplished in BES with simultaneous current production. Glass BES reactors were set up using sediment collected from an hydrocarbon contaminated marine site as microbial inoculum, and artificial ocean water as growth medium. Anode potentials of 0 mV and +300 mV (vs Ag/AgCl) were tested in order to check their influence on current production, enrichment of electrocatalytically active microorganisms and hydrocarbon degradation rate. At the end of the experiment microbial characterization of the communities attached to the electrodes and in the bulk of each reactor was performed by Illumina sequencing of the 16S rRNA. Degradation of toluene was directly linked to current generation up to 431 mA/m, but over time decreasing peak currents were obtained upon renewed toluene spiking. In both the conditions a degradation rate of 1 mg/(L d) was observed. Monitoring of sulfate/sulfide concentrations during bioelectrochemical experiments suggested that sulfur metabolism might play an important role in toluene degradation on a bio-anode, potentially leading to passivation over time. The microbial communities were dominated by sulfate reducing microorganisms, particularly the family Desulfobulbaceae appeared to be linked both with current production and toluene degradation.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
Spatio-temporal survey of bacterial and archaeal diversity and community composition in four contrasting sediments of the Western English Channel Observatory

Sediment samples were taken from four sites in the Western English Channel as part of the Plymouth Marine Laboratory Benthic Survey. The four sites were chosen due to their contrasting combinations of depth, sediment type and level of exposure. Jennycliff (50? 20.91 N, 04? 07.71 W) and Cawsand (50? 19.81 N, 04? 11.50 W) represent shallow habitats (approximately 10 m deep), are sheltered from the prevailing south westerly winds but have different sediments types (Jennycliff is coarse silt whereas Cawsand is very fine sand). Rame Head (50? 17.75 N, 04? 16.00 W) and L4 (50? 13.30 N, 04? 11.40 W) are exposed sites with a depth of approximately 50 m, again with contrasting sediment type, Rame Head being medium silt and L4 fine sand. Samples used in this study were taken approximately bimonthly from July 2009 to May 2010. However, samples could not be taken at L4 in November 2009 due to adverse weather conditions at this site. DNA was extracted and bacterial and archaeal abundance, diversity and community composition assessed using both quantitative PCR and 454 pyrosequencing of the V4-V5 region of archaeal 16S rRNA genes. DNA libraries were prepared for sequencing using the Roche emPCR Method Manual Lib-L MV and the Roche Sequencing Method Manual for the GS FLX Titanium Series at PML. Picotitre plates were used with an 8 lane gasket.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
The studies presented here aim to gain evaluate the potential of an anaerobic microbial consortium to biologically translate Cr(VI) from sediments amended with NPs (i.e., Fe2O3 and Fe3O4).

Chromium has been listed as one of the top 20 contaminants on the superfund priority list of hazardous substances for the past few years due to its tremendous toxicity. In general, chromium mainly exists in trivalent (Cr(III)) and hexavalent (Cr(VI)) species. Carbon sources and electron shuttles compounds, some novel materials, like nanoparticls (NPs), would play an important role in Cr(VI) reduction in anaerobic condition. Thus, the studies presented here aim to gain evaluate the potential of an anaerobic microbial consortium to biologically translate Cr(VI) from sediments amended with NPs (i.e., Fe2O3 and Fe3O4).

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Response of the sediment bacterial community to a spring phytoplankton bloom at the Western English Channel Observatory site L4

The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded only when it reached the sediment surface: the nature of the chlorophyll degradation products was indicative of grazing activity. The abundance of bacterial 16S rRNA genes per gram sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the sediment surface. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of 16S rRNA genes was also performed on four replicate samples from eight sampling point throughout the duration of the spring bloom. This indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period; primarily due to an increase in the abundance of members of the Flavobacteria.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Investigation of the response of the active microbial community to CO2 exposure from a controlled sub-seabed CO2 leak in Ardmucknish Bay (Oban, Scotland)

The impact of a controlled sub-seabed CO2 leak on the composition of the active community of benthic bacteria was assessed before, during and after CO2 release. A total of 4.2 tonnes of CO2 was injected into the overlying unconsolidated sediments, over a 37 day period, during which flow was increased from 10 to 210 kg per day. Five replicate sediment samples were taken from the epicentre and 450m distant during 4 time points (7 days before CO2 exposure, after 14 and 36 days of CO2 release, and 6 after the CO2 release had ended). RNA was extracted from the top 1 cm sediment and possible changes to the composition of the active benthic bacterial community assessed by in depth sequencing of 16S rRNA. CO2 related changes were detected to the relative abundance of both major and minor bacterial taxa: most notably an increase in the relative abundance of the Planctomycetacia after 14 days of CO2 release.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Shotgun metagenomic study of sedimentary ancient DNA (sedaDNA), from four strata of sediment core taken from an Bouldner Cliff, a submarine archaeological site in the Solent. Dates of

The Mesolithic to Neolithic transition in Europe marked the transition of humans from hunter-gathers to agriculturalists. This event coincided with rising sea levels in the area and submergence of numerous paleosols, obscuring the earliest evidence of the transition from the archaeological record. A combination of archaeological and molecular approaches of sediment cores dating from 8030-7980 cal BP show the presence of domesticated plant species, suggesting neolithicisation of the area 2,000 years earlier than expected. The submitted raw sequence data here correspond to four strata of a core sample within this time range. Using a shotgun metagenomic approach we identified sequences of domesticated plant species amongst background ecology of the early Neolithic, around 8,000 cal BP.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Trying to sew with a needle from a haystack: cautionary tales of assembly and taxonomy assignment from a White Oak River sediment metagenome

We analyzed a short read metagenome dataset from estuarine sediment in the White Oak River, NC to examine microbial community composition and functional potential. The dataset was assembled through multiple methods into longer reads, which were analyzed for functional and taxonomic content. While different assemblies yielded somewhat similar functional calls showing anaerobic metabolic pathways, the taxonomic calls varied depending on the pipeline applied. Homology-based assignment for taxonomy was most consistent with direct ribosomal RNA amplicon analysis, yet wide variations were seen between amplicon and metagenome identifications. Deep branching organisms may result in misidentification of genes through pipelines. We questioned whether assembly was creating chimeras and if fragment recruitment could assist in assembly. We show that close relatives may assist in assembly refinement, but that many relatives are missing for this environment in the databases. In total, we have a cautionary tale of the potential for bias and misidentification in metagenomic annotation, depending on analysis method

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Linking DNRA community structure and activity in a shallow lagoonal estuarine system

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between structure and activity of DNRA communities has yet to be discovered. We examined the composition, abundance and activities of DNRA communities at five sites along salinity gradients in the New River Estuary, North Carolina, USA, a shallow eutrophic system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates while abundance of DNRA communities was estimated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, which is unique to DNRA.  A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine diversity and composition of DNRA communities within the estuarine sediment communities. We found a positive correlation between nrfA gene abundance and DNRA rates. Among the environmental variables, %organic and sulfide in sediments might support higher activities of DNRA communities. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the saline gradient of New River Estuary. Relative abundance of dominant populations was found to have significant influences on overall activities and abundance of DNRA communities. Thus, we found that abundance of dominant DNRA bacteria was an important regulator of DNRA activities in the eutrophic New River Estuary.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Anthropogenic contamination in Red Sea and their potential impact on marine water microbial community

Good water quality in the Red Sea is imperative for the continued sustenance of key industries like desalination and aquaculture, as well as to ensure minimal public health impact. Through the use of next-generation sequencing, this study aims to evaluate the impact anthropogenic contamination has on seawater microbiota at four sampling zones of near-shore water (<1.5km from the coast) and from two swash zones of local beaches. Conventional water quality parameters relating to nutrient content and enterococci numbers were also monitored. Occasional breaches in the enterococci numbers (> 35 MPN/100ml) and significantly higher abundance of genera associated with opportunistic pathogens were detected in the water samples collected from swash zones of beaches. Total organic carbon (1.48-2.18 mg/L) and nitrogen (0.15-0.27 mg/L) content in these water samples were also significantly higher than that detected in the near-shore waters (1.13 mg/L for organic carbon and 0.09 mg/L for total nitrogen). The abundance of certain genera, for example Clostridia group, was observed to correlate with the nutrient content (Spearman?s rank > 0.503). Furthermore, Enterococcus faecalis and E. faecium isolated from the beach sands showed resistance to up to 5 types of antibiotics (i.e., kanamycin, erythromycin, chloramphenicol, ceftazidime and meropenem). OTUs associated with cyanobacteria, Prochlorococcus and Ostreococcus were more prevalent in the near-shore waters collected in closest proximity to a sewage outfall. Microbial richness at these sites was on average 702 OTUs, and was significantly lower than the average 1062 OTUs determined from all other samples. Our findings suggest that anthropogenic contamination arising from sewage discharge and recreational activities resulted in different extent of perturbations on marine water community in near-shore and swash zones of the Red Sea.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline
This study utilizes a metagenome-based approach to elucidate the phylogenetic and functional gene diversity of fecal microbiome in Galapagos land and marine iguanas.

While much has been known about the fecal microbiome of mammalian herbivorous, little is known about the fecal microbiome of reptilian herbivores. To elucidate the functional gene diversity of reptilian herbivores, we performed a metagenome-based analysis of the fecal samples from the algae-consuming marine iguana (Amblyrhynchus cristatus) and terrestrial flora-consuming land iguanas (genus Conolophus) that are indigenous on the Gal?pagos Archipelago. Further comparison was made against the mammalian herbivorous hosts, and our findings suggested that the phylogenetic affiliations of both land iguanas (LI) and marine iguanas (MI) fecal microbiota clustered apart, and shared low similarity with the mammalian herbivorous hosts. Furthermore, functional gene diversities in both iguana hosts showed differentiation based on the diet, in which the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-flora consuming LI iguana and herbivorous mammalian hosts. The differentiation in the functional gene diversity of MI fecal microbiota is likely attributed to a distinctly unique diet that is based on marine algae. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM) and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous mammalian and reptilian hosts, reiterating the important roles these genes have in the breakdown and metabolism of herbivorous diet. However, some classes of carbohydrates-degrading families like GH2, GH13, GT2, GT4, CBM50, CBM48, CE4 and CE11, as well as genes associated with sulfur metabolism and dehalogenation were highly expressed or unique to the MI fecal microbiota. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and carbohydrate-degrading families like GH13, GH66, GT2, GT4, CBM50, CBM13, CE4 and CE8 were highly abundant in the LI. Certain bacterial populations were enriched over ten generations in various substrates (e.g. glucose, arabinose, xylose), and the enriched populations exhibited differences based on the iguana host and the type of enrichment substrate. Majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g. GT2, GT4, GT28, GT35 and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.

Biome: root:Host-associated:Reptile
Multiple approaches detect the presence of fungi in human breast milk samples.

BackgroundHuman breast milk contains a variety of bacteria, which is transmitted to the infant and contributes to microbiota development and immune maturation. The description of fungal organisms in breastmilk from healthy mothers is uncovered although the presence of fungal species has been reported in the human gut and in other mammalians? milk.  Methods  Breast milk samples from healthy lactating mothers (n=65) within 1 month after birth were analyzed. Fungal presence was confirmed by microscopy using fungal-specific fluorescent probes (FISH), isolation in culture media and isolates identification by specific ITS and 18S PCR and Sanger-sequencing.  Total fungal load was estimated by qPCR using fungal-specific primers, and the fungal composition was determined by 28S high-throughput rDNA sequencing. In addition, milk macronutrients and human somatic cells were also quantified by spectrophotometry and cytometry. ResultsUsing different culture media, we isolated 18 strains, whose ITS and 18S rDNA genes sequencing led to confirm the presence of viable fungal species. The qPCR data showed that 89% of the samples had detectable levels of fungal DNA, at an estimated median load of 4,1x105 cells/ml in colostrum, 4,5x105 cells/ml in transition milk and 2,8x105 cells/ml in mature milk samples. Pyrosequencing of the PCR-amplified 28S rDNA gene showed that the most common genera detected were Malassezia (44%), followed by Candida (19%) and Saccharomyces (12%). Nutrient analysis of the milk samples showed significant positive correlations of Malassezia presence with lactose content, and Candida presence with protein content. We also found a significant negative correlation between Lodderomyces genus and human somatic cells, as well as positive correlations of Cladosporium and Alternaria with bacterial load. ConclusionsIn this study we have detected the presence of viable fungal species in human breast milk.  Interaction between fungi and milk?s components and bacteria present may have a relevant role for infant?s health development. However, further research should be performed to understand the origin and role of these microorganisms and their potential transmission to the developing infant.

Biome: root:Host-associated:Human:Milk
Metagenomic analysis of anaerobic reactors for wastewater treatment

Differently seeded but functionally identical anaerobic sequencing batch reactors were analysed using metagenomic and metaproteomic analyses

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
A Metagenomic Anlaysis of a Winogradsky Column Supplemented with Molybdate

Two Winogradsky Columns were constructed from the University of Strathclyde burn. A control column and a column supplemented with Molybdate were created. The columns were homogenised and metagenomic analysis was carried out using WGS sequencing on an Ion Torrent PGM Sequencer. It was hypothesised that the column containing Molybdate should be enriched with nitrate reducing bacteria.

Biome: root:Engineered:Bioremediation:Hydrocarbon
Citrate addition enhanced anaerobic hydrocarbon degrader activity

Citrate addition can increase phosphorus and hydrocarbon bioavailability to enhance hydrocarbon bioremediation, but the overall microbial community response is poorly understood. In order to elucidate the potential mechanisms of citrate addition for hydrocarbon biostimulation, the structure and function of microbial communities were investigated in a gasoline-contaminated site in calcareous cold region soil.There are three treatments (no amendment, phosphate amendment, phosphate and citrate amendment) for the biostimulation deliveries. DNA was extracted from soils for different biostimulation treatments. 16S metagenomics sequencing library was constructed with primers 926F and 1392R and was sequenced on an Illumina Miseq sequencer.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Microbes present in feed to Atlantic salmon

THe samples are to investigate the type of microbes that Atlantic salmon are feed through feed

Biome: root:Engineered:Food production
Disentangling facilitation drivers in arid environments: the role of soil microorganisms

1.\tNurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking. \n2.\tIn three microhabitats (gaps, small and large Retama shrubs), we placed 6 microcosms with sterilized soil, two per soil origin (i.e., from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing. \n3.\tGermination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage.\n4.\tNurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse belowground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.

Biome: root:Environmental:Terrestrial:Soil:Desert
Samples from salt marshes in the south of England

Samples were collected from natural and realigned sites, and during Summer and Winter.

Biome: root:Environmental:Terrestrial:Soil
Citrate may stimulate the anaerobic hydrocarbon degraders in the groundwater

Citrate addition can increase phosphorus and hydrocarbon bioavailability to enhance hydrocarbon bioremediation, but the overall microbial community response is poorly understood. In order to elucidate the potential mechanisms of citrate addition for hydrocarbon biostimulation, the structure and function of microbial communities were investigated in a gasoline-contaminated site in calcareous cold region soil.There are three treatments (no amendment, phosphate amendment, phosphate and citrate amendment) for the biostimulation deliveries. DNA was extracted from Tenax beads incubated in two infiltrators for different biostimulation treatments. 16S metagenomics sequencing library was constructed with primers 926F and 1392R and was sequenced on an Illumina Miseq sequencer.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Atlantic salmon Microbiota

Pilot study to determine if it was possible to isolate DNA from the commensal microbiota present on healthy Atlantic salmon skin-mucus and intestinal content to be used for PacBio sequencing

Biome: root:Host-associated:Fish
Gut microbiome from patients obtained by 16s rRNA sequencing.

Advento study is a research about chronic diseases that are frequent in adult population, specially diabetes and cardiovascular conditions.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Comparison between samples obtained from Curua Una reservoir

Three samples were collected from Curua Una reservoir to compare metagenomic features between samples.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems