SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2013

This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2013 from a number of low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples.  Previous work at this site determined the taxonomic structure and distribution of microbial communities in venting fluids, but the contribution and mechanisms of the different redox driven metabolisms and the impact these reactions have on vent chemical signatures have not been fully characterized. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
biogas

biogas from swine manure

Biome: root:Engineered:Wastewater:Water and sludge
Microbial community structure in six deep crystalline bedrock fracture zones

Bacterial and archaeal communities from six fracture zones from 180-2300 m depths in Outokumpu crystalline bedrock were characterized using high-throughput amplicon sequencing.

Biome: root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada

Most streams receive substantial inputs of allochthonous organic material in the form of leaves and twigs (CPOM, coarse particulate organic matter). Mechanical and biological processing converts this into fine particulate organic matter (FPOM). Other sources of particles include flocculated dissolved matter and soil particles. Fungi are known to play a role in the CPOM conversion process, but the taxonomic affiliations of these fungi remain poorly studied. The present study seeks to shed light on the composition of fungal communities on FPOM and CPOM as assessed in a natural stream in Nova Scotia, Canada. Maple leaves were exposed in a stream for four weeks and their fungal community evaluated through pyrosequencing. Over the same period, four FPOM size fractions were collected by filtration and assessed. Particles had much lower ergosterol contents than leaves, suggesting major differences in the extent of fungal colonization. Pyrosequencing documented a total of 821 fungal operational taxonomic units (OTU), of which 726 were exclusive to particles and 47 to leaf samples. Most fungal phyla were represented, including yeast lineages (e.g., Taphrinaceae and Saccharomycotina), Basidiomycota, Chytridiomycota and Cryptomycota, but several classes of Pezizomycontina (Ascomycota) dominated. Cluster dendrograms clearly separated fungal communities from leaves and from particles. Characterizing fungal communities may shed some light on the processing pathways of fine particles in streams and broadens our view of the phylogenetic composition of fungi in freshwater ecosystems.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Assessing the groundwater quality at a Saudi Arabian agricultural site and the occurrence of antibiotic-resistant opportunistic pathogens on irrigated food produce

This study monitors the groundwater in wells situated near to agricultural fields of Saudi Arabia. Vegetables irrigated with the groundwater were also assessed for their microbial safety. The amount of total nitrogen exceeded the 15 mg/L permissible for agricultural irrigation in most of the sampled groundwater. Fecal coliforms in density >12 MPN/100 mL were detected in some of the groundwater wells of close proximity to a chicken farm. Coupled with qPCR-based fecal source tracking, monitoring effort showed that groundwater in two of the wells nearest to the chicken farm were relatively more perturbed than the other wells. Anthropogenic contamination resulted in a shift of predominant bacterial phylum within the groundwater microbial communities. Specifically, there was an elevated presence of Proteobacteria but a lower microbial richness in the groundwater perturbed by anthropogenic contamination. Acinetobacter was detected at high relative abundance of up to 48.6% in the total microbial community of groundwater but culture-based analysis did not recover any antibiotic-resistant bacteria and opportunistic pathogens from the groundwater. Although Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the vegetables irrigated with the groundwater, quantitative microbial risk assessment suggests that the annual risk incurred from consumption of these vegetables are within the acceptable limits of 10-4. Our findings highlighted that the groundwater quality at this agricultural site in the western Saudi Arabia was not as pristine as commonly perceived. Despite the poor groundwater quality, there was no significant impairment of food quality arising from the groundwater.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Bioremediation and metal resistant bacteria in a closed, cold northern mine

Closed, water filled mined produce heavy metal rich acid mine draining that affects the environment in many ways. In this study we have characterized the bacterial community on the water of closed Kotalahti mine by 16S rRNA gene targeted 454 amplicon sequencing as well as by heavy metal resistance gene targeting clone libraries combined with Sanger sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Mine drainage
Microbial and geochemical sampling in high pressure, low biomass terrestrial subsurface Pyhäsalmi mine.

Microbial and geochemical sampling in high pressure, low biomass terrestrial subsurface Pyh?salmi mine. Pyrosequencing of bacterial and archaeal 16S rDNA and rRNA and fungal ITS DNA and cDNA fractions.

Biome: root:Environmental:Terrestrial:Soil:Mine
Probing the texture of the rare biosphere

Probing the texture of the rare biosphere: We have bracketed the dimensions of the rare biosphere in two marine bacterial samples by comparing a deep (1 million sequences per sample) pyrosequencing analysis of the two samples and the cultures isolated from one of them.

Biome: root:Environmental:Aquatic:Marine
Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland

In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 m to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths.

Biome: root:Environmental:Terrestrial:Geologic
Canonical correlation methods for exploring microbe-environment interactions in deep subsurface

The active and general sulphate reducing bacterial popilation of crystalline bedrock fracture fluids from Olkiluoto Island, Finland, were investigated by dsrB gene and transcript trageted 454 amplicon sequencing. The effect of geochemical parameters on the SRB community was tested by canonical correlation methods.

Biome: root:Environmental:Terrestrial:Geologic
Microbial communities and nutrient dynamics in experimental microcosms are altered after the application of a high dose of Bti

Bacillus thuringiensis subsp. israelensis (Bti) is the most widely used biopesticide against mosquitoes and blackflies, with a history of high specificity and efficacy. However, interactions of Bti with native microfauna in the environment are poorly understood. High and low Bti (VectoBac G) applications, in addition to an untreated control, were assigned to replicate ?1 m^2? mesocosms in a completely randomized design under field conditions. The abundance of Culex spp., phytoplankton, sestonic particulates, nutrients and other water quality parameters were assessed throughout this large-scale 82-day field study. Bacterial communities present in the water column were assessed by next generation sequencing of 16S rRNA genes, comparing treatments and sampling dates. The high Bti application rate significantly reduced mosquito abundance, phytoplankton biomass, sestonic particulates, nutrients, and other physicochemical variables in the water, and was also associated with higher bacterial diversity. Beta diversity analysis revealed that bacterial communities in the water column were influenced significantly by the high Bti treatment. Together, our results demonstrate significant dose-dependent changes to aquatic ecosystem chemistry and bacterial community composition associated with Bti application.

Biome: root:Engineered:Modeled
Microbiota, microbiome, and virome of an aquaculture sample

This study aims to characterize the microbial ecology of a water sample collected from a salmonid aquaculture plant.

Biome: root:Environmental:Aquatic:Aquaculture
Uncultured archaeal communities in anoxic, saline groundwater were characterized using 16S rRNA and rDNA targeted 454 amplicon sequencing.

Uncultured archaeal communities in anoxic, saline groundwater were characterized using 16S rRNA and rDNA targeted 454 amplicon sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Bacterial diversity in groundwater of three hard-rock aquifers in the Armorican massif (Brittany, France)

Hard-rock aquifers are widespread subsurface habitats that are readily colonized by microorganisms. These environments are characterized by heterogeneous hydrologic circulation, which strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. However, little is known about the effects of hydrologic circulation on microbial communities. Groundwater of different ages (residence time) was sampled along hydrogeologic flow paths in three contrasting hard-rock aquifers in Brittany (France). Residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by community RNA extraction and 454 sequencing of 16S rRNA amplicons.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling

Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Additionally, bacterial cell numbers and bacterial production were assessed . Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs) affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas "Pelagibacterales" were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads) was affiliated with "Pelagibacterales" and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads) was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Photic zone
The microbial community of aquatic sediments influenced by heavy metals

Microbial communities within sediments regulate biogeochemical cycling throughout aquatic ecosystems.  However, microbial community structure can become influenced through heavy metal toxicity, often caused by anthropogenic disturbance.  Toxicity of heavy metals can become reduced over time through mineralization and/or sorption of previously bioavailable metal ions.  As consequence, it is anticipated that microbial communities should exhibit a more pronounced observable response to available metal concentrations within the local environment.  In this study, lake sediments collected from two heavy metal impacted geographical regions (Poyang Lake, China and sites adjacent to the Muskegon Watershed, MI, USA) were analyzed for microbial community structure using high-throughput sequencing technology.  Total and available metal concentrations were also investigated in order to elucidate the relative strengths each fraction exerted on local sediment microbial communities.  Results indicate a weak relationship of metal influence on microbial community diversity, but strong positive and negative correlations of available heavy metals with specific taxonomic groups and OTUs of bacteria and archaea.  This shows the importance of analyzing available metals when examining the impact of this disturbance on microbial community structure within aquatic sediments.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Bacterial diversity assessment of Tulshi shyam hot spring using metagenomic appraoch

A taxonomic description of bacteria was deduced from 5.78 MB metagenomic sequence retrived from Tulshi shyam Hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Changeability of bacterial community composition caused by seawater exposure to crude oil at low temperature

A crude oil contamination at sea causes changes in marine bacterial abundance and composition. Microorganisms that are initially undetectable in a pristine environment become prevalent following an exposure to petroleum compounds. The overarching goal of the study were examine through laboratory experiments changes in abundance and composition of bacteria. Here we present laboratory data obtained with crude oil in the range 30ppb ? 2000ppb (nominal concentration) during an 11 days exposure. Changes in chemical composition coincided with major changes in total number of bacteria as well as in bacterial composition.

Biome: root:Engineered:Biotransformation:Microbial enhanced oil recovery
Microbial diversity and the implications of sulfide levels in an anaerobic
reactor used to remove an anionic surfactant from laundry wastewater

The objective of this study was to evaluate the removal of linear alkylbenzene sulfonate (LAS) from commercial laundry wastewater using an expanded granular sludge bed (EGSB) reactor with two specific LAS\nloading rates (SLLRs), 1.0 and 2.7 mg LAS gVS ?1 d ?1. The biomass was characterized using denaturing gradient gel electrophoresis (DGGE) and 16S Ion Tag sequencing. Higher LAS removal (92.9%) was observed\nin association with an SLLR of 1.0 mg LAS gVS ?1 d ?1 than with an SLLR of 2.7 mg LAS gVS ?1 d ?1 (58.6%). A\nrelationship between the S ?2 concentration in the effluent and the surfactant removal efficiency was\nobserved. This result is indicative of the inhibition of LAS-removing microbiota at S ?2 concentrations\ngreater than 20 mg S L?1. By using DGGE, microbial stratification was observed in the reactor in association with granule size, even though the reactor is considered to be a completely mixed regime. The\nRDP-classifier identified 175 genera, 33 of which were related to LAS degradation.

Biome: root:Engineered:Wastewater:Industrial wastewater
A flow-through rolling tank allows to conduct experiments on particulate organic matter at near in-situ conditions.

Downward fluxes of particulate organic matter (POM) are the major sink of atmospheric CO2 into aquatic sediments, remaining there for thousands of years. Budget calculations of the biological carbon pump are greatly based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, thus, strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities follow those in-situ, contrary to rapidly changing ones in closed rolling tanks. The active particle-associated community in the flow-through system is stable over several days contrary to several hours previously reported. Decrease in particles photosynthetic rates is much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes, using our new experimental tool.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
Functional redundant and similar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here we describe our findings regarding the functional redundancy and similarity of involved microorganisms in four continuously-stirred tank lab-scale biogas reactors (CSTRs, 39 ?C, 12 L volume) supplied with different mixtures of sugar beet silage (SBS) and maize silage (MS) resulting in similar biogas yields in all reactors. CSTRs were set-up with inoculum from a full-scale biogas plant, fed with mixtures of MS and SBS in the ratios of 1:0 (CF1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kg VS m-3 d-1) and operated for 140 d. The compositions of bacterial and archaeal communities degrading the different substrate mixtures were analyzed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. As the compositional shifts within the microbial communities did not influence the respective biogas production, similar process dynamics indicate functional redundant archaeal and functional similar bacterial communities in each individual CSTR.

Biome: root:Engineered:Biogas plant:Wet fermentation
Mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diet

Feeding alternative diet to replace the conventional fishmeal diet has been the focus in aquaculture nutrition. This study investigates the effect of two alternative diets on the GIT of rainbow trout raised in a cultured environment.

Biome: root:Host-associated:Fish:Digestive system
Removal of bacterial contaminants and antibiotic resistance genes by conventional wastewater treatment processes in Saudi Arabia: Is the treated wastewater safe to reuse for agricultural irrigation?

This study aims to assess the removal efficiency of microbial contaminants in a local wastewater treatment plant over the duration of one year, and to assess the microbial risk associated with reusing treated wastewater in agricultural irrigation. The treatment process achieved 3.5 logs removal of heterotrophic bacteria and up to 3.5 logs removal of fecal coliforms. The final chlorinated effluent had 1.8 x 102 MPN/100 mL of fecal coliforms and fulfils the required quality for restricted irrigation. 16S rRNA gene-based high-throughput sequencing showed that several genera associated with opportunistic pathogens (e.g. Acinetobacter, Aeromonas, Arcobacter, Legionella, Mycobacterium, Neisseria, Pseudomonas and Streptococcus) were detected at relative abundance ranging from 0.014 to 21 % of the total microbial community in the influent. Among them, Pseudomonas spp. had the highest approximated cell number in the influent but decreased to less than 30 cells/100 mL in both types of effluent. A culture-based approach further revealed that Pseudomonas aeruginosa was mainly found in the influent and non-chlorinated effluent but was replaced by other Pseudomonas spp. in the chlorinated effluent. Aeromonas hydrophila could still be recovered in the chlorinated effluent. Quantitative microbial risk assessment (QMRA) determined that only chlorinated effluent should be permitted for use in agricultural irrigation as it achieved an acceptable annual microbial risk lower than 10-4 arising from both P. aeruginosa and A. hydrophila. However, the proportion of bacterial isolates resistant to  6 types of antibiotics increased from 3.8% in the influent to 6.9% in the chlorinated effluent. Examples of these antibiotic-resistant isolates in the chlorinated effluent include Enterococcus and Enterobacter spp. Besides the presence of antibiotic-resistant bacterial isolates, tetracycline resistance genes tetO, tetQ, tetW, tetH, tetZ were also present at an average 2.5 x 102, 1.6 x 102, 4.4 x 102, 1.6 x 101 and 5.5 x 103 copies per mL of chlorinated effluent. Our study highlighted that potential risks associated with the reuse of treated wastewater arise not only from conventional fecal indicators or known pathogens, but also from antibiotic-resistant bacteria and genes.

Biome: root:Engineered:Wastewater:Water and sludge
Impact of the diet on the intestinal microbiota in African children moving from rural to urban areas

We studied the intestinal microbial changes in groups of African children belonging to the same ethnicity in which transition from a rural environment to urban areas, together with improvement of socio-economic conditions, results in exposure to a ?globalized? western type diet. Introduction of foods from animal origin and rich in fat and simple sugar into a traditional African diet, composed by cereals, legumes and vegetables, causes gut microbiota shift, leading to progressive loss of biochemical functions associated to production of Short Chain Fatty Acids. Key microbial profiles are lost in the course of urbanization and improvement of economic conditions independently from geography and ethnicity, resulting in a marked shift in bacterial communities, typical of western populations.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomics of the mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diets

Rainbow trout is an important aquaculture species. Feeding alternative diet to replace the conventional fishmeal diet has been the focus in aquaculture nutrition. This study investigates the effect of two alternative diets on the GIT of rainbow trout raised in a cultured environment.

Biome: root:Host-associated:Fish:Digestive system