SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Biogeography of bacterioplankton communities in freshwater boreal ecosystems

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S rRNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Qu?bec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams towards larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (i.e., the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
metagenome of thermophilic anaerobic sludge before and after antibiotic exposure

metagenome of thermophilic anaerobic digested sludge before and after oxytetracycline exposure was sequenced using Illumina Hiseq. And, the mobilomes of both sludge were analyzed.

Biome: root:Engineered:Wastewater:Water and sludge
Performance and microbial community composition in a long-term operated sequential anaerobic-aerobic bioreactors treating coking wastewater

The anaerobic and aerobic combined biosystem is assumed to consume less energy for the treatment of high strength industrial wastewater. In this study, the pollutant removal performance and microbial diversity were revealed in a long run (over 300 days) bench scale sequential anaerobic-aerobic biosystem treating coking wastewater. Anaerobic treatment could remove one third of COD and more than half of phenols at a hydraulic retention time of 42 hours, while the combined system with a total HRT of 114 hours removed COD, TOC, total phenols, thiocyanate and cyanide by 81.6?3.3%, 85.2?4.2%, 99.9?0.02%, 98.2?0.3, 87.2?3.9% respectively. Comprehensive two dimensional gas chromatography with time-of-flight mass spectrometric analysis revealed almost complete removal of phenol derivatives and nitrogenous heterocyclic compounds (NHCs) by the combination in which anaerobic process alone contributed in average 58.4% and 59.1% removal, respectively. In order to appraise microbial activity in bioreactors, the bacterial, archaeal and fungal communities were analyzed by 454 pyrosequencing. Proteobacteria (relative abundance 61.2 - 93.4%), particularly Betaproteobacteria (34.4-70.1%) were the most predominant bacterial group. Phenol degrading and hydrolytic bacteria like Ottowia (14.1-46.7%), Soehngenia (3.0-8.2%) and Corynebacterium (0.9-12.0%) were most abundant genera in anaerobic sludge, whereas in aerobic sludge Thiobacillus (6.6- 43.6%), Diaphorobacter (5.1-13.1%) and Comamonas (0.2-11.1%)were speculated as major degraders of phenol, thiocyanate and NHCs, respectively. Despite of low density of fungi, oleaginous yeast Trichosporon which degrades phenolic compounds was found abundant in aerobic sludge. The results revealed that the removal of pollutants was related with phylogenetic abundance of microbial diversity. This study revealed the feasibility of less energy intensive optimization for the removal of organic pollutants from coking wastewater, and the potential association between some important bacterial groups and key pollutants.

Biome: root:Engineered:Wastewater:Industrial wastewater
High habitat-specificity in fungal communities of an oligo-mesotrophic, temperate lake

Freshwater fungi are a poorly studied paraphyletic group that include a high diversity of phyla. Most studies of aquatic fungal diversity have focussed on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in meso-oligotrophic, temperate Lake Stechlin in northern Germany, including the pelagic and littoral water column, sediments, and biotic substrates. We pyrosequenced a universal eukaryotic marker within the ribosomal large subunit (LSU) in order to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1024 fungal OTUs (97% criterion). Diversity was highest in the sediment, biofilms, and benthic samples (293-428 OTUs), intermediate in water and reed samples (36-64 OTUs), and lowest in plankton (8 OTUs) samples. NMDS clustering clearly grouped the eight studied habitats into six clusters, indicating that total diversity was strongly influenced by turnover among habitats. Fungal communities exhibited pronounced changes at the levels of phylum and order along a gradient from littoral to pelagic habitats. The large majority of OTUs could not be classified below the order level due to the lack of aquatic fungal entries in taxonomic databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat-specificity to total fungal diversity. This remarkable diversity is probably an underestimate, because most lakes undergo seasonal changes and previous studies have uncovered differences in fungal communities among lakes.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Metatranscriptomes from Blanes Bay, Barcelona, mesocosm experiments

Water from Blanes Bay was incubated for nine days in mesocosms. The water was treated with nutrients (NO3, PO4, SiO4; NA and NB samples) and acidified using CO2 (KA and KB samples). RNA after stable RNA depletion and poly-T depletion was Illumina sequenced.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
Ammonia oxidizing microorganisms are an important source of nitrous oxide (N2O) in aquatic environments

Ammonia oxidizing microorganisms are an important source of nitrous oxide (N2O) in aquatic environments, , but the impact that acidification has on the rate and mechanism of N2O production by these organisms is not well understood. Here we present evidence from 15N-tracer incubations that acidification (from pH 7.54 to 7.20) significantly enhances N2O production by the ammonia oxidizer community in the shallow hypolimnion (17 m) of Lake Lugano in southern Switzerland. This community is dominated by the ammonia oxidizing bacteria of the genus Nitrosospira. Although ammonia oxidation rates were not significantly different among the pH treatments, the pH reduction did enhance the yield, or the ratio of N2O relative to NOx- (nitrite + nitrate) produced by ammonia oxidizers, from 2.6 × 10-5 to 8.8 × 10-5 mol N-N2O/mol N-NOx- at an O2 concentration of 290 μM, and from 5.7 × 10-5 to 12.1 × 10-5 mol N-N2O/mol N-NOx- at an O2 concentration of 70 μM. The increases were due at least in part to enhanced incorporation of N derived from exogenous NO2- into N2O. Incorporation of N from this exogenous NO2- is consistent with hybrid N2O formation, where the N2O produced contains one ammonia- (NH3-) derived N atom and one nitrite- (NO2-) derived N atom but it is not consistent with nitrifier denitrification (enzymatic reduction of 2 NO2- to N2O). In all incubations, most of the N incorporated into N2O appears to have been derived from NH3 rather than exogenous NO2-. We also present evidence of hybrid N2O formation during similar incubations of seawater (at its unaltered pH) from 200 m depth off the coast of Namibia, a coastal upwelling zone and known hotspot of N2O production whose ammonia oxidizer community is dominated by archaea.

Biome: root:Environmental:Aquatic
Acidification and warming affect prominent bacteria during two seasonal phytoplankton bloom mesocosms

In contrast to clear stimulatory effects of rising temperature, recent studies reported conflicting results of CO2 effects on planktonic bacteria. To obtain a better understanding of the impact of future climate scenarios on the development of bacterial communities, we performed bifactorial mesocosm experiments (pCO2 and temperature) with Baltic Sea water, during a diatom bloom in autumn and during a summer bloom. The development of bacterial community composition BCC followed well-known bloom dynamics with Alphaproteobacteria dominating during the bloom peak and Bacteroidetes dominating during bloom decay. A principle coordinate analysis (PCoA) of bacterial OTUs (operational taxonomic units) revealed that phytoplankton succession and temperature were the major bacterial community structuring variables whereas only a weak impact of pCO2 was found. This was corroborated by the trends in bacterial bulk parameters. However, significant and potentially direct effects of pCO2 on the relative abundance of several dominant OTUs occurred and were in some cases accompanied by an antagonistic temperature effect. Our results suggest the necessity of high-resolution BCC analyses and statistical analyses on OTU level to observe strong effects of CO2 on specific bacterial groups, which in turn might influence also particular organic matter degradation processes.

Biome: root:Environmental:Aquatic:Marine
Four metagenomes and four metatranscriptomes sampled along a transect in the plume of the Sarno River in the Gulf of Naples (Italy).

The study aimed to investigate closely related samples under the influence from the Sarno River, the most polluted river in Europe, to inform about differences within the taxonomical and functional diversity along a transect from the rivers mouth to the open Gulf of Naples.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Fecal microbiome transplantation between chow-fed and high fat diet-fed rats

Obesity, insulin resistance and the metabolic syndrome are associated with changes to the gut microbiota; however, the mechanism by which modifications to the gut microbiota might lead to these conditions is unknown. Here we show that increased production of acetate by an altered gut microbiota leads to activation of the parasympathetic nervous system which in turn promotes increased glucose-stimulated insulin secretion (GSIS), increased ghrelin secretion, hyperphagia, obesity and its related sequelae. Taken together, these data identify increased acetate production by a nutrient-gut microbiota interaction and subsequent parasympathetic activation as possible therapeutic targets for obesity.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Minimum Effective Concentration of Streptomycin in Inducing Antibiotic Resistance

It has been demonstrated that antibioticresistancecould be selected for and enrichedunder high antibiotic concentrations in biological wastewater treatment systems. However, limit knowledge is known about the antibiotic concentrations in influents that exert selection for antibiotic resistance in biological wastewater treatment systems.Herein, this study investigated the long-term effects of different streptomycin concentrations on selection of antibiotic resistance in an aerobic biofilm reactor treating simulated antibiotic production wastewater(606 days)by using multiple culture-independent andculture-dependent methods. qPCR, high-throughput quantitative PCR and metagenomic sequencing were used to detected ARGs and MGEs.Although the efficient COD removal from 88.52% to 92.83%was observed across all six stages (streptomycin: 0, 0.1, 1, 5, 25, 50 mg/L), increasing streptomycin concentration caused proliferation of ARB, ARGs and MGEs.And the Minimum effectiveconcentration of streptomycin causing a significant increase of relative abundance of ARGs and MGEs was at the levels ranging from 1 to 5 mg•L-1. This work proposed an experimental significant effect concentration which can guide implementation of antibiotic emission limits into biological treatment systems.

Biome: root:Engineered:Wastewater:Water and sludge
Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

This study aimed to reveal how antibiotic resistance genes (ARGs) and their horizontal and vertical transfer-related items (mobilome and bacterial hosts) respond to the transformation of anaerobic digestion (AD) from mesophilic to thermophilic using the strategy of one-step temperature increase. The resistomes and mobilomes of mesophilic and thermophilic sludge were investigated using metagenome sequencing, and the changes in twenty-four representative ARGs belonging to three categories, class 1 integron and bacterial genera during the transition period were further followed using qPCR and 454-pyrosequencing. After temperature increase, the abundance of the resistome of digested sludge decreased from 125.97 ppm (day 0, mesophilic) to 50.65 ppm (day 57, thermophilic) with the reduction of most ARG types except for the aminoglycoside resistance genes. Thermophilic sludge also had a smaller mobilome, including plasmids, insertion sequences and integrons, than that of mesophilic sludge, suggesting the lower horizontal transfer potential of ARGs under the thermophilic condition. On the other hand, the total abundance of 18 bacterial genera, which were suggested as the possible hosts for 13 ARGs through network analysis, was decreased from 23.27% in mesophilic sludge to 11.92% in thermophilic sludge, indicating less hosts for the vertical expansion of ARGs after the hike of temperature. The results highlighted that the better reduction of resistome abundance by thermophilic AD might be associated with the decrease of both the horizontal and vertical transferabilities of ARGs.

Biome: root:Engineered:Wastewater:Water and sludge
A metaproteomic analysis of the response of a freshwater microbial community under nutrient enrichment

Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
anaerobic digestion

anaerobic digestion

Biome: root:Engineered:Wastewater:Water and sludge
Organic micropollutants in aerobic and anaerobic membrane bioreactors (MBR): changes in microbial communities and gene expression

The effect of organic micro-pollutants (OMPs) in wastewater on the microbial populations essential to the aerobic activated sludge and anaerobic digestion processes is not well understood. The purpose of this study was to examine the effect of OMPs on microbial population dynamics associated with both aerobic and anaerobic wastewater treatment. It was also desired to determine what OMPs show better biodegradability in aerobic compared to anaerobic membrane bioreactor (MBR) systems while monitoring biodegradation-related and antibiotic resistance-related gene expression levels in both reactors. To achieve this, two MBR systems (aerobic and anaerobic) were operated under the same conditions, treating wastewater spiked with a cocktail of 27 OMPs. Next-generation sequencing platforms were used to monitor changes in the microbial populations in the MBRs and their gene expression levels. Results show that spiking of OMPs in the wastewater feed had a clear effect on predominant and keystone bacterial populations in both MBRs while also significantly impacting gene expression levels associated with biodegradation. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while also ultimately impacting the presence of associated antibiotic resistance genes in both systems.

Biome: root:Engineered:Wastewater:Water and sludge
Metagenomic analysis of microbes attached to fuel cell electrodes

Whole genome shotgun metagenomics of microbes attached to closed circuit and open circuit fuel cells.

Biome: root:Engineered
Alterations of the Fecal Microbiome in Parkinson's Disease

In the course of Parkinson's disease (PD), the enteric nervous system is probably the first structure being affected by alpha-synuclein pathology. Recent research has shown that there is an intense bidirectional interaction between gut microbiota and the brain via diverse pathways. We speculated that intestinal microbiota may be implicated in PD. We compared the fecal microbiomes of 72 PD patients and 72 control subjects by pyrosequencing the bacterial 16S rRNA gene.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Influence of carbon sources and concrete on microbially induced corrosion of carbon steel in subterranean groundwater environment

Microbially induced corrosion of carbon steel was assessed in environment simulating deep geological repository of radioactive waste. A dense and diverse biofilm was formed on surfaces of steel in biotic systems without concrete. Addition of nutrients changed the bacterial communities forming biofilm, increased corrosion rate and changed the properties of corrosion products i.e. composition and resistance. Presence of concrete altered the corrosion behaviour of steel and hindered the biofilm formation on steel. The corrosion rate was consistently radically decreased, as the properties of the corrosion product, were different from those in the other systems.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing DS10

High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and alpha-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Microbial biogeography of grapes predicts regional metabolite patterns in wine

Microbial activity is an inherent feature of wine production. The microbial communities of grapes present regionally defined patterns, influenced by vineyard and climatic conditions. However, the degree to which these microbial patterns associate with the chemico-sensory qualities of wine is unclear. We demonstrate that both grape microbiota and wine metabolite profiles distinguish growing sub-regions and individual vineyards within Napa and Sonoma County, California. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate closely with the chemical composition of the finished wines. Grape must microbiota serve as highly accurate biomarkers for predicting metabolite abundance in finished wines using machine-learning models. The use of pre-harvest microbiota as an early predictor of wine qualities is unprecedented and poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is a definable feature that quantitatively contributes to wine terroir.

Biome: root:Host-associated:Plants
Thermophilic two-phase anaerobic digestion using innovative fixed-bed reactor for enhanced organic matter removal and bioenergy recovery from sugarcane vinasse

Thermophilic two-phase anaerobic digestion using innovative fixed-bed reactor for enhanced organic matter removal and bioenergy recovery from sugarcane vinasse

Biome: root:Engineered:Biotransformation:Mixed alcohol bioreactor
Nitrification at different salinities: biofilm community composition and physiological plasticity

The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities in nitrifying moving bed bioreactors operated at different salinities; freshwater, brackish (20 ‰) and seawater. The microbial communities from the biofilm carriers were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. The nitrifying fraction of the communities were identified and compared between the reactors operated at distinct salinities.

Biome: root:Engineered:Bioreactor
Inhibition factors in biofilm N removal systems treating wastes generated by amine based CO2 capture

The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities associated with bioreactors for biological nitrogen removal for treating wastes generated by amine based CO2 capture. In order to identify limiting factors for successful up-scaling, we compared the nitrifying activity of moving bed biofilm reactors (MBBR) with or without chronic exposure to organic loading in the form of acetate. Three moving bed biofilm reactors (MBBR) were operated for 48 days in continuous mode. Reactor 1 was run as a control to confirm process stability, while chronic exposure to organic loading was tested in duplicate (Reactor 2 and 3) in order to verify reproducibility. To study inhibition and the effect on the relative abundance of nitrifying bacteria within the nitrifying biofilm over time, the bacterial communities were characterized by pyrosequencing of 16S rDNA amplicons. The sequence data were used for determining the relative abundance of ammonia and nitrite oxidizing bacteria.

Biome: root:Engineered:Bioreactor:Continuous culture