SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Relationship between co-substrate and microbial composition in the degradation of anionic surfactant

Different carbon sources were used as co-substrate to evaluate the removal of linear alkylbenzene sulfonate (LAS) from laundry wastewater, as well as the related microbial community. An anaerobic fluidized bed reactor (AFBR) was operated in three stages, after the biomass adaptation without LAS (stage I). Those stages were differentiated by the co-substrate supplementation: stage II, sucrose plus ethanol, stage III, only ethanol, stage IV, no co-substrate. Laundry wastewater was diluted to obtain approximately 20 mg.L-1 of LAS in the AFBR influent. The replacement of sucrose plus ethanol in the substrate composition with only ethanol favored the removal efficiency of LAS, and that removal remained high after the co-substrate was removed (Stage II: 52%; Stage III: 73%; Stage IV: 77%). Those results suggest that the microbial community favored by only ethanol was more capable of degrading LAS than the community favored by sucrose plus ethanol. The presence of sucrose favored the Comamonadaceae family (stage II). After the sucrose was removed (stage III), the Comamonadaceae family decreased and the Rhodocyclaceae family increased. Some genera from the Rhodocyclaceae family are possibly related to LAS degradation. The relative abundance of these genera increased in stage IV in the absence of the co-substrate. Therefore, only ethanol is suggested as a more suitable co-substrate than sucrose plus ethanol in the co-metabolic process of LAS removal.

Biome: root:Engineered:Wastewater:Industrial wastewater
RNA and DNA based biodiversity of sea ice protists over the central Arctic Ocean

Sea ice is a large ecosystem contributing significantly to Polar primary productivity. Especially in the northern hemisphere sea ice consists of often several meters thick multi-year ice (MYI) and thinner first-year ice (FYI). Current global warming is most severe in Arctic regions and as a consequence sea ice cover, especially for MYI is decreasing. Despite its apparent hostile nature sea ice interior is inhabited by a microbial community of bacteria and protists, many of which are photosynthetic. The composition of these communities is yet not known in detail and the relation between active cells versus those just entrapped has not been studied. Here we present data on eukaryotic biodiversity in MYI and FYI from the Central Arctic Ocean using high-throughput sequencing of 18S rRNA and rDNA amplicons. By analyzing datasets from environmental DNA versus RNA we compare the DNA-based total biodiversity to that from RNA amplicons representing the more active part of the community. We found differences between these two in that Bacillariophyceae OTUs are over-represented in the active part of the community. The important arctic diatom Melosira arctica seems to be more abundant in MYI.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Bacterial communities in thermophilic H2-producing reactors investigated using 16S rRNA 454 pyrosequencing

In this study, the composition and diversity of the bacterial community in thermophilic H2-producing reactors fed with glucose were investigated using pyrosequencing. The H2-producing experiments in batch were conducted using 0.5 and 2.0 g.l-1 glucose at 55o C. Under the two conditions, the H2 production and yield were 1.3 and 1.6 mol H2/mol glucose, respectively. Acetic, butyric, iso-butyric, lactic and propionic acids were detected in the two reactors. The increase in substrate concentration favored a high H2 yield. In this reactor, a predominance of acetic and iso-butyric acids, 27.7% and 40%, were measured, respectively. By means of pyrosequencing, a total of 323 and 247 operational taxonomic units were obtained, with a predominance of the phylum Firmicutes (68.73 ? 67.61%) for reactors with 0.5 and 2.0 g.l-1glucose, respectively. Approximately 40.55% and 62.34% of sequences were affiliated with Thermoanaerobacterium and Thermohydrogenium, microorganisms that produce H2 under thermophilic conditions.

Biome: root:Engineered:Bioreactor:Continuous culture
Picoplankton diversity in the South Adriatic Sea during a strong deep winter convection year

The South Adriatic is a key area for the Adriatic and the deep Eastern Mediterranean mainly because it is a dense water source and a driving engine of the Eastern Mediterranean deep circulation cell. In addition, the South Adriatic is an entry point for water masses in the Adriatic. It is the place where Ionian saltier and warmer waters are mixing with Adriatic fresher waters through the process of open-ocean winter convection. The biodiversity and seasonality of bacterial picoplankton before, during and after deep winter convection in the oligotrophic South Adriatic waters were assessed combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the euphotic zone in spring when the maximum value of chlorophyll a was recorded in response to deep winter convection. The communities were dominated by Bacteria while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values in the winter convection and spring post-convection period, and maximum values during summer stratified conditions. SAR11 was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group strongly depending on the convection event when minimal cyanobacterial abundance was observed. Euphotic zone in spring and autumn were characterized by Bacteroidetes and Gammaproteobacteria. The Bacteroidetes clades NS2b, NS4 and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. SAR324, SAR202 and SAR406 were present in the deep layer exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are strongly impacted by strong winter convection.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Using Illumina MiSeq platform to sequence the partial 16S rRNA library of the hot spring sample

A comprehensive investigation of the microbial community composition and taxonomy of Sungai Klah, which is located in Perak, Malaysia. It is the second hottest geothermal springs in Malaysia. The hot spring is a streamer-like and several spring heads with boiling temperature (100-110 ?C) are presence. Other parts of the streaming water exhibit the temperature ranging from 50?100 ?C. Little knowledge on the types of hyper- and thermophilic within this hot spring is known. Furthermore, this high temperature environment condition serves as a source for understanding the genetic diversity, population structure, and ecological roles of these boiling point-tolerant microorganisms.

Biome: root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C)
Exploring the River Continuum Concept for Bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared to macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water column samples collected from the river channel across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel, were characterised using pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from Bacteroidetes dominated in the headwaters to an Actinobacteria dominated community downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature above other measures of position such as Euclidian distance between sites and site catchment area; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid (LNA) bacteria relative to high nucleic acid (HNA) bacteria were found to correspond with these downstream changes in community structure, indicating that functional changes correspond with the taxonomic succession. Our findings suggest that bacterial communities across the Thames basin exhibit a marked ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physiochemical status of the river.

Biome: root:Environmental:Aquatic:Freshwater:Lotic
Microbial communities in deep crystalline bedrock aquifers of Olkiluoto, Finkand

The deep subsurface microbial communities in the crystalline bedrock aquifers of Olkiluoto, Finland, were studied. The actively transcribing community was examined by targeting the archaeal and bacterial 16S rRNA and the mRNA transcripts of the mcrA genes of the  methanogens and the dsrB gene transcripts of the sulphate reducers using 454 amplicon sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Growth of heterotrophic aquatic bacteria in winter is controlled by organic matter availability rather than temperature

In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (NE Germany). Extraordinary high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae. The ice-cover was blanketed by snow leading to a significant reduction of the incident light. This exerted a pronounced physiological stress on the cyanobacteria. These were rapidly colonized by heterotrophic bacteria resulting in a sudden proliferation of associated and subsequently of free-living bacteria. Total bacterial protein production reached 201 ?g C l-1 d-1 - ca. five times higher than previously measured values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed a sharp change in bacterial community structure coinciding with changes in cyanobacteria physiology. Pyrosequencing of 16S rRNA genes revealed that during cyanobacteria breakdown diversity of cyanobacteria-associated and free-living bacteria communities were reduced to a few dominant families. Some of these families were not detectable during the early stages of the cyanobacterial bloom indicating that senescent cells of cyanobacteria select for specific and well adapted bacterial communities. This massive bacterial bloom was rapidly terminated by heterotrophic nanoflagellates shortly before ice-off. Our case study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. This highlights the need for year-round studies of aquatic ecosystems including the winter season to correctly understand and model element and energy cycling through aquatic food webs, particularly the microbial loop.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Through the pyrosequencing analysis of samples from support mateial and phase separator from the anaerobic fluidized bed reactor total of 83 genera was found, which 18 are involved to the nonionic surfactant degradation.

Through the pyrosequencing analysis of samples from support mateial and phase separator from the anaerobic fluidized bed reactor total of 83 genera was found, which 18 are involved to the nonionic surfactant degradation as well as its byproducts. The genera with the highest relative abundance were Sporomusa, Geobacter, Desulfobulbus, Synergistes, Sedimentibacter, Holophaga, Serpens and Azonexus. All samples showed high phylogenetic diversity in which found genera are somehow related to the degradation of LAE and were favored by the configuration of the anaerobic fluidized bed reactor.

Biome: root:Engineered:Biotransformation:Mixed alcohol bioreactor
Assessing polychlorinated biphenyl degradation by an anaerobic microbial consortium in batch reactors with biofilm

Anaerobic biomass was used as inoculum in batch reactors undergoing fermentative-methanogenic conditions aiming to removal PCBs congeners (0.7 mg mL-1). Ethanol (460 mg L-1) and sodium formate (680 mg L-1) was used as co-substrate and polyurethane foam (PF) as support for biomass immobilization. Control reactors (RWCS, RCS and RCS-PF) did not contain PCBs, and biomass received a heat-treatment (RCS-PCB-HT). Ethanol and sodium formate stimulate the metabolism of biomass, since there was an increased methane production in reactors RCS and RCS-PF. The low yield of methane in reactors RCS-PCB and RCS-PCB-PF suggests an inhibitory effect of PCB over the methanogenic community. Reactors RCS-PCB presented a substantial reduction of the initial concentration of PCBs from 0.7 to 0.2 mg mL-1 after 60 days. For domain Bacteria, the reactors with PCBs (RCS-PCB and RCS-PCB-PF) were grouped with 86% similarity and only 55% with free-PCBs reactors (RWCS, RCS and RCS-PF) suggesting a selection of specific population in the presence of PCBs. For Archaea domain the reactors RCS-PCB and RCS-PCB-PF were grouped with 94% similarity and those without PCBs (RWCS, RCS and RCS-PF) with 86%. However, between these groups the similarity was 59% indicating that besides the selection of specific populations induced by PCBs the variation was not as evident as observed for the Bacteria domain. Reactors containing PCBs (RCS-PCB and RCS-PCB-PF) had an increased prevalence of Firmicutes and Chloroflexi phyla and, a pronounced relative abundance of Sedimentibacter, (7.4 and 12.4, respectively) a bacterium correlated with reductive dechlorination of PCBs.

Biome: root:Engineered:Bioreactor
Targeted population genomics of marine Synechococcus cyanobacteria

Large-scale sequencing of nucleic acids extracted from diverse sources is now widely used to study the structure and function of bacterial communities. However, the biological complexity of natural environments, combined with both technical and practical difficulties in analysing large datasets often means the full potential of this technique is rarely achieved. In this respect, we present a targeted metagenomic pipeline, focusing on extracting one component of a complex bacterial community. We used a 3 step process: flow cytometric sorting, followed by direct whole genome amplification on purified cells, then high throughput sequencing. We selected Synechococcus, a ubiquitous marine picophytoplankton, as a target and tested our methods on defined mixtures of cultivated isolates before applying the approach on environmental samples. We show that this targeted approach can provide precise and in-depth assessment of the genomic potential of a selected group where low environmental abundance would limit the return of metagenomic information from community-wide DNA surveys. This approach will help to explore fine-scale population structure and biogeography in a genomic context and therefore the underlying mechanisms that allow specific keystone populations, e.g., marine Synechococcus, to cohabit and contribute to nutrient cycling across a range of habitats.

Biome: root:Host-associated:Plants
Metatranscriptome of a marine bacterioplankton in the North Sea assessed by total RNA sequencing

Marine metatranscriptome data was generated as part of a more detailed study investigating the bacterioplankton communities towards the end of a diatom-dominated spring phytoplankton bloom. This genomic resource article reports a metatranscriptomic dataset from amidst the winter time prior the occurrence of the spring diatom bloom. Up to 58% of all sequences could be assigned onto ORFs and taxonomic analysis based on expressed 16S rDNA revealed identified Gammaproteobacteria, Alphaproteobacteria and to a lesser extend Flavobacteria as the most active community members.

Biome: root:Environmental:Aquatic:Marine
Black Water Project

Bacterial community characterization from a sewage system

Biome: root:Engineered:Wastewater
PCR-amplified 16S rRNA gene tag sequencing from Banyoles karstic area (Catalonia, Spain).

16S rRNA gene was sequenced using the primers set 341F-907R covering the hypervariable regions V3?V5. Amplicons were pyrosequenced using the 454 FLX system (454 Life Sciences, Branford, CT, USA) at the Research and Testing Laboratory (Lubbock, TX). Lakes Cis?, Vilar, and Lake Banyoles-basin III (C-III) are in the Banyoles karstic area northeastern Spain (42?8''N, 2?45''E), samples from the metalimnion and hypolimnion of these lakes are explored in this study. These stratified aquatic ecosystems have incoming sulfate-rich water seeping in through bottom springs resulting in deep waters rich in sulfur-reduced compounds. An oxic-anoxic interface, or redoxcline, is established in the water column where light and sulfide usually coexist.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Diversity of Haptophytes in two years (2009-2011) of monthly samples of subsurface water in the Skagerrak revealed by 454 pyrosequencing.

At station OF2 (59.186668 N, 10.691667 E) in the Skagerrak, samples of the subsurface (1m) pico- and nanoplankton were collected monthly for two years (September 2009-June 2011). 20L were prefiltered through 45 micron, and size-fractionated into 0.8-3 micron and 3-45 micron size fractions. The haptophytes were targeted by amplification of cDNA with haptophyte-specific SSU rDNA V4 primers Hap454 described in Egge et al. 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0074371).

Biome: root:Environmental:Aquatic:Marine
Metagenomic Study of North East Lakes and Ponds

Conditions that favor cyanobacterial dominance in algal blooms, and thus facilitate microcystin production, are not well understood (2). To address this issue we designed an experiment to measure taxonomic diversity during different stages of algal blooms across a geographic region. Microcystin levels and bulk algal counts are reported over a fourteen week period from samples taken once weekly at five different locations in four northeastern states. In addition, we conducted a 16S survey and metagenomic sequencing of directly sampled blooms at three different time points from each of the five sites.  Water samples were collected from five lakes and ponds in the northeast United States over a fourteen-week period from July 20 to October 21, 2010 by investigators at partner institutions across the North East Cyberinfrastructure Consortium (NECC) (Table 1). Samples were collected in triplicate once weekly from Lake Champlain at Highgate Springs, VT, Lake Winnipesaukee, NH, Sebasticook Lake, Maine and Trustum and Yawgoo Ponds in Rhode Island (Figure 1). Whole water was shipped overnight to the University of Vermont DNA Sequencing Facility where all further processing was carried out. A total of 204 samples were collected and processed. Microcystin levels and raw algae counts were measured for all samples. Total flourescent particle counts from flow cytometry analysis were used to select three time points representing the beginng, midpoint and end of the blooms at each location. These selected time points were further processed for DNA sequencing.   Whole DNA was extracted from each of the three selected time points for all locations and subjected to 16S rRNA amplicon sequencing. Samples were barcoded, multiplexed and sequenced on a single plate of a 454 Life Sciences Genome Sequencer FLX at the Genetic Analysis Genomics Core Facility,?Huck Institutes for Life Sciences, Penn State University producing 1.1M sequence reads.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Dysbiosis of gut microbiota contributes to the pathogenesis of hypertension

Hypertension is one of the most prevalent cardiovascular diseases worldwide. Recent findings have identified a link between gut microbiota and blood pressure, yet the contributions of gut microbes and bacterial metabolites towards hypertension remain largely uncharacterized. We carried out metagenomic and metabonomics analyses, in combination with faecal microbiota transplantation, and elucidate that dysbiosis of gut microbiome triggers the pathogenesis of hypertension through altering the metabolic effects.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
454-pyrosequencing technology was employed to investigate the microbial communities from anaerobic fluidized bed reactor treating laundry wastewater.

In this study, 454-pyrosequencing technology was employed to investigate the microbial communities from anaerobic fluidized bed reactor treating laundry wastewater. Biomass from the support material (S) and phase separator (PS) were analysed in two stages, with (S-I and PS-I) and without sucrose (S-II and PS-II) as co-substrate. The pyrosequencing generated in total 18,523 sequences of the 16S rRNA representing from 4 samples that widely represented the diversity of the microbial communities. Among them 17 phyla, 30 classes, 49 orders, 64 families and 92 genera of Bacteria. While Proteobacteria followed by Bacteroidetes was found to be the dominant  phylum in the samples from the stage I (with sucrose), in samples from the stage II (without sucrose) were Proteobacteria and Gemmatimonadetes. The absence of sucrose in the last stage did not affect the Shannon-Weiner and Simpson indices. Regarding the Pielou index the most heterogeneous samples in terms of microbial distribution was PS-I, followed by S-I. The differences found between the samples indicated that the treatment process likely had effects on the microbial structure. Gemmatimonas, Desulfobulbus and Zoogloea were the most abundante genus related with surfactants degradation.

Biome: root:Engineered:Wastewater:Industrial wastewater
Metagenomics of the Respiratory disease complex in Broilers

To collect the respiratory fluid for the poultry for the diagnosis of the Respiratory disease complex.

Biome: root:Host-associated:Birds:Respiratory system
Analysis of plant derived alkaloids on rumen microbiota using an in vitro Rusitec system

Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and predicted metabolic pathways using an in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA) using MiSeq paired ends sequencing and PICRUSt predicitve metabolic pathway analysis. The measurement of community diversity  showed an exponential increase and eventual plateau for all samples. Beta diversity analysis showed high levels of variation between individual fermenters, resulting in high variation within treatments.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Microbial diversity associated with Sphagnum mosses

Bryophytes belong to the phylogenetically oldest land plants. The bryophyte genus Sphagnum is the dominant component of the mire and bog vegetation, which are of high importance for our world climate. Recently, it was shown that Sphagnum mosses are colonized in high abundances with special microbial communities, which fulfil important functions for the moss plantlets as well as for the whole bog ecosystem. However, data obtained resulted in a lot of new scientific questions; which are the objective of the current project. The major aim of this project was to illuminate the biodiversity and ecological characteristics of the Sphagnum-associated microbiome as a bio-resource.

Biome: root:Host-associated:Plants