SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Four samples were collected from biological reactors treating wastewater containing an anionic surfactant (linear alklybenzene sulfonate - LAS)

Four samples were collected from biological reactors treating wastewater containing an anionic surfactant (linear alklybenzene sulfonate - LAS), aiming to analyze the microbial structure. Two reactors were fed with wastewater containing LAS (~10 mg/L), at a hydraulic retention time (HRT) of 35 h. Reactor R1L was fed with a synthetic wastewater containing LAS and reactor RL1 was fed with a laundry wastewater diluted (1:25). LAS degradation rate was 82?9% and 45?16% in the reactors RL1 and RS1, respectively. The samples were collected from the biomass in the sludge-blanket (SB) and phase-separator (PS) from reactors RL1 and RS1. These samples were named as SB-RL1, PS-RL1, SB-RS1 and PS-RS1. The samples were sequenced in a 454 platform. The four samples were sequenced in a run using barcodes (SBRL1: CGACGTGACT; PS-RL1: TACACACACT; SB-RS1: TACACGTGAT; PS-RS1: TACAGATCGT).

Biome: root:Engineered:Wastewater:Water and sludge
Microbial community response during the iron fertilization experiment LOHAFEX

Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phae- ocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine up- take) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition ???uorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were re- markably constant without development of typical bloom-related succession patterns. Members of groups usually found in phy- toplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but signi???cantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession- like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled mem- bers like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Photic zone
The dynamic bacterial communities of a melting High Arctic glacier snowpack

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland?s ice sheet in 2012 merits further investigation.

Biome: root:Environmental:Aquatic:Freshwater:Ice
Salmo intestinal mucus microbes

Pilot study to determine if it was possible to isolate DNA from the commensal microbiota present on healthy Atlantic salmon and sepparate fecal amd omtestinal mucus content to be used for metagenomics

Biome: root:Host-associated:Fish:Digestive system:Foregut
Micromes on salmon skin and surrounding sea water

Pilot study to investigate if sampled Atlantic salmon skin mucus surrounding sea water could prodce quality metagenome sequence reads.

Biome: root:Host-associated:Fish:Skin
study of microbial communities of a lake during winter

three different depth points, sediment and water(2 levels)

Biome: root:Environmental:Aquatic:Freshwater:Lake
Metagenomes of Danish EBPR WWTPs

Metagenome sequencing of activated sludge from Danish enhanced biological phosphorus removal wastewater treatment plants.

Biome: root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge
metagenomics of medieval human remains from Sardinaia, Italy

Medieval skeletons from Sardinia in which Lesions indicative of pathologies were present were sampled and DNA extracted and sequenced by shotgun metagenomics  in order to find evidence of a bacterial cause to the pathologies observed.

Biome: root:Host-associated:Human
Analysis of stool samples from sickle cell disease patients and healthy controls

Analysis of stool samples from sickle cell disease patients and healthy controls

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Sedimentary ancient DNA over a period of last ~14,500 years

Biodiversity of Eukaryotes was described using universal phylogenetic marker gene with a well-preserved sediment core over last post-glacial period - a period of last ~14,500 years in North-Eastern Europe. Sedimentary ancient DNA (sedaDNA) was extracted from the minuscule sediment samples with ~150 year intervals step and amplified at a low amplification level from each sub-sample.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Bacterial, archaeal and eukaryotic diversity associated with hydrothermal sediments retrieved from the Menez Gwen, Lucky Strike, and Rainbow vent fields was assessed by rRNA gene tag pyrosequencing.

Menez Gwen, Lucky Strike, and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through autotrophy, feeding, and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. Here we provide the first comparative survey of the sediment-associated microbial communities from these three neighboring vent fields. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene tag pyrosequencing. The Menez Gwen, Lucky Strike, and Rainbow studied sites presented distinct microbiomes. The occurrence of anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggest that the sediment communities are potentially enriched in subseafloor microbes, rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Trace metal contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
Oil spill impacted sediments

Offshore spilled oils can cause long-term ecological effects in the marine environment. Environmental DNA metasystematics (EDMS) was applied to characterize the ecological effects of the Hebei Spirit oil spill on micro- and macro-biomes of sediments. Alterations on diversities and structures of micro- and macro-biomes were observed in the contaminated area with elevated concentration of total polycyclic aromatic hydrocarbons (?PAHs; sum of concentrations of parent- and alkyl-PAHs). EDMS potentially provides a powerful tool for ecological assessment of multiple communities in ecosystems affected by oil spills.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated sediments
Viral metagenome study of Han River body

Viral metagenomic study was performed on the Han River body, one of the major river in South Korea. Surface samples were collected from upstream to downstream of the waterbody.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Metagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment

Marine sediments harbor a vast amount of Earth?s microbial biomass, yet little is understood regarding how cells subsist in these low-energy environments without forming endospores. DNA methylation, a reversible process that involves the addition of a methyl group to a nucleotide base via a methyltransferase, exists as a possible epigenetic mechanism for non-sporulated cells in low-energy sediment environments to regulate gene expression and potentially lower cellular activity. To investigate the presence and scope of this phenomenon in estuarine sediment microbial communities, we sequenced three metagenomic and 16S rRNA gene amplicon libraries extracted from a sediment core collected from the banks of the Oyster Rocks site of the Broadkill River, Milton, Delaware, USA. We targeted 5-methylcytosine at CpG sites by digesting metagenomic libraries with the methylation-sensitive restriction endonuclease HpaII. By quantitatively distinguishing ?mixed? methylation states for populations of CpG site copies, we identified dynamic, non-binary shifts in CpG methylation for community taxa and function.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
Ammonium influences microbial community composition in anaerobic digestion of swine manure

Objectives?To reveal the shift of microbial communities along ammonium gradients, and to examine the relationship between microbial community composition and the AD performance.Results: The CH4 production declined with increasing ammonium concentration, and was inhibited when ammonium exceeded 4000 mg/L. The VFAs especially acetate accumulated with elevated ammonium. The prokaryotic community composition and structure varied along the ammonium gradients. In particular, genera Clostridium, Tepidimicrobium, Sporanaerobacter, Peptostreptococcus, Sarcina and Peptoniphilus showed good tolerance to ammonium. However, Syntrophomonas with poor tolerance to ammonium may be inhibited during anaerobic digestion. Methanosarcina was the dominant methanogen. Conclusions: Excessive ammonium would decouple the linkage between acidification and methanogenesis. The shift of specific taxa under ammonium gradients may reflect their adaptations to different niches, which finally results in different efficiency in anaerobic digestion.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Metagenome of "hand-picked" Achromatium cells from Lake Stechlin, NE, Germany

Polyploid bacteria are more common than previously believed; however, little is known about the genetic and functional diversity incurred by having multiple chromosomes. We show, using the largest known freshwater bacterium, Achomatium sp., that single cells can host a genetic diversity equal to that of entire populations. No correlation was found between genetic diversity and functional role.  The cells contain an excessive number of transposable elements and we hypothesize that these are involved in, intracellular, inter- and intra-chromosome gene re-arrangements; however, the integrity of operons is maintained. We further hypothesize that gene convergence is strongly reduced in these cells as suggested by the high diversity of the usually conserved 16S rRNA gene. Imaging the 16S rRNA distribution inside the cells points to the potentially spatial-differential expression of genes. Thus, intracellular gene transfer (iGT) leads to a large genetic diversity and potentially accelerated evolution. Polyploidy, multiple alleles, and localized gene expression, suggests Achromatium (and perhaps other polyploid bacteria) uses a genetic machinery similar to multicellular eukaryotes.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Bioprospecting for genes encoding hydrocarbon-degrading enzymes from metagenomic samples isolated from northern Adriatic Sea sediments

Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been selected using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM-profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
microbial diversity and function

studyed microbial diversity and function which is in the sediment polluted by antimony

Biome: root:Environmental:Aquatic:Marine:Sediment
Sequencing the bacterial metatranscriptome associated with the marine sponge Crambe crambe

Crambe crambe was sampled from the Western Mediterranean and immediately presserved in RNA later. Total RNA was extracted en rRNA and eukaryotic mRNA were removed and the remaining bacterial mRNA (and unremoved rRNAs and eukaryotic mRNAs) were sequenced with the Illumina HiSeq using paired end sequencing.

Biome: root:Host-associated:Porifera
Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454 pyrosequencing

The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing freshwater anammox consortia that were adapted to salinities of 3 and 30 g/L NaCl. While adaption from 0 to 3 g/L salinity took 153 days, adaption from 3 to 30 g/L salinity took only 40 days, and no inhibition was observed. A major succession in the anammox community wasobserved at 3 g L-1 where the dominating population shifted from Ca. Brocadia fulgida to Ca. Kuenenia stuttgartiensis. The latter dominated at high salinity and seemed to be essential for the high (? 96%)ammonium and nitrite removal efficiencies achieved.

Biome: root:Environmental:Aquatic:Marine
Plasmidomes of aerobic biofilm under long-term oxytetracycline exposure

Aerobic biofilm was exposed to oxytetracycline with gradually increased concentration from 0mg/L to 5mg/L and 25mg/L. Plasmid of the aerobic biofim bacteria from different exposure stages was extracted and sequenced by using illumina Hiseq sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Postglacial viability and colonization in North America's ice-free corridor

During the Last Glacial Maximum (LGM) continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By ~15-14 thousand years ago (cal. kyr BP), glacial retreat opened a 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by ~12.6 cal. kyr BP, followed by open forest, with evidence of moose and elk at ~11.5 cal. kyr BP, and boreal forest ~10 cal. kyr BP. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr BP, are unlikely to have travelled this route into the Americas. However, later groups may have used this north-south passageway.

Biome: root:Environmental:Aquatic:Marine:Sediment
Evaluating the diversity and activity of marine archaea via 16S rRNA gene and transcript sequencing

This study evaluates the diversity and activity of marine archaea via 16S rRNA gene and transcript sequencing. This method is complementary to evaluation of the activity of these organisms by evaluating the differential uptake of isotope labeled bicarbonate and amino acids with nano-scale secondary ion mass spectrometry and isotope ratio mass spectrometry.

Biome: root:Environmental:Aquatic:Marine
Comparison of samples and mock communities amplified with single-base variations in 515-Forward universal primer

This study is a comparison of marine environmental and marine mock community samples amplified with different versions of a commonly used universal forward primer 515.  A mismatch in the 4th position in the 515F primer to the Thaumarchaea was corrected by replacing the (C) in that position with an ambiguity (N).

Biome: root:Environmental:Aquatic:Marine
Monthly time-series analysis of the marine microbial community from surface to seafloor at the San Pedro Ocean Time-series station

This study primarily evaluates the monthly dynamics of the marine microbial community at the San Pedro Ocean Time-series station (SPOT; near Los Angeles, CA, USA). Other marine samples from two different locations in the San Pedro Channel (Pacific Ocean) have also been analyzed to compare the microbial communities to the SPOT station.

Biome: root:Environmental:Aquatic:Marine
Studying the metagenomic diversity of tiger gut

Tiger gut metagenome is studied in order to asses the diversity of microbes residing in gut of tigers occupying different territories.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Environmental alkali multi-extreme Diamante Lake Red Biofilm WGS

Diamante Lake is a multi-extreme environment located in Catamarca province, Argentina. Developing on the bottom of calcareous rocks we found Red Biofilms (DLRB). The taxonomic composition metabolic potential was determined by shotgun sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Lake
18S rRNA genes from benthic Antarctic sediments

We sampled surface sediment from 24 sites across a 5,500 km region of western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities (both 16S and 18S) and sediment geochemistry.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic