SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
microbial communities in long-term e-waste contaminated river sediments

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and examined how community functions respond to the complex combined pollution. High throughput 16S rRNA sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, with genes encoding key enzymes (including dioxygenase, dehydrogenase, aldolase, decarboxylase, hydroxylase and hydrolase) in organic pollutants-degradation pathways largely harbored by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and function (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and BaP, available lead and EC were the key contributors. Given the ecological significance of microbes in sediments, long-term e-waste pollution has the potential to alter nutrient cycling and contribute to functional perturbation of freshwater systems.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Archaeal Raw sequence reads

Abstract: Archaeal is very important in the nitrogen cycle.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Taihu Raw sequence reads

Abstract: AOA and AOB were the important nitrogen microbes

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
bacterial diversity of lake sediments

To determine influence of inflow-rivers on bacterial community of the lake

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Prokaryotic microbial communities structure in the  headwater watchment of Dongjiang River in the south of China

Prokaryotic microbial communities structure in the headwater watchment of Dongjiang River in the south of China

Biome: root:Environmental:Aquatic:Freshwater:Lotic
Eucaryotic microbial communities structure in the  headwater watchment of Dongjiang River in the south of China

Eucaryotic microbial communities structure in the headwater watchment of Dongjiang River in the south of China

Biome: root:Environmental:Aquatic:Freshwater:Lotic
Bacterial and fungal diversity in Ashumet Pond, MA (USA), and prevalence of manganese-oxidizing isolates

Distinct black manganese oxide mineral coatings have long been observed on a portion of the shores of Ashumet Pond, a freshwater pond impacted by heavily contaminated groundwater emanating from a nearby decommissioned wastewater treatment facility. The goal of this study is to identify the microbial communities contributing to the biogeochemical cycling of Mn, and thus to the remediation of metals and organics in this environment.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Microbial community in PAH-contaminated riverine sediments

Co-occurrence patterns of microbial community

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Lake sediment sequencing

This study can provide novel insights into basin pollution control in plain river networks

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Surface Diatom Sediments of Deep Freshwater Lake Baikal

In this work we analyzed the structure and diversity of bacterial and archaeal communities in the surface sediment core. Microscopy has shown that this core is rich in siliceous diatom valves (frustules), whose degrees of preservation varied with the depth and diatom species as revealed by SEM. Pyrosequencing targeting bacterial V3-V4 and archaeal V1-V3 regions of 16S rRNA were performed to profile procaryotic community structure.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Archaea microbial communities structure in the  sediment and downarea soil of the Fengshuba Reservoir in the Guangdong Provinve, South China

Archaea microbial communities structure in the sediment and downarea soil of the Fengshuba Reservoir in the Guangdong Provinve, South China

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Qinghai Lake sediments Metagenome

Investigation of microbial diversity

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Anaerobic Photosynthetic Consortia 16s rRNA profiling

Anaerobic photosynthetic consortia that degrade cellulose and fix nitrogen.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
sediment microorganism Metagenome

Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of microbial communities in sediments site Posolskay Banka, of Lake Baikal

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
rRNA, rDNA bacteria thaw ponds Targeted loci environmental

Present (rDNA) and active (rRNA) arctic bacterial communities under an increased temperature incubation

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
freshwater sediment metagenome Metagenome

To investigate the influence of nitrate on soil microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Lonar sediment Raw sequence reads

Identifying total microbiota of the extreme ecosystem

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Surface sediment raw sequence reads 1

Diversity of bacteria in surface sediment from Lake Bosten in xinjiang Province, China

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Swan lake bacteria Raw sequence reads

bacterial 16S V3 region sequences

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Baikal Archaea Metagenome

Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of archaeal communities in methane hydrate- and oil bearing sediments, c different component composition of pore water in six districts of Lake Baikal

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Characteristics of bacterial communities in the deep sediment Lake Baikal from the regions with oil and gases discharging

Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of bacterial communities in methane hydrate- and oil bearing sediments, c different component composition of pore water in six districts of Lake Baikal.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Thermokarst ponds Targeted Locus (Loci)

The objective of our study was to evaluate the release and potential for GHG emissions in the poorly studied runnel ponds compared with polygonal ponds of northeastern Canada. Archaeal community composition in the sediments was analyzed with high-throughput 16S rRNA gene pyrosequencing.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
bacterial diversity of lake sediment

To determine influence of allochthonous rivers on bacterial communities of the lake

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Sediment Raw sequence reads

to study the denitrifying microorganisms in Lake Taihu

Biome: root:Environmental:Aquatic:Freshwater:Lentic
Marine (Aarhus) and freshwater (Lake Constance) sediment Raw sequence reads

General marine and freshwater sediment community in low iron environment; Distribution, abundance and activity of iron metabolizers

Biome: root:Environmental:Aquatic:Freshwater:Lake
Amino acid addition experiment Metagenome

Amino acid addition experiments using freshwater lake bacterioplankton

Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 17MAY2012 deep hole epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Trout Bog Lake, WI - 28MAY2007 hypolimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Trout Bog Lake, WI - 22MAY2008 epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Trout Bog Lake, WI - 29MAY2008 epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 05MAY2012 deep hole epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 03MAY2011 deep hole epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 18MAY2011 deep hole epilimnion ns metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 18MAY2010 deep hole epilimnion ns metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Freshwater microbial communities from Lake Mendota, WI - 20MAY2010 deep hole epilimnion metagenome


Biome: root:Environmental:Aquatic:Freshwater:Lake
Effect of climate-change induced glacier melting on the benthic prokaryotic diversity in the West Antarctic Peninsula

West Antarctic Peninsula (WAP) is recognized as one of the fastest warming area on Earth. Climate change and the consequent warming of the oceans has reduced the polar icecaps resulting in a change of the regulation of the biological pump, with altered conditions of primary production and nutrient cycling and circulation. Moreover, the increased melting of coastal glacier and scouring events may have a strong impact on local communities, potentially affecting the local biodiversity and ecosystem functioning. We investigated community structure and diversity of benthic prokaryotes in a fast warming region of the WAP.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Cryoconite sediments Targeted Locus (Loci)

Biological processes on glacier surfaces affect the physical behaviour of glaciers and ice sheets and carbon and nutrient fluxes in the cryosphere. Changes in rates of biological processes are often associated with changes in diversity, yet there is little knowledge of the diversity of active microbes on glacier surfaces and its controls. We examined the microbial abundance, community structure, and the proportion of the active microbes at two contrasting surface sites located at the margin and in the interior of the Greenland ice sheet over the course of a melting season, using DNA and RNA co-extraction from the same samples, quantitative PCR and pyrosequencing of 16S rRNA and rDNA. Whereas the rDNA abundances were similar at both sites (108  109 copies g-1), the rRNA abundance was significantly higher in the interior (1010 copies g-1). Significant differences in diversity were found between the sites, with the DNA diversity significantly higher at the margin and the RNA diversity higher at the interior site. The bulk of the active communities at both sites comprised Cyanobacteria and Alpha- and Betaproteobacteria, suggesting a truncated food web structure dominated by few bacterial primary producers and decomposers. We suggest that the ice sheet margin contains a more diverse but less active assemblage of microbes while the interior harbours a less diverse but well-adapted active community. We propose that the process of community assembly at the surface of the GrIS can be understood as species sorting from a metacommunity of airborne microbes which land on the ice surface.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Aldegondabreen cryoconite Targeted Locus

The aggregation of surface debris (cryoconite) on melting glaciers into larger may provide microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (surface debris, ice and meltwater), quantitative PCR (targeting the 16S rRNA and amoA genes), pyrosequencing and multivariate statistical analysis to better understand the ecology of prokaryotic microbes on the surface on Aldegondabreen and their role in nitrogen cycling. The combination of high nutrient input, supraglacial melt water flow and the presence of fine, claylike particles supports the formation of cmscale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are wellknown in supraglacial environments. Allochthonous material including plant tissuederived chloroplasts was also identified in the molecular analysis. Importantly, ammonia oxidizing archaea (AOA) were detected in the aggregates for the first time on an Arctic glacier.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
16S rDNA metagenomes of Western Balkans glacial lakes sediments

Since the Balkan Peninsula is situated in the climatic transition between the temperate zone and Mediterranean conditions, it can be assumed that this region will become dryer and warmer in the course of global climatic change. Potential vanishing of glaciers in this part of Europe could endanger existing glacial lakes, which points to the need of conservation and biodiversity studies of this ecological niche. The studies of microbial communities in glacial lakes, especially in southeast Europe are rare and even neglected. It is well recognized that unexplored ecological niches and metabolic potential as well as new molecular frameworks of their microbial communities could be a gold mine of secondary metabolites with importance for biotechnology, medicine and pharmacy. Our goal was to assess the bacterial communities from selected Western Balkans glacial lakes. Selection of lakes was based on exposure to anthropological influences. Thus we analyzed bacterial communities from Plav lake (designated as D in the project, located in the town of Plav), Black lake (designated as C in the project, outside of human settlements but tourist attraction) and Donje Bare lake (isolated lake without significant human impact, designated as Z in the project).

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
VAG Mine Pit Pond Metagenome

The Vermont Asbestos Group (VAG) mine provides an experimental model to investigate resident microbial communities exposed simultaneously to multiple environmental stressors. The VAG Pit Pond and its Outlet present an alkaline aquatic environment, contaminated with asbestos-laden mine tailings and a variety of heavy metals.As no information is available on the microbial community structure of this aquatic ecosystem, our first goal was to characterize the taxonomic profile of its resident microorganisms. Investigations of human-induced perturbation have provided little understanding of microbial community dynamics. The overarching goal of this project is to expand our knowledge of these microbial community interactions using a combination of sequence-based and function-based methodologies. The work lays the foundation for study of microbial dynamics in ecological and geochemical processes of human-impacted environments.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Mine drainage
Bacterial community profiles in  a bioreduced uranium contaminated site after reoxidation

A site contaminated with uranium was bioreduced through multiple injections of ethanol to immobilize the uranium in situ. Then it was allowed to reoxidize via the invasion of low-pH , high-nitrate groundwater back into the reduced zone for about 4 years. To examine the biogeochemical response, high-throughput sequencing were applied to characterize bacterial population shifts.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Long distance electron transfer by cable bacteria in aquifer sediments

Investigation of BTEX contaminated groundwater sediments for the abundance of cable bacteria which could enhance biodegradation by long distance electron transfer at the plume fringes

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Aquifer sediment nitrate reducing community change

Microbial community composition change over the course of a heterotrophic nitrate reducing enrichment. Sediments used in this experiment were collected from a nitrate contaminated shallow aquifer at a depth of 58-61ft from Alda, NE. Illumina sequencing of the V5 hypervariable region of the 16S rRNA gene is used.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Impacts of crude oil and chemical dispersant exposure on marine microbial biofilm formation and steel corrosion

The release of hydrocarbons and dispersants in the marine environment may place at risk the preservation of historic steel shipwrecks on the seafloor. In this study, we exposed steel biofilm communities to crude oil and dispersants and monitored compositional and functional changes after exposure, and the impact of oil exposure on steel corrosion processes.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Sediment of acid mine drainage Targeted loci environmental

Sediments from an ancient gold mine in La Carolina, San Luis, Argentina.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
Uncultured Environmental Isolate Targeted loci environmental

This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from groundwater during radioactive waste geodisposal.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Groundwater microbiome


Biome: root:Environmental:Aquatic:Freshwater:Groundwater
hospital shower hose biofilms metagenomes

Drinking water (DW) biofilms are well known to harbor opportunistic pathogens, however, these biofilm communities remain poorly characterized by culture-independent approaches that circumvent the limitations of conventional monitoring efforts. In this study we characterize the composition of microbial communities growing on five hospital shower hoses using shotgun metagenomics.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
Biofoam biofilm sample 16S rRNA gene libraries

Small scale biosand filters (BSFs) utilized as point of use (POU) water treatment technologies can provide quality drinking water in arid regions. In this current study, biofilms within a novel biologically active POU technology that removes pathogens from water were studied. The biofilms develop across porous foam cartridge filters termed biofoam, and were assayed for community membership. Biofilms within the POU filter medium were developed at three different locations in the US using three different surface waters. Biofilm microbial communities that developed on biofoam were analyzed utilizing 454 pyrosequencing of the 16S rDNA genes, and showed a remarkable degree of shared community membership among the three locations. A large, diverse shared microbiome was found as defined by the top 100 shared operational taxonomic units (OTUs) at 0.03 cut off (97% similarity). This represented 280,000 of the 306,000 sequences (>90%). Of those, 25% were classified within the genus Pseudomonas. Members of the microbial communities found within the shared microbiome of the biofoam were closely associated with organisms commonly found in activated sludge, drinking water biofilms, rhizosphere, phyllosphere, and soil ecosystems. The biofoam provides a unique and effective porous matrix for biofilm formation, which appears to allow for the establishment of consistent microbial communities, even when developed at different locations utilizing different water sources. Improving our understanding of the biofoams microbial ecology may provide insights into mechanisms of pathogen removal, and allow development of customized biofilms for targeted remediation projects, as part of a lightweight and energy efficient water filtration system.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
Sundarbans estuarine ecosystem Metagenome

This work will provide a model for the large-scale extension of molecular phylogenetic-type analysis of direct study, characterization, and secondary metabolite biosynthetic gene clusters that remain hidden in soil microbiomes of Sundarbans. Genome base study with the theoretical prediction of structures will provide importance for the discovery of natural products in the future from Sundarbans ecosystem. The expansion of the genomic sequence will exhibit potential route for synthetic biology approaches and metabolic research. Preliminary data on this screening will demonstrate great economic interest.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Ammonia monooxygenase biogeography and sequence diversity in the Cape Fear Estuary

This project is focused on exploring the spatial and temporal distribution of microbes involved in nitrification within the sediments of the Cape Fear Estuary. 454 Sequencing of both bacterial and archaeal amoA genes was conducted with DNA extracts obtained from estaurine surface sediment samples. Spatial patterns were evaluated by collecting sediment along the salinity gradient of the estuary. Temporal patterns were evaluated by collecting sediment samples seasonal over a three year period. The interaction of community composition with environmental conditions was evaluated using in situ sediment transplant experiments within the estuary, where sediment bundles were moved from one location in the estuary to another and changes in the microbial community were observed over time following transplantation. These data are relevant to understanding the diversity and distribution of microbes involved in microbial nitrogen cycling and how the diversity of these functional groups interact with environmental conditions within an estuary.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Chesapeake Bay Sediment nirS Metagenome

Amplicon sequences of nirS, encoding nitrite reductase

Biome: root:Environmental:Aquatic:Estuary:Sediment
Estuarine wetland Targeted Locus (Loci)

At the salt marsh Dongtan, the effect of Spartina alterniflora invasion on the structure of bacteria were investigated at three points where the first was uninvaded, the second was partially invaded and the third was completely displaced.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Estuarine wetland Targeted Locus (Loci)

This study aimed to understand the abundance and diversity of methanogens in salt marsh sediments with S. alterniflora invasion.  mcrA of methanogens collected by 454-pyrosequencing from Dongtan salt marsh.

Biome: root:Environmental:Aquatic:Estuary:Sediment
sediment metagenome Raw sequence reads

It was used to reflect the microbial community diversity for the sediment samples collected from the Yellow River Estuary.

Biome: root:Environmental:Aquatic:Estuary:Sediment
estuary metagenome Raw sequence reads

Anaerobic Dechlorination of Tetrachlorobisphenol A

Biome: root:Environmental:Aquatic:Estuary:Sediment
estuary metagenome Raw sequence reads

Continent-wide Pollution of Estuaries with Antibiotic Resistance Genes

Biome: root:Environmental:Aquatic:Estuary:Sediment
Microbial communities in estuarine sediments

Microbial communities from estuarine sediments differing in anthropogenic contamination

Biome: root:Environmental:Aquatic:Estuary:Sediment
Newfoundland sediment pyrosequencing

16S rRNA gene sequencing for bacterial community composition of sediment collected on the West coast of Newfoundland, Canada

Biome: root:Environmental:Aquatic:Estuary:Sediment