SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Fringing reef Metagenome

This study used 16S and 18S rRNA genes pyrosequencing derived metagenomic DNA to obtain the microbial profiles of a marine tropical reef surface of Kham island, Trat province, Thailand

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Microbiome variation in Agaricia undata with distinct depth distribution ranges

Here, we study the prokaryotic community associated with reef-building coral (Agaricia undata) over a depth gradient (38-80 m)

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Coral or reef-seawater associated bacteria Targeted Locus (Loci)

SSU rRNA gene amplicons from Ctenactis crassa, Herpolithia limax or reef seawater.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Environmental zooplankton Targeted Locus (Loci)

This study investigated the diversity of metazoan plankton around three reef systems in the central/southern Red Sea utilising 18S rRNA amplicon sequencing.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Coral

Characterization of fungal and bacterial communities associated with inlets, ocean water, and coral tissue samples

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Zhoushan intertidal zone sediments Raw sequence reads

We reported the ANME archaea in the intertidal zone.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
sediment metagenome Raw sequence reads

This study focus on the effect of tidal zonation and the rhizosphere on the distribution of microeukaryotes.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
Intertidal Mixing Zone Targeted Locus (Loci)

Submarine groundwater must pass through an Fe-mineralized barrier before being discharged to coastal environments. Our goal was to assay the microbial members of this subsurface aquifer environment, looking at both pore water and surface sediments from a shore-perpendicular transect down to 4 m depth.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
Hydrothermal Deposit Targeted Locus (Loci)

Understanding the distribution and activity of sulfate reduction at hydrothermal vents requires a more thorough interrogation of the community ecology and metabolic activity of vent hosted microorganisms in the context of the extreme physico-chemical environment.   To date, many studies have quantified rates of sulfate reduction in hydrothermal-influenced sediments and vent isolated microorganisms, but only one study of sulfate reduction exists for hydrothermal deposits.  Here we present rates of microbially-mediated sulfate reduction as determined via 35S tracer studies- from three distinct hydrothermal deposits recovered from the Middle Valley vent field on the Juan de Fuca Ridge.  We further evaluate these rates in the context of the in situ geochemistry and microbial community structure of each chimney to better constrain linkages between phylogeny and function.   Middle Valley hydrothermal deposits Chowder Hill, Dead Dog, and Needles collected July 2010 AT15-67 on Alvin Dive 4625.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
marine sediment metagenome Targeted loci environmental

Compare the bacterial communities of hydrothermal deposits and other deep-sea sediments in Okinawa Trough

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
Sediment Metagenome

This study presents an evaluation of the impacts of DNA extraction methods, targeted 16S rRNA hypervariable regions and sample origins on the microbial diversity detected by 454-pyrosequencing in sediments from cold seep and hydrothermal vent ecosystems

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
Loihi Seamount Targeted loci environmental

We propose 16s tag sequencing from subsurface fluid samples and microbial mats sampled directly above the venting fluids to further our understanding of subsurface microbial populations in a low sulfide, high iron hydrothermal environment, and to determine the extent of interaction between microbial communities in the subsurface diffuse fluids and seafloor microbial mats. We will test the following hypotheses:1. The subsurface microbial communities in the Hiolo area and Spillway area have different compositions that are related to local fluid chemistry, and2. The dominant species in microbial mats at Loihi Seamount are seeded by subsurface populations present in diffuse flow fluids. It is likely that the dominant mat species are present but not dominant in the subsurface, and bloom in the transition zone at the seafloor where warm, reduced anoxic fluids mingle with cool,oxic seawater.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
AT26-10 Crab Spa IGT incubations raw sequence reads

These are sequences from the final time point of ~24 h incubations of diffuse-flow hydrothermal vent fluids from "Crab Spa" (9o50.3981 N, 104o17.4942 W). All but two samples were incubated at 24 C, the remaining two were incubated at 50 C. Further details about sampling and experimental conditions are available in an accepted publication by McNichol et al (2016) entitled "Assessing Microbial Processes in Deep-Sea Hydrothermal Systems via Incubations at In Situ Temperature and Pressure" to be published in Deep-Sea Research Part I. A forthcoming publication will also use these data.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
Comparative 16S analysis of hydrothermal vent samples from the Mid-Atlantic Ridge (MAR)

The samples were collected as part of a comparative 16S amplicon sequencing-based analysis of hydrothermal vent samples from the Mid-Atlantic Ridge (MAR)

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Bacterial community of cold seeps Metagenome

Spatial scaling of bacterial diversity of cold seeps in the deep Eastern Mediterranean sea

Biome: root:Environmental:Aquatic:Marine:Cold seeps:Sediment
Preservation of ancient eukaryotic DNA in methane hydrate-associated marine sediments.

Ancient eukaryotic DNA in marine sediment can provide valuable information on the paleo-environment. However, labile nucleic acids are generally considered to be microbially degraded in water and sediment columns. Previously, ancient eukaryotic DNA has been retrieved from sediments associated with anoxic water column in lake and semi-closed sea, due to the minimized effect of oxic biodegradation. Cold seep sediment is characterized by high upward flux of methane, where there is the possibility that the excess energy source might suppress the degradation of deposited organic matter including nucleic acids by microbial activity. We investigated the preservation of ancient eukaryotic DNA in marine sediments associated with and without methane hydrate in the eastern Japan Sea, between which the dominant prokaryotic populations are clearly distinct. Marine sediments were retrieved from the eastern Japan Sea during a cruise onboard R/V Marion Dufresne in June 2010. Two-step alkaline DNA extractions were conducted with 0.1 g of marine sediments. DNA from living organisms such as fungi was removed by the first extraction under mildly heated conditions at 65 degrees Celsius, which was followed by the second extraction at 95 degrees Celsius. Triplicate DNA extraction and subsequent clone library analysis were more reproducible for marine sediments associated with methane hydrate. Based on highly variable18S rRNA gene sequences, terrestrial and marine organisms were taxonomically identified at the species level. The diversity of ancient eukaryotic DNA represented by Alveolata, Fungi, Stramenopiles and Viridiplantae was comparable between this study and previous ones. As only 0.1g of g wet sediment is required, the overall methodology developed in this study has great potential to reconstruct terrestrial and marine ecology at high time resolution. In addition, methane hydrate-associated sediments, which are globally distributed along the continental margin, have great potential to reconstruct the past terrestrial and marine ecology around the world over geological timescales.

Biome: root:Environmental:Aquatic:Marine:Cold seeps:Sediment
archaeal community in Haima cold seep in SCS

archaeal community

Biome: root:Environmental:Aquatic:Marine:Cold seeps:Sediment
Incubation of marine methane seep sediments with a bioorthogonal amino acid

In marine sediments, anaerobic oxidation of methane (AOM) is primarily catalyzed by syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). We applied bioorthogonal non-canonical amino acid tagging (BONCAT) using a high-throughput approach to detecting protein synthesis in individual cells, on sediments from deep-sea methane seeps. Sediment samples have been incubated in the presence or absence of methane and a bioorthogonal amino acid. V6 regions of bacterial and archaeal 16S rRNA genes were amplified using general primers, tagged, and analyzed for shifts in the microbial community during time of incubation.

Biome: root:Environmental:Aquatic:Marine:Cold seeps:Sediment
seawater metagenome

Methane seep mesocosms

Biome: root:Environmental:Aquatic:Marine:Cold seeps
marine methane seep Targeted Locus (Loci)

Analysis of microbial diversity (e.g., 16S rRNA gene diversity) in folliculinid ciliates found at methane seeps along the Pacific margin.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Marine methane seep Targeted Locus (Loci)

Analysis of 16S rRNA gene diversity in methane-derived authigenic carbonate nodules and their host sediments, across two previously established marine methane seep sites off the west coast of North America.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Santa Monica Basin seep sediment incubations to assess C and N sources for F430 synthesis

Santa Monica methane seep sediment incubations

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Hydrate Ridge, OR - Deep sea cold seep ecosystem Targeted Locus (Loci)

The goal of this study was to examine how various sources and scales of heterogeneity within a methane seep ecosystem off the coast of Oregon influenced microbial eukaryote community composition and diversity.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
16S Amplicon Data from an Antarctic Cold Seep

Benthic fauna from a high Antarctic cold seep

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Marine methane seep Targeted Locus (Loci)

Microbial 16S rRNA diversity associated with various samples at marine methane seeps along the western North American margin.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Heterogeneity of methane seep microbiomes in the NE Pacific

Data from 16S rRNA sequencing of marine sediment samples collected from both methane seep and reference sediments along the Cascadia Margin (NE Pacific) during three separate research cruises. Included 8 newly discovered seeps, 2 known seeps, and 2 reference sediments.

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Denitrification bacteria in sediment cores of Daya Bay, China

nirS gene

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial ecology of AOA community in sediment from adjacent waters of Rushan Bay

Microbial ecology of AOA community

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial ecology of AOB community in sediment from adjacent waters of Rushan Bay

Microbial ecology of AOB community

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
coastal sediment Raw sequence reads

Diversity of Rhodopirellula and related planctomycetes. This study investigates the diversity of Rhodopirellula and related planctomycetes in an intertidal sediment of Sylt island, Germany, employing carB gene, coding for the large subunit of carbamoylphosphate synthetase, as a marker gene.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial diversity before and after tidal re-instatement

Microbial community diversity from four surface sediment sites collected in duplicates. Two of the sites are below sea level and two are above sea level. The data set includes samples before and after a tidal re-instatement project. Greenhouse gas fluxes, water levels, and salinity were also collected to identify the potential of blue carbon in coastal wetlands.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Bacterial community structure and their predicted functions in coastal sediments

The main objectives of the present study were investigation of bacterial community compositions and their predicted functions in coastal sediments, considering the impacts of natural processes and anthropogenic activities.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
seawater bacterial community Raw sequence reads

We report the sediment derived dissolved organic matter degradation in incubation experiment with the overlying seawater, shifts in microbial community structure during the incubation were investigated. Microbial genomic DNA was extracted from the polycarbonate membranes (microbial cells filtered) and the 16S rRNA gene sequences (v3+v4) were amplified by PCR.We classified the OTUs based on their phylogenetic affiliations and determined their relative proportions on the total number of sequencing reads.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Coastal Sediment Bacterial Community Alterations in Association with Sudden Vegetation Dieback

This study analyses the alterations in the sediment microbial communities in a coastal wetland in response to the die off of the dominant plant, Spartina alterniflora

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial ecology of archaeal community in sediment from adjacent waters of Rushan Bay

Microbial ecology of archaeal community

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial ecology of bacteiral community in sediment from adjacent waters of Rushan Bay

Microbial ecology of bacterial community

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
coastal sediment diversity study

The main objectives of the present study were the in-depth characterization of bacteria and archaea diversity and community distribution in the coastal sediments along a pollution gradient subject to costal anthropogenic disturbances and the riverine input.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

Microbial communities play a crucial role in microbial loop process that constitute the foundation of the ecosystem structure and function. The goal of this study was to monitor microbial community shift in the Gulf of Mexico coastal sediments following exposure to MC252 oil in a laboratory microcosm experiment. We used bacterial tag encoded FLX pyrosequencing (bTEFAP) approach targeting the 16S rRNA gene. We also studied the presence of the biodegradative genes in pure cultures of bacteria from oil-treated sediments samples.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Microbial diversity of Oslo Fjord Pockmark sediments

The non-active pockmarks of the Oslo Fjord are excellent seabed features for studying the effects of geology on the microbial diversity. Geological features such as pockmarks effect the waterflow over the seabed. Here we studied the microbial communities from pockmarks sediments to understand how the diversity is affected by these structures.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Mudflat sediment Metagenome

Microorganisms are important in gulf ecosystem, they are more sensitive to environmental changes and are better indicators for environmental quality assessment. Therefore, understanding the microbial community compositions is important to improve the environmental assessment indicators.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Marine Sediment Targeted Locus

Marine sediment samples collected from the Bay of Fundy, New Brunswick.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Comparison of marine sediments from the Beguela upwelling zone

Comparing the microbial communities present in the marine sediments off the coast of Namibia and their relationship to phosphogensis.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Development and validation of a multi-trophic metabarcoding biotic index for benthic organic enrichment biomonitoring using a salmon farm case-study.

Salmon farms are often associated with strong benthic enrichment gradients. Routine monitoring is usually required by regulation, and has traditionally been based on benthic macrofaunal communities. This is reliant on taxonomic expertise, excludes analsyis of micro-organisms and turn-around times can be slow, limiting opportunities for adaptive management. Environmental metabarcoding is a powerful high-throughput sequencing-based technique that is promising for identifying and quantifying assemblages of benthic organisms for biomonitoring. Previous studies have demonstrated relationships between specific taxonomic groups (e.g., bacteria, foraminifera or other eukaryotes) and anthropogenic effects. However, there is uncertainty around applicability at larger spatial and temporal scales, and the absence of fixed categorical scales makes the use of data challenging for routine biomonitoring. In this study, we analysed 105 sediment samples collected over three years from three salmon farms spanning two separate bioregions. Environmental DNA and RNA (eDNA/eRNA) metabarcoding of three taxonomic groups (foraminifera [For], bacteria [Bac], and general eukaryotes [Euk]) was undertaken in parallel with traditional macrofaunal and biochemical analysis (which were used to calculate an Enrichment Stage [ES] index for each sample). The most abundant 200 to 250 Operational Taxonomic Units in each taxonomic group were assigned to Eco-Groups (EG) using a quantitative, quality-based method. These were then used to develop a Metabarcoding Biotic Index (MBI) for each group individually (For-MBI, Bac-MBI, and Euk-MBI) and in combination (multi-trophic MBI; mt-MBI). Based on our assessment criteria we robustly allocated ca. 500 EG to a wide range of known and unknown taxa. Using both the development (year 1 [Y1] and 2 [Y2]) and independent validation (year 3) datasets the weakest correlation was between For-MBI and ES (eDNA/RNA, R2 = 0.731 to 0.850), whereas strong correlations were obtained between the mt-MBI and, or when just Bac and Euk data (mt[Bac+Euk]-MBI) were combined (eDNA/RNA, R2 > 0.900). Consequently, we suggest that foraminifera be excluded from the mt-MBI, which will reduce analytical time and costs. The strong correlations obtained between the mt-MBI and ES confirms that it has the potential to complement or even replace current fish farm biomonitoring techniques in the near future.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Mangrove soil sediment Targeted Locus (Loci)

Biodiversity is at present receiving increasing attention due to need of conservation and sustainable utilization. Proper sampling and identification of organisms at the baseline is prerequisite to monitor any disturbances in future. This is particularly significant in the context of sea level rise and climate changes. The Indian coastal and marine habitat includes near shore, creeks, tidal flats, mud flats, coastal dunes, mangroves, seaweed, sea grass beds and coral reefs. These marine habitats are potential natural resources playing significant role in ecological and economic stabilities of the country. The present study aims at to inventorize the present microbial diversity on Indian coast and construct a detailed strategy for bridging the gaps with sampling plan for creating a database available in public domain.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
UCYN-A diversity in the Pacific

UCYN-A nifH amplicons were recovered from a coastal and oligotrophic site in the Pacific to characterize the diversity of UCYN-A sublineages.

Biome: root:Environmental:Aquatic:Marine:Coastal
Effects of different types of wastewater on microbial degradation of 2,2'',4,4''-tetrabromodiphenyl ether (BDE-47) in anaerobic sediment.

Surface sediments (from 0 to 10 cm depth) were collected from the southern coastal area (30.9844? N, 120.1411? E) at Taihu Lake, with a low-level of PBDE contamination as reported previously.

Biome: root:Environmental:Aquatic:Marine:Coastal
Future climate change affects the microbiome and condition of habitat-forming kelp

Climate change can cause effect on marine ecosystem. As a result, higher temperature and enrichment of carbon dioxide of seawater would be expected in the future scenario. In this study, we experimentally investigated the independent and interactive effects of warming and acidification on the habitat-forming kelp Ecklonia radiata and its associated microbiome, then 16S rRNA sequencing data of microbial communities associated with E. radiata on healthy and blistered samples under current and future environmental conditions were collected.

Biome: root:Environmental:Aquatic:Marine:Coastal
Marine Bacteria 16S V4 Raw sequence reads

Analysis of Bacterioplankton Community Distribution Pattern in Bohai Bay

Biome: root:Environmental:Aquatic:Marine:Coastal
Metagenomics of Jacarepagua Lagoon

The Jacarepagua lagoon is a coastal shallow water body in the Rio de Janeiro city (Brazil) historically contaminated by Microcystins ("MCs" - toxin produced by cyanobacteria with carcinogenic potential for mammals). These molecules are stable and resistant to variation in some physical and chemical factors (i.e. temperature, pH) and some common proteases. Besides, many studies have evidenced the process of bioaccumulation of MCs in different organisms, its adsorption to sediment particles and also its biodegradation by microorganisms from the environment. Previously, we evaluated the removal of MC from water by microorganism assemblages and biodegradation process was observed in the sediment as well as in the interstitial water. Furthermore, we analysed the microbial community through sequencing 16S rDNA by Illumina and showed the differences between these two microbiomes. Moreover, major identified phyla were Chloroflexi, Proteobacteria, Firmicutes, OP3 and the identified OTUs several genera described as MC-degraders were detected

Biome: root:Environmental:Aquatic:Marine:Coastal
water sample Raw sequence reads

seawater bacterial diversity in Dongji Island

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbial community diversity in Arctic marine sediments and Planktonic microbial

This study assessed the microbial community composition in Arctic marine sediments by 454 pyrosequencing of the 16S rRNA gene and planktonic microbial community composition in an Arctic fjord by 454 pyrosequencing of the 16S rRNA and 18S rRNA genes.

Biome: root:Environmental:Aquatic:Marine:Coastal
coastal suspended particulate matter North Sea surface Raw sequence reads

Microbial diversity in the North Sea coastal surface water during an annual cycle

Biome: root:Environmental:Aquatic:Marine:Coastal
seawater PCC7002M CCMP1334M Raw sequence reads

publish a paper

Biome: root:Environmental:Aquatic:Marine:Coastal
Coastal Marine Environment Targeted loci environmental

Marine protist samples were taken from Tolo Harbour in Hong Kong, before during and after a severe hypoxic episode.

Biome: root:Environmental:Aquatic:Marine:Coastal
Metagenome from mudbank Area,Alappuzha Kerala India

The Water samples are collected from 3 locations in the Coastal waters of Alappuzha during the monsoon and pre-monsoon period.

Biome: root:Environmental:Aquatic:Marine:Coastal
Marine sample from an Antarctic Bay Raw sequence reads

Describe microbial diversity

Biome: root:Environmental:Aquatic:Marine:Coastal
Marine waters Raw sequence reads

Microbial community structure of ballast and harbor waters

Biome: root:Environmental:Aquatic:Marine:Coastal