http://lod.bco-dmo.org/id/dataset/553959
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2015-03-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments collected on R/V Atlantis cruise AT18-14 in the Eastern Mediterranean (35.3 N, 21.7 E) in 2011
2015-05-22
publication
2015-05-22
revision
BCO-DMO Linked Data URI
2015-05-22
creation
http://lod.bco-dmo.org/id/dataset/553959
Joan M. Bernhard
Woods Hole Oceanographic Institution
principalInvestigator
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Bernhard, J. M., Edgcomb, V. P. (2015) 454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments collected on R/V Atlantis cruise AT18-14 in the Eastern Mediterranean (35.3 N, 21.7 E) in 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-05-22) Version Date 2015-05-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/553959 [access date]
454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments Dataset Description: <p>Pyrotags of eukaryotes obtained from Urania, Discovery, and L’Atalante DHAB halocline sediments.</p>
<p>Small subunit ribosomal RNA V4 hyper variable region eukaryotic pyrotags prepared from total RNA extracted from sediments below haloclines of 3 deep hypersaline anoxic basins in the Eastern Mediterranean Sea and from nearby control sites (normal saline deep marine sediments in close proximity to deep hypersaline anoxic basins). Total RNA was transcribed to cDNA, and eukaryotic V4 pyrotags amplified from cDNA.</p>
<p><strong>Related References:</strong><br />
Bernhard, J.M., CM Morrison, E Pape, DJ Beaudoin, MA Todaro, MG Pachiadaki, K Ar Kormas, &amp; VP Edgcomb. 2015 (submitted). Metazoans of redoxcline seidments in Mediterranean deep-sea hypersaline anoxic basins.</p>
<p>Bernhard, J.M., Kormas, K.A., Pachiadaki, M.G., Rocke, E., Beaudoin, D.J., Morrison, C., Visscher, P.T., Cobban, A., Starczak, V.R., and Edgcomb, V.P. 2014. Benthic protists and fungi of Mediterranean deep hypersaline anoxic basin redoxcline sediments. Frontiers in Microbiology, doi: <a href="http://dx.doi.org/10.3389/fmicb.2014.00605" target="_blank">10.3389/fmicb.2014.00605</a>.</p> Methods and Sampling: <p>ROV Jason was used to collect push cores 6.35cm diameter obtained from the Deep Submergence Lab at Woods Hole Oceanographic Institution (<a href="http://www.whoi.edu/groups/DSL/">www.whoi.edu/groups/DSL/</a>) and configured with a seal to prevent contamination during ascent from the halocline sediments of L’ Atalante, Urania and Discovery basins in the eastern Mediterranean Sea at a depth of about 3500-4000m. Sediments were profiled for oxygen and immediately frozen upon return to surface.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061391 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1061391
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0849578 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0849578
completed
Joan M. Bernhard
Woods Hole Oceanographic Institution
508-289-3480
Department of Geology and Geophysics Woods Hole Oceanographic Institution, MS#52
Woods Hole
MA
02543
USA
jbernhard@whoi.edu
pointOfContact
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
508-289-3734
Department of Geology and Geophysics 220 McLean Lab, MS #8
Woods Hole
MA
02543
USA
vedgcomb@whoi.edu
pointOfContact
asNeeded
Dataset Version: 2015-05-22
Unknown
project_id
seq_target
BioSample_id
SRA
sample_location
cruise_id
lat
lon
ROV Jason
Automated Sequencer
Thermal Cycler
theme
None, User defined
No BCO-DMO term
sample identification
station
cruise id
latitude
longitude
featureType
BCO-DMO Standard Parameters
ROV Jason
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AT18-14
service
Deployment Activity
Eastern Mediterranean; 35.3 N 21.7 E
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Pickled Protists or Community Uniquely Adapted to Hypersalinity?
https://www.bco-dmo.org/project/2134
Pickled Protists or Community Uniquely Adapted to Hypersalinity?
<p>Protists are an essential component of microbial food webs and play a central role in global biogeochemical cycles, and thus are key players in sustaining the healthy functioning of any ecosystem. Over the past few years a rich diversity of protists has been revealed in a range of extreme environments, indicating that the frontiers of eukaryotic life are still being explored. Only recently, one of the most extreme marine environments known to science was discovered in the eastern Mediterranean Sea at a depth of ~3500m, namely deep hypersaline anoxic basins (DHABs). These basins are characterized by extremely high salt concentrations (up to saturation) that have been considered anathema to life. Instead, highly diverse communities of bacteria exist in the waters of these basins. With the exception of a preliminary study to this proposal that indicated a diverse and active assemblage of protists in the water column along the halocline and below the halocline, these DHABs remain largely unexplored regarding eukaryotic life forms. The sediments of the DHABs have not been explored for protists at all. </p>
<p>The investigators will collect water column and sediment samples on a short cruise to two basins with different brine chemistries. An exciting combination of molecular, cultivation-independent and culture-based approaches will be used to study the microbial communities of two basins. Investigators will use those approaches to determine adaptive strategies of marine protist communities to hypersaline, anoxic environments and the degree of their potential impact on biogeochemical cycling as a result of their predation activities, the degree to which the dominant protists maintain bacterial or archaeal symbionts, and the identity of those symbionts. The original research proposal identified Bannock and Discovery Basins as the field study areas, however the 2009 cruise collected samples at Discovery and Urania Basin. Methods to be employed include RNA-based sequence analysis of diversity based on 18S rDNA genes, statistical analyses of community composition and phylotype richness, geochemical documentation of the water column and sediments using classical and microelectrode approaches, expression profiling using 3'-UTR fragments of mRNAs, sequencing of complete gene transcripts for proteins appearing to confer adaptation to hypersalinity, analysis of the proteome signatures, FISH-SEM to characterize novel extremophiles, CARD-FISH to identify eukaryote prey and putative symbionts, and TEM to assess morphology and endobiont presence in common benthic morphotypes. </p>
<p>Hypersaline environments rank highly in the list of extreme systems that have attracted increasing notice in science as well as by the lay public. For example, considering predictions of increasing temperatures and drought in certain regions of our planet, the number of hypersaline habitats may increase dramatically causing this ecosystem to gain importance on a global scale. Thus, an understanding of the ecosystem in these habitats will help predict future ecosystem functioning due to global change. From a different perspective, revealing the mechanisms of adaptation to high salinity has become a major objective, both for biological science and for potential commercial exploitation of natural products associated with those adaptations. </p>
Pickled Protists
largerWorkCitation
project
Investigations into the Physiological State of DHAB Metazoans
https://www.bco-dmo.org/project/2177
Investigations into the Physiological State of DHAB Metazoans
<p>Invasion of the Body Snatchers!</p>
<p>Description text from the NSF award abstract:<br />
Although it has been known for many decades that metazoans inhabit anoxic habitats either on a periodic, transient, or semi permanent basis, none have been shown to complete an entire life cycle without access to oxygen. The remarkable recent observation that loriciferan metazoans complete a full life cycle without access to dissolved oxygen raises questions in the fields of physiology and evolution. The habitat from which the anaerobic animals were collected is sediment from a Deep Hypersaline Anoxic Brine (DHAB) in the eastern Mediterranean Sea at a water depth greater than 3 kilometers. DHABs are one of the most extreme marine environments known to science, with a water chemistry considered anathema to eukaryotic life. While the possibility of anaerobic metazoa is exciting, there are other potential explanations that warrant investigation before biology textbooks are rewritten. One alternative scenario is that remnant metazoa bodies were inhabited by anaerobic bacteria and/or archaea.</p>
<p>The overall goal of this project is to determine if the dominant loriciferan and nematode taxon in each of three DHABs represent living populations. Because remnant DNA can be preserved in anoxic settings for long periods of time, the project will include in situ preservation for RNA analysis. Further, because there is also some chance of RNA preservation in these anoxic sedimentary environments, the study will include analyses of the more ephemeral mRNA and also Transmission Electron Microscopy (TEM). On three ship days added to a funded cruise to sample DHABs for other purposes, an ROV will be used to preserve samples in situ. The specific aims are to: (1) Use RNA and DNA analysis to establish if metazoan ribosomal RNA and functional genes were active at the time of in situ preservation in the dominant two metazoan taxa from each DHAB. (2) Identify the prokaryotes associated with DHAB metazoans using RNA analysis and FISH/CARD FISH. (3) Assess the state of cellular ultrastructure in metazoans using TEM to determine the state of organelles (e.g., nuclei, Golgi, hydrogenosomes) and if DHAB metazoans have specialized cellular structures.</p>
<p>Regardless of results, significant information will be obtained. If the metazoans are not living in the DHABs, then a paradigm shift is unnecessary and physiology text books do not need to be rewritten. If the metazoans are living in the DHAB, then a paradigm shift is required.<br />
</p>
DHAB Metazoans
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Mediterranean; 35.3 N 21.7 E
2015-05-22
From projects that focused on the following 2 locations: 1. Mediterranean Sea 2. Eastern Mediterranean; 35.3 N, 21.7 E
0
BCO-DMO catalogue of parameters from 454 pyrotags for Eukaryote taxa in deep hypersaline anoxic basin (DHAB) halocline sediments collected on R/V Atlantis cruise AT18-14 in the Eastern Mediterranean (35.3 N, 21.7 E) in 2011
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/553971.rdf
Name: project_id
Units: unitless
Description: GenBank Project identification
http://lod.bco-dmo.org/id/dataset-parameter/553972.rdf
Name: seq_target
Units: unitless
Description: sequence target
http://lod.bco-dmo.org/id/dataset-parameter/553973.rdf
Name: BioSample_id
Units: unitless
Description: GenBank BioSample identification number and hyperlink.
http://lod.bco-dmo.org/id/dataset-parameter/553974.rdf
Name: SRA
Units: unitless
Description: GenBank Sequence Read Archive identification
http://lod.bco-dmo.org/id/dataset-parameter/553975.rdf
Name: sample_location
Units: unitless
Description: sampling location
http://lod.bco-dmo.org/id/dataset-parameter/553976.rdf
Name: cruise_id
Units: unitless
Description: cruise identification
http://lod.bco-dmo.org/id/dataset-parameter/553977.rdf
Name: lat
Units: decimal degrees
Description: latitude; north is positive
http://lod.bco-dmo.org/id/dataset-parameter/553978.rdf
Name: lon
Units: decimal degrees
Description: longitude; east is positive
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
964
https://datadocs.bco-dmo.org/file/P66Gw0nF0g9lE2/sediment_pyrotags_euk.csv
sediment_pyrotags_euk.csv
Primary data file for dataset ID 553959
download
https://www.bco-dmo.org/dataset/553959/data/download
download
onLine
dataset
<p>ROV Jason was used to collect push cores 6.35cm diameter obtained from the Deep Submergence Lab at Woods Hole Oceanographic Institution (<a href="http://www.whoi.edu/groups/DSL/">www.whoi.edu/groups/DSL/</a>) and configured with a seal to prevent contamination during ascent from the halocline sediments of L’ Atalante, Urania and Discovery basins in the eastern Mediterranean Sea at a depth of about 3500-4000m. Sediments were profiled for oxygen and immediately frozen upon return to surface.</p>
Specified by the Principal Investigator(s)
<p>RNA from approximately 8 g of the top 2 cm from each frozen syringe subcore was extracted using an optimized protocol with the RNA Power Soil kit (MoBio, USA). Major modifications included introduction of 3 cycles of freeze-thaw (-80 degrees C, 5 min., 65 degrees C, 5 min.), bead beating with 2× 5 min. intervals on a horizontal vortexer, an overnight nucleic acid precipitation, and a one-hour centrifugation during the precipitation step. In addition, we introduced two DNAase treatments using TurboDNAase (Ambion, USA). Removal of DNA was confirmed by PCR using general eukaryotic primers. RNA was purified using the MEGAclear kit (Ambion, USA). Reverse transcription of the purified RNA samples was performed using the QuantiTect kit (Qiagen, USA). Tag-pyrosequencing of the eukaryotic small subunit rRNA (18S rRNA) gene was performed using PCR amplification of the V4 region of the 18S rRNA gene and the primer pair TAReuk454FWD1 (5′-CCAGCA(G/C)C(C/T)GCGGTAATTCC-3′) and TAReukREV3 (5′-ACTTTCGTTCTTGAT(C/T)(A/G)A-3′). Following PCR, all amplicon products (ca. 450 bp) from different samples were purified using the MinElute Reaction Cleanup kit (Qiagen, USA). Amplicon libraries were sequenced utilizing the Roche 454 FLX Titanium platform and reagents following manufacturer’s guidelines at the MR DNA (Molecular Research LP, Shallowater, TX, USA) sequencing facility.&nbsp;</p>
<p>Denoising of the flowgrams was performed using Acacia. Processing of the resulting sequences, i.e. trimming and quality control, was performed using QIIME. Sequences with 380 bp or more and no ambiguous base calls and no homopolymers of 6 bp or more were included in further analysis. All sequences were binned into Operational Taxonomic Units (OTUs) and were clustered (average neighbor algorithm) at 97% sequence similarity identity. Taxonomic assignments were made using BLAST within QIIME.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- original file: EdgcombDHABeukaryoteTags.xlsx<br />
- replaced positions for Discovery and Urania with those in event log for pushcores<br />
- added html links to GenBank BioProject<br />
- added cruise_id, lat, lon<br />
- added html links to the GenBank BioSample (22 May 2015)</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:Sampled with push cores of 6.35cm diameter and configured with a seal to prevent contamination during ascent. Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument Description: The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:Roche 454 FLX Titanium platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: AT18-14
AT18-14
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-14
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel