http://lod.bco-dmo.org/id/dataset/553979
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 Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments from the R/V Atlantis AT18-14 cruise in the Eastern Mediterranean; 35.3 N 21.7 E in 2011 (Pickled Protists project)
2015-03-19
publication
2015-03-19
revision
BCO-DMO Linked Data URI
2015-03-19
creation
http://lod.bco-dmo.org/id/dataset/553979
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Joan M. Bernhard
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: Edgcomb, V. P., Bernhard, J. M. (2015) 454 pyrotags for Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments from the R/V Atlantis AT18-14 cruise in the Eastern Mediterranean; 35.3 N 21.7 E in 2011 (Pickled Protists project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-03-19) Version Date 2015-03-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/553979 [access date]
454 pyrotags for Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments Dataset Description: <p>Pyrotags of bacteria and archaea&nbsp;obtained from Urania, Discovery, and L’Atalante DHAB halocline sediments.</p>
<p>Sequences have been submitted to GenBank under BioProject PRJNA270764. They will be publicly available once the manuscript is accepted (Kormas et al. submitted to Extremophiles)</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-0849578 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0849578
completed
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
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
asNeeded
Dataset Version: 2015-03-19
Unknown
project_id
seq_target
sample
SRA
sample_location
cruise_id
lat
lon
Automated Sequencer
ROV Jason
Thermal Cycler
theme
None, User defined
No BCO-DMO term
sample identification
station
Cruise identfier
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
ROV Jason
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://osprey.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
eng; USA
biota
oceans
Eastern Mediterranean; 35.3 N 21.7 E
2015-03-19
Mediterranean Sea
0
BCO-DMO catalogue of parameters from 454 pyrotags for Bacterial and Archaeal taxa in deep hypersaline anoxic basin (DHAB) halocline sediments from the R/V Atlantis AT18-14 cruise in the Eastern Mediterranean; 35.3 N 21.7 E in 2011 (Pickled Protists 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
http://lod.bco-dmo.org/id/dataset-parameter/553991.rdf
Name: project_id
Units: unitless
Description: <p>GenBank Project identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/553992.rdf
Name: seq_target
Units: unitless
Description: <p>sequence target</p>
http://lod.bco-dmo.org/id/dataset-parameter/553993.rdf
Name: sample
Units: unitless
Description: <p>GenBank Sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/553994.rdf
Name: SRA
Units: unitless
Description: <p>GenBank Sequence Read Archive identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/553995.rdf
Name: sample_location
Units: unitless
Description: <p>sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/553996.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/553997.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/553998.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
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
1048
https://datadocs.bco-dmo.org/file/QAAXxYoUlwqY9z/sediment_pyrotags_prok.csv
sediment_pyrotags_prok.csv
Primary data file for dataset ID 553979
download
https://osprey.bco-dmo.org/dataset/553979/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 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 16S rRNA gene was performed using PCR amplification of the V4-V6 region of the 16S rRNA gene and the primer pair S-DBact-0341-b-S-17 (5’-CCTACGGGNGGCWGCAG-3’) and S-D-Bact-0785-a-A-21 (5’-GACTACHVGGGTATCTAATCC-3’) for Bacteria (Klindworth et al. 2012), and&nbsp;archaea349F (5’-GYGCASCAGKCGMGAAW-3’) and archaea806R (5’-GGACTACVSGGGTATCTAAT-3’) for Archaea (Takai &amp; Horikoshi 2000), as described in Dowd et al., (2008). A one-step, 30-cycle PCR reaction was performed using HotStarTaq Plus Master Mix Kit (Qiagen, USA).&nbsp; Following PCR, all amplicon products (ca. 450 bp) from different samples were mixed in equal concentrations and purified using Agencourt Ampure beads (Agencourt Bioscience Corporation, USA). Samples were sequenced utilizing the Roche 454 FLX Titanium platform and reagents according to the guidelines at the MRDNA Ltd. (Shallowater, TX, USA) sequencing facility. Processing of the resulting sequences, i.e. trimming and quality control, was performed with the MOTHUR software (v 1.30)&nbsp; including denoising of the flowgrams using PyroNoise and data normalization to the smallest number of sequences in the resulting libraries. Sequences ≥250 bp with no ambiguous base assignments and no homopolymers ≥8 bp were included in downstream analyses. Single singletons, i.e. sequences that appeared only with once in the whole dataset, were excluded from further analysis. These sequences were aligned using the SILVA SSU database (release 108). All sequences were binned into Operational Taxonomic Units (OTUs) and were clustered (average neighbor algorithm) at 97% sequence similarity. Coverage values were calculated with MOTHUR (v 1.30).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- original file: EdgcombDHABprokaryoteTags.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</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
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: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
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. https://ndsf.whoi.edu/jason/
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