http://lod.bco-dmo.org/id/dataset/3568
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
2011-10-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Scientific sampling event log from R/V Atlantis cruise AT18-14 in the Eastern Mediterranean; 35.3 N 21.7 E (Pickled Protists project, DHAB Metazoans project)
2011-12-21
publication
2011-12-21
revision
BCO-DMO Linked Data URI
2011-12-21
creation
http://lod.bco-dmo.org/id/dataset/3568
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. (2011) Scientific sampling event log from R/V Atlantis cruise AT18-14 in the Eastern Mediterranean; 35.3 N 21.7 E (Pickled Protists project, DHAB Metazoans project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 21 December 2011) Version Date 2011-12-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3568 [access date]
scientific sampling event log Dataset Description: <p>The science party used the Rolling Deck to Repository (R2R) event log application (ELOG with cruise-specific custom configuration files) to create a digital event log to record all instrument deployments during the cruise.&nbsp; The log includes information about all scientific sampling events recorded during the cruise including time, position, instrument name and additional comments regarding sampling details.</p> Methods and Sampling: <p>According to the event log, 5 ROV Jason dives, 10 SID-ISMS deployments, 3 CTD/Niskin rosette casts and one XBT profile were completed during the cruise.&nbsp; A multi-corer (MC800) deployment was conducted as well, but was not successful in collecting any cores, and therefore no data will be reported. It is unlikely that the XBT profile data will be reported either as it was done simply to calibrate some shipboard instrumentation.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061391 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1061391
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: 21 December 2011
Unknown
TZ
event
date
time
latitude
longitude
instrument
action
cast
seafloor
author
comment
dive
sample_type
basin
habitat
CTD Sea-Bird SBE 911plus
Deep Submersible Incubation Device
XBT
ROV Jason
Submersible Incubation Device-In Situ Microbial Sampler
theme
None, User defined
time_zone
event
date
time of day
latitude
longitude
instrument
event type
cast
depth_bottom
investigator
comments
dive_id
sample type
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Deep Submersible Incubation Device
Expendable Bathythermograph
ROV Jason
Submersible Incubation Device-In Situ Microbial Sampler
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
Investigations into the Physiological State of DHAB Metazoans
https://osprey.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
oceans
Eastern Mediterranean; 35.3 N 21.7 E
2011-12-21
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 Scientific sampling event log from R/V Atlantis cruise AT18-14 in the Eastern Mediterranean; 35.3 N 21.7 E (Pickled Protists project, DHAB Metazoans 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/26457.rdf
Name: TZ
Units: dimensionless
Description: <p>timezone (offset from UTC) in which sampling event was conducted</p>
http://lod.bco-dmo.org/id/dataset-parameter/26458.rdf
Name: event
Units: dimensionless
Description: <p>unique sampling event number derived from local YYYYMMDD.HHMM</p>
http://lod.bco-dmo.org/id/dataset-parameter/26459.rdf
Name: date
Units: dimensionless
Description: <p>date (UTC) as YYYYMMDD</p>
http://lod.bco-dmo.org/id/dataset-parameter/26460.rdf
Name: time
Units: dimensionless
Description: <p>time (UTC) using 24 hour clock HHMM format</p>
http://lod.bco-dmo.org/id/dataset-parameter/26461.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude (North is positive; South is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/26462.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude (East is positive; West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/26463.rdf
Name: instrument
Units: dimensionless
Description: <p>name of instrument or sampling system used to collect data</p>
http://lod.bco-dmo.org/id/dataset-parameter/26464.rdf
Name: action
Units: dimensionless
Description: <p>activity performed with the instrument; e.g. deploy/recover, start/end, etc.</p>
http://lod.bco-dmo.org/id/dataset-parameter/26465.rdf
Name: cast
Units: dimensionless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/26466.rdf
Name: seafloor
Units: meters
Description: <p>depth of water; seafloor depth from the shipboard 12 kHz Knudsen echosounder</p>
http://lod.bco-dmo.org/id/dataset-parameter/26467.rdf
Name: author
Units: dimensionless
Description: <p>name of person entering the event</p>
http://lod.bco-dmo.org/id/dataset-parameter/26468.rdf
Name: comment
Units: dimensionless
Description: <p>free text comment</p>
http://lod.bco-dmo.org/id/dataset-parameter/26469.rdf
Name: dive
Units: dimensionless
Description: <p>unique dive identification or number</p>
http://lod.bco-dmo.org/id/dataset-parameter/26470.rdf
Name: sample_type
Units: dimensionless
Description: <p>Sample type is a custom field created for this cruise, used to describe the types of samples taken. See the dataset documentation for a detailed explanation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/26471.rdf
Name: basin
Units: dimensionless
Description: <p>A term describing the basin location where sampling occurred. For this cruise it one of three possible terms: L'Atalante, Urania or Discovery.</p>
http://lod.bco-dmo.org/id/dataset-parameter/26472.rdf
Name: habitat
Units: dimensionless
Description: <p>Habitat is a custom field added to the event log for this cruise. It is one of three terms: control, halocline or brine.</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
36565
https://datadocs.bco-dmo.org/file/KAAGonvhBqjYPp/event_log.csv
event_log.csv
Primary data file for dataset ID 3568
download
https://osprey.bco-dmo.org/dataset/3568/data/download
download
onLine
dataset
<p>According to the event log, 5 ROV Jason dives, 10 SID-ISMS deployments, 3 CTD/Niskin rosette casts and one XBT profile were completed during the cruise.&nbsp; A multi-corer (MC800) deployment was conducted as well, but was not successful in collecting any cores, and therefore no data will be reported. It is unlikely that the XBT profile data will be reported either as it was done simply to calibrate some shipboard instrumentation.</p>
Specified by the Principal Investigator(s)
<p>A preliminary version of the event log was generated by BCO-DMO after the cruise.&nbsp; A quality assurance review was done to ensure unique event numbers, and some cleanup was done to move comments from other fields into the comment field.&nbsp; Several comments had been entered in the notebook page and seafloor depth field.&nbsp; On December 20 and 21, 2011 updates were made to the event after iterative review and consultation with the Chief Scientist.&nbsp; About two dozen events had to be adjusted for the correct date and time (including all of the Deep-SID events).&nbsp; The few entries in the station column were entered as cast numbers instead, and the station column removed as it was no longer needed.&nbsp; The 21 December 2011 version includes all modifications requested by the Chief Scientist.</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
CTD Sea-Bird SBE 911plus
CTD Sea-Bird SBE 911plus
PI Supplied Instrument Name: CTD Sea-Bird SBE 911plus PI Supplied Instrument Description:For this cruise aboard R/V Atlantis, the Seabird CTD 9 included dual conductivity and temperature sensors, a SBE 43 oxygen sensor and a Wet Labs C*Star transmissometer (660nm wavelength). The CTD was deployed in a frame with a 24-position, 10-liter bottle Rosette system. Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Deep Submersible Incubation Device
Deep Submersible Incubation Device
PI Supplied Instrument Name: Deep Submersible Incubation Device PI Supplied Instrument Description:The Deep-SID was used by Dr. Joan Bernhard to conduct timed, in situ grazing experiments during AT18-14. Instrument Name: Deep Submersible Incubation Device Instrument Short Name:Deep-SID Instrument Description: The Deep Submersible Incubation Device (Deep-SID) is capable of collecting a 4-liter sample that can then be pushed to 8 subsample chambers that contain a fixative. The Deep-SID was used by Dr. Joan Bernhard to conduct in situ grazing experiments during AT18-14. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
XBT
XBT
PI Supplied Instrument Name: XBT PI Supplied Instrument Description:According to the event log, one XBT probe was fired. The Chief Scientist did not know the type (T-5 or T-7). Instrument Name: Expendable Bathythermograph Instrument Short Name:XBT Instrument Description: An XBT is an expendable free-fall temperature probe that provides a profile of measured temperature against depth calculated from a fall-rate model. For example, two popular XBT models are the T-5 and T-7 probes from Sippican. More information is available from Lockheed Martin Sippican at URL: http://www.sippican.com/. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/132/
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:During the ROV Jason dives for this cruise, two types of sampling were conducted: injector push cores or.sediment scooped into chamber pots each injected with one of three types of preservatives: RNAlater, formalin, or glutaraldehyde. 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/
Submersible Incubation Device-In Situ Microbial Sampler
Submersible Incubation Device-In Situ Microbial Sampler
PI Supplied Instrument Name: Submersible Incubation Device-In Situ Microbial Sampler PI Supplied Instrument Description:The SID-ISMS was developed for and first deployed during this cruise. Instrument Name: Submersible Incubation Device-In Situ Microbial Sampler Instrument Short Name:SID-ISMS Instrument Description: The Submersible Incubation Device-In Situ Microbial Sampler (SID-ISMS) system was developed for the 2011 NSF funded DHAB Metazoans Mediterranean Brine research project and first used on cruise AT18-14. The system includes several integrated components including: a 2 liter incubation chamber; fixation filters and water sample bottles; a High Range CTD (Neil Brown Ocean Sensors, Inc., USA) equipped with two turbidity sensors (Wet Labs ECOView); an Aanderra 2808F oxygen optode; an SDSL-data link; and a sonardyne beacon, a pinger and a 24 volt deep-sea battery. The sensors and sampling devices are mounted on a frame that is attached to the hydro-wire. Lowering rate and recovery speed are controlled by a winch mounted on the surface vessel. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
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