Woods Hole Oceanographic Institution

Cruise Planning Synopsis

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R/V Atlantis


HOV Alvin

Cruise Party

Peter Girguis: Principal Investigator
16 Divinity Ave room 3085 Cambridge, MA United States 02138
+1 617 496 8328

Jeremy Rich: Principal Investigator
Brown University Providence, RI USA 02912
+1 401 863 6748

Kathleen Scott: Principal Investigator
University of South Florida 4202 East Fowler Avenue Tampa, FL USA 33620
+1 813 480 3908

Stefan Sievert: Chief Scientist, Principal Investigator
Woods Hole Oceanographic Institution Watson Building 207, MS#52 Woods Hole, Ma. USA 02543
+1 508 289 2305

Craig Taylor: Principal Investigator
Woods Hole Oceanographic Institution Watson Building 209, MS#52 Woods Hole, Ma. USA 02543
+1 508 289 2354

Scott White: Principal Investigator
University of South Carolina USA
+1 803 777 6304

Departure: Nov 2, 2014

Manzanillo Mexico

Arrival: Nov 26, 2014

Puntarenas Costa Rica

Operations Area

9° North Integrated Study Site
Lat/Lon: 9° 50.0′ N / 104° 18.0′ W
Depth Range: 2500 / 2600
Will the vessel be operating within 200 NM of a foreign country? no

Science Objectives

Sievert/Taylor/Rich: Knowledge of the in situ metabolism of microorganisms carrying out CO2-fixation at deep-sea hydrothermal vents is very limited. Particularly lacking are studies measuring rates of autotrophic carbon fixation in situ, which is a measurement ultimately needed to constrain production in these ecosystems. Although recent data suggests that nitrate reduction either to N2 (denitrification) or to NH4+ (dissimilatory reduction of nitrate to ammonium, DNRA) might be responsible for a significant fraction of chemoautotrophic production, NO3--reduction rates have never been measured in situ at hydrothermal vents. We hypothesize that chemoautrophic growth is strongly coupled to nitrate respiration in vent microbial communities. As part of this cruise, we are going to deploy and test a newly developed robotic micro-laboratory, the Vent-Time Series Submersible Incubation Device (Vent-TSSID) for measuring rates of relevant metabolic processes at hydrothermal vents at both in situ pressures and temperatures.

Scott and Girguis:
The relative importance of the two carbon fixation pathways (CBB, rTCA) in Riftia is impossible to infer from the existing data.  Bulk stable carbon isotopic compositions, and the presence and activities of enzymes allied to rTCA and CBB in Riftia symbionts,  do not definitively answer whether one or both pathways are operational in a single individual, and the contribution of each pathway to net carbon fixation.  The objective of this study is to clarify whether the activity of these pathways in Riftia are regulated by environmental conditions (e.g., the relative abundance of redox substrates), internal heterogeneity, or whether both pathways operate simultaneously.  

Science Activities

Sievert/Taylor/Rich: Our component of the cruise has 12 dives with DSV Alvin, to allow time for deployment and collection of experiments and for sampling of discrete vents along the axis of the 9°46’N to 9°53’N segment of the East Pacific Rise (EPR). We will focus our activities at Crab Spa, a diffuse flow vent site near Tica, and deploy experiments and sampling equipment, including the Vent-TSSID and a large volume pump (LVP). During the course of the cruise we will perform several deployments of the Vent-TSSID, as well as collect biomass from fluids and biofilms (deployment/recover experimental microbial colonizers) by utilizing a the LVP. Both the Vent-TSSID and the LVP will be deployed as an elevator. It is planned to deploy the instruments and bring them close to the deployment site the night before a dive, and then to position the instruments at the site with Alvin the next day. Alvin will be releasing the instrument either on the same dive or any subsequent dive, after which the instrument will be picked up at the surface. Furthermore, we will carry out additional opportunistic sampling of other diffuse-flow vents. Fluid samples for chemical analyses will be collected at each deployment site using isobaric gas-tight samplers, which will also be used to sample fluids from the focus site for the shipboard incubations. Finally, we will deploy/recover experimental microbial colonizers to collect microbial biofilms, as well as collect Riftia for subsequent ‘omic analyses. We will also perform several water casts at night, using the CTD/Niskin rosette on board Atlantis. 

Scott and Girguis:
  To address our objectives, it is critical for us to get freshly collected Riftia tubeworms that have been placed in a thermally insulated biobox and sent to the surface as soon after collection as possible (elevators would be fine as long as they were retrieved as soon as they surfaced).  Collected tubeworms would be incubated in high-pressure aquaria in the Girguis lab's pressure van for respirometry experiments.  After they reach steady-state, they will be subsampled for tissues, enzyme assays, and symbiont preparations (we will need some bench space in one of the ship's labs). Symbiont metabolism will be interrogated via 14C-labelling experiments (we will need to use a radioisotope van and have submitted our radioactive materials use request to WHOI).

Additional Info

Pre-cruise Planning Meeting: Teleconference
Meeting Notes: Sievert/Taylor are at WHOI
Media personnel on board: not sure yet


  Station 1
  Distance: null
  Days: null
  Latitude: 9° 50.0’ N
  Longitude: 104° 18.0’ W

Supporting documentation:



Funding Agency: NSF
Grant or contract number: IOS-1257532, OCE-1131095

Scientific Instrumentation for R/V Atlantis

Other Science Vans:

Shipboard Equipment

Navigation - Position
Navigation - Heading
Sippican XBT System (Mark 21)
Transponder Navigation - Sonardyne USBL
Deionized Water System
Fume Hood
Relay Transponder for Wire Use

Shipboard Communication

Basic Internet access via HiSeasNet
Is there a need to receive data from shore on a regular basis?
Is there a need to transfer data to shore on a regular basis?
Is there an expectation to use Skype or any other real-time video conference program?

CTD/Water Sampling

911+ Rosette 24-position, 10-liter bottle Rosette with dual T/C sensors
SBE43 oxygen sensor
Wet Labs FLNTURTD Combination Flourometer and Turbidity Sensor

Critical CTD Sensors

Sample Storage

Climate Controlled Walk-in
Freezer -70°C 3.2 cu. ft. ea.
Freezer -70°C 25 cu. ft.
Refrigerator 8.6 cu. ft.
Storage Notes: Girguis/Scott: It would be helpful to have a climate controlled space at 15C with bench space and room for two scientists to work.  Let us know if this is possible.


Will you be using Long Base Line (LBL) navigation? no
How many nets? null
How many tansponders? null
Will you be using Ultra-short baseline (USBL) navigation?no


Navigation Notes:


CTD Winch with .322" Electro-mechanical wire
Hydro Winch with .25" hydro wire
Winch Notes:

Wire use and application

CTD Winch with .322" Electro-mechanical wire
Hydro Winch with .25" hydro wire
Winch Notes:

Standard Oceanographic Cables

Slip ring required? no
Non-standard wire required? no
Traction winch required? no

Portable Vans

Isotope Van
Chemical Storage Van
Science Van 1
Type/size: Girguis lab pressure van Location:
Water: Power:
Science Van 2
Type/size: Location: 01 deck next to the emergency generator room
Water: we need clean seawater, as well as freshwater in the pressure van Power:480VDC (three phase); two circuits @ 60A each

Specialized Deck Equipment

Mooring Deployment/Recovery Equipment Required: no Type: 
Cruise Specific Science Winch Required: no Type: 
Nets Required: no Type: 

Over the Side Equipment

Will you be bringing any equipment (winches, blocks, etc.) that lowers instruments over the side? no

Special Requirements

Elecrical Power: yes Identify See Girguis Lab pressure van above
Equipment Handling: no Identify: 
Inter/intraship Communications: no Identify: 
Science Stowage: yes Identify: We would like to consider leaving the pressure van on the ship until we reach a US port.
Water: yes Identify: See pressure van

Additional Cruise Items/Activities

Explosive Devices:no Portable Air Compressors:no Flammable Gases:yes Small Boat Operations:no SCUBA Diving Operations:no

Hazardous Material

Will hazardous material be utilized?yesDescribe deployment method and quantity:

Radioactive Material


Additional Information

Is night time work anticipated on this cruise?yesSpecialized tech support (Seabeam, coring, other):
Sievert/Taylor/Rich/White: We will be perfoming water casts using the ship-board CTD/Rosette systemOther required equipment and special needs:

Scientific Instrumentation for HOV Alvin

Current Chart(s):

What type of samples do you expect to collect?Sievert/Taylor/Rich/White: water samples primarily with isobaric samplers, animals (Riftia, mussels), rocks, slurp samples, pick up larval colonization blocks and microbial colonization devices Girguis/Scott: Riftia tubeworms. We would be very happy to have these deployed to the surface in elevators as long as they were in thermally insulated bio collection boxes and the elevators were retrieved immediately upon surfacing. We do not want all six collections on one dive; it would be best to have the 6 collections spaced throughout the cruise. We have two dives funded; each collection will take a small portion of each dive in which they occur. We would be happy for our two dives to instead translate into six collections over the course of the cruise, as long as we had a little bottom time to collect environmental data and samples associated with each Riftia collection. null null null

Site Survey

Will you provide detailed charts of the work area(s)?no
If no, willl you need R/V Atlantis to generate maps of the work area(s)?no
Will you need post-dive maps of the work area generated?no


Will you be using Long Base Line (LBL) navigation? no
How many nets? 0
How many tansponders? 0
Will you be using Ultra-short baseline (USBL) navigation for other than Alvin operations?yes

Vehicle Equipment

Push corers (12-pack rack)
Search sonar
High temperature probe (0-480°C)
Low temperature probe
Scoop nets
Small capacity slurp samplers
Large capacity slurp samplers: multi-chamber
Bio collection boxes: 12 x 12 x 12
Bio collection boxes: 12 x 12 x 24


Will you be using elevators to transport samples to the surface?yes
If yes, how many would you anticipate? 6 (G/S), 10 (S/T/R)

Science Supplied Equipment

Are you supplying equipment to be used on HOV Alvin yes
Has this equipment been used on Alvin before? no
Please give a brief description of the equipment, its intended purpose, the cruise # it was last used on if any and its deployment method.
Sievert/Taylor/Rich: We are going to use a a number of instruments, msot of which have been used with Alvin:

1. We will be using Jeff Seewald's isobaric samplers, which have been used frequently with Alvin

2. We will be using chemical in situ sensors developed by Nadine LeBris, these are self-contained units that have been frequently used with Alvin (last time on AT15-38)

3. A McLane in situ large volume pump is going to be deployed as an elevator. Alvin will need to move the pump to the deployment site and also release it after filtration is finished (6-8 hours)

4. Vent-TSSID: This is a newly devleoped isntrument that has not yet been used with Alvin. The pressure senstive components will be pressure tested according to Alvin specificications. Fred Thwaites who is engeering the isntruemnt has been in touch with Alvin group.  

The LVP and Vent-TSSID are independent units. They will be moved by Alvin and positioned at the sampling site. 

We may possibly be gringing in situ blenders to preserve tubeworms on the seafloor.  They are not pressurized.
Does this equipment use an external pressure housing? no
Has the pressure housing been tested per Alvin Pressure Test requirements? no
Pressure housing schematic with dimensions and include air and water weights.
Air weight of this equipment? 12
Water weight of this equipment?
Does the equipment require a power interface from Alvin? no
Voltage required null
Power required
Data Interface
Does the equipment meet the electrical requirements of the Alvin User Manual? no
Please provide power and comms specifics, wiring diagram, pinout, and wiring harness in advance of the cruise.
Does this equipment require hydraulic inputs from the vehicle? yes
How many? 2 Single
Pressure requirements?
Flow requirements?
Hydraulic schematic of the equipment requirements.
Does this equipment require manipulation? yes
If yes, please describe how the equipment is to be manipulated:
Girguis/Scott: PIlot needs to open and close lid.  Very minor.  Specifications are included in the diagram uploaded for the hydraulic schematic.  Device has been successfully used with the JASON.

Sievert/Taylor:  LVP and Vent-TSSID need to be moved by Alvin, intake wand needs to be placed in opening of vent, instrument weights need to be released at end of operation
Will this equipment be deployed off the vehicle? no
If yes, please describe how the equipment is intended for deployment:
If yes, will the equipment be disconnected from the vehicle and left in situ? no
How long will the deployment be?
Will the equipment be recovered by the same vehicle? no
Do you intend to recover any other previously deployed equipment? no
If yes, please describe this equipment:
Does this equipment use any glass spheres for either buoyancy or as pressure housings? no
Does the equipment have an associated computer or control panel for remote operation from the personnel sphere? no
Has the computer or control panel been gas tested for use in the personnel sphere? no

Hazardous Material

Will hazardous material be utilized?no
Describe deployment method and quantity:

Additional Information

Brief operations description or comments:
Navy Clearance:
Granted 11/04/14:
WITHIN 10 NM RADIUS OF 09-50N 104-17W DURING PERIOD 020000T THRU 262400T NOV 14.
WITHIN 10 NM RADIUS OF 09-39N 104-14W DURING PERIOD 020000T THRU 262400T NOV 14.
WITHIN 10 NM RADIUS OF 09-54N 104-15W DURING PERIOD 020000T THRU 262400T NOV 14.

Checklist & Notes


U.S. Customs Form: yes
Diplomatic Clearance: yes
Date Submitted: Feb 27, 2014
Date Approved: Sep 18, 2014
Agent Information:

Mexico (Manzanillo)

Primary Agent:
Vasile Tudoran Transport
819 Ohio Ave.
Long Beach, CA 90804

Contact: Vasile Tudoran
Phone: (562) 882-5590
Fax: (562) 434-9800
Email : vtudoran@aol.com

Master R/V Ship Name
Attn: Scientist's Name
c/o Transmex Shipping, S de R.L de C.V.

Colhuas No.83 Centro
Manzanillo, Colima

Contact: Daniel Arias Romo
Phone: 011 52
314 33 2 20 65 / 33 2 80 22
Fax: 011 52 55 10 842917
Cell: 011 52 1 314 12 1 48 42
Email: danielromo2007@gmail.com

Note: Agent and WHOI contacts should be copied on all communications. It is requested that shipment information of any equipment be communicated to the Agent and WHOI contacts

Costa Rica

Master R/V Atlantis
Attn: Scientist's Name - AT26-23
c/o Vasile Tudoran Transport
819 Ohio Ave.
Long Beach, CA 90804

Contact: Vasile Tudoran
Phone: (562) 882-5590
Fax: (562) 434-9800
Email: vtudoran@aol.com

Local Address for Large Shipments:

Master R/V Ship Name
Attn: Scientist's Name
Aptdo 76
Puntarenas, Costa Rica
Manuel Fernandez
Phone: 011-506-2661-1529
Fax: 011-506-2661-2779

Manuel Fernandez, cell #011 506 8862 6787

Note: Agent and WHOI contacts should be copied on all communications. It is requested that shipment information of any equipment be communicated to the Agent and WHOI contacts

Mexico and Costa Rica.  All work done outside EEZs.
Forms to Eric by Oct 17.  San Fran load port.

Isotope Use Approval: yes
Isotope Notes:
Stefan Dystick.
SCUBA Diving: no


SSSG Tech:
Dave Sims, Allison Heater
Pre load BAE San Fran Oct 20 and 21.
Puerto Caldera will be dock on arrival Nov 26 to off load lab van and science samples and equipment.    Caldera address is:
INCOOP / Puerto Caldera, Costa Rica.  Container Terminal.    Leave container terminal out of the google search.