Woods Hole Oceanographic Institution

Cruise Planning Synopsis

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R/V Atlantis

Cruise Party

Bonnie Chang: Principal Investigator
University of Washington USA
+1 206 685 9613

Amal Jayakumar: Principal Investigator
Princeton University USA
+1 609 258 6294

Margaret Mulholland: Chief Scientist, Principal Investigator
Old Dominion University 4600 Elkhorn Avenue Norfolk, VA USA 23529-0276
+1 757 683 3972

Departure: Dec 31, 2014


Arrival: Jan 23, 2015


Operations Area

Eastern Tropical South Pacific Ocean adjacent to Peru
Lat/Lon: 14° 0.0′ S / 78° 0.0′ W
Depth Range: 0 / 2000
Will the vessel be operating within 200 NM of a foreign country? Peru and possibly Chile
Are visas or special travel documents required? no

Science Objectives

In much of the world ocean, the bioavailability of dissolved nitrogen (N) limits primary production in surface waters. While dinitrogen (N2) is abundant in marine waters, it is biologically unavailable to all but certain groups of prokaryotic marine organisms that fix N2 (diazotrophs). Diazotrophs can stimulate biological production via the introduction of new N into otherwise N-depleted oceanic systems.  Recent work suggests that planktonic diazotrophs are geographically more widely distributed than previously thought.  Recent studies suggest that there is active N2 fixation in relatively warm (14-23oC) aphotic oxygenated pelagic waters and in aphotic waters within OMZs. Because the volume of aphotic water in the ocean is large, if N2 fixation is widely distributed at sub-euphotic depths, this could result in a dramatic upward revision of global N inputs via this process. However, at present there are few measurements of rates and we know little about how vertical chemical and physical gradients affect N2 fixation and the diazotrophic communities mediating these N inputs.

Nitrogen loss from the ocean, via pelagic marine denitrification, occurs primarily in oceanic OMZs and, like N2 fixation, is accomplished by a diverse group of microbes that occupy these regions. The juxtaposition of N2 fixation and denitrification (including anammox) has not been widely examined. Heterotrophic diazotrophy has now been observed in areas within and adjacent to oxygen minimum zones where concentrations of dissolved inorganic N (DIN) are high. In fact, if DIN is not inhibitory to active N2 fixation of the resident diazotrophs, oxygen minimum zones should be havens for diazotrophic activity because nitrogenase, the enzyme complex that mediates N2 fixation, is extremely sensitive to oxygen and many diazotrophic organisms employ physiological or behavioral strategies for removing or avoiding oxygen.  Expression of nifH was previously observed in the Arabian Sea OMZ suggesting active N2 fixation occurs there. In addition, N2 fixation and proteobacterial nifH phylotypes, were detected in the low oxygen, nitrate-rich, waters of coastal California and in the OMZ region of the Eastern Tropical South Pacific where it co-occurred spatially and temporally with denitrification, refuting the paradigm of spatial and/or temporal uncoupling between the two processes. 

While aphotic N2 fixation could substantially increase our estimates of depth-integrated rates of oceanic N2 fixation and therefore oceanic N inventories, there are still very few measurements of N2 fixation from oxic or suboxic aphotic waters and these measurements are poorly resolved with respect to vertical chemical and biological gradients in the ocean. It is imperative that we understand how diazotrophy varies along these gradients so that we can better predict and model the distribution of marine N2 fixation past, present, and future. The expansion of oxygen minimum zones will undoubtedly affect the marine N and C cycles through the expansion of oceanic N losses from denitrification. However, here we hypothesize that this may be offset by N inputs from N2 fixation by diazotrophic communities that thrive at low oxygen concentrations.

We propose to examine N2 fixation rates and nifH gene diversity in the context of light, nutrient, and oxygen gradients (and necessarily temperature gradients) along vertical profiles that penetrate into to the ETNP and ETSP OMZs.  These oceanic realms have contrasting surface productivity which may control rates of microbial growth and processes at depth.  We will compare rates of N2 fixation and diazotrophic community composition in vertical profiles within the OMZs to those in water masses adjacent to OMZs.  Rates will be measured using stable isotope tracer techniques that account for slow gas dissolution and that we have already applied successfully in the ETNP; we will continue to refine those methods as part of this project.  We will compare rate measurements of N2 fixation with the abundance and expression of nifH genes and nirS genes as a proxy for active denitrification in the region to better understand the juxtaposition of these two processes in association with OMZs. 

The overarching questions that we will address are:

  1. What is the contribution of diazotrophy to the total productivity in the euphotic zone of the ETP?
  2. Is N2 fixation occurring in and above the ETP OMZs and if so, how do the rates compare to N2 fixation rates in euphotic and aphotic N2 fixation in adjacent oxic waters?
  3. How does the community composition of N2 fixing microbes vary with respect to the vertical gradients of light, oxygen, and dissolved inorganic N concentrations with depth?
  4. What is the contribution of heterotrophic N2 fixation to depth integrated N2 fixation in the ETP both in and adjacent to the OMZs?
  5. Is the rate of N2 fixation (N inputs) within and above the ETP OMZs enough to partially offset denitrification (N losses) from these regions? 

Science Activities

During cruises we will measure water column hydrography, light, nutrient concentrations (total dissolved nitrogen, ammonium, nitrate, nitrite, urea, dissolved free amino acids, oxygen, and phosphate), and rates of primary productivity and dinitrogen (N2) fixation in detailed depth profiles at stations within and adjacent to oxygen minimum zones in the ETSP (this cruise) and the ETNP (2016).  In addition, we will measure the abundance and expression of nifH genes, concentrations of particulate carbon (C) and nitrogen (N) and the natural abundance of 13C and 15N in particles, chlorophyll a, and cyanobacterial and heterotrophic bacterial abundance. These measurements will be compared with rates of dissolved N uptake (NO3-, NO2-, NH4+, urea, and amino acids).  We will conduct experimental incubations wherein we examine the effect of organic C additions on N2 fixation rates.  Collaborators will measure rates of denitrification and measure the natural abundance of stable isotopes in nitrate.

We will examine the distribution of N2 fixation and the diversity of diazotrophs with respect to vertical gradients in oxygen, light, and dissolved N, and spatial gradients of productivity in the mesotrophic Eastern Tropical South Pacific (ETSP), one of the most productive oceanic regions on Earth, and the more oligotrophic Eastern Tropical North Pacific Oceans (ETNP).  We will to make detailed vertical profiles (e.g., 20 depths sampled over several days) of N2 fixation and the abundance and activity of diazotrophs with respect to chemical and biological gradients in the ETNP and ETSP both within and adjacent the OMZs.

Additional Info

Pre-cruise Planning Meeting: Teleconference


Supporting documentation:



Funding Agency: NSF
Grant or contract number: NSF-OCE 1356056

Scientific Instrumentation for R/V Atlantis

Other Science Vans:

Shipboard Equipment

Deionized Water System
Science Underway Seawater System
Navigation - Heading
Fume Hood
Navigation - Position

Shipboard Communication

Basic Internet access via HiSeasNet
Is there a need to receive data from shore on a regular basis?

CTD/Water Sampling

911+ Rosette 24-position, 10-liter bottle Rosette with dual T/C sensors
Biospherical underwater PAR (1000m depth limit) with reference Surface PAR
SBE43 oxygen sensor
Wet Labs ECO-AFL fluorometer
Wet Labs FLNTURTD Combination Flourometer and Turbidity Sensor

Critical CTD Sensors

MET Sensors

Barometric Pressure
Air temperature
Relative Humidity
Wind speed and direction
Short Wave Solar Radiation

Sample Storage

Climate Controlled Walk-in
Freezer -70°C 25 cu. ft.
Freezer -70°C 3.2 cu. ft. ea.
Refrigerator 8.6 cu. ft.
Scientific Walk-in Freezer
Storage Notes: Science will have three 4' x 4' x 1.5' incubators on deck.  They will bring hoses.


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
Trawl Winch with 9/16th trawl wire
Other Portable Winch
Winch Notes:

Wire use and application

CTD Winch with .322" Electro-mechanical wire
Trawl Winch with 9/16th trawl wire
Winch Notes:

Standard Oceanographic Cables

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

Portable Vans

Cold Storage Van
Science Van 1
Type/size: UNOLS COLD LAB VAN Location: 01 Deck inboard
Water: no Power:yes
Science Van 2
Type/size: Location: 01 deck inboard
Water: Power:yes

Specialized Deck Equipment

Mooring Deployment/Recovery Equipment Required: no Type: 
Cruise Specific Science Winch Required: yes Type: Pump Profiler System (sci).
Nets Required: no Type: 

Over the Side Equipment

Will you be bringing any equipment (winches, blocks, etc.) that lowers instruments over the side? yes Details: Pump Profiler system (PPS) from Chilean collaborators.

Special Requirements

Elecrical Power: yes Identify 220V clean to PPS on main deck
Equipment Handling: no Identify: 
Inter/intraship Communications: no Identify: 
Science Stowage: yes Identify: storing gear with pre-loading in San Francisco
Water: yes Identify: Cold storage and freezer storage req.

Additional Cruise Items/Activities

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

Hazardous Material

Will hazardous material be utilized?yesDescribe deployment method and quantity:
Chemicals such as acetone for nutrient and chlorophyll analysis.  Stable isotopes for conducting incubations.

Radioactive Material


Additional Information

Is night time work anticipated on this cruise?noSpecialized tech support (Seabeam, coring, other):
noneOther required equipment and special needs:
Science will have THREE 4' x 4' x 1.5' incubators on deck.  They will bring hoses.

Checklist & Notes


U.S. Customs Form: yes
Diplomatic Clearance: yes
Date Submitted: Jul 3, 2014
Date Approved:
Agent Information:

Chile (Arica)

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
Edificio Empresarial
Arturo Prat 391, piso 15, Of. 154

Contact: Claudio Silva
Phone: (56-58) 584495
Fax: (56-58) 230088
Cell: (56-9)-93469068
Email: csilva@agunsa.cl, agunsaari@agunsa.cl

AGUNSA Chile Head Office Contact: Gonzalo J. De la Sotta
Ship's Operations
Valparaiso Head Office
Phone: (56-32)-2556282
Fax: (56-32)-2257586
Cell: (56-9)-97484109
email: gdelasotta@agunsa.cl, operations@agunsa.cl
All Customs paperwork (4455's) recieved by Oct 20 and forwarded onto Atlantis in San Fran.
Shipments back to USA from Arica must have 4455's with them.
Isotope Use Approval: no
Isotope Notes:
STABLE istotopes being used in Wet lab.  C13 & N15.
SCUBA Diving: no


SSSG Tech:
Dave Sims, Catie Graver
Pre Loading San Fran OCT 20 and 21, 2014. 
LOADING in Arica = Chilean lab van and small ctd / winch.