Ship Request

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  Methane in OMZs  -  2017  -  Sally Ride  
  Project Information  
Project Title: Microbial processes of pelagic anaerobic methane cycling in oxygen minimum zones Project Status: Submitted
Principal Investigator: Frank J. Stewart, MSU Project Institution: GaTech
Project ID: 104979 Version #: 8
Date Submitted: 8/9/2015 3:31:00 PM Created By: Frank J. Stewart
Date Last Modified: 10/7/2016 10:31:00 AM URI Serial #: None
Funding Agencies: NSF/OCE/BIO - 1558916 - Funded
Summary of Field Work: Recent evidence suggests that marine oxygen minimum zones (OMZs) support microorganisms that couple pelagic methane consumption to processes of nitrogen (N2) loss. However, the metabolic pathways and microbial taxa responsible for these transformations are just beginning to be characterized, and the full extent of pelagic microbial methane cycling in OMZs remains unconstrained. In addition, the role of denitrification-dependent methane oxidation as a potential 3rd route of oceanic nitrogen loss (in addition to classical denitrification and anammox) has not been quantified. Here, we propose to investigate the diversity, activity, and global distribution of microorganisms mediating methane-nitrogen cycle linkages in OMZs. We focus primarily on characterizing pelagic members of the candidate division NC10, a recently described bacterial group that couples methane oxidation to a unique pathway of nitrite-dependent N2 and O2 production. Recent molecular studies in our lab suggest that NC10 bacteria are present and active in nitrite-replete anoxic OMZs of the Eastern Tropical Pacific. Here, we aim to quantify the environmental drivers shaping NC10 distributions in OMZs, measure rates of NC10 methane oxidation and N2 production in OMZs, and analyze the metabolic gene content and evolutionary history of pelagic NC10 bacteria relative to those from other habitats.

We propose a combination of meta-omic (community DNA and RNA) sampling, single-cell genomics, shipboard stable isotope experiments, and microbial enrichments to characterize anaerobic methane cycling in the permanent OMZ of the Eastern Tropical North Pacific (ETNP) and the hypoxic “dead zone” in the Gulf of Mexico (GOM). Results will be contextualized relative to molecular surveys of existing samples from the Eastern Tropical South Pacific OMZ (Chile/Peru) and three silled anoxic basins (Golfo Dulce off Costa Rica; Cariaco Basin off Venezuela; Soledad Basin off Baja), thereby establishing a comparative framework for understanding the diversity and ecology of pelagic anaerobic-methane oxidizer communities in diverse low-oxygen regions.

Fieldwork will consist of two cruises, one to the ETNP in early summer 2016 and one to the GoM in summer 2017. We have worked at both sites in prior years in support of other OMZ-related projects. We propose sampling in the ETNP OMZ at 10-15 stations along two transects starting roughly from Manzanillo, Mexico and running southeast-northwest along the coast (~19-24°N, 106-116°W) and northeast-southwest off the coast (~14-18°N, 106-115°W). Proposed sampling in the GOM will span 5-10 stations on an east-west transect through the hypoxic zone on the Louisiana shelf (~28-29°N, 89-94° W). At each station, general water column parameters will be assessed via vertical depth surveys using a CTD equipped with sensors for fluorometry, PAR, and dissolved oxygen. Seawater collections for DNA, RNA, and microscopy samples and chemical measurements (of methane, nitrate, nitrite, ammonium, concentrations) will be done via rosette casts to discrete depths spanning the oxycline and suboxic zones. More extensive sampling will be done at ~3-5 process stations. At these sites, additional seawater samples will be collected for shipboard stable isotope and microcosm experiments to measure methane oxidation and nitrogen transformation rates and community transcriptional responses to methane and nitrogen additions. These seawater collections will also be used as inocula for incubations to enrich for denitrification-dependent anaerobic methane oxidizers. We therefore anticipate ~6-10 CTD-rosette casts (~24 hrs) per process station (initial CTD profile + nutrient collection + RNA/DNA casts) and 1-2 casts (~4 hrs) per non-process station.
Summary of Facility Requirements: The proposed shipboard microcosm experiments will involve maintaining temperature and ambient light at in situ levels. To do so, we will require access to a dedicated cold van that can be kept dark during the incubations, though external shading could also be used to regulate light levels. In addition, the project requires access to a rosette and CTD equipped with sensors for fluorometry, PAR, and dissolved oxygen. We will likely also mount high-resolution STOX oxygen sensors to the CTD, in addition to sensors available via UNOLS. We will need wet lab bench and storage space (estimated 30-40 sq ft) for filtering and preserving rosette-based water samples, as well as space to put a liquid nitrogen dewar for flash-freezing and temporarily storing RNA samples, and pressurized gases for experiments (methane, helium, argon). RNA samples can then be moved into a -80C freezer (if available) for longer-term storage. Access to a - 20C freezer and 4C refrigerator will be needed for storing DNA samples, reagents, and samples for enrichment cultures.
Summary of other requirements and comments:  
Ship Request Identification
Type of Request: Collaborative Ship Use Request Status: Submitted
Request ID: 1007993 Created By: Frank J. Stewart
Date Last Modified: 10/7/2016 10:31:00 AM Date Submitted: 8/9/2015 3:31:00 PM
Requested Ship, Operating Days and Dates
Year: 2017 Ship/Facility: Sally Ride
Optimum Start Date: 5/1/2017 Dates to Avoid: We would like to avoid sampling in the ETNP from October-April (Winter), due to teaching requirements. We also strongly prefer to sample earlier (May) in the summer rather than later to avoid the potential for hurricanes.
Earliest Start Date: 4/24/2017 Multi-Ship Op: No
Latest Start Date: 6/14/2017 Other Ship(s): N/A

Operating Days Needed: Science Days Mob Days De-Mob Days Estimated Transit Days Total Days
14 2 2 8 26
Repeating Cruise?
(within same year)
No Interval: N/A # of Cruises:  

Description of Repeating cruise requirements: N/A
Justification/Explanation for ship choice, dates,
conflicts, number of days & multi-ship operations:
R/V Sally Ride is based out of San Diego, the US port closest to the ETNP. Ideally, we would like to avoid sampling in the ETNP from October-April (Winter), due to teaching requirements. However, we may be able to accommodate winter sampling if absolutely necessary. We also strongly prefer to sample earlier (May) in the summer rather than later to avoid the potential for hurricanes.
Work Area for Cruise
Short Description of Op Area
for use in schedules:
Description of Op Area: Eastern Tropical North Pacific oxygen minimum zone (OMZ), off Colima Mexico, south of Baja
Op Area Size/Dia.: 600
  Lat/Long Marsden Grid Navy Op Area
24° N / 116° W map
84 map
NP13 map
14° N / 115° W map
48 map
NP13 map
  Show Degrees Minutes    
Foreign Clearance and Permitting Requirements
Foreign Clearance Required? Yes Coastal States:

 Important Info on Foreign Research Clearances  

Are you or any member in your science party bringing in any science equipment items which are regulated for export by the International Traffic in Arms Regulations (ITAR) and/or the Export Administration Regulations (EAR)?
No If yes, have you applied for the necessary permits through your export control office? No
 Questions about ITAR/EAR regulations?

Comments about foreign clearance requirements or
description of any other special permitting requirements
(e.g., MMPA, ESA, IHA, Marine Sanctuaries, etc.)
Port Calls
Requested Start Port Intermediate Port(s) Requested End Port
San Diego, CA, USA None, , None, San Diego, CA, USA
Explanation/justification for requested
ports and dates of intermediate stops
or to list additional port stops
San Diego is the port closest to the study area.

 Important Info on Working in Foreign Ports

Science Party
Chief Scientist: Frank J. Stewart, MSU
# in Science Party 8 # of different science teams 3 # Marine Technicians to be
provided by ship operator:
(include in science party total)
Explanation of Science Party Requirements and Technician Requirements Science party: 2 from Co-I Jen Glass lab, 3 from collaborator Bo Thamdrup lab, 3 from PI Stewart lab. Two technicians are requested to deploy and operate the CTD-rosette during 24-hr ops. Additional party members are required for water collection and processing and shipboard experiments.
Instrumentation Requirements That Impact Scheduling Decisions
Unselected Dynamic PositioningUnselected ADCPUnselected MultibeamUnselected Seismic
Unselected Dredging/Coring/Large Dia. Trawl WireUnselected Stern A-frameUnselected Fiber Optic (.681)Unselected 0.680 Coax Wire
Unselected SCUBA DivingUnselected Radioisotope use - briefly describeUnselected NO Radioisotope use/Natural level workUnselected Other Operator Provided Inst. - Describe
0 PI-Provided Vans - briefly describe Unselected MOCNESS  
Explain Instrumentation or Capability
requirements that could affect choice
of ship in scheduling.

We will need access to a dedicated cold van and radioisotope van for shipboard experiments and sample processing.

Major Ancillary Facilities (that require coordination of schedules with ship schedule)
Unselected Helicopter Ops (USCG)Unselected Twin OtterUnselected Unmanned Aerial Systems (UAS) 
Autonomous Underwater Vehicle (AUV)
Unselected Other AUVUnselected Sentry  
Coring Facility
Unselected Jumbo Piston CoringUnselected Large Gravity Core Unselected MC800 multicorer w/ MISO camera/telemetryUnselected OSU Coring Facility (MARSSAM)
Unselected Other Large Coring FacilityUnselected WHOI Long Core  
Human Occupied Vehicle (HOV)
Unselected AlvinUnselected Clelia (HBOI)Unselected JSL I & II (HBOI)Unselected Other HOV
Other Facility
Unselected MISO Facility - deep-sea imagingUnselected Other FacilityUnselected Potential Fields Pool Equipment 
Remotely Operated Vehicle (ROV)
Unselected JasonUnselected Other ROV  
Seismic Facility
Unselected Ocean Bottom Seismograph Instrument Center (OBSIC)Unselected Ocean Bottom Seismograph Instrument Pool (OBSIP)Unselected Ocean-Bottom Seismometer Program (UTIG)Unselected Other Seismic/OBS Facility
Unselected PASSCALUnselected Portable MCS groupUnselected Portable MCS/SCS groupUnselected U.S. Geological Survey Ocean Bottom Seismometer Facility (USGS at WHOI)
Towed Underwater Vehicle
Unselected ARGO IIUnselected Hawaii MR1 (HMRG)Unselected IMI12 (HMRG)Unselected IMI120 (HMRG - formerly DSL 120A)
Unselected IMI30 (HMRG)Unselected Other Towed Underwater VehicleUnselected Towfish 
UNOLS Van Pool
Unselected AUV Lab Van #1Unselected Clean Lab VanSelected Cold Lab VanUnselected General Purpose Lab Van
Selected Radioisotope Lab VanUnselected Wet Lab Van  
UNOLS Winch Pool
Unselected Mooring SpoolerUnselected Portable WinchUnselected Turn Table 
Explain Major Ancillary Facilities
Requirements and list description
and provider for "other" systems.
We will need access to a dedicated cold van and radioisotope van for shipboard experiments and sample processing.

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