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Assessing the Efficacy of the Aerobic Methanotropic Biofilter in Methane Hydrate Environments
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The goal of this project is to assess the efficacy of aerobic methanotrophy in preventing the escape of methane from marine, hydrate-bearing reservoirs to the atmosphere and ultimately to better define the role of aerobic methanotrophy in the global carbon cycle.

Methane seeps with the resulting methane plume, Geophysical Research Letters, November 2007Methane seeps with the resulting methane plume, Geophysical Research Letters, November 2007


University of California – Santa Barbara, Santa Barbara (UCSB), CA 93106


The global methane reservoir in the form of gas hydrate is estimated at 500–10,000 Gt (KVENVOLDEN, 1995; MILKOV, 2004). This pool of carbon resides in permafrost/sub-permafrost and sub-seafloor settings. Neither the rates of methane generation/loss from the reservoir are known, nor if the reservoir is currently growing, shrinking, or at steady state. Evidence suggests that the hydrate reservoir has been unstable in the geologic past (JAHREN et al., 2001; THOMAS et al., 2002), and the reservoir is now considered as a capacitor on geologic time-scales (DICKENS, 2003). Given the magnitude and potential instability of at least some portion of this reservoir, combined with the potency of methane as a greenhouse gas, it is critical to understand the natural processes that act to control the release of subsurface methane to the ocean and atmosphere.

One fundamental knowledge gap standing between methane hydrates and the carbon cycle at earth’s surface is an understanding of the physical, chemical, geological, and biological controls on methane release from the subsurface to the ocean and atmosphere. Physical, chemical, and geological controls tend to trap or otherwise hinder methane transport from the subsurface, and are of primary importance in determining the magnitude, distribution, and phase of subsurface methane reservoirs, as well as the flux of methane departing the subsurface to the ocean and atmosphere (ETIOPE and KLUSMAN, 2002; ETIOPE and MILKOV, 2004). However, only methanotrophy (biological methane consumption) is known to destroy methane in the ocean and shallow subsurface, and the efficiency of this “methanotrophic biofilter” through space and time is a critical factor controlling how much subsurface methane ultimately reaches the atmosphere.

The potential impacts of methanotrophy in marine waters extend beyond the issue of methane transport to the atmosphere. The biological consumption of methane in the ocean is potentially an important process in the global carbon cycle in its own right, particularly at times of enhanced subsurface methane flux, as might be associated with broad hydrate destabilization. Methanotrophy not only removes methane, but also consumes O2 and produces both CO2 and abundant biomass (HANSON and HANSON, 1996). These processes have potentially far reaching consequences, including contributions to ocean anoxia (SLUIJS et al., 2007), ocean acidification (ZACHOS et al., 2005), and direct inputs of organic carbon to the deep ocean. In order to understand the linkage between methanotrophy and these factors, and how they might feed into the carbon cycle and broader earth system, it is critical to first understand the nature of the process and the associated controls.

A) Methanotroph-containing mat from Coal Oil Point, CA (COP), B) In-situ incubation of a methanotrophic mat at COP, C) Ongoing in-situ incubation of mats at Santa Monica Basin (SMB), D) Vein filling orange mats at the SMB methane seep, E) Mosaic of orange and white mats at SMB site, F) Methane hydrate was formed from an active seep at the SMB site-released here.A) Methanotroph-containing mat from Coal Oil Point, CA (COP), B) In-situ incubation of a methanotrophic mat at COP, C) Ongoing in-situ incubation of mats at Santa Monica Basin (SMB), D) Vein filling orange mats at the SMB methane seep, E) Mosaic of orange and white mats at SMB site, F) Methane hydrate was formed from an active seep at the SMB site-released here.


This project will provide insight into the relationship between the global carbon cycle and methane hydrate in regions of sub-marine methane hydrate occurrence and gas seepage. Results should create awareness of how benthic microbial communities impact the flux of methane from subsurface reservoirs to the ocean, the organisms involved, how active they are in several settings, and how they go about metabolizing methane. Results from both the closure of a basin-scale methane budget and research to identify the factors that most impact the aerobic biofilters can potentially be fed directly into global carbon cycle models to predict what might happen to the carbon cycle if a period of large-scale methane release into the oceans were to occur (i.e., gas hydrate dissociation).

Accomplishments (most recent listed first)

In October 2008, the University of California – Santa Barbara (UCSB) initiated investigations of water column methane oxidation in methane hydrate environments. Benthic microbial mat samples incubated in situ at Coal Oil Point (COP) and in the Santa Monica Basin were collected and fed 13C isotopically labeled methane in the lab to determine methane uptake and turnover rates. Experiments revealed rapid turnover of methane and uptake of carbon 13 into COP mat biomass. Incubated microbial mats from the Santa Monica Basin showed sluggish rates of methane oxidation and little uptake of carbon 13. However, another mat community was identified in direct contact with methane hydrate that showed strong suggestions of active methanotrophy, which was used for subsequent analyses. Stable isotope probing (SIP) and DNA extractions from these samples were used to apply new phylochip technology developed at Lawrence Berkeley National Laboratory (LBNL) to provide a robust assessment of microbial community structure and population dynamics as they relate to methane oxidation.

Water sampling in both shallow and deep water in the Santa Barbara and Santa Monica basins was conducted on several independent excursions as well as during the Study on the Ecology and Evolution of Petroleum Seeps (SEEPS) 2009 (September 13–29, 2009) and SEEPS 2011 (September 13–29, 2011) cruises aboard the R/V Atlantis.The SEEPS 09 cruise provided enormous benefits to this DOE project by providing a platform for sampling known seep sites and for locating and verifying potential seep sites. Using the AUV Sentry, a new methane hydrate site at 900m water depth was discovered in the Santa Monica Basin and a significant previously unknown seep field at 200–250m water depth was found in the Santa Barbara Basin. This latter seep field will help project personnel better understand and model the methane budget within the Santa Barbara Basin, particularly in shallower waters, which have long been enigmatic as they display a persistent methane maxima but with an unknown previous source.

Methane budget analysis for the Santa Barbara Basin was the focus of an article published in Continental Shelf Research (doi:10.1016/j.csr.2011.10.016). Initial analysis of the methane budget showed natural distinctions among the deep basin, mid-water, and surface waters, suggesting three divisions into three discrete depth horizons for budgeting purposes. In a separate journal article published in Limnology and Oceanography(doi:10.4319/lo.2012.57.2.0420), UCSB scientists present the results of methane concentration and turnover rate analyses of water column methane flux data in the Santa Monica Basin. The findings suggest that physical factors, including nature of methane input, water mass history, water mass residence time, and basin topography contribute to methane dynamics within the basin.

In May 2010, UCSB requested that their project scope be expanded to include sampling of oil-laden waters near Mississippi Canyon site 252. On June 11, researchers left Gulfport, MS onboard the R/V Cape Hatteras to study the fate of large methane releases in the Gulf of Mexico (GoM). UCSB researchers collected water samples during the 10-day “PLUMES” expedition to determine methane concentrations and develop a spatial distribution of the methane at the surface and at underlying depths. Researchers returned to the GoM on three additional expeditions between June and October to collect additional samples. UCSB researchers have analyzed over five hundred samples collected during these expeditions. These analyses included isotope labeling experiments and DNA extractions to assess methane oxidation rates and analyze the microbial communities in the GoM waters. In an article published January 6, 2011, in Sciencexpress (see Additional Information below), scientists on the PLUME and subsequent sampling expeditions in the Gulf suggest that within approximately 120 days from the onset of the BP incident nearly all the release methane was respired by a deepwater bacterial bloom. In one of two recent articles published in the Proceedings of the National Academy of Sciences (see Additional Information below) pertaining to the BP accident and its aftermath, researchers at UCSB have isolated the microbial communities responsible for degrading natural gas and heavier hydrocarbon plumes—ethane and propane—found in the Gulf of Mexico following the Deepwater Horizon spill. Based on stable isotope probing and DNA sequencing, the researchers discovered the advantage that certain cold-loving bacteria have in responding to deep water plumes where cooler temperatures (4°C) prevail.

Current Status

(January 2013) 
This project has been completed. The final report is available below under "Additional Information".

Project Start
Project End
DOE Contribution

Phase 1 - DOE Contribution: $210,461 
Phase 2 - DOE Contribution: $278,817
Phase 3 - DOE Contribution: $323,641 

Total Funding:
DOE Contribution: $812,919

Performer Contribution

Phase 1 - Performer Contribution: $80,642
Phase 2 - Performer Contribution: $71,153
Phase 3 - Performer Contribution: $61,441

Total Funding:
Performer Contribution: $213,236

Contact Information

NETL - Robert Vagnetti ( or 304-285-1334)
University of California Santa Barbara – David Valentine ( or 805-893-2973)
If you are unable to reach the above personnel, please contact the content manager.

Publications and Draft Manuscripts in Review


  • Mau S, Heintz MB, Kinnaman FS, Valentine DL (2010) Compositional variability and air-sea flux of ethane and propane in the plume of a large, marine seep field near Coal Oil Point, CA. Geo-Marine Letters 30: 367–378.
  • Redmond MC, Valentine DL, Sessions AL (2010) Identification of Novel Methane-, Ethane-, and Propane-Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing. Applied and Environmental Microbiology 76: 6412-6422.
  • Valentine DL (2010) Measure methane to quantify the oil spill. Nature 465: 421–421.
  • Valentine DL, Kessler JD, Redmond MC, Mendes SD, Heintz MB, et al. (2010) Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill. Science 330: 208–211.
  • Valentine DL, Reddy CM, Farwell C, Hill TM, Pizarro O, et al. (2010) Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters. Nature Geoscience 3: 345–348.
  • Valentine, DL. (2010) An opportunity to assess the behavior of methane released in the deep ocean. Fire in the Ice 10 (2)5.
  • Valentine DL (2011) Emerging Topics in Marine Methane Biogeochemistry. Annual Review of Marine Science, Vol 3 3: 147–171
  • *Kessler JD, *Valentine DL, Redmond MC, Du MR, Chan EW, et al. (2011) A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico. Science 331: 312–315. *Kessler and Valentine are co-first authors
  • Pack MA, Heintz MB, Reeburgh WS, Trumbore SE, Valentine DL, et al. (2011) A method for measuring methane oxidation rates using low-levels of (14)C-labeled methane and accelerator mass spectrometry. Limnology and Oceanography-Methods 9: 245–260.
  • Redmond MC, Valentine DL (2011) Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proceedings of the National Academy of Sciences of the United States of America. Doi:10.1073/pnas.1108756108
  • Mau S, Heintz MB, Valentine DL (2011) Quantification of CH4 loss and transport in dissolved plumes of the Santa Barbara Channel, California. Continental Shelf Research 32, 110-120. doi:10.1016/j.csr.2011.10.016
  • Ryerson T, Camilli R, Kessler J, Kujawinski EB, Reddy CM, et al. (2012) Chemical composition measurements quantify Deepwater Horizon hydrocarbon emissions and
  • distribution in the marine environment. Proceedings of the National Academy of Sciences, USA.doi/10.1073/pnas.1110564109
  • Heintz MB, Mau S, Valentine DL (2012) Physical Control on Methanotrophic Potential in Waters of the Santa Monica Basin, Southern California. Limnology and Oceanography 57(2) 420–432. doi:10.4319/lo.2012.57.2.0420
  • Valentine DL, Mezic I, Macešic S, Crnjaric-Žic N, Ivic S, et al. (2012) Dynamic auto-inoculation and the microbial ecology of a deep water hydrocarbon irruption. Proceedings of the National Academy of Sciences of the United States of America.doi/10.1073/pnas.1108820109

Manuscripts Submitted or in Draft Form

  • Farwell CA, MB Heintz, AL Sessions and DL Valentine (in preparation for Geochimicaet Cosmo-chimica Acta) Stable isotope probing for lipids of marine methanotrophs using deuterium and carbon-13.
  • Heintz MB, JW Pohlman, SC Bagby, M Elvert, MJ Wooler, C Ruppel and DL Valentine (in preparation for PLoS ONE) Enhanced Methane Consumption in Ice Covered Arctic Lakes.
  • Pack MA, MB Heintz, WS Reeburgh, SE Trumbore, DL Valentine, X Xu and ERM Druffel (submitted in revised form) Methane oxidation in the eastern tropical north Pacific water col-umn. Limnology and Oceanography.
  • Paul BG, H Ding, SC Bagby, MC Redmond, GL Anderson and DL Valentine (in preparation for Applied and Environmental Microbiology) Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep.
  • Redmond MC, PA Tavormina, VJ Orphan and DL Valentine (in preparation for Applied and Environmental Microbiology) Dynamics of Hydrocarbon Monooxygenase Genes in the Deep Ocean Following the Deepwater Horizon Spill.
Additional Information

Technology Status Assessment [PDF-137KB]

Project Kick-Off Presentation [PDF-4.69MB]

Article in Sciencexpress [PDF-1.85] - Kessler, Valentine, et. al. - Published January, 2011

Chemical Data Quantify Deepwater Horizon Hydrocarbon Flow Rate and Environmental Distribution [PDF-1.08] - National Academy of Sciences Proceedings

Dynamic Autoinoculations and the Microbial Ecology of a Deep Water Hydrocarbon Irruption [PDF-1.60] - National Academy of Sciences Proceedings

Final Project Report [PDF-2.50MB]