Ocean carbon cycle dynamics, remote sensing, aquatic chemistry, marine biogeochemistry, land - ocean biogeochemistry, chemical oceanography, ocean sensors and autonomous observing systems.
Degrees: B.Sc. (hon) Physical and Inorganic Chemistry, University of British Columbia; Sc.D. in Marine Chemistry, MIT/Woods Hole Oceanographic Institution Joint Program in Oceanography.
Path to Berkeley: Columbia University, Lamont Doherty Earth Observatory and NASA Goddard Institute for Space Studies, both in New York; University of Victoria, School of Earth and Ocean Sciences, BC, Canada; and Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley. I joined the EPS faculty in 2006.
Our research investigates the mechanics of biogeochemical processes of aquatic and marine systems.
At sea, we explore new ways to follow the very fast --- but largely unobserved --- biological carbon cycle: photosynthesis, grazing, sedimentation, and respiration. These processes, collectively known as the "ocean biological carbon pump" transform CO2 into organic matter and sequester it in the deep sea, impacting levels of CO2 in the atmosphere. The biotic carbon flows in the ocean are substantial and there are open questions regarding the stability of these flows in the face of human induced warming and acidification of the ocean. Is the ocean biological carbon pump strengthening (good) or weakening (bad)? Every time we go to sea on ships we get surprises. We need to find out how this system works so it can be predicted.
On land, we study how water changes its chemistry as it moves from rain, through soils and fractured rock to ground water, to creek, to river, and to the ocean. This process transports micro-nutrient elements such as iron from land to ocean and is thus important to the biological productivity of coastal waters.
Carbon Flux Explorers
Follow us when at sea on Twitter @OC_Explorer.
Trace Metal Biogeochemistry
Aquatic Geochemistry at the Angelo Coast Mountain Reserve.
The Ocean Biogeochemical Processes Laboratory and field facilities are located in the Lawrence Berkeley National Laboratory's Earth Sciences Division. LBNL is a 15 minute walk (or bus ride) from McCone Hall.
Courses I enjoy teaching in the Department of Earth and Planetary Science include EPS 103/203, "Introduction to Aquatic and Marine Geochemistry"; EPS C82 "Oceans", EPS 24 "Oceans in the News". I am EPS marine science track advisor.
What I like most about oceanography is that I need to draw on all my undergraduate basics (math, physics, chemistry, biology, computers, engineering...) to answer the difficult questions about where carbon goes in the ocean. There are always new things to discover and we've just only begun.
I really enjoy going to sea and bicycling in the Berkeley Hills. The forested hillslopes of the Angelo Coast Range Reserve are amazingly fun as well.
Bishop at sea aboard R/V Knorr - May 2009 - North Pacific Gyre 30oN 140oW
1971 B.Sc (Hon) - Chemistry, University of British Columbia
1977 Sc.D. Massachusetts Institute of Technology - Woods Hole Joint Program in Oceanography
Selected Peer Reviewed Papers since 2000: (*student #post-doc)
(for downloads of these send request to the author, for a more complete list and some down-loads see www-ocean.lbl.gov)
*Kim, H., J.K.B. Bishop, W. Dietrich, I.Y. Fung (2014). Process dominance
shift in solute chemistry as revealed by long-term high-frequency water
chemistry observations of groundwater flowing through weathered
argillite underlying a steep forested hillslope. Geochimica et
Cosmochimica Acta 140, 1-19. DOI:10.1016/j.gca.2014.05.011.
*Kim, H., J.K.B. Bishop, T.J. Wood, and I.Y. Fung (2012), Autonomous water sampling for a long-term monitoring of trace metals in remote environments. Environ. Sci. Technol., 46, 11220-11226; DOI:10.1021/es3006404
Bishop, J. K. B., P. J. Lam and T. J. Wood (2012), Getting good particles: Accurate sampling of particles by large volume in-situ filtration. Limnology and Oceanography Methods 10:681-710; DOI:10.4319/lom.2012.10.681
Lam. P.J., S.C. Doney, and J.K.B.Bishop (2011) The dynamic ocean biological pump: Insights from a global compilation of particulate organic carbon, CaCO3, and opal concentration profiles from the mesopelagic. Global Biogeochemical Cycles, 25, GB3009, doi:10.1029/2010GB003868.
Bishop, J.K.B. and T.J. Wood(2009) Year Round Observations of Carbon Biomass and Flux Variability in the Southern Ocean. Global Biogeochemical Cycles. 23. doi:10.1029/2008GB003206.
Bishop, J.K.B (2009) Autonomous Observations of the Ocean Biological Carbon Pump. Oceanography, 22 (2). 182-193.
Bishop, J.K.B.and Wood, T.J. (2008) Particulate Matter Chemistry and Dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites. Deep-Sea Research I 55, 1684-1706. 10.1016/j.dsr.2008.07.012
*Lam, P.J., and J.K.B. Bishop, (2008) The continental margin is a key source of iron to the HNLC North Pacific Ocean , Geophys. Res. Lett., 35, L07608, doi:10.1029/2008GL033294.
*Lam, P. J., and J.K.B. Bishop (2007), High Biomass Low Export Regimes in the Southern Ocean , Deep-Sea Research II 54 601-638.
*Lam, P.J., J.K.B. Bishop, C.C. #Henning, M. A. Marcus, G.A. Waychunas, and I.Y. Fung (2006) Wintertime phytoplankton bloom in the Subarctic Pacific supported by continental margin iron. Global Biogeochemical Cycles 20, GB1006, doi:10.1029/2005GB002557.
Bishop, J.K.B., T.J. Wood, R.E. Davis and J.T. Sherman (2004) Robotic Observations of Enhanced Carbon Biomass and Export at 55S. Science 304, 417-420.
Bishop, J.K.B., R.E. Davis and J.T. Sherman (2002) Robotic Observations of Dust Storm Enhancement of Carbon Biomass in the North Pacific. Science 298, 817-821.
Fung, I.Y., S.K. Meyn, I. Tegen, S.C. Doney, J.G. John, and J.K.B. Bishop (2000) Iron supply and demand in the upper ocean. Global Biogeochemical Cycles. V14(N1):281-295.
Visiting Postdoctoral Fellow:
Jill Sutton (Institute of Ocean Sciences, BC, Canada) Marine Phytoplankton Ecophysiology (2012-2013). Now at Université de Bretagne Occidentale, IUEM - Institut Universitaire Européen de la Mer (http://univ-brest.academia.edu/JillSutton).
Ben Thurnhoffer M.Sc. F2013 - Geochemistry at the Eel River Critical Zone Observatory.
Hannah Bourne Ph.D. F2013 - Ocean Particulate Geochemistry and Sedimentation
Hyojin Kim Ph.D. S2009-2014:
"Water chemistry evolution through the critical zone"
Aug 2014- Post Doctoral Scientist: Shale Hills Critical Zone Observatory
Phoebe Lam Ph.D. 2001-2005:
"Marine Particulate Matter in the Twilight Zone: Insights on Iron Cycling
and remineralization of Particulate Organic Carbon in the Ocean"
- 2011: Associate Scientist, Woods Hole Oceanographic Institution.
- 2014: Faculty, UC Santa Cruz
Atif Saleem MA 2010-11. "Climate Change, Oceans and Human Health"
Undergraduate Research Apprentice Program Interns:
Project: Angelo Coast Range Reserve - water chemistry
Areeb Aslam (Chem Eng. F2012) CO2
Robert William Nicklas (Chemistry, summer 2012; F2012) Soil Chemistry
Stacy Nagelstad (Engineering; F2011, S2012)
Ernesto Martinez (EPS; F2011)
Michael Fong (EPS; S2011-F2011)
Nolan Wong (EPS, Chemistry; F2010-S2011)
Tim Ault (engineering; F2009-S2010)
Kelsey Jones (EPS; S2009)
Project: Carbon Flux Explorer
Andrew Bower (engineering; S2011-F2011)
Sarah Dendy (EPS, F2009 -F2010)
Project: Ocean Particulate matter dynamics/ PIC Sensor development
Paul Lerner (EPS, F2011-S2012)
Gabrielle Weiss (EPS; F2010-F2011)
Ralph Till (EPS, S2009-S2010)
Undergraduate Honors Thesis Projects
Christina Hamilton (2013-2014) "Carbon FLux Explorer imagery"
Paul Lerner (2012) "Line P transmissometer POC estimates 2012 vs. 1996" (now PhD at Woods Hole)
Michael Fong (2012) "Effects of temperature and Zn-Co substitution on the variability of del-13C in Thalassiosira psudonana" (now PhD at Scripps)
Courtney Hann (2012) "Carbon Flux Explorer biology". (now PhD OSU)
Gabrielle Weiss (2012) "PIC sensor sensitivity to major particle phases" (now PhD at Univerity of Hawaii)
Ralph Till (2011) "Particulate Mo Geochemistry"
Sara Walkup (2010) "trace metal regulation of carbon" (now at Scripps)
Big Ideas Course: EPS/IB/GEOG C82 "Oceans" F2014 MWF 10-11 Pimentel 1.
EPS290 "Group Seminar: Marine and Aquatic Geochemistry" TBD
EPS 103/203 "Aquatic and Marine Geochemistry" 325 McCone Tu Th 9:30-11
EPS 024 "Oceans in the News" freshman seminar, 325 McCone W 10-11 AM
EPS 290 "Group Seminar: Marine and Aquatic Geochemistry" TBD
Th 2:00 - 3:45
Or by arrangment (email jkbishop AT berkeley.edu)
Marine Science Track Adviser:
Tu 1:30 - 3:00 - sign up sheet on door for 15 minute blocks
Or by arrangement (email jkbishop AT berkeley.edu)
Marine Science Adviser:
Tu 1:30 - 3:00
or by arrangement (email jkbishop AT berkeley.edu)
M or F 10-11 or by arrangement (email jkbishop AT berkeley.edu)
R/V New Horizon May 21-31 2011 CTD deployment to test new optical sensors
recovery of Carbon Flux Explorer May 27 2011 - Santa Cruz Basin
Deployment of Carbon Flux Explorer at beginning of a nasty 3 day gale. Santa Cruz Basin. It surfaced from a depth of 300 m every 7 hours to relay position data to the ship and we recovered it as planned on May 30 2011.
Below is a heavier than water BUOY-system with twinned sample collecting optical
sedimentation recorders of the same kind that are on the CFE.
June 2013 +CCGS JP Tully, Subarctic North Pacific, PIC, Carbon Flux Explorers, 16 days
Mar 2013 *R/V New Horizon, NSF Carbon Flux Explorer/PIC, 6 days
Feb 2013 +CCGS JP Tully, Subarctic North Pacific, PIC, Carbon Explorers, 16 days
Jan 2013 *R/V New Horizon, NSF Carbon Flux Explorer/PIC, 6 days
Oct 2012 *R/V Point Sur, NSF Carbon Flux Explorer/PIC, 6 days
Aug. 2012 +CCGS JP Tully, Subarctic North Pacific, PIC, 16 days
May 2012 *R/V New Horizon, NSF Carbon Flux Explorer/PIC, 10 days
Feb 2012 *R/V Point Sur, NSF PIC/POC sensor tests/CFE 7 days
Sept 2011 *R/V Point Sur, NSF Carbon Flux Explorer recovery/PIC, 7 days
July 2011 *R/V Point Sur, NSF Carbon Flux Explorer deployment/PIC, 6 days
May 2011 *R/V New Horizon, NSF Carbon Flux Explorer/PIC, 11 days
Oct 2010 *R/V Sproul, NSF Carbon Flux Explorer, 6 days
July 2009 S.S.V. Robert Seamens (Sea Education) 5 days.
May 2009 R/V/ Knorr, NSF GEOTRACES -MULVFS, 3.5 weeks
June 2008 R/V Knorr, NSF GEOTRACES -MULVFS, 2 weeks
June 2007 *R/V Sproul, CarbonFlux Explorer, ONR/NOPP, 3 days
+ Highlighted in the News section and on Department Web site.
* Bishop - Expedition Chief Scientist
June 21 2013
Following an 8 day deployment, Carbon Flux Explorers, CFE002 and CFE003 were recovered today from the subarctic North Pacific ocean by Todd Wood with the expert help of captain and crew and science party aboard the Canadian Coast Guard Vessel J.P. Tully. Todd was aided by UC Berkeley, Earth and Planetary Science marine science program (2013) graduate, Amelia Weiss. Recoveries took place in hours of darkness and first light at 49N 135W in the open subarctic North Pacific. While CFE003 operated perfectly and relayed its GPS positions during its mission and at the planned end of mission, CFE002 failed to report any positions during its mission and refused to acknowledge satellite commands to abort its mission. We only had two 20-30 minute windows for recovery of this float. It was recovered on its first surfacing.
At 3 am on June 21st, the Tully had positioned slightly to the west of the last estimated position for CFE002. CFE002 surfaced within 50 m of the bow of the ship. It was spotted within 1 minute of its first ARGOS transmission; CFE002 was then lost in poor visibility, but found again and recovered within 30 minutes of it's first transmission. It was hauled from the ocean by the Tully's small boat just as it was beginning to sink for its next dive. CFE003 was recovered at first light.
We owe a huge thank you to the crew and science party of the John P Tully and to the Institute of Ocean Sciences for so expertly helping out.
I've posted a few tweets as the saga developed on @OC_Explorer.
This was the first truly open ocean test of the new CFEs since a 41 day mission on 2011. They are expected to be deployed for a year long mission in Feb 2014 at station PAPA (50N 145W).
Carbon Flux Explorers are autonomous ocean profiling robots designed to follow hourly variations of carbon sedimentation in the ocean, a barely observed process, but a critical process governing the sequestration of carbon in the ocean. The Carbon Flux Explorer program is supported by the National Science Foundation. Engineering of the CFE was a joint effort by UC Berkeley, Lawrence Berkeley National Laboratory and the Instrument Developmennt Group at Scripps Institution of Oceanography.
March 28 2013: Science Short on the return of Carbon Explorers to sea.
August 14 2012: Canadian Coast Guard Ship John P Tully departed Vanconver Island destined for ocean station PAPA (50N 145W). Aboard the Tully, EPS marine science undergraduate student Ernesto Martinez is conducting an optical survey of particulate organic carbon (POC) and particulate inorganic carbon (PIC) at 26 locations from surface to sea-floor along the 1600 km transect. Along the way he will filter particles from water samples to validate our optical sensors.
PIC is produced by calcifying organisms, including coccolithophores, foraminifiera, and pteropods. PIC, composed of calcium carbonate minerals calcite and aragonite, is sensitive to the effects of fossil fuel acidification of the surface ocean. We have very few observations of PIC in the ocean. Our new optical sensor for PIC addresses this gap of observations. It uses transmitted cross polarized light to detect photons that interact with biologically produced calcium carbonate minerals calcite and aragonite. This cruise is the first science application of our new PIC sensor. In 2013 we will launch Carbon Explorer floats outfitted with POC and PIC sensors at PAPA which will operate in real time on a 24/7/365 schedule and return data to shore in real time.
This work is supported by the National Science Foundation. WETLabs, Inc. Philomath, OR is our industrial partner on this project.
Students at Sea with Group (First time; number of expeditions)
Mar-13 (1) Mitchel Bartolo; May-11 (1) Andrew Bower; Oct-10 (1) Sarah Dendy; May-12 (1) Bryce Dewees; Mar-13 (1) John Domingo; Aug-11 (2) Michael Fong; May-11 (1) Nin Gan; May-12 (1) Courtney Haan; Oct-12 (2) Christina Hamilton; Oct-12 (3) Heidi Hansen; Aug-11 (2) Megan Hayes; Mar-13 (1) Oliver Heggie; Oct-12 (2) Jessica Kendall-Bar; May-11 (6) Paul Lerner; May-11 (5) Ernesto Martinez; Oct-12 (1) James Meyer; Jan-13 (1) Nichole Ornelas; Oct-10 (1) Atif Saleem; Jan-13 (1) Aurora Smedley; Oct-10 (2) Ralph Till; May-12 (2) Doriane Weiler; Aug-11 (5) Amelia Weiss; Oct-10 (6) Gabrielle Weiss; May-11 (2) Nolan Wong; Feb-12 (3) Addien Wray
Jul-11 (1) Hyojin Kim; Mar-13 (1) Susan Willis
Post Doctoral Scientists
Oct-12 (2) Jill Sutton; Oct-10 (1) Shala Ali
Science Party R/V New Horizon (May 21-31 2011) Santa Catalina Basin, Santa Cruz Basin. left to right: Brian, Alex Morales, Todd Wood, Ralph Till, Nin Gan, Wes Strubhar, Jim Bishop, Andrew Bower, Gabrielle Weiss, Ernesto Martinez, Nolan Wong, Paul Lerner