About me:

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. I am a Faculty Senior Scientist at Lawrence Berkeley National Laboratory.

Research Overview: 
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 Explorers

Carbon Flux Explorers

Follow us when at sea on Twitter @OC_Explorer.

Trace Metal Biogeochemistry

Aquatic Geochemistry at the Angelo Coast Mountain Reserve.

 
Laboratory:
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.

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 )

Bishop, J.K.B., M. B. *Fong, T.J. Wood (2016). Robotic observations of high wintertime carbon export in California coastal waters. Biogeosciences 13, 3019-3129, doi:10.5194/bg-13-3109-2016.

*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.

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).

Graduate Students:

Naomi Intrator  Ph.D. F2016 - Biogeochemical dynamics of the Vadose Zone of the Eel River Critical Zone Observatory.

Hannah Bourne Ph.D. F2013 - Ocean Particulate Geochemistry and Sedimentation

Ben Thurnhoffer M.Sc. F2013-2015 
     "Relationship of hillslope orientation and ground water chemical
       end members to spatial and temporal variation in surface water
       chemistry from catchment mouth to headwater springs."

Hyojin Kim Ph.D. S2009-2014:
      "Water chemistry evolution through the critical zone"
        Aug 2014- Post Doctoral Scientist: Shale Hills Critical Zone Observatory
        (http://criticalzone.org/shale-hills/)

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 / Eel River CZO - water chemistry

Project: Carbon Flux Explorer

Project: Ocean Particulate matter dynamics/ PIC Sensor development 

Undergraduate Honors Thesis Projects

  Athena Ngheim (2015-2016) "Particulate Composition and Subsurface Dynamics
at the Eel River Critical Zone Observatory" (now at Lamont Doherty Earth Observatory)

  Imari Walker (2015-2016) "Quantification of particulate inorganic carbon
sedimentation using autonomous carbon flux explorer"

   Alexandra Niebergal (2015-2016) "Evaluation of chemical defenses and aposematic potential in the ‘disco’ clam, Ctenoides ales" (joint with Lindsey Dougherty, IB).

  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"

  Courtney Hann (2012) "Carbon Flux Explorer biology".

  Gabrielle Weiss (2012) "PIC sensor sensitivity to major particle phases"

  Ralph Till (2011) "Particulate Mo Geochemistry"

  Sara Walkup (2010) "trace metal regulation of carbon"

Teaching Schedule
Fall 2016
Big Ideas Course: EPS/IB/GEOG C82 "Oceans"  F2016 TuTh 5:00-6:30 PM Pimentel 1.
EPS290  "Group Seminar: Marine and Aquatic Geochemistry" F2016 M 12:00-13:30 McCone 401.

Spring 2017
EPS 103/203 "Aquatic and Marine Geochemistry" 325 McCone Tu Th TBD
EPS 024 "Oceans in the News" freshman seminar, 325 McCone W 10-11 AM
EPS 290 "Group Seminar: Marine and Aquatic Geochemistry" TBD

Office Hours
Fall 2016

"Oceans"
  Tu 1:30 - 3:30
  Or by arrangment (email jkbishop AT berkeley.edu)
Marine Science Track Adviser: 
  Th 10:00 - 11:30. 
   in times of high demand... sign up sheet on door for 15 minute blocks
  Or by arrangement (email jkbishop AT berkeley.edu)

Spring 2016
EPS103/203 
  TBD
Marine Science Adviser: 
  TBD
  or by arrangement (email jkbishop AT berkeley.edu)
EPS024 
   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. 

Aug     2016  *R/V Ocanus, NSF Carbon Sedimentation iN the Ocean Watercolumn (C-SNOW), 12 days

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 

August 13-23 2016

Follow science writer Sarah Yang aboard our recent expedition aboard R/V Oceanus to study the ocean biological carbon pump.

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)

Undergraduates: 

Aug-16 Jessica Kendall-Bar, Will Kumler, Yuzhuang Liu, Xiao Fu 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

Graduate Students:

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