Kolby Jeremiah Jardine

Research Scientist

Building 074B, Room 0106

M/S 74R316C

Phone: 510-495-8231

kjjardine@lbl.gov

Curriculum Vitae

Biography

Kolby Jardine studies plant and microbial metabolism by working at the interface of biochemistry, ecology, and atmospheric sciences (Biochemical Ecology) and is a research scientist in the Ecology Department within the Climate & Ecosystem Sciences Division of Lawrence Berkeley National Laboratory.

The primary goal of the research is to characterize quantitative relationships between biochemical, optical, and volatile organic signals emitted by plants during climate extremes in order to characterize processes and mechanisms of potentially high global importance. This presents exciting opportunities for the development of new methods for the continuous local and global monitoring of the physiological, energetic, and oxidative status of plants and ecosystems and their associated cycling of carbon and water.

Field, greenhouse, and laboratory methods are developed for the quantification of carbon dioxide and gas-phase volatile organic compound concentrations, fluxes, and isotopic composition from leaves to ecosystems and seconds to seasons. Methods include IR spectrometry, proton transfer reaction mass spectrometry (PTR-MS), and thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS).

Current Projects

Working with Phase 2 of the Next Generation Ecosystem Experiments (NGEE) Tropics project in the Brazilian Amazon, Kolby installed an isotope trace gas laboratory and maintains a small research group at the National Institute for Amazon Research in Manaus, Brazil to study photosynthesis, respiration, and defense. Prior to returning to Berkeley Lab, he was based in Manaus where he led the BrazilianAIR campaign (5 mo), the terrestrial ecosystem component of the GoAmazon project (4 yr), and NGEE Tropics Phase I (2 yr).
More Brazil Research Photos (Dropbox)
360 Degree Tropical Research Videos (YouTube)

Together with postdoc Rebecca Dewhirst and collaborators at the Joint Bioenergy Institute (JBEI) and Environmental Molecular Sciences Laboratory (EMSL), a DOE BER early career research project (ECRP) is underway entitled, “O-Acetylation and methylation engineering of plant cell walls for enhanced biofuel production”. Also known as the poplar esterified cell wall transformations and metabolic integration (PECTIN) study, this project studies the metabolism of cell wall esters and their roles in forest response to climate in the emerging biofuel tree species California poplar (Populus trichocarpa). See PECTIN project website.
Exploring the role of volatile organic compounds in soil biogeochemistry.

Experience

Research Scientist, Lawrence Berkeley National Laboratory, Climate and Ecosystem Sciences Division, 2014-Present
Project Scientist, Lawrence Berkeley National Laboratory (Berkeley, CA, USA) and Instituto Nacional de Pesquisas da Amazônia (Manaus, Brazil), 2012-2014
Visiting Scientist, Green Ocean Amazon (GoAmazon) Terrestrial Ecosystem Project, University of Bielefeld, Bielefeld, Germany, 2012
Assistant Research Professor, Biosphere 2, University of Arizona, Tucson, AZ, 2009-2012
Visiting scholar, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil, 2010
Postdoctoral Research Fellow, National Center for Atmospheric Research, Boulder, CO and Biosphere 2, University of Arizona, Tucson, AZ, 2008-2009
Biosphere-Atmosphere Research and Training (BART) Doctoral Research Fellowship, University of Michigan Biological Station, 2004-2008
Instructor, San Juan College, Farmington New Mexico, 2001-2002
Graduate Student, NSF fellow in Optical Biomolecular Devices, Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 1999-2000
Undergraduate Research Assistant, Department of Chemistry, New York University, New York City, NY, 1997-1999
Research Internship, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 1994-1996

Scholarly Service

Reviewer, Analytical Chemistry
Reviewer, Geophysical Research Letters
Reviewer, Atmospheric Measurement Techniques
Reviewer, Biogeosciences
Reviewer, Atmospheric Chemistry and Physics
Reviewer, Global Change Biology
Reviewer, Oecology
Reviewer, New Phytologist
Reviewer, Phytochemistry
Reviewer, Atmospheric Environment
Reviewer, Austrian Science Foundation, 2013-2015
Reviewer, Environmental Protection Agency (EPA), 2013-2015
Reviewer, DOE Terrestrial Ecosystem Science, 2013-2015
Reviewer, NSF Atmospheric Chemistry, 2013-2015
Editor, Biogeosciences, 2013-2015
Session Co-Chair, AGU, 2011-2012

Description of Research

PECTIN: 2018 – Present (LBNL-EMSL): “O-Acetylation and methylation engineering of plant cell walls for enhanced biofuel production”. This 5-year project started Nov 1st, 2018 studies the metabolism of cell wall esters and volatile intermediates as well as their role in central physiological processes in the emerging biofuel tree species California poplar (Populus trichocarpa) using field settings and controlled environmental conditions.
NGEE Tropics: Jan 2016 – Present (INPA-LBNL): Integration of water and carbon cycling in Amazonia. Installation of an automated Basin wide sensor network for leaf temperature and sap flux for dominant trees within the footprint of LBA CO₂/H₂O flux towers including Caxuana, Santarem, and Manaus. Lead teams of researchers in advanced sensor installations and manual field collections of trace gas exchange, tissue specific organic compound analysis, and stable isotope sampling. Establish a stable isotope ecology/hydrology laboratory at INPA based on mass spectrometry and spectroscopy.
GoAmazon 2014/5, June 2012-Dec 2015 (INPA-LBNL): Establishment of a new analytical atmospheric plant biochemistry lab consisting of PTR-MS, TD100 thermal desorption-GC-MS, and cavity ringdown carbon isotope spectrometry. Tested instrumentation in California before deploying to the central Amazon for leaf to ecosystem level carbon metabolism studies using stable carbon isotope techniques and leaf photosynthesis systems. Current activities also include ecosystem level mapping of volatile metabolite emissions in the central Amazon through high vertical resolved ambient concentrations within and above the forest canopy as a part of GoAmazon 2014/15.
Visiting Scientist, University of Bielefeld, Germany, April-June 2012: Development of a unified theory of plant primary and secondary metabolism. Experiments include stable carbon isotope leaf feeding experiments (H¹³CO₃, pyruvate-2-¹³C, and glucose-2-¹³C) followed by stable carbon isotope analysis of CO₂ and volatile organic compound emissions.
BrazillianAir 2010, June 2010-July 2011: Lead PI of 6-month remote field campaign in the central Amazon Basin. Vertical concentration gradients and branch/soil enclosure flux measurements of volatile organic compounds and ozone at the K34 tower at ZF2, Manaus, Brazil. Analytical techniques include PTR-MS, GC-PTR-MS, and GC-FID.
CREosote ATmosphere Interactions through Volatile Exchange (CREATIVE 2009), May-October 2009: Lead PI of 5 month remote off the grid field site with a mobile laboratory (PTR-MS and a GC-MS) in the Santa Rita Experimental Range. Goal to investigate the emissions of volatile organic compounds from creosotebush during the summer monsoon season. Branch and ecosystem scale fluxes were measured using enclosures, eddy covariance, and relaxed eddy accumulation techniques.
Biosphere 2, 2008-2012: Designed and installed the Ecosystem Metabalomics Laboratory (EML) in the Biosphere 2 complex and integrated it via heated tubing to the tropical rainforest and desert biomes. Instruments installed:
• A high sensitivity proton transfer reaction mass spectrometer (PTR-MS), Thermal desorption-gas chromatograph-mass spectrometer (TD-GC-MS).
• VOC calibration systems based on the permeation tube and dynamic solution injection techniques.
• A Licor 7000 and a Licor 840 CO₂/H₂O analyzer.
• Programmable custom light and temperature controlled glass leaf chamber.
• CO₂ and water vapor concentration and isotope calibration equipment.
• A Picarro isotopic H₂O cavity ringdown spectrometer.
• An Aerodyne quantum cascade laser CO₂ isotopic analyzer.
National Center for Atmospheric Research, Boulder, CO, spring 2007: Identify the biochemical pathways that lead to the production and consumption of acetaldehyde in plants and its relationship between photosynthesis and respiration. Determine the plant physiological and environmental controls over the exchange of acetaldehyde between plants and the atmosphere. Development of a canopy scale compensation point model for acetaldehyde.
Canopy Horizontal Array Turbulence Study (CHATS) field experiment, Dixon, CA, summer 2007: Characterize the turbulent structure of the fields of aerosols and trace chemical species within and above the orchard canopy. Measurements included aerosol vertical concentration and flux measurements including species such as volatile organic compounds, ozone, NOx, NOy, H₂O, CO₂, etc.
Intercontinental Chemical Transport Experiment (INTEX-B), Seattle, WA, spring 2006: NASA/NCAR aircraft study designed to better understand the transport and transformation of gases and aerosols on transcontinental/intercontinental scales. Primary responsibilities were the operation of a PTR-MS instrument for fast VOC concentration measurements aboard the NCAR C-130 research airplane.
Stony Brook University, Stony Brook, NY, Fall 2005 – May 2008, Design, fabrication, and control of instrumentation for gas chromatography-combustion-isotope ratio mass spectrometry. Branch enclosure measurements of carbon isotope ratio signatures of oxygenated volatile organic compounds from various biological sources. Investigation into biochemical pathways and plant physiological controls over OVOC exchange.
University of Michigan Biological Station, Pellston, MI, summer 2005 and 2006, Part of NSF Biosphere Atmosphere Research and Training Fellowship. Participated in climate change, plant ecology, atmospheric chemistry, and science and society workshops. Conducted flux measurements of oxygenated volatile organic compounds from soils and litter by GC-FID. Testing of an experimental dehydration membrane for removing water vapor from VOCs in air samples.
National Center for Atmospheric Research (NCAR), Boulder, CO, summer 2004, Visiting scientist. Design and fabrication of a cryogenic automated thermal desorption system for the analysis of volatile organic compounds by GC-MS.
Black Hills Ameriflux tower, South Dakota and Duke University Experimental Forrest (CELTIC study), summer 2003: Above canopy disjunct eddy covariance flux measurements of biogenic VOCs and vertically resolved flux estimates from inverse Lagrangian modeling. Comparison of VOC flux measurements between two Ionicon PTR-MS instruments and a Fast Isoprene Sensor. Gas Chromatography/Proton Transfer Reaction Mass Spectrometry to verify identity of molecules.
Arizona State University, Tempe, AZ, Fall 1999 – Fall 2000: Utilization of artificial photosynthetic reaction centers inserted in liposome membranes to pump protons in a light dependent manner into the interior of the vesicles creating a proton motive force. This was then used by the enzyme CFoF1 ATPsynthase to synthesize ATP from ADP and Pi. The ATP was then used be to power the fixation of carbon dioxide.
University of Washington, Center for Nanotechnology, Seattle Washington, summer 2001: Project to develop light powered nanotrains for nanoscale transport of material by integrating biological and biomimetic components. Techniques included protein purification, surface nanopaterning with Teflon, liposome reconstitution of biological and biomimetic components, assembly of microscope flow cells, flowing in individual components and generating fluorescence microscopy movies.
New York University, NY, NY, Spring 1998 – Spring 1999: DNA nanotechnology experiments with Ned Seeman in the Chemistry Department at NYU. Techniques included DNA sequence design and self-assembly engineering, molecular modeling, operation of automated DNA synthesizers, gel electrophoresis, DNA sequencing, and atomic force microscopy to visualize the products of self-assembly.
Harvard University, Cambridge MA, summer 1997: Summer research internship in the Department of Organismic and Evolutionary Biology. Using forward genetics techniques we investigated the ability of the transposase gene product to excise the transposable element mariner from a target sequence. Techniques involved fly mutagenesis, mutant collection, element amplification by PCR, bacterial transformation, gel electrophoresis, and DNA sequencing.
Colorado School of Mines, Golden CO, Spring 1997: Worked with Dr. Kevin Mandernack on microbial influences of biogeochemical cycles.