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Director

Adam Arkin is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering at the University of California, Berkeley and Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. He and his laboratory develop experimental and computational technologies for discovery, prediction, control and design of microbial and viral functions and behaviors in environmental contexts.

He is the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA(Ecosystems and Networks Integrated with Genes and Molecular Assemblies, http://enigma.lbl.gov), designed to understand, at a molecular level, the impact of microbial communities on their ecosystems with specific focus on terrestrial communities in contaminated watersheds. He also directs the Department of Energy Systems Biology Knowledgebase (KBase) program: (http://kbase.us) an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants and their communities, and for sharing results and methods with other scientists. He is director of the newly announced Center for Utilization of Biological Engineering in Space which seeks microbial and plant-based biological solutions for in situ resource utilization that reduce the launch mass and improves reliability and quality of food, pharmaceuticals, fuels and materials for astronauts on a mission to Mars. Finally, he is the Co-Director of the Berkeley Synthetic Biology Institute, which brings together U.C. Berkeley and Lawrence Berkeley National Laboratory Scientists with Industry Partners to forward technology and applications for sustainable biomanufacturing.

Faculty

Dr. Coleman-Derr received his graduate education at the University of California at Berkeley in the lab of Dr. Daniel Zilberman in the Plant and Microbial Biology Department, studying mechanisms of epigenetic regulation of transcription in the model plant Arabidopsis. He then completed a post-doctoral research position at the Joint Genome Institute in the group of Dr. Susannah Tringe studying the microbial ecology of the root systems of desert succulents; in this role he also served as bioinformatic support on multiple JGI collaborative metagenomic research efforts involving analysis of 16S rRNA tag data from a variety of environmental and host-associated samples. Dr. Coleman-Derr now leads a research team for the United States Department of Agriculture’s Agricultural Research Service, where he aims to improve our understanding of the effect of abiotic stress on the plant microbiome, and to help identify plant growth promoting microbes capable of alleviating drought stress in their plant hosts. Current research involves several projects related to drought stress response in Sorghum bicolor (sorghum), including investigations into the changes in rhizosphere community composition under drought stress, a genome wide association study to reveal host loci controlled by drought tolerance-inducing root endophytes, and a screen of a collection of cereal endophytes for the ability to confer drought tolerance in sorghum. Dr. Coleman-Derr was awarded the USDA’s Scientist of the Year Award in 2017 for his contributions in this area.
 

Postdoctoral Scholar

Kristian is an NSERC post-doctoral fellow in Environmental Engineering and Science at Stanford University. His current research focuses on: Hard-wiring bacteria in a microbial battery, salinity gradient energy production from a mixing entropy battery, and PHB bioplastic production from C. Necator. His PhD was in Chemical and Biological Engineering from the University of British Columbia in Vancouver.
 

Wenyu Gu is currently a postdoc at Stanford University. 
 

Sunggeun Woo earned his B.S. and M.S. from Yonsei University in South Korea. During his B.S. and M.S. programs, he studied in the civil and environmental engineering department and he narrowed down his research focus to environmental biotechnology in his M.S. program, where he wrote fifteen papers for about two and a half years including five of them as the lead-author. At that time, the research topics were various in the field of environmental biotechnology including wastewater treatment systems, isolation and cultivation of microorganisms and harnessing renewable bio-diesel from microalgae. Based on the wide range of understandings, Sunggeun Woo joined the Criddle group for his Ph.D. program in September, 2012 focusing on the Coupled Aerobic-anoxic Nitrous Decomposition Operation (CANDO) project. Sunggeun Woo participated in developing the CANDO process which produces a renewable energy, nitrous oxide (N2O), from nitrogen pollutants through microorganisms. During his Ph.D. program, Sunggeun Woo's main focus was to elucidate the microbial members that produce N2O and the metabolic pathways in them related to N2O and polyhydroxybutyrate (PHB) production. He graduated from Ph.D. program in January, 2018 and he is now continuing his research as a post-doctoral scholar in the Criddle group. His research is currently focusing on the recovery of renewable energy and materials from waste or wastewater using microorganisms. 
 

He is currently working as a Researcher with Professor Dr. Lance C. Seefeldt at Utah State University. He received his PhD in Organic Chemistry from Nankai University, Tianjin, China in 2007 and PhD in Biochemistry from Utah State University in 2013. After that, he continuously worked with Dr. Lance Seefeldt as postdoctoral fellow focusing on understanding nitrogenase mechanism with a broad range of interdisciplinary strategies, including biochemical, biophysical, and electrochemical methods. His research interests include metalloenzymes, small molecule activation, and relevant catalyst design and mechanistic studies.

Shuyang is a post-doctoral research associate working with Dr. Bruce Bugbee in the Crop Physiology Laboratory at the Utah State University. Her current research is focused on improving the understanding of whole-plant photosynthetic and morphological responses of food crops to light quality and quantity, primarily under artificial light in controlled environments. She received her PhD from the horticulture department at the University of Georgia in August 2017.
 

Graduate Student

Wakuna is a PhD candidate in the environmental engineering program working with Prof. Craig Criddle. Her research focuses on the microbial degradation of methane in mixtures (biogas and natural gas) for the production of biodegradable polymers called polyhydroxyalkanoates (PHAs). Wakuna is interested in understanding the impact these methane mixtures have on microbial communities, the dynamics between the microbial interactions under certain complex conditions, while optimizing the polymer production process and bacterial growth rates. In addition to research, Wakuna is quite passionate about tutoring and mentoring.

Paul Kusuma received a bachelor’s degree in horticulture from the University of Florida, and is now pursuing a PhD in plant physiology at Utah State University. 
 

Rhesa discovered her scientific interest many years ago in a high school chemistry class. Her inspirational teacher, Mr. Best—the stereotypical science geek with large bug-eye glasses—taught Rhesa many scientific lessons, but perhaps the greatest was that science is not just for nerdy boys (as her flawed logic thought), it is for anyone.

Currently, a Ph.D. student in the Department of Chemistry and Biochemistry at Utah State University, Rhesa can be found at the laboratory bench doing research focused on understanding and harnessing the amazing abilities of microorganisms. Specifically, she studies the microbial transformation of nitrogen (N2) to ammonia (NH3). This process is a critical part of nature as the majority organisms cannot utilize N2 directly, but need it in a form like NH3 for growth and reproduction. The few microbes that facilitate this conversion provide valuable insight into one of the most biologically challenging reactions and may serve as a catalyst for developing systems for sustainable ammonia production on Mars. 

In additional to research, Rhesa also serves as a science reporter for Utah Public Radio and plans to pursue a career in science education and/or communication. Her excitement for not only doing science, but communicating it just might stem from growing up doing musical theater, which she loves. She also enjoys experiencing other cultures, and hot-potting is always on her list of things to do (and yes, it’s partly to see the beautiful microbial mats)!

Jorge is originally from Chicago where he attended Loyola University Chicago and received his B.S. in Environmental Science with a Chemistry Minor. After his undergraduate studies, he attended Stanford where he obtained his M.S. in Environmental Engineering and where he has continued as a PhD student working with Professor Craig Criddle. His research focuses on biotechnology with an emphasis on efficiently utilizing waste streams to produce biological materials (e.g., bioplastics, biofuels). As part of the CUBES effort, Jorge's research involves identifying organisms that can thrive on the limited amount of resources available for long-range space travel.

Alex graduated from Georgetown University in 2014 with a B.S. in Environmental Biology with a focus in community ecology. Following graduation, he moved to the University of Kentucky to study how bacterial symbionts mediate insect ecology in agricultural systems.

Now, pursuing a PhD in Plant Biology at UC Berkeley, Alex studies plant-associated microbial communities from shoots to roots. In cassava, a tropical root crop, Alex  investigates the phyllosphere ecology and carryover of the microbiome between planting seasons. For CUBES, he aims to construct synthetic bacterial communities via host-mediated selection to better grow rice in space. As both a Trekkie and wannabe farmer, Alex is very excited to be a member of FPSD.

Kelly Wetmore is a graduate student in Adam Arkin’s lab at UC Berkeley with over 15 years of experience in microbial physiology and genetics before and during graduate school. She has been instrumental in developing a number of next-generation tools and protocols for microbial functional genomics. Kelly is supporting the CUBES team in applying these tools to optimize the core biomanufacturing microbes in physiologically more-or-less relevant conditions. She is also part of a large DOE environmental systems biology project in which she is developing a new technology to query high-throughput genetic interactions.