November 24, 2014










H. James (Jim) Tripp     Publications CV (Hyperlinked) AS OF JAN 3, 2012, I HAVE MOVED TO THE JOINT GENOME INSTITUTE IN WALNUT CREEK, CA.

Jim Tripp, PhD
Earth and Marine Sciences Bldg A433
University of California Santa Cruz
1156 High Street, Santa Cruz, CA 95064
T: 831-459-4490
F: 831-459-4882
email: htripp(at)ucsc.edu

Research Interest: Streamlined Genomes of Marine Bacteria

As a high school student attending an NSF program in oceanography at the University of Rhode Island, I was introduced to what became known as "The Great Plate Anomaly", or the fact that most aquatic bacteria do not grow in "standard" media.  I pondered this mystery as my education unfolded at Cornell University, covering biochemistry, ecology, and planetary sciences; remote sensing and limnology at the University of Wisconsin; and then genomics at Oregon State University.  In the last seven years, I've helped take the first steps toward solving this problem for three marine bacteria that impact ocean-atmosphere exchanges.  The biological component of atmosphere to ocean exchanges is something upon which we rely and for which we must act as stewards for future generations.

UCYN-A:  Since joining the Zehr Lab in July of 2008, I've contributed to a paper (Science, 2008) demonstrating that the nitrogen-fixing UCYN-A cyanobacterium lacks Photosystem II and have written a Nature paper (in press, Feb. 2010, DOI 10.1038/nature08786) reconstructing the entire metabolism of UCYN-A from a complete genome sequence.  These studies suggest that UCYN-A has a photofermentative metabolism uniquely suited to nitrogen fixation by avoidance of oxygen production.  Its highly streamlined metabolism suggests that it is highly dependent on other organisms for nutrition.  UCYN-A was discovered by Jon Zehr in 2001 by culture-independent means, and remains uncultured, but studies show that it is globally distributed and periodically abundant.

Inference of metabolism from genome


SAR11:  At the Giovannoni Lab from 2003 to 2008, I earned a Ph.D. in Molecular and Cellular Biology writing or co-authoring a set of papers demonstrating that some clades of the diverse SAR11 marine bacteria require reduced sulfur (Nature, 2009), glycine or a precursor of glycine (Environ. Microbiol. 2009), and pyruvate or selected organic acids (Environ. Microbiol. 2010) for growth.  The unique nutritional requirements of SAR11 have been a mystery since its discovery in 1990 by Steve Giovannoni and its first cultivation in natural seawater in 2002 by Mike Rappé.

OM43:  Also at the Giovannoni Lab, I shared first authorship on a paper demonstrating the nutrient requirements of this highly streamlined methylotroph found in coastal waters (Environ. Microbiol. 2008).  Surprisingly, the only apparent sole carbon source for this organism is methanol, suggesting that coastal areas might be more abundant in this compound than previously thought.

My hyperlinked CV describes how I accumulated the training and experience to do this research.







Jim Tripp, PhD
Earth and Marine Sciences Bldg A433
University of California Santa Cruz
1156 High Street, Santa Cruz, CA 95064
T: 831-459-4490
F: 831-459-4882