James Shapleigh

I received my BS in Microbiology from Clemson University and Ph.D. in Microbiology from the University of Georgia. I continued my post-doctoral training in the laboratory of Prof. Robert Gennis at the University of Illinois. My research emphasis prior to coming to Cornell focused on aerobic and anaerobic respiration in bacteria. I have continued this focus at Cornell, with a specific interest in denitrification, the respiration of nitrogen oxides. My laboratory studies denitrification in related bacteria that occupy environmental niches ranging from the soil to the human body. We are interested in better understanding how these different bacteria adapt to environmental changes and deal with the stresses that arise from denitrification. I am currently Director of Undergraduate Studies in the Department of Microbiology.

Research Focus

Understanding the nitrogen cycle in natural and managed ecosystems is a great challenge in environmental biology and critical to improving the sustainability of human activities from agriculture to energy generation to transportation to urbanization. Impetus for nitrogen cycle studies have become more compelling in recent years with the recognition that human activities have more than doubled the annual global production of reactive nitrogen, resulting in considerable increases in the deposition of nitrogen onto ecosystems and the leaching of nitrogen from excess fertilizer use to ground- and drainage waters. Uncertainty about the fate of nitrate in ecosystems has led to increased interest in nitrogen transformations and gaseous losses via the microbial biogeochemistry of nitrogen but many drivers of nitrogen transformation remain poorly understood, regardless of scale. While nitrate is produced via microbial nitrification and consumed via microbial denitrification, the reduction of nitrate to nitrogen gas, recent studies have shown that both processes are more dynamic and complicated than expected and the diversity of microorganisms playing prominent roles has been underestimated.

Denitrification is the process by which the most problematic reactive nitrogen, nitrate, is converted to unreactive nitrogen gas. This conversion occurs in four reductive steps requiring four enzymes: nitrate, nitrite, nitric oxide and nitrous oxide reductase, each reducing a separate product in the pathway .While excess nitrate can cause significant environmental problems, the ‘downstream’ products of denitrification are also environmentally important because of the roles they play in atmospheric chemistry. To better understand the factors that can impact the production and flux of these various nitrogen oxides it is essential to have a realistic model of the factors controlling denitrification. Our research is focused on studying denitrification at various scales to help provide information that will allow better understanding of the factors controlling flux through the denitrification pathway. We have used model organisms for many studies but have recently begun to use soil isolates to provide additional insight into the complexity of the denitrification landscape.

Teaching Focus

My teaching focuses on several aspects of bacteriology including physiology, genomics and structure/function aspects of bacterial cells. This will expand in the coming year to include a more general course in Public Health Microbiology.

Teaching involves both introducing basic concepts to students but also providing students with the skills to gain knowledge through their own activities. This latter is critical for making students lifelong learners. In every course I teach I make an effort to make learning as active as possible. These efforts have ranged from helping guide freshman analyze and compare bacterial genomes to working with seniors to construct pathway flowcharts from a variety of web based sources. I will continue to utilize new approaches and techniques to aid in this effort to have students actively involved in learning new material.

Areas Of Expertise

• Bacteria
• Denitrification
• Genomics
• Laboratory Methods
• Nitrate
• Nitrogen Cycle
• Physiology
• Public Health
• Structure And Function

Graduate Fields

• Microbiology

Selected Publications

Journal Publications

• Stern, A. M., Liu, B., Bakken , L. R., Shapleigh, J. P., & Zhu, J. (2013). A novel protein protects bacterial iron-dependent metabolism from nitric oxide. Journal of Bacteriology. 195:4702-4708 .
• Liu, B., Frostegard, A., & Shapleigh, J. P. (2013). Draft Genome Sequences of Five Strains in the Genus Thauera. Genome Announcements. 1:e00052-12.
• Hartsock , A., & Shapleigh, J. P. (2011). Physiological roles for two periplasmic nitrate reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025). Journal of Bacteriology. 193:6483-6489.
• Shapleigh, J. P. (2011). Oxygen control of nitrogen oxide respiration, focusing on _-proteobacteria. Biochemical Society Transactions. 39:179-183.
• Hartsock, A., & Shapleigh, J. P. (2010). Identification, functional studies, and genomic comparisons of new members of the NnrR regulon in Rhodobacter sphaeroides. Journal of Bacteriology. 192:903-911.
• Hartsock, A., & Shapleigh, J. P. (2010). Mechanisms of oxygen inhibition of nirK expression in Rhodobacter sphaeroides. Microbiology. 156(Pt 10):3158-3165.
• Lee, B., Usov, O., Grigoryants, V., Myers, W., Shapleigh, J. P., & Scholes, C. (2009). The role of arginine-127 at the proximal NO-binding site in determining the electronic structure and function of 5-coordinate NO-heme in cytochrome c' of Rhodobacter sphaeroides. Biochemistry. 48:8985-8993.
• Bergaust, L., Shapleigh, J. P., Frostegard, A., & Bakken, L. (2008). Transcription and activities of NOx reductases in Agrobacterium tumefaciens: the influence of nitrate, nitrite and oxygen availability. Environmental Microbiology. 10:3070-3081.
• Baek, S., Hartsock, A., & Shapleigh, J. P. (2008). Agrobacterium tumefaciens C58 Uses ActR and FnrN To Control nirK and nor Expression. Journal of Bacteriology. 190:78-86.
• Basaglia, M., Toffanin, A., Baldan, E., Bottegal, M., Shapleigh, J. P., & Casella, S. (2007). Selenite-reducing capacity of the copper-containing nitrite reductase of Rhizobium sullae. FEMS Microbiology Letters. 269:124-130.

Presentations and Activities

• Nitric oxide production in soils: respiration, communication or something else? Workshop on rhizospere immunity engineering. December 2017. Hainan University. Haikou, China.