Lisa Y. Stein, PhD

Professor, Climate Change Microbiology, Faculty of Science - Biological Sciences
Associate Dean, Mentorship & Awards, Faculty of Science - Deans Office


Professor, Climate Change Microbiology, Faculty of Science - Biological Sciences
(780) 492-4782
M-528A Bio Science - Microbiology Wing
11355 - Saskatchewan Drive
Edmonton AB
T6G 2E9

Associate Dean, Mentorship & Awards, Faculty of Science - Deans Office


Area of Study / Keywords

Climate Change Microbiology



Research Interests

•   Physiology, genomics, and ecology of nitrification, denitrification, and single carbon metabolism. 

•   Influence of microbial metabolism on greenhouse gas production. 

•   Industrialization of microorganisms using single-carbon feedstocks. 

•   Increasing nitrogen use efficiency in soil-free (aquaponics) systems

Work in our laboratory focuses on the numerous and diverse pathways of inorganic nitrogen and single carbon metabolism in bacteria and archaea. Using the tools of comparative genomics, molecular biology, physiology, and biochemistry we study how microorganisms process nitrogen and methane at the molecular, whole-cell, and ecosystem levels. Our goals are to track the evolution of nitrogen metabolism, predict how and when deleterious nitrogen oxide products are released to the environment, and define linkages between methane and nitrogen metabolism. The greenhouse gas nitrous oxide, the ozone depleting nitric oxide, and the groundwater polluting nitrate are the most significant of the nitrogen oxide pollutants created and released by microbial nitrogen metabolism. Single carbon metabolism, i.e. methane oxidation and carbon fixation, are intimately connected to the biogeochemical nitrogen cycle. By interrogating the linkages between single carbon and nitrogen metabolism, we can harness microorganisms to generate commercially viable bioproducts using single-carbon waste streams as feedstocks. We can also maximize microbial activities to increase productivity of vertical agriculture aquaponics systems without production of greenhouse gases.

Current Projects

Methane Oxidizing Bacteria (MOB Squad):

a) Uncovering Linkages Between Methane and the Nitrogen Cycle: Some methane-oxidizing bacteria metabolize methane and nitrate to release nitrous oxide when exposed to exceedingly low oxygen levels. Methane-dependent denitrification is an important process in permafrost, coastal oxygen minimum zones, hypoxic soils, and other ecosystems where methane, nitrate, and low oxygen co-exist. Through the collaborative Organization for Methanotroph Genome Analysis (OMeGA), we have gained access to a wealth of genome sequences and cultures of methanotrophic bacteria, allowing us to test and map functional pathways responsible for methane-dependent denitrification and nitrous oxide production.

b) Industrialization of Microorganisms using Single-Carbon Feedstocks: Using the genome-sequenced culture collection of methanotrophic bacteria, we are working with Dr. Dominic Sauvageau in Chemical and Materials Engineering and industrial partners to screen for value-added products created by bacteria as they consume methane, methanol and carbon dioxide. The resurgent interest in synthetic biology and green chemistry has placed methane-consuming microorganisms at the forefront of new bioindustrial developments. Projects in this area include screening methanotrophic bacteria for products, optimization of growth and product formation, and pathway engineering.

The Nitrogen Cycle (Team Nitro):

Ammonia-oxidizers & Greenhouse Gases: Specialized groups of bacteria and archaea make a living by oxidizing ammonia to nitrite as their sole energy-generating metabolism. Due to alarming increases in the greenhouse gas, nitrous oxide, to the atmosphere, there has been intensive interest in understanding how these chemolithotrophic microorganisms contribute to the nitrogen cycle and nitrous oxide release. We are using cutting-edge technologies of microrespirometry and RNAseq to show that ammonia-oxidizing bacteria and archaea have distinct mechanisms for metabolizing nitrogen and releasing nitrogen oxides. The metabolic intermediate, nitric oxide, plays a critical (albeit different) role in the pathways of both bacteria and archaea, although only the bacteria have enzymology to convert nitric oxide to nitrous oxide. This very exciting and novel line of research is changing the way we understand the microbial nitrogen cycle and makes use of one of the largest collections of genome-sequenced ammonia-oxidizing isolates in the world. Projects in the lab involve collaboration with many distinguished colleagues around the world.

Aquaponics: In collaboration with local companies, we are investigating and manipulating microbial communities in aquaponics agricultural systems to increase nitrogen use efficiency for improved plant growth without greenhouse gas production.


MICRB 606 - Microbiology Seminar

Intended for all Microbiology and Biotechnology graduate students, except those in their second year who should register for MICRB 607. Credit may be obtained more than once.

MICRB 607 - Microbiology Seminar

Graded seminar course intended for second-year graduate students.

Browse more courses taught by Lisa Y. Stein

Scholarly Activities

Research - Professional Activities

2022: Invited participant for the Rockefeller Philanthropy Advisor workshop on How Can Agrigenomics Help to Address Climate Change?

2021: Invited participant for the Rockefeller Philanthropy Advisors workshop on Climate Change Mitigation and Adaptation in Agriculture: 

what can biotechnology do?

2020: Editor-in-Chief for The ISME Journal

2016: Invited participant for ASM-AGU Collaborative Colloquium on the Effects of Climate Change on Microbial Ecosystems

2015: Invited chair for Nitrification section of NSF INFEWS workshop on the Nitrogen Cycle

2015: Chair and Organizer of 4th International Conference on Nitrification and Related Processes (ICoN4), Edmonton AB

Featured Publications

Cavicchioli et al.

Nature Reviews Microbiology. 2019 June; 17

Lisa Y. Stein, Martin G. Klotz

Current Biology. 26 (3):R94-R98

Kozlowski, J.A., M. Stieglmeier, C. Schleper, M.G. Klotz and L.Y. Stein

ISME Journal. doi:10.1038/ismej.2016.2