Lisa Stein, PhD

Professor, Faculty of Science - Biological Sciences
Associate Chair (Research), Faculty of Science - Biological Sciences


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

Associate Chair (Research), Faculty of Science - Biological Sciences


Area of Study / Keywords

Environmental Microbiology & Microbial Physiology


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 vertical agriculture (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 311 - Microbial Physiology

The structure, growth, and metabolic pathways used by bacteria, archaea, and unicellular eukaryotes. Emphasis is placed on the comparative biochemical aspects of microbial life. Prerequisites: MICRB 265 and BIOCH 200 or 205. Credit cannot be obtained for both MICRB 311 and 511.

Fall Term 2020
MICRB 315 - Applied Microbiology and Biotechnology

Microbial production of commercially important metabolites, drugs, food grade enzymes and platform chemicals; use and modification of microbes for industrial-scale processes including biofuel production; bioprospecting for novel activities; strain improvement and synthetic biology; fundamentals of fermenter operation. Prerequisite: MICRB 265.

Fall Term 2020
MICRB 511 - Advanced Microbial Physiology

The structure, growth, and metabolic pathways used by bacteria, archaea, and unicellular eukaryotes. Lectures are the same as MICRB 311, but with additional assignments and evaluation appropriate to graduate studies. Prerequisite: consent of the instructor. Credit cannot be obtained for both MICRB 311 and 511.

Fall Term 2020

Browse more courses taught by Lisa Stein

Scholarly Activities

Research - Professional Activities

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)
2011-present: Member, Editorial Board, Applied and Environmental Microbiology, 2010-present: Member, Editorial Board, Environmental Microbiology

2010-present: Specialty Chief Editor, Frontiers in Terrestrial Microbiology

2010-2011: Co-Editor for “Nitrification and Related Processes.” Meth. Enzymol. Vol 496
2010: Founder of Organization for Methanotroph Genome Analysis (OMeGA)

2009-present: Member of US Regional Council, Univ. of Alberta
2009-2013: Nitrification Network Steering Committee


The Nitrogen Cycle
Author(s): Lisa Y. Stein, Martin G. Klotz
Publication: Current Biology
Volume: 26
Issue: 3
Page Numbers: R94-R98
External Link:
Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1
Author(s): K. Dimitri Kits, Martin G. Klotz and Lisa Y. Stein
Publication: Environmental Microbiology
Volume: 17
Issue: 9
Page Numbers: 3219-3232
External Link:
Cyanate Fuels the Nitrogen Cycle
Author(s): Lisa Y. Stein
Publication: Nature
Volume: 524
Page Numbers: 43-44
External Link:
Pathways and key intermediates required for obligate ammonia-dependent chemolithotrophy
Author(s): Kozlowski, J.A., M. Stieglmeier, C. Schleper, M.G. Klotz and L.Y. Stein
Publication: ISME Journal
Volume: doi:10.1038/ismej.2016.2
External Link: