Alyse Kathleen Hawley

Assistant Professor

Civil, Engineering, School of Engineering
Office: EME3273
Phone: 250.807.8215

Graduate student supervisor

Research Summary

Systems Ecology; Big Data Science; Microbial Metabolic Interactions; Natural and Engineered Microbial Ecosystem; Multi-omics (DNA, RNA and protein sequencing).

Courses & Teaching

ENGR 548 - Engineering Microbiology

ENGR 446 – Biological Treatment Processes


Dr. Hawley is an Assistant Professor of environmental genomics in the School of Engineering at University of British Columbia Okanagan. Her research interests focus on how microbial metabolisms shape our environment. Working at the interface of natural and engineered environments, Dr. Hawley’s research leverages microbial metabolic activities found in natural environments to carry out processes in engineered environments. Her work addresses challenges in waste management, bio-products and bioenergy production. Using microbial systems ecology approaches paired with big-data analyses of multi-omic datasets (microbial community DNA, RNA and proteins) her work reconstructs microbial metabolic interactions within the context of environmental and engineering outcomes.  Her extensive research experience in natural settings coupled with her work in engineered ecosystems enables Dr. Hawley to understand microbial metabolic interactions within the engineered environments of anaerobic digester thereby leading to improved bioprocess controls, reactor design and bio-product development.

Dr. Hawley earned her PhD at the University of British Columbia for her research into how microbial metabolisms alter nitrogen and carbon flow in low oxygen marine systems. Her findings demonstrate how metabolic interactions between microbes contribute to nitrogen availability in marine systems, impacting carbon fixation and other ecosystem services on a global scale.

Prior to arriving at UBC Okanagan, Dr. Hawley held NSERC Postdoctoral fellowship at University of Calgary with the Engineering Bioenergy and Geomicrobiology group.  Her work there explored the impact of viruses that infect microbes on the stability of engineered microbial communities responsible for carbon capture and bio-product production. Using advanced protein sequencing she developed analytical approaches to chart microbial interactions within both natural and engineered microbial communities.

Her research at UBC Okanagan explores microbial processes and metabolic interactions in anaerobic digester environments. Using microbial systems ecology, long-read DNA sequencing platforms and large-scale multi-omic datasets Dr. Hawley compares microbial metabolic interactions in engineered environments of anaerobic digesters with the natural environments of wetlands. This comparison supports identification of organic matter degradation and methane production pathways, and explores the potential roll of viruses and microdiversity (diversity within a species) in these processes. This information will inform improvements to bioprocess controls, reactor design, waste degradation and the production of bioenergy and other bio-products.


Post-Doctoral Fellowship – University of Calgary

PhD – (Microbial Ecology) University of British Columbia

BSc – (Biochemistry) University Victoria (with distinction)

Research Interests & Projects

  • Role of viruses in anaerobic digester performance
  • Bioinformatic approaches to microbial metabolic networks in natural and engineered environments
  • Experimental approaches to microbial metabolic networks in natural and engineered environments
  • Role of microbial micro-diversity in stability of anaerobic digestors

Selected Publications & Presentations

Selected Publications:

(Full list:

Khot, V., Dong, X., Strous, M., Hawley, A. K. Computational approaches in viral ecology. Computational and Structural Biotechnology IN PRESS

Hawley, A.K.*, Nobu, M.K.*, Wright, J.J., Durno, W.E., Morgan-Lang, C., Sage, B., Schwientek, P., Swan, B.K., Rinke, C., Liu, W-T., Stepanauskas, R., Woyke, T., Torres Beltrán, M., Mewis, K., Hallam, S.J. (2017). Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nature Communications 8(1507)

(* authors contributed equally)

Hawley, AK*, Torres-Beltrán, M*, Zaikova, E., Walsh, D.A., Mueller, A., Scofield, M., Kheirandish, S., Payne, C., Pakhomova, L., Bhatia, M., Shevchuk, O., Gies, E.A., Fairley, D., Malfatti, S.A., Norbeck, A.D., Brewer, H.M., Paša-Tolic, L., Glavina del Rio, T., Suttle, C.A., Tringe, S., Hallam, S.J. (2017). A compendium of multi-omic sequence information from the Saanich Inlet water column. Nature Scientific Data 4(170160) (* authors contributed equally)

Torres-Beltrán, M.*, Hawely, A.K.*, Capelle, C., Zaikova, E., Walsh, D.A., Mueller, A., Scofield, M.,Payne, C., Pakhomova, L., Kheirandish, S., Finke, F., Bhatia, M., Shevchuk, O., Gies, E.A., Fairley, D., Michiels, C., Suttle, C., Whitney, F., Crowe, S.A., Tortell, P.D., Hallam, S.J. (2017). A compendium of geochemical information from the Saanich Inlet water column. Nature Scientific Data 4(170159) (* authors contributed equally)

Capelle, D., Hawley, A.K., Hallam, S.J., and Tortell, P.D. (2017). A multi-year time-series of N2O dynamics in Saanich Inlet, British Columbia, a seasonally anoxic coastal fjord. Limnology and Oceanography. DOI:10.1002/lno.10645

Torres Beltrán M., Hawley, A.K., Capelle, D., Bathia, M.P., Durno, W.E., Tortelle, P.D., Hallam, S.J. (2016). Methanotrophic community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Frontiers in Marine Science. 3(268)

Louca, S., Hawley, A.K., Katsev, S., Beltran, M.T., Bhatia, M.P., Michiels, C., Sihota, N., Capelle, D., Doebeli, M., Crowe, S.A., Hallam, SJ. (2016). Integrating biogeochemistry with multi-omic sequence information in a model oxygen minimum zone. Proceedings of the National Academy of Sciences. 113(40):E5925-5933.
Roux, S., Hawley, A.K., Torres Beltrán, M., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S.J., Sullivan, M.B. (2014). Ecology and evolution of viruses infection uncultivated SUP05 bacteria as revealed by single-cell and meta-genomics. eLife. 3:e03125.

Hawley, A.K., Brewer, H.M., Norbeck, A.D., Paša-Tolic L., Hallam, S.J. (2014). Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. 2014. Proceedings of the National Academy of Sciences 111(31):11395-11400.

Hawley, A.K., Kheirandish, S., Mueller, A., Leung, H.T.C., Norbeck, A.D., Brewer, H.M., Paša-Tolic L., Hallam, S.J. (2013) Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters. Methods in Enzymology, Microbial Metagenomics, Metatranscriptomics, and Metaproteomics. 531:305-329.

Hanson, N.W., Konwar, K.M., Hawley, A.K., Tomer, A., Karp, P.D., Hallam, S.J. (2014). Metabolic pathways for the whole community. BMC Genomics. 15:619.

Selected Grants & Awards

NSERC Post-doctoral fellowship (2019-2021)

John Richard Turner Fellowship in Microbiology (2014)


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