Ryan Ziels
Research Classification
Research Interests
Relevant Thesis-Based Degree Programs
Affiliations to Research Centres, Institutes & Clusters
Recruitment
The Environmental Microbial Biotechnology for Resource Recovery (EMBeRR) Lab (https://emberrlab.civil.ubc.ca/) at the University of British Columbia (Vancouver, BC, Canada) is seeking a PhD student to start in September, 2025, focusing on anaerobic biotechnology for resource recovery from wastes. The research project will involve the development of anaerobic microbial bioprocesses, metagenomics, bioinformatics, and process modeling. A primary focus will be on microbiomes involved in carbon dioxide upgrading to value-added commodities.
The position will be supported by a grant from the Natural Sciences and Engineering Research Council of Canada (NSERC), and will provide unique opportunities at the interface of academia, private sector, and water utilities, combining conventional process engineering fundamentals with microbiome science, bioinformatics, and modeling. The PhD student will become a member of a dynamic and collaborative research group, and will coordinate between project team members and communicate results via peer-reviewed journal articles and presentations at national and international conferences.
Qualifications:
- Undergraduate or Masters degree in environmental, chemical, civil engineering, or a related engineering program. Students with a previous focus on microbiology and biotechnology are also encouraged to apply.
- Previous research experience in environmental biotechnology, wastewater treatment, microbiology, and bioinformatics is desired.
- Previous experience in command-line programming (e.g., R, python, bash, MatLab) is desired.
- A high degree of motivation to learn new topics and scientific approaches.
Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged. We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.
To apply, please email a cover letter describing relevant research experience and interests, a curriculum vitae, the names and contact information of three references to Dr. Ryan Ziels (ziels [at] mail.ubc.ca). Please send applications as a single pdf file. In the subject line of the email, please put ‘EMBERR Lab Prospective Student: [surname]’.
Complete these steps before you reach out to a faculty member!
- Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
- Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Admission Information & Requirements" - "Prepare Application" - "Supervision" or on the program website.
- Identify specific faculty members who are conducting research in your specific area of interest.
- Establish that your research interests align with the faculty member’s research interests.
- Read up on the faculty members in the program and the research being conducted in the department.
- Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.
- Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
- Do not send non-specific, mass emails to everyone in the department hoping for a match.
- Address the faculty members by name. Your contact should be genuine rather than generic.
- Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
- Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
- Demonstrate that you are familiar with their research:
- Convey the specific ways you are a good fit for the program.
- Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
- Be enthusiastic, but don’t overdo it.
G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.
ADVICE AND INSIGHTS FROM UBC FACULTY ON REACHING OUT TO SUPERVISORS
These videos contain some general advice from faculty across UBC on finding and reaching out to a potential thesis supervisor.
Supervision Enquiry
Graduate Student Supervision
Master's Student Supervision
Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Global plastic production has increased exponentially since the 1950s, ushering in an era of cheap synthetic polymers that have revolutionized human manufacturing and promoted socioeconomic development. However, the benefits of this plastics revolution are contrasted with human and environmental health problems resulting from its disposal. Not only has plastic waste contributed to burgeoning accumulation in landfills and the ocean, but additives and leachates from plastic polymers have been linked to negative health effects including endocrine disruption and cancer. Less well understood is the potential impact of microplastic particles and fibers (MPs) between 0.3mm and 5mm on human and environmental health. MPs frequently enter coastal marine waters through wastewater treatment where they are rapidly colonized by microbes. The drivers of community assembly on MPs remain unconstrained with implications for carbon cycling, antimicrobial resistance and mobilization of additives and leachates through marine food webs. Here, I investigated microbial community assembly on marine plastic fibers and the impact of MP pollution on planktonic microbial community composition. A time-resolved mesocosm experiment using different concentrations of MP fibers indicated that increased fiber concentrations did not have a significant effect on planktonic microbial community composition or chemical concentrations but did induce finer-scale taxonomic changes. A related in-situ textile degradation experiment indicated rapid microbial colonization coalescing into relatively stable community structures after one month. Plastic-attached communities varied significantly by polymer type but not by chemical additive or color. These results demonstrate that marine microbial community assembly varies by plastic type, but MP pollution may not significantly affect the surrounding planktonic microbial community.
View record
Anaerobic digestion (AD) is a well-established organic waste treatment biotechnology that enables resource recovery in the form of biomethane and nutrient-rich biosolids. AD systems treating municipal organic waste are prone to reduced biomethane yields and process upsets due to ammonia inhibition within their underlying microbial community. Microbial communities that are resilient to high ammonia conditions within AD are therefore of interest, given their ability to maintain stable and efficient AD reactor operation. Such microbial communities are generally characterized by the presence of a microbial guild performing syntrophic acetate oxidation (SAO) in partnership with hydrogenotrophic methanogens. So far, few members of the SAO guild have been identified and characterized. The objective of this study was to characterize the microbial community present within a high ammonia AD system and identify the taxa that were performing SAO. In this study, a commercial-scale biogas facility with a dry mesophilic AD system treating municipal organic wastes was monitored over the course of a year. Chemical monitoring of the AD system revealed high in situ ammonia concentrations, while a microbial community profile obtained via 16S rRNA gene amplicon sequencing suggested SAO as a dominant means of acetate utilization. In situ activity profiling was performed in batch microcosms with biomass sampled from the AD reactor using DNA stable isotope probing (SIP) amended with universally labelled ¹³C-acetate. DNA extracts recovered from the SIP incubations revealed a 5% shift in total community DNA ¹³C content. Following a consensus-based approach of high-resolution and quantitative SIP data analysis, 13 bacterial amplicon sequencing variants (ASVs) belonging to 8 genera were determined as isotopically enriched. Linking short-read 16S rRNA ASVs to long-read metagenomic assemblies allowed for accurate phylogenetic placement of acetate-incorporating taxa, as well as for an examination of potential metabolic pathways used for acetate oxidation by the active members. The results of this study provide new insights that can help guide process operations and optimization of the study AD system, as well as contribute to the emerging body of knowledge regarding SAO and microbial communities underpinning dry AD systems with high ammonia levels.
View record
The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.
View record
Over the past few years, microplastics (MPs) have emerged as contaminants of global environmental concern, but important questions remain regarding their source, transport and fate. Because of their complexity, quantification and identification of MPs remain a major analytical challenge. The goals of this study were to examine the importance of Combined Sewer Overflows (CSOs) as one of the pathways for MPs to urban watersheds, and the fate of urban MPs in the receiving waters. In addition, a new statistical protocol to guide efficient and accurate analysis of MPs was also developed. Focusing on the Vancouver metropolitan area, this study provides novel data on MPs in CSOs in Canada and in the Fraser River, BC – a major river in western North America. MPs were detected in all CSOs and the Fraser River samples, ranging in concentration from 1,833─13,673 MPs/m³ and 4─30 MPs/m³, respectively. A preliminary assessment of the annual emission rates of MPs by the two CSOs under study was carried out, with values ranging from 0.82 to 14.6 × 10⁹ MPs/year. This implies that CSO emissions of MPs require further research and should not be overlooked in management strategies. The much lower concentrations of MPs in the receiving waters of CSOs and significantly shorter fibers suggest a complex fate, which may involve mixing with other sources, sinking and/or rapid dilution upon entry to the environment. This research also suggests that the Fraser River is an important conduit for MPs to the Strait of Georgia, given the estimates of 0.67─3.35 trillion annual microparticles flux derived in this study. While the dimensions, polymer types, and shapes of MPs varied in space and time, synthetic fibers were most common (58─78% in CSO samples and 76─86% in river samples) and were dominated by polyester. Fibers emitted with CSOs had a median width of 24 µm, which is consistent with the average width of textile fibers. Fragments were also present and comprised mostly of polyethylene in both CSOs and river samples (0─70%). This study helps better understand the sources and transfer of MPs in urbanized watersheds, with management strategies and other solutions are also discussed.
View record
Partial nitritation/anammox (PN/A) is a novel pathway for nitrogen removal in wastewater treatment that offers advantages of low oxygen and organic carbon demands as well as high potential for energy recovery. However, the partial nitritation process remains a key hurdle for the widespread implementation of the PN-A process in mainstream treatment due to the difficulty in washing out nitrite-oxidizing bacteria (NOB) from active sludge. Exposing biomass to high concentrations of free ammonia (FA) has been reported as an effective strategy to achieve partial nitritation. This study examined the effectiveness of treating 20% of return activated sludge with synthetic centrate containing FA at 200 mg N/L for 24 hours to promote partial nitritation in mainstream wastewater treatment. Experimental and control bioreactors were operated under two different conditions, with or without FA treatment, respectively, after reaching similar nitrification performance. Biokinetic parameters of ammonium-oxidizing bacteria (AOB) and NOB were estimated by performing respirometric batch tests with activated sludge biomass from the two bioreactors under different operational conditions, and calibrating a process model based on oxygen mass balance. The bioreactor performance showed that the FA treatment strategy promoted the PN process, with a maximum nitrite accumulation ratio (NAR) of 41.9 ± 2.1% after treating return sludge with high FA solution for 37 days. However, this nitrite accumulation was not stable, and the NAR decreased to 10.9 ± 6.0% after 33 days, indicating that NOB were able to acclimate to the temporary exposure to a high FA concentration. The biomass yield coefficient (Y) of AOB increased during FA treatment, while the maximum specific growth rate (μmax) of AOB and NOB decreased under this condition. Microbial community analysis on activated sludge under FA treatment, and further investigations on the optimization of the FA treatment strategy combined with other NOB out-selection strategies are required to better facilitate the application of PN-A to full-scale mainstream wastewater treatment.
View record
Biofilm photobioreactors rely on cooperation between algae and bacteria within a single biofilm to treat wastewater. Algae growth produces oxygen, which can subsequently be utilized by aerobic bacteria to degrade organic matter and produce carbon dioxide, which is then utilized as a carbon source by algae. Due to their relatively low maintenance and energy inputs, biofilm photobioreactors could be amenable for decentralized wastewater treatment. However, the impact of biofilm photobioreactor design on treatment efficiency has received little attention. Here, it was hypothesized that open (i.e. unsealed) versus closed (i.e. sealed) photobioreactors could promote different nitrogen removal pathways by altering redox conditions throughout a diel cycle. This study explored the effect of open versus closed photobioreactor configurations on nitrogen removal and the microbial community structure in two parallel photobioreactors treating microscreened decentralized wastewater. The reactors were intermittently lit in a 16hr-8hr light-dark cycle, and operated at an HRT of 2 days and SRT of 9 days. The influent feed regime and alkalinity addition were varied over three successive 30-day experimental phases. Microscreening was an effective primary treatment step, removing 70 ± 6% (95% c.i.) of suspended solids and 39 ± 9% of COD. The photobioreactors removed 90 ± 6 % and 83 ± 3% of the remaining suspended solids and COD respectively, independent of operating conditions. Alternating oxic and anoxic conditions were observed in both reactors during the lit and unlit periods, respectively, resulting nitrification and denitrification. Optimal nitrogen removal conditions were observed under a sequencing batch feed regime with alkalinity addition. Under these conditions, TKN removal was significantly higher in the open reactor at 93 ± 5% compared to 78 ± 6% in the closed reactor due to higher rates of nitrification and N assimilation. TN removal was similar at 77 ± 9% and 76 ± 8% in the open and closed systems, respectively. The dominant bacterial genus in the reactors was Tychonema, a cyanobacteria which comprised up to 87% of 16S rRNA gene amplicon reads. Overall, this study demonstrated that nitrogen removal pathways differ significantly in open and closed photobioreactors when operated at the same COD loading rate.
View record
If this is your researcher profile you can log in to the Faculty & Staff portal to update your details and provide recruitment preferences.
