Research Associate, Department of Biological Sciences, Faculty of Science
University of Calgary
Reporting to the Principal Investigator of the Geomicrobiology Group the Research Associate will be responsible for participating in research in the area of microbial ecology and ecophysiology of marine and hydrocarbon systems using bioinformatics, genomics and metagenomics, biogeochemistry, and microbiology.
Using these approaches the research associate will assess microbial community changes at taxonomic, phylogenetic, and functional levels. The work will include computational biology and large dataset analysis, with complementary laboratory work and fieldwork components. Work will be undertaken in collaboration with other researchers at the University of Calgary and other research institutions. The role will include presenting results to diverse audiences (academia, end users, industry), and publishing the findings in peer-reviewed journals.
Regular collaboration with other team members in the broader Energy Bioengineering and Geomicrobiology Group (EBG) is expected and encouraged. The successful candidate will conduct research with support of other team members and PI as well as provide support and mentorship to other team members (graduate students, undergraduate, and summer students).
This position will focus on characterisation of microbial communities in marine ecosystem(s) that are (or may be) at risk of oil spill pollution in the Canadian Arctic Ocean, including seawater, bottom sediments, and sea ice (thin, thick, first year, multi-year, etc). In addition to determining in situ microbial community structure and function, the successful candidate will study the effect of pollutants and microbial remediation of pollutants (i.e. mock oil spills in experimental microcosms or larger scale mesocosms) in different sample types and/or geographic areas. This will include screening genomes and metagenomes for genes associated with hydrocarbon biodegradation (e.g., https://www.biorxiv.org/content/10.1101/2021.06.10.447808v1).
This successful candidate will carry out assessments of microbial diversity and ecophysiology using existing and emerging genomic technologies related to metagenomic and amplicon sequence analysis (e.g., different sequencing strategies and platforms). The candidate should be able to carry out sequence analysis in aid of ecological interpretations, which may involve using or developing bioinformatics tools. The samples currently available for this work span the Canadian Arctic and sub-Arctic marine ecosystem. Future sampling can or will be carried out through small and/or large research vessels. including the Canadian Coast Guard’s research icebreaker Amundsen, and in experimental mesocosms at the Churchill Marine Observatory on the shores of Hudson Bay. Field experience is an asset but not a requirement.
The Energy Bioengineering and Geomicrobiology (EBG) labs at the University of Calgary main campus in the EEEL building are equipped with fully functional omics facilities, microscopy, and flow cytometry. EBG has in-house Illumina MiSeq and Nanopore sequencing platforms, as well as readily accessible additional sequencing platforms at the University of Calgary’s Centre for Health Genomics and Informatics (https://cumming.ucalgary.ca/research/cat/health-genomics/home). All bioinformatics and large sequence data analyses are carried out on the research cluster maintained by the university’s Research Computing Services. Accordingly, this position will combine and blend ecology, molecular microbiology, microbial metabolism (e.g., hydrocarbon degradation), statistics, and bioinformatics.
This position will have an emphasis on using genomics as a form of environmental baseline information that can be provided to policy makers and industry regarding the state of pristine environments. This information can be leveraged in an event of an accidental spill of oil, shipping fuel, or other forms of marine pollution. Environmental Effects Monitoring in Canada and elsewhere does not currently routinely include microbial genomics, which offers an important opportunity for recent advances in microbial ecology and DNA sequencing to make an important contribution to this endeavour. Hence, an ability to communicate genomics and other scientific information to a non-scientific audience is desirable.
Summary of Key Responsibilities (job functions include but are not limited to):
o Installing and running bioinformatics tools for assessing and contrasting microbial communities
o Metagenomic library preparation, troubleshooting, analysis, and interpretation
o Amplicon library preparation, troubleshooting, analysis, and interpretation
o Incorporating environmental metadata for statistically tested ecological interpretations of marine microbial biodiversity and its potential to respond to different pollution events
o Nucleic acid extraction (DNA, RNA) from different kinds of samples using multiple approaches
o Microscopy applications for cell counting
•Reporting and Publications
o Participating in publication of results in peer-review journals is expected
o Maintain a clear and well-documented log of all data, data analyses, results, and lab work
o Meet with supervisor(s) regularly (e.g., monthly meetings, as well as interactions on a day-to-day basis) to provide update on status of experimental results
o Presentation of results to the EBG research group in weekly lab meetings (e.g., once every 6 weeks) and when applicable to project end users, sponsors or other researchers (e.g., at a conference)
•Safety and Environment
o Understanding of standard operating procedures of the equipment used in the experimental protocols
o Maintain a clean and safe laboratory work environment
o Manage time effectively to complete project work and contribute yearly research updates to program sponsors
o Perform other duties, as assigned by the Research Supervisor
o Contribute daily towards a positive work environment within a large and diverse team of colleagues in the EBG group
• PhD in area of Molecular Biology, Microbial Ecology, Microbiology, Bioinformatics, Computational Biology, or a similar area
• Familiarity with bioinformatics software applications and/or development, including those applied in but not limited to genomics, metagenomics and other microbial multi-omics applications
• Experience in and knowledge of environmental microbiology
• Familiarity and interest in marine microbial ecology and biogeography
• Knowledge of WHMIS
• Ability to multi-task and deal with some repetitive tasks
• Strong organizational and time management skills
• Good verbal and written communication skills
• Understanding of hydrocarbon degradation and bioremediation
• Proficiency in Microsoft Office Programs, Unix/Linux, R (or other statistical softwares), scripting in Python (or Perl), server use and SLURM
• Experience in analysing terabyte-scale sequencing data
• Must be comfortable working in a diverse research team and have good interpersonal skills
• Previous experience with mentoring early career scientists (e.g. graduate students)
Application Deadline: October 4, 2021
To apply please visit the UCalgary Careers page: https://science.careers.ucalgary.ca/jobs/7438955-research-associate-marine-microbial-metagenomics-and-bioinformatics-biological-sciences-faculty-of-science
We would like to thank all applicants in advance for submitting their resumes. Please note, only those candidates chosen to continue on through the selection process will be contacted.
This position is part of the AUPE bargaining unit, and falls under the Technical Job Family, Phase II.
To find out more about management and staff opportunities at the University of Calgary and all we have to offer, view our Management and Staff Careers website. For more information about the Faculty of Science visit Careers in the Faculty of Science.
About the University of Calgary
The University of Calgary is Canada’s leading next-generation university – a living, growing and youthful institution that embraces change and opportunity with a can-do attitude. Located in the nation’s most enterprising city, the university is making tremendous progress on its Eyes High journey to be recognized as one of Canada’s top five research universities, grounded in innovative learning and teaching and fully integrated with the community it both serves and leads. The University of Calgary inspires and supports discovery, creativity and innovation across all disciplines. For more information, visit ucalgary.ca.
The University of Calgary has launched an institution-wide Indigenous Strategy in line with the foundational goals of Eyes High, committing to creating a rich, vibrant, and culturally competent campus that welcomes and supports Indigenous Peoples, encourages Indigenous community partnerships, is inclusive of Indigenous perspectives in all that we do.
The University of Calgary recognizes that a diverse staff/faculty benefits and enriches the work, learning and research experiences of the entire campus and greater community. We are committed to removing barriers that have been historically encountered by some people in our society. We strive to recruit individuals who will further enhance our diversity and will support their professional success while they are here. We encourage all qualified applicants to apply, however preference will be given to Canadian citizens and permanent residents of Canada.