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Research Associate - Microbial Diversity & Metagenomics, Biological Sciences, Faculty of Science

Job ID: 11120

Updated: March 9, 2017

Location: Main Campus

Position Overview

The Department of Biological Sciences in the Faculty of Science invites applications for a Research Associate - Microbial Diversity and Metagenomics. This Full-time Fixed Term position is for approximately 2 years (based on length of grant funding), with the possibility of extension.

The Energy Bioengineering & Geomicrobiology Group (EBG) is a collaborative research effort at the University of Calgary that began in 2014 as part of the Campus Alberta Innovation Program (www.ucalgary.ca/ebg). EBG occupies new state of the art environmental microbiology laboratories in the U of C’s Energy Environment and Experiential Learning Building (www.ucalgary.ca/eeel). The Group consists of two faculty (Marc Strous in the Department of Geosciences and Casey Hubert in the Department of Biological Sciences) joined by a diverse and talented team of staff, students and post docs, as well as many collaborators on campus and internationally. We work on various projects where environmental microbiology and bioengineering can improve how society approaches meeting our energy needs. This includes research related to both fossil fuel and renewable energy resources. EBG is supported by research funding from the University of Calgary, Province of Alberta, the Canada Foundation for Innovation, the Natural Sciences and Engineering Research Council of Canada, and Genome Canada. We are seeking new colleagues to join our team as post-doctoral research associates.

The Research Associate will report to two (2) Principal Investigators. Regular collaboration with other team members in EBG is expected and encouraged. The post-doctoral research associate will conduct her/his own experiments as well as provide support and mentoring to other team members (e.g., grad students, undergraduate project and summer students, visitors, etc) who need to set up similar experiments. Research Associates are part of the Alberta Union of Public Employees (AUPE) group. Applicants who have recently completed a PhD (<3 years) can alternatively join the University of Calgary through the post-doctoral scholars program (http://www.ucalgary.ca/research/postdoc).    

This position will focus on characterising microbial communities in marine samples that are (or may be in the future) at risk of oil spill pollution in the Canadian Arctic. Investigations will include samples of different types of sea ice (thin, thick, first year, multi-year etc), seawater and marine sediments. In addition to determining in situ microbial diversity, community profiles before and after experimental exposure to pollution (i.e. mock oil spills in experimental microcosms or larger scale mesocosms) will also be compared for different sample types and geographic areas. This may promote enrichment of numerically rare taxa from the pristine environmental samples, with important catalytic potential in a pollution context. With genomic baseline data companies and policy makers can be provided with critical information on the state of pristine environments that will be needed should an accidental spill of oil, shipping fuel, or other marine pollution ever occur. 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.

The project will assess different nucleic extraction methods and how they influence downstream applications for determining microbial diversity and community profiles involving both PCR amplicon based assessments of diversity as well as metagenomic approaches. Since it is difficult to predict when future spills may occur, both existing and emerging genomic technologies for determining environmental baselines must be considered and incorporated into this research, e.g. different sequencing strategies and platforms will be used. Sequence analysis for ecological interpretations will require use and/or development of bioinformatics tools allowing samples to be compared and baseline data to be archived for future use.

Sampling will primarily focus on the Hudson Bay region in the central Canadian sub-Arctic, accessible through small and large research vessels including the CCGS research icebreaker Amundsen. Other marine samples from elsewhere in Canada including other regions of the high Arctic and Northwest Passage will also be investigated. EBG has an in-house Illumina MiSeq platform that is part of the Western Canada Microbiome Centre with access to additional sequencing platforms. The EBG labs are also equipped with fully functional omics facilities, microscopy and flow cytometry. EBG has also developed in-house bioinformatics tools for sequence analysis (e.g. http://ebg.ucalgary.ca/metaamp/) and is continually pursuing improvements in this area. As such this position will involve a blend of ecology, molecular biology and bioinformatics.

Candidates interested in more than one of the vacancies in EBG (see Job ID #11117, #11118, #11119) are encouraged to indicate this in a covering letter but do not need to submit more than one application.

 

Position Description

Summary of Key Responsibilities (job functions include but are not limited to):

Technical

  • Nucleic acid extraction from different kinds of environmental samples using multiple approaches
  • Microscopy applications for cell counting
  • Amplicon library preparation, troubleshooting, analysis and interpretation
  • Metagenomic library preparation, troubleshooting, analysis and interpretation
  • Bioinformatics tools for assessing microbial diversity and comparing different samples
  • Incorporating environmental metadata into ecological interpretations of marine microbial biodiversity and its potential to respond to different pollution events
  • Conduct fieldwork

Reporting and Publications

  • Publication of results in peer-review journals is expected
  • Maintain a clear and well-documented log of all data
  • Meet with supervisor regularly (e.g. monthly meetings, as well as interactions on a day to day basis) to provide update on status of experimental results
  • Presentation of results to the EBG research group in weekly lab meetings (e.g. once a month) and if necessary to industry sponsors

Safety and Environment

  • Understand standard operating procedures of the equipment used in the experimental protocols
  • Maintain a clean and safe laboratory work area

Other

  • Manage time effectively to complete project work and contribute yearly research updates to program sponsors
  • Perform other duties, as assigned by the Research Supervisor
  • Contribute on a daily basis towards a positive working environment within a large and diverse team of colleagues working in the EBG group

Qualifications / Requirements:

  • PhD in area of Molecular Biology, Ecology, Microbiology or a similar area
  • Experience with bioinformatics software applications and/or development
  • Experience in assessing microbial diversity in environmental samples
  • Experience in and knowledge of environmental microbiology
  • Familiarity and interest in marine microbial ecology and biogeography
  • Proficiency in Microsoft Office Programs
  • 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
  • Must be comfortable working in a diverse research team and have good interpersonal skills
  • Ability and willingness to teach and mentor early career scientists (e.g. graduate students)
  • Willingness to conduct fieldwork in the Arctic and on research vessels

Application Deadline:  This position will remain open until it is filled. Review of applications will begin in October, 2016.

Candidates interested in more than one of the vacancies in EBG (see Job ID #11117, #11118, #11119) are encouraged to indicate this in a covering letter but do not need to submit more than one application.

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. All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority.

 

Additional Information

This position is part of the AUPE bargaining unit, and falls under the Technical Job Family, Phase 2 (range of $4,718.35 to $6,831.07).

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.

In support of the University of Calgary’s promotion of a diverse workforce, EBG is committed to showing leadership in diversity, equity and inclusion and nurturing a healthy and respectful workplace environment for all.

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 become 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. Ranked as the top young university in Canada and North America, the University of Calgary inspires and supports discovery, creativity and innovation across all disciplines. For more information, visit ucalgary.ca.

The University of Calgary believes that a respectful workplace, equal opportunity and building a diverse workforce contribute to the richness of the environment for teaching, learning and research, and provide faculty, staff, students and the public with a university that reflects the society it serves. All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority.


 

 

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