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Evaluating the Biogeochemistry and Microbial Function in the Athabasca Oil Sands Region: Understanding Natural Baselines for Reclamation End-Points

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Evaluating the Biogeochemistry and Microbial Function in the Athabasca Oil Sands Region: Understanding Natural Baselines for Reclamation End-Points University of Windsor Scholarship at UWindsor Electronic Theses and Dissertations Theses, Dissertations, and Major Papers 2019 Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points Thomas Reid University of Windsor Follow this and additional works at: https://scholar.uwindsor.ca/etd Recommended Citation Reid, Thomas, "Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points" (2019). Electronic Theses and Dissertations. 7732. https://scholar.uwindsor.ca/etd/7732 This online database contains the full-text of PhD dissertations and Masters’ theses of University of Windsor students from 1954 forward. These documents are made available for personal study and research purposes only, in accordance with the Canadian Copyright Act and the Creative Commons license—CC BY-NC-ND (Attribution, Non-Commercial, No Derivative Works). Under this license, works must always be attributed to the copyright holder (original author), cannot be used for any commercial purposes, and may not be altered. Any other use would require the permission of the copyright holder. Students may inquire about withdrawing their dissertation and/or thesis from this database. For additional inquiries, please contact the repository administrator via email ([email protected]) or by telephone at 519-253-3000ext. 3208. Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points By Thomas Reid A Dissertation Submitted to the Faculty of Graduate Studies through the Great Lakes Institute for Environmental Research in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy at the University of Windsor Windsor, Ontario, Canada 2019 © 2019 Thomas Reid Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points By Thomas Reid APPROVED BY: ______________________________________________ G. Ferris, External Examiner University of Toronto ______________________________________________ J. Ciborowski Department of Biological Sciences ______________________________________________ S.R. Chaganti Great Lakes Institute for Environmental Research ______________________________________________ S. Mundle Great Lakes Institute for Environmental Research _______________________________________________ C. Weisener, Advisor Great Lakes Institute for Environmental Research ______________________________________________ I.G. Droppo, Co-Advisor Environment and Climate Change Canada April 26, 2019 DECLARATION OF CO-AUTHORSHIP / PREVIOUS PUBLICATION I. Co-Authorship I hereby declare that this thesis incorporates material that is result of joint research, as follows: Chapter 2 of the thesis was co-authored with S.R. Chaganti, I.G. Droppo, and C.G. Weisener, under the supervision of both I.G. Droppo and C.G. Weisener. In all cases, the key ideas, primary contributions, data analysis, interpretation, and writing were performed by the author, and the contribution of co-authors was primarily through the provision of grant funding alongside experimental design. All co-authors also provided feedback for the purpose of editing and refining the manuscript. Chapter 3 of the thesis was co-authored with S.R. Chaganti, I.G. Droppo, and C.G. Weisener, under the supervision of both I.G. Droppo and C.G. Weisener. In all cases, the key ideas, primary contributions, data analysis, interpretation, and writing were performed by the author, and the contribution of co-authors was primarily through the provision of grant funding alongside experimental design. All co-authors also provided feedback for the purpose of editing and refining the manuscript. Chapter 4 of the thesis was co-authored with S.R. Chaganti, I.G. Droppo, and C.G. Weisener, under the supervision of both I.G. Droppo and C.G. Weisener. In all cases, the key ideas, primary contributions, data analysis, interpretation, and writing were performed by the author, and the contribution of co-authors was primarily through the provision of grant funding alongside experimental design. All co-authors also provided feedback for the purpose of editing and refining the manuscript. I am aware of the University of Windsor Senate Policy on Authorship and I certify that I have properly acknowledged the contribution of other researchers to my iii thesis, and have obtained written permission from each of the co-author(s) to include the above material(s) in my thesis. I certify that, with the above qualification, this thesis, and the research to which it refers, is the product of my own work. II. Previous Publication This thesis includes 3 original papers that have been previously published/submitted for publication in peer reviewed journals, as follows: Thesis Publication title/full citation Publication status* Chapter Chapter [2] Reid, T., Chaganti, S.R., Droppo, I.G., Weisener, Published C.G., 2018. Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box. Water Res. 136, 1–11. https://doi.org/10.1016/j.watres.2018.02.039 Chapter [3] Reid, T., Droppo, I.G., Chaganti, S.R., Weisener, Published C.G., 2019. Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes? Sci. Total Environ. 665, 113–124. https://doi.org/10.1016/j.scitotenv.2019.02.032 Chapter [4] Reid, T., Droppo, I.G., Chaganti, S.R., Weisener, Submitted by mid- C.G., 2019. Tracking Functional Bacterial May 2019 Biomarkers in Response to a Gradient of Contaminant Exposure within the Oil Sands River Sediment Continuums I certify that I have obtained a written permission from the copyright owner(s) to include the above published material(s) in my thesis. I certify that the above material describes work completed during my registration as a graduate student at the University of Windsor. iv III. General I declare that, to the best of my knowledge, my thesis does not infringe upon anyone’s copyright nor violate any proprietary rights and that any ideas, techniques, quotations, or any other material from the work of other people included in my thesis, published or otherwise, are fully acknowledged in accordance with the standard referencing practices. Furthermore, to the extent that I have included copyrighted material that surpasses the bounds of fair dealing within the meaning of the Canada Copyright Act, I certify that I have obtained a written permission from the copyright owner(s) to include such material(s) in my thesis. I declare that this is a true copy of my thesis, including any final revisions, as approved by my thesis committee and the Graduate Studies office, and that this thesis has not been submitted for a higher degree to any other University or Institution. v ABSTRACT Understanding the biogeochemical processes governed by the complex metabolic pathways of microbial communities is paramount in understanding overall ecosystem services. Their ability to adapt to the world’s harshest environments allows them to thrive in otherwise hostile environments. The Athabasca Oil Sands of Northern Alberta, Canada, constitutes one of the largest oil sands deposits in the world. This uniquely hydrocarbon- rich environment is a diverse and complex ecosystem governed by strong anthropogenic (i.e. industrial mine sites) and natural environmental gradients (i.e. substantial bitumen outcroppings). The economically significant oil sands deposit produces millions of barrels of bitumen daily, with waste materials (i.e. sands, clays, residual bitumen etc.) pumped into large settling basins called tailings ponds. The Government of Alberta requires oil sands operators to return their mine sites to a reclaimed landscape after mining has completed, thus leaving an enormous task of determining appropriate reclamation procedures, target end-points and water quality targets. However, what remains unknown is an understanding of the baseline biogeochemical fingerprint of the natural McMurray Formation (MF) – the geological strata constituting the mineable bitumen ore. Additionally, there has yet to be any studies focusing on the microbial function in the MF, a vital research gap that would provide insight into how the indigenous microbial communities deal with this ubiquitous, natural hydrocarbon presence. The research comprising the chapters of this dissertation, are the first to reveal the active, in-situ metabolism of the bacterial communities within the MF. Novel metatranscriptomics approaches from in-situ samples are used to characterize the microbial vi metabolic processes governing these ecosystems, to better understand what may constitute viable ecosystem reclamation end-points. Functional characterizations are compared to hydrocarbon signatures and redox state of the various study sites. Results indicate a unique microbial consortium with both energy and xenobiotic metabolic pathways tailored to the complex hydrocarbon substrate of the MF. Further, the sensitivity of this metatranscriptomics approach was tested and validated as a means of tracking hydrocarbon exposure down a river continuum. Clusters of closely related co-expressing genes revealed patterns of expression indicative of exposure to the hydrocarbons of the MF, providing interesting methodologies to track pollution exposure in a hydrodynamic
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    Bibliography Abella, C.A., X.P. Cristina, A. Martinez, I. Pibernat and X. Vila. 1998. on moderate concentrations of acetate: production of single cells. Two new motile phototrophic consortia: "Chlorochromatium lunatum" Appl. Microbiol. Biotechnol. 35: 686-689. and "Pelochromatium selenoides". Arch. Microbiol. 169: 452-459. Ahring, B.K, P. Westermann and RA. Mah. 1991b. Hydrogen inhibition Abella, C.A and LJ. Garcia-Gil. 1992. Microbial ecology of planktonic of acetate metabolism and kinetics of hydrogen consumption by Me­ filamentous phototrophic bacteria in holomictic freshwater lakes. Hy­ thanosarcina thermophila TM-I. Arch. Microbiol. 157: 38-42. drobiologia 243-244: 79-86. Ainsworth, G.C. and P.H.A Sheath. 1962. Microbial Classification: Ap­ Acca, M., M. Bocchetta, E. Ceccarelli, R Creti, KO. Stetter and P. Cam­ pendix I. Symp. Soc. Gen. Microbiol. 12: 456-463. marano. 1994. Updating mass and composition of archaeal and bac­ Alam, M. and D. Oesterhelt. 1984. Morphology, function and isolation terial ribosomes. Archaeal-like features of ribosomes from the deep­ of halobacterial flagella. ]. Mol. Biol. 176: 459-476. branching bacterium Aquifex pyrophilus. Syst. Appl. Microbiol. 16: 629- Albertano, P. and L. Kovacik. 1994. Is the genus LeptolynglYya (Cyano­ 637. phyte) a homogeneous taxon? Arch. Hydrobiol. Suppl. 105: 37-51. Achenbach-Richter, L., R Gupta, KO. Stetter and C.R Woese. 1987. Were Aldrich, H.C., D.B. Beimborn and P. Schönheit. 1987. Creation of arti­ the original eubacteria thermophiles? Syst. Appl. Microbiol. 9: 34- factual internal membranes during fixation of Methanobacterium ther­ 39. moautotrophicum. Can.]. Microbiol. 33: 844-849. Adams, D.G., D. Ashworth and B.
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