A list of microbe-related research published by members of the Waterloo Centre for Microbial Research since 2017. This collection is organized by member using the newest APA citation guidelines.
William Anderson
Bai, Y., Moo-Young, M., & Anderson, W. A. (2019). A mechanistic model for gas–liquid mass transfer prediction in a rocking disposable bioreactor. Biotechnology and Bioengineering, 116(8), 1986–1998. https://doi.org/10.1002/bit.27000
Bai, Y., Moo-Young, M., & Anderson, W. A. (2019). Characterization of power input and its impact on mass transfer in a rocking disposable bioreactor. Chemical Engineering Science, 209, 115183. https://doi.org/10.1016/j.ces.2019.115183
Cholewinski, A., Dadzie, E., Sherlock, C., Anderson, W. A., Charles, T. C., Habib, K., Young, S. B., & Zhao, B. (2022). A critical review of microplastic degradation and material flow analysis towards a circular economy. Environmental Pollution (Barking, Essex: 1987), 315, 120334. https://doi.org/10.1016/j.envpol.2022.120334
Derraik, J. G. B., Anderson, W. A., Connelly, E. A., & Anderson, Y. C. (2020). Rapid Review of SARS-CoV-1 and SARS-CoV-2 Viability, Susceptibility to Treatment, and the Disinfection and Reuse of PPE, Particularly Filtering Facepiece Respirators. International Journal of Environmental Research and Public Health, 17(17), Article 17. https://doi.org/10.3390/ijerph17176117
Harfoot, R., Yung, D. B. Y., Anderson, W. A., Wild, C. E. K., Coetzee, N., Hernández, L. C., Lawley, B., Pletzer, D., Derraik, J. G. B., Anderson, Y. C., & Quiñones-Mateu, M. E. (2022). Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators. Pathogens, 11(1), Article 1. https://doi.org/10.3390/pathogens11010083
Kaur, A., Anderson, W. A., Tanvir, S., & Kansal, S. K. (2019). Solar light active silver/iron oxide/zinc oxide heterostructure for photodegradation of ciprofloxacin, transformation products and antibacterial activity. Journal of Colloid and Interface Science, 557, 236–253. https://doi.org/10.1016/j.jcis.2019.09.017
Liu, M., Bauman, L., Nogueira, C. L., Aucoin, M. G., Anderson, W. A., & Zhao, B. (2022). Antimicrobial polymeric composites for high-touch surfaces in healthcare applications. Current Opinion in Biomedical Engineering, 22, 100395. https://doi.org/10.1016/j.cobme.2022.100395
Muralidharan, S. K., Bauman, L., Anderson, W. A., & Zhao, B. (2020). Recyclable antimicrobial sulphonated poly (ether ether ketone) – copper films: Flat vs micro-pillared surfaces. Materials Today Communications, 25, 101485. https://doi.org/10.1016/j.mtcomm.2020.101485
Schmidt, T., & Anderson, W. A. (2017). Biotrickling Filtration of Air Contaminated with 1-Butanol. Environments, 4(3), 57. https://doi.org/10.3390/environments4030057
Tanvir, F., Yaqub, A., Tanvir, S., & Anderson, W. A. (2017a). Colorimetric enumeration of bacterial contamination in water based on β-galactosidase gold nanoshell activity. Enzyme and Microbial Technology, 99, 49–56. https://doi.org/10.1016/j.enzmictec.2017.01.006
Tanvir, F., Yaqub, A., Tanvir, S., & Anderson, W. A. (2017b). Poly-L-arginine Coated Silver Nanoprisms and Their Anti-Bacterial Properties. Nanomaterials, 7(10), Article 10. https://doi.org/10.3390/nano7100296
Marc Aucoin
Blondeel, E. J. M., & Aucoin, M. G. (2018). Supplementing glycosylation: A review of applying nucleotide-sugar precursors to growth medium to affect therapeutic recombinant protein glycoform distributions. Biotechnology Advances, 36(5), 1505–1523. https://doi.org/10.1016/j.biotechadv.2018.06.008
Boegel, S. J., Gabriel, M., Sasges, M., Petri, B., D’Agostino, M. R., Zhang, A., Ang, J. C., Miller, M. S., Meunier, S. M., & Aucoin, M. G. (2021). Robust Evaluation of Ultraviolet-C Sensitivity for SARS-CoV-2 and Surrogate Coronaviruses. Microbiology Spectrum, 9(2), e00537-21. https://doi.org/10.1128/Spectrum.00537-21
Bruder, M. R., & Aucoin, M. G. (2022). Utility of Alternative Promoters for Foreign Gene Expression Using the Baculovirus Expression Vector System. Viruses, 14(12), Article 12. https://doi.org/10.3390/v14122670
Bruder, M. R., & Aucoin, M. G. (2023). Evaluation of Virus-Free Manufacture of Recombinant Proteins Using CRISPR-Mediated Gene Disruption in Baculovirus-Infected Insect Cells. Vaccines, 11(2), 225. https://doi.org/10.3390/vaccines11020225
Bruder, M. R., Walji, S.-D., & Aucoin, M. G. (2021). Comparison of CRISPR–Cas9 Tools for Transcriptional Repression and Gene Disruption in the BEVS. Viruses, 13(10), Article 10. https://doi.org/10.3390/v13101925
Dare, E. V., Gabriel, M., Begum, A., Sasges, M., & Aucoin, M. G. (2017). The effect of hydrogen peroxide produced during ultraviolet disinfection of CHO cell culture media. Process Biochemistry, 61, 147-–155. https://doi.org/10.1016/j.procbio.2017.06.025
Delumeau, L.-V., Asgarimoghaddam, H., Alkie, T., Jones, A. J. B., Lum, S., Mistry, K., Aucoin, M. G., DeWitte-Orr, S., & Musselman, K. P. (2021). Effectiveness of antiviral metal and metal oxide thin-film coatings against human coronavirus 229E. APL Materials, 9(11), 111114. https://doi.org/10.1063/5.0056138
Gabriel, M. A., Dare, E. V., Meunier, S. M., Campbell, J. L., Sasges, M. R., & Aucoin, M. G. (2019). Ultraviolet irradiation of trypsin, lysozyme and β-galactosidase: How does UVC affect these enzymes when used as a secondary barrier against adventitious agents? Vaccine, 37(43), 6518–6525. https://doi.org/10.1016/j.vaccine.2019.08.063
Ganobis, C. M., Al-Abdul-Wahid, M. S., Renwick, S., Yen, S., Carriero, C., Aucoin, M. G., & Allen-Vercoe, E. (2020). 1D 1H NMR as a Tool for Fecal Metabolomics. Current Protocols in Chemical Biology, 12(3), e83. https://doi.org/10.1002/cpch.83
Havaei, S. M., Aucoin, M. G., & Jahanian-Najafabadi, A. (2021). Pseudomonas Exotoxin-Based Immunotoxins: Over Three Decades of Efforts on Targeting Cancer Cells With the Toxin. Frontiers in Oncology, 11, 781800. https://doi.org/10.3389/fonc.2021.781800
Lall, D., Miscevic, D., Bruder, M., Westbrook, A., Aucoin, M., Moo-Young, M., & Perry Chou, C. (2021). Strain engineering and bioprocessing strategies for biobased production of porphobilinogen in Escherichia coli. Bioresources and Bioprocessing, 8(1), 1–16.
Liu, M., Bauman, L., Nogueira, C. L., Aucoin, M. G., Anderson, W. A., & Zhao, B. (2022). Antimicrobial polymeric composites for high-touch surfaces in healthcare applications. Current Opinion in Biomedical Engineering, 22, 100395. https://doi.org/10.1016/j.cobme.2022.100395
Logan, M., Manalil, J., Notte, C., Kearse, C., George, S., Zeiser, A., Farrell, P., & Aucoin, M. G. (2019). A flow cytometric granularity assay for the quantification of infectious virus. Vaccine, 37(47), 7090-7099. https://doi.org/10.1016/j.vaccine.2019.02.059
Logan, M., Rinas, K., McConkey, B., & Aucoin, M. G. (2022). Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. Scientific Reports, 12(1), Article 1. https://doi.org/10.1038/s41598-022-10221-z
Lourenco Nogueira, C., Boegel, S. J., Shukla, M., Ngo, W., Jones, L., & Aucoin, M. G. (2022). Antiviral Activity of Contemporary Contact Lens Care Solutions against Two Human Seasonal Coronavirus Strains. Pathogens, 11(4), Article 4. https://doi.org/10.3390/pathogens11040472
Marcali, M., Aucoin, M. G., & Ren, C. (2021). Hemagglutination Assay to Quantify Influenza A Virus Like Particles in Droplets. MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 985–986. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755515/
Marcali, M., Chen, X., Aucoin, M. G., & Ren, C. L. (2022). Droplet formation of biological non-Newtonian fluid in T-junction generators. II. Model for final droplet volume prediction. Physical Review E, 105(2), 025106. https://doi.org/10.1103/PhysRevE.105.025106
Meunier, S. M., Sasges, M. R., & Aucoin, M. G. (2017). Evaluating ultraviolet sensitivity of adventitious agents in biopharmaceutical manufacturing. Journal of Industrial Microbiology and Biotechnology, 44(6), 893–909. https://doi.org/10.1007/s10295-017-1917-0
Moussa, H. I., Chan, W. Y., Logan, M., Aucoin, M. G., & Tsui, T. Y. (2020). Limitation in Controlling the Morphology of Mammalian Vero Cells Induced by Cell Division on Asymmetric Tungsten-Silicon Oxide Nanocomposite. Materials, 13(2), Article 2. https://doi.org/10.3390/ma13020335
Moussa, H. I., Logan, M., Chan, W. Y., Wong, K., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2018). Pattern-dependent mammalian cell (Vero) morphology on tantalum/silicon oxide 3D nanocomposites. Materials, 11(8). https://doi.org/10.3390/ma11081306
Moussa, H. I., Logan, M., Siow, G. C., Phann, D. L., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2017). Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips. Science and Technology of Advanced Materials, 18(1), 839–856. https://doi.org/10.1080/14686996.2017.1388135
Moussa, H. I., Logan, M., Wong, K., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2018). Nanoscale-textured tantalum surfaces for mammalian cell alignment. Micromachines, 9(9). https://doi.org/10.3390/mi9090464
Nogueira, C. L., Boegel, S. J., Shukla, M., Ngo, W., Jones, L., & Aucoin, M. G. (2022). The impact of a rub and rinse regimen on removal of human coronaviruses from contemporary contact lens materials. Contact Lens and Anterior Eye, 45(6), 101719. https://doi.org/10.1016/j.clae.2022.101719
Quattrociocchi, M., Boegel, S. J., & Aucoin, M. G. (2021). Enhanced characterization of yeast hydrolysate combining acid digestion and 1D-1H NMR targeted profiling. The Canadian Journal of Chemical Engineering, 99(S1), S7–S17. https://doi.org/10.1002/cjce.24018
Shafiee, F., Aucoin, M. G., & Jahanian-Najafabadi, A. (2019). Targeted Diphtheria Toxin-Based Therapy: A Review Article. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.02340
Srirangan, K., Akawi, L. K., Chou, C. P., Aucoin, M. G., Stacey, L. E., & Newton, C. (2017). Use of a case on metabolically engineered Escherichia coli to develop a framework for the design and analysis of bioprocesses. International Journal of Engineering Education, 33(2), 751–760.
Tsui, T. Y., Logan, M., Moussa, H. I., & Aucoin, M. G. (2018). What’s happening on the other side? Revealing nano-meter scale features of mammalian cells on engineered textured tantalum surfaces. Materials, 12(1). https://doi.org/10.3390/ma12010114
Varga, J. F. A., Brunner, S. R., Cheng, G., Min, D., Aucoin, M. G., Doxey, A. C., & Dixon, B. (2022). Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae. Developmental & Comparative Immunology, 137, 104518. https://doi.org/10.1016/j.dci.2022.104518
Walji, S.-D., & Aucoin, M. G. (2020). A critical evaluation of current protocols for self-sterilizing surfaces designed to reduce viral nosocomial infections. American Journal of Infection Control, 48(10), 1255–1260. https://doi.org/10.1016/j.ajic.2020.02.008
Walji, S.-D., Bruder, M. R., & Aucoin, M. G. (2021). Virus matrix interference on assessment of virucidal activity of high-touch surfaces designed to prevent hospital-acquired infections. Antimicrobial Resistance & Infection Control, 10(1), 133. https://doi.org/10.1186/s13756-021-01001-x
Wulff, D., Chan, A., Liu, Q., Gu, F. X., & Aucoin, M. G. (2020). Characterizing internal cavity modulation of corn starch microcapsules. Heliyon, 6(10). https://doi.org/10.1016/j.heliyon.2020.e05294
Yip, A., Smith-Roberge, J., Khorasani, S. H., Aucoin, M. G., & Ingalls, B. P. (2022). Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLOS Computational Biology, 18(10), e1010533. https://doi.org/10.1371/journal.pcbi.1010533
Trevor Charles
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979–990. https://doi.org/10.1111/mmi.14588
Brumwell, S. L., MacLeod, M. R., Huang, T., Cochrane, R. R., Meaney, R. S., Zamani, M., Matysiakiewicz, O., Dan, K. N., Janakirama, P., Edgell, D. R., Charles, T. C., Finan, T. M., & Karas, B. J. (2019). Designer Sinorhizobium meliloti strains and multi-functional vectors enable direct inter-kingdom DNA transfer. PloS One, 14(6), e0206781. https://doi.org/10.1371/journal.pone.0206781
Cheng, J., Lam, K. N., Engel, K., Hall, M., Neufeld, J. D., & Charles, T. C. (2017). Metagenomic cosmid libraries suitable for functional screening in proteobacteria. In Functional Metagenomics: Tools and Applications (pp. 1–11). https://doi.org/10.1007/978-3-319-61510-3_1
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545. https://doi.org/10.1371/journal.pone.0172545
Cholewinski, A., Dadzie, E., Sherlock, C., Anderson, W. A., Charles, T. C., Habib, K., Young, S. B., & Zhao, B. (2022). A critical review of microplastic degradation and material flow analysis towards a circular economy. Environmental Pollution (Barking, Essex: 1987), 315, 120334. https://doi.org/10.1016/j.envpol.2022.120334
D’Alessio, M., Nordeste, R., Doxey, A. C., & Charles, T. C. (2017). Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. MSystems, 2(5), e00035-17. https://doi.org/10.1128/mSystems.00035-17
Donovan, M., Lynch, M. D. J., Mackey, C. S., Platt, G. N., Washburn, B. K., Vera, D. L., Trickey, D. J., Charles, T. C., Wang, Z., & Jones, K. M. (2020). Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome. Microbiology Resource Announcements, 9(2), e01310-19. https://doi.org/10.1128/MRA.01310-19
Eckhard, U., Bandukwala, H., Mansfield, M. J., Marino, G., Cheng, J., Wallace, I., Holyoak, T., Charles, T. C., Austin, J., Overall, C. M., & Doxey, A. C. (2017). Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications, 8(1), 521. https://doi.org/10.1038/s41467-017-00599-0
Fuentes, A., Herrera, H., Charles, T. C., & Arriagada, C. (2020). Fungal and Bacterial Microbiome Associated with the Rhizosphere of Native Plants from the Atacama Desert. Microorganisms, 8(2), 209. https://doi.org/10.3390/microorganisms8020209
Gupta, P. K., Gharedaghloo, B., Lynch, M., Cheng, J., Strack, M., Charles, T. C., & Price, J. S. (2020). Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions. Environmental Research, 191, 110167. https://doi.org/10.1016/j.envres.2020.110167
Heil, J. R., Lynch, M. D. J., Cheng, J., Matysiakiewicz, O., D’Alessio, M., & Charles, T. C. (2017). The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid. Genome Announcements, 5(49), e01349-17. https://doi.org/10.1128/genomeA.01349-17
Lam, K. N., Martens, E. C., & Charles, T. C. (2018). Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome. MSystems, 3(3), e00195-17. https://doi.org/10.1128/mSystems.00195-17
LeBlanc, N., & Charles, T. C. (2022). Bacterial genome reductions: Tools, applications, and challenges. Frontiers in Genome Editing, 4, 957289. https://doi.org/10.3389/fgeed.2022.957289
Lobb, B., Hodgson, R., Lynch, M. D. J., Mansfield, M. J., Cheng, J., Charles, T. C., Neufeld, J. D., Craig, P. M., & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2), e00145-20. https://doi.org/10.1128/mSystems.00145-20
Martinez, A. R., Heil, J. R., & Charles, T. C. (2019). An engineered GFP fluorescent bacterial biosensor for detecting and quantifying silver and copper ions. Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine, 32(2), 265–272. https://doi.org/10.1007/s10534-019-00179-3
Nett, R. S., Nguyen, H., Nagel, R., Marcassa, A., Charles, T. C., Friedberg, I., & Peters, R. J. (2020). Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon. MSphere, 5(3), e00292-20. https://doi.org/10.1128/mSphere.00292-20
Ryan, M. J., Schloter, M., Berg, G., Kostic, T., Kinkel, L. L., Eversole, K., Macklin, J. A., Schelkle, B., Kazou, M., Sarand, I., Singh, B. K., Fischer, D., Maguin, E., Ferrocino, I., Lima, N., McClure, R. S., Charles, T. C., de Souza, R. S. C., Kiran, G. S., … Sessitsch, A. (2021). Development of Microbiome Biobanks—Challenges and Opportunities. Trends in Microbiology, 29(2), 89–92. https://doi.org/10.1016/j.tim.2020.06.009
Smyth, S. J., & Charles, T. C. (2021). Impacts on International Research Collaborations from DSI/ABS Uncertainty. Trends in Biotechnology, 39(5), 430–433. https://doi.org/10.1016/j.tibtech.2020.10.011
Soto, J., Ortiz, J., Herrera, H., Fuentes, A., Almonacid, L., Charles, T. C., & Arriagada, C. (2019). Enhanced Arsenic Tolerance in Triticum aestivum Inoculated with Arsenic-Resistant and Plant Growth Promoter Microorganisms from a Heavy Metal-Polluted Soil. Microorganisms, 7(9), 348. https://doi.org/10.3390/microorganisms7090348
Thakor, A., Cheng, J., & Charles, T. C. (2023). Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities. Methods in Molecular Biology (Clifton, N.J.), 2555, 115–123. https://doi.org/10.1007/978-1-0716-2795-2_8
Thomas-Barry, G., St Martin, C. C. G., Lynch, M. D. J., Ramsubhag, A., Rouse-Miller, J., & Charles, T. C. (2021). Driving factors influencing the rhizobacteriome community structure of plants adapted to multiple climatic stressors in edaphic savannas. The Science of the Total Environment, 769, 145214. https://doi.org/10.1016/j.scitotenv.2021.145214
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., … Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457–463. https://doi.org/10.1038/nature24621
Tran, T. T., & Charles, T. C. (2020). Lactic acid containing polymers produced in engineered Sinorhizobium meliloti and Pseudomonas putida. PloS One, 15(3), e0218302. https://doi.org/10.1371/journal.pone.0218302
Varaljay, V. A., Charles, T. C., & Daniel, R. (2022). Editorial: Functional Metagenomics for Enzyme Discovery. Frontiers in Microbiology, 13, 956106. https://doi.org/10.3389/fmicb.2022.956106
Zhang, X., Liang, S., Wu, Q., Charles, T. C., He, R., Wu, J., Zhao, Y., Zhao, Z., & Wang, H. (2022). Mode of action of nanochitin whisker against Fusarium pseudograminearum. International Journal of Biological Macromolecules, 217, 356–366. https://doi.org/10.1016/j.ijbiomac.2022.07.056
Alexis Dolphin
Hodgins, H. P., Chen, P., Lobb, B., Tremblay, B. J., Mansfield, M. J., Lee, V. C., Lee, P.-G., Coffin, J., Wei, X., Duggan, A. T., Dolphin, A. E., Renaud, G., Dong, M., & Doxey, A. C. (2022). Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains (p. 2022.06.30.498301). bioRxiv. https://doi.org/10.1101/2022.06.30.498301
Andrew Doxey
Adegboye, M. F., Lobb, B., Babalola, O. O., Doxey, A. C., & Ma, K. (2018). Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil. Genome Announcements, 6(26), e00632-18. https://doi.org/10.1128/genomeA.00632-18
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979–990. https://doi.org/10.1111/mmi.14588
Banerjee, A., Doxey, A. C., Mossman, K., & Irving, A. T. (2021). Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2. Trends in Ecology & Evolution, 36(3), 180–184. https://doi.org/10.1016/j.tree.2020.12.002
Banerjee, A., Doxey, A. C., Tremblay, B. J.-M., Mansfield, M. J., Subudhi, S., Hirota, J. A., Miller, M. S., McArthur, A. G., Mubareka, S., & Mossman, K. (2020). Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. The Journal of General Virology, 101(12), 1251–1260. https://doi.org/10.1099/jgv.0.001491
Banerjee, A., El-Sayes, N., Budylowski, P., Jacob, R. A., Richard, D., Maan, H., Aguiar, J. A., Demian, W. L., Baid, K., D’Agostino, M. R., Ang, J. C., Murdza, T., Tremblay, B. J.-M., Afkhami, S., Karimzadeh, M., Irving, A. T., Yip, L., Ostrowski, M., Hirota, J. A., … Mossman, K. (2021). Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. IScience, 24(5), 102477. https://doi.org/10.1016/j.isci.2021.102477
Bano, L., Kiel, M., Sales, G., Doxey, A. C., Mansfield, M. J., Wami, H. T., Schiavone, M., Rossetto, O., Pirazzini, M., Dobrindt, U., & Montecucco, C. (2020). Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae. Microbiology Resource Announcements, 9(16). https://doi.org/10.1128/MRA.01575-19
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545. https://doi.org/10.1371/journal.pone.0172545
D’Alessio, M., Nordeste, R., Doxey, A. C., & Charles, T. C. (2017). Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. MSystems, 2(5), e00035-17. https://doi.org/10.1128/mSystems.00035-17
Doxey, A. C., Mansfield, M. J., & Lobb, B. (2019). Exploring the Evolution of Virulence Factors through Bioinformatic Data Mining. MSystems, 4(3). https://doi.org/10.1128/mSystems.00162-19
Doxey, A. C., Mansfield, M. J., & Montecucco, C. (2018). Discovery of novel bacterial toxins by genomics and computational biology. Toxicon : Official Journal of the International Society on Toxinology, 147, 2–12. https://doi.org/10.1016/j.toxicon.2018.02.002
Eckhard, U., Bandukwala, H., Mansfield, M. J., Marino, G., Cheng, J., Wallace, I., Holyoak, T., Charles, T. C., Austin, J., Overall, C. M., & Doxey, A. C. (2017). Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications, 8(1), 521. https://doi.org/10.1038/s41467-017-00599-0
Eckhard, U., Blöchl, C., Jenkins, B. G. L., Mansfield, M. J., Huber, C. G., Doxey, A. C., & Brandstetter, H. (2020). Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Scientific Reports, 10(1), 19052. https://doi.org/10.1038/s41598-020-76010-8
Ghasemi, M., Jenkins, B., Doxey, A. C., & Sivaloganathan, S. (2020). A study of nitric oxide dynamics in a growing biofilm using a density dependent reaction-diffusion model. Journal of Theoretical Biology, 485, 110053. https://doi.org/10.1016/j.jtbi.2019.110053
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Mansfield, M. J., Wentz, T. G., Zhang, S., Lee, E. J., Dong, M., Sharma, S. K., & Doxey, A. C. (2019). Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins. Scientific Reports, 9(1), 1634. https://doi.org/10.1038/s41598-018-37647-8
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Bernard Duncker
Zhao, K., Larasati, Duncker, B. P., & Li, D. (2019). Continuous Cell Characterization and Separation by Microfluidic Alternating Current Dielectrophoresis. Analytical Chemistry, 91(9), 6304–6314. https://doi.org/10.1021/acs.analchem.9b01104
John Honek
Honek, J. F. (2019). Commentary on “Current Challenges in the Development of Vaccines and Drugs Against Emerging Vector-borne Diseases” by Professor Kwang-sun Kim, Pusan National University, Republic of Korea. Current Medicinal Chemistry, 26(17), 3201–3204. https://doi.org/10.2174/092986732617190820145226
Suttisansanee, U., & F. Honek, J. (2017). Hydroxamate Inhibitor Profiling of Both Zn2+- and Ni2+-Activated Glyoxalase I Metalloenzymes Having Diverse Quaternary Structures. Letters in Drug Design & Discovery, 14(7), 843–852. https://doi.org/10.2174/1570180814666161128115808
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Laura Hug
Co, R., & Hug, L. A. (2020). A Need for Improved Cellulase Identification from Metagenomic Sequence Data. Applied and Environmental Microbiology, 87(1), e01928-20. https://doi.org/10.1128/AEM.01928-20
Co, R., & Hug, L. A. (2021). Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill. FEMS Microbiology Ecology, 97(5), fiab065. https://doi.org/10.1093/femsec/fiab065
Collins-Fairclough, A. M., Co, R., Ellis, M. C., & Hug, L. A. (2018). Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River. MSphere, 3(5), e00346-18. https://doi.org/10.1128/mSphere.00346-18
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Douglas, A. J., Hug, L. A., & Katzenback, B. A. (2021). Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure. Microbial Ecology, 81(1), 78–92. https://doi.org/10.1007/s00248-020-01550-5
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Hilts, A. S., Hunjan, M. S., & Hug, L. A. (2021). Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes. MSystems, 6(6), e00790-21. https://doi.org/10.1128/mSystems.00790-21
Hinz, A., Xing, L., Doukhanine, E., Hug, L. A., Kassen, R., Ormeci, B., Kibbee, R. J., Wong, A., MacFadden, D., & Nott, C. (2022). SARS-CoV-2 detection from the built environment and wastewater and its use for hospital surveillance. FACETS, 7, 82–97. https://doi.org/10.1139/facets-2021-0139
Hug, L. A. (2018). Sizing Up the Uncultured Microbial Majority. MSystems, 3(5), e00185-18. https://doi.org/10.1128/mSystems.00185-18
Hug, L. A., & Co, R. (2018). It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs. MSystems, 3(2), e00152-17. https://doi.org/10.1128/mSystems.00152-17
Jensen, G., Krogstad, K., Rezanezhad, F., & Hug, L. A. (2022). Microbial Community Compositional Stability in Agricultural Soils During Freeze-Thaw and Fertilizer Stress. Frontiers in Environmental Science, 10, 908568. https://doi.org/10.3389/fenvs.2022.908568
Johnson, L. A., & Hug, L. A. (2019). Distribution of reactive oxygen species defense mechanisms across domain bacteria. Free Radical Biology and Medicine, 140, 93–102. https://doi.org/10.1016/j.freeradbiomed.2019.03.032
Johnson, L. A., & Hug, L. A. (2022). Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum. Environmental Microbiology Reports, 14(4), 520–529. https://doi.org/10.1111/1758-2229.13061
Krogstad, K., Gharasoo, M., Jensen, G., Hug, L. A., Rudolph, D., Van Cappellen, P., & Rezanezhad, F. (2022). Nitrogen Leaching From Agricultural Soils Under Imposed Freeze-Thaw Cycles: A Column Study With and Without Fertilizer Amendment. Frontiers in Environmental Science, 10. https://doi.org/10.3389/fenvs.2022.915329
Méheust, R., Castelle, C. J., Matheus Carnevali, P. B., Farag, I. F., He, C., Chen, L.-X., Amano, Y., Hug, L. A., & Banfield, J. F. (2020). Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. The ISME Journal, 14(12), Article 12. https://doi.org/10.1038/s41396-020-0716-1
Mendler, K., Chen, H., Parks, D. H., Lobb, B., Hug, L. A., & Doxey, A. C. (2019). AnnoTree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Research, 47(9), 4442–4448. https://doi.org/10.1093/nar/gkz246
Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., … Reysenbach, A.-L. (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5(8), Article 8. https://doi.org/10.1038/s41564-020-0733-x
Sauk, A. H., & Hug, L. A. (2022). Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities. ISME Communications, 2(1), Article 1. https://doi.org/10.1038/s43705-022-00141-4
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Viljakainen, V. R., & Hug, L. A. (2021a). The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic-degrading genes. Environmental Microbiology, 23(3), 1717–1731. https://doi.org/10.1111/1462-2920.15409
Viljakainen, V. R., & Hug, L. A. (2021b). New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes. Computational and Structural Biotechnology Journal, 19, 6191–6200. https://doi.org/10.1016/j.csbj.2021.11.023
Brian Ingalls
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Yilan Liu
Chen, J., Liu, Y., Diep, P., Jo, A., Nesbø, C., Edwards, E., Papangelakis, V., & Mahadevana, R. (2020). Complete Genome Sequence of Acidithiobacillus ferridurans JAGS, Isolated from Acidic Mine Drainage. Microbiology Resource Announcements, 9(13). https://doi.org/10.1128/MRA.00033-20
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Kesen Ma
Adegboye, M. F., Lobb, B., Babalola, O. O., Doxey, A. C., & Ma, K. (2018). Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil. Genome Announcements, 6(26), e00632-18. https://doi.org/10.1128/genomeA.00632-18
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Lobb, B., Adegoke, A. A., Ma, K., Doxey, A. C., & Aiyegoro, O. A. (2018). Metagenomic Sequencing of Wastewater from a South African Research Farm. Microbiology Resource Announcements, 7(16). https://doi.org/10.1128/MRA.01323-18
Ma, K. (2018). Beneficial Characteristics and Evaluation Criteria of Probiotics. Int J Food Biosci Vol: 1, Issu: 1 (19-26).
Rahman, Md. S., Xu, C. (Charles), Ma, K., Guo, H., & Qin, W. (2017). Utilization of by-product glycerol from bio-diesel plants as feedstock for 2,3-butanediol accumulation and biosynthesis genes response of Klebsiella variicola SW3. Renewable Energy, 114, 1272–1280. https://doi.org/10.1016/j.renene.2017.07.080
Rahman, Md. S., Xu, C. (Charles), Ma, K., Nanda, M., & Qin, W. (2017). High Production of 2,3-butanediol by a Mutant Strain of the Newly Isolated Klebsiella pneumoniae SRP2 with Increased Tolerance Towards Glycerol. International Journal of Biological Sciences, 13(3), 308–318. https://doi.org/10.7150/ijbs.17594
Sun, Y., Wang, H., Ma, K., & Shao, W. (2018). Construction and characterization of the GFAT gene as a novel selection marker in Aspergillus nidulans. Applied Microbiology and Biotechnology, 102(18), 7951–7962. https://doi.org/10.1007/s00253-018-9185-0
Tse, C., Ibrahim, N. E., & Ma, K. (2017). Characterization of an Alcohol Dehydrogenase of the Hyperthermophilic Archaeon Hyperthermus Butylicus. Journal of Applied Microbiology and Biochemistry, 2(1). https://doi.org/10.21767/2576-1412.100018
Wang, Q., Sha, C., Wang, H., Ma, K., Wiegle, J., Abomohra, A. E.-F., & Shao, W. (2021). A novel bifunctional aldehyde/alcohol dehydrogenase catalyzing reduction of acetyl-CoA to ethanol at temperatures up to 95 °C. Scientific Reports, 11, 1050. https://doi.org/10.1038/s41598-020-80159-7
Wang, Y., Liu, H., Peng, Y., Tong, L., Feng, L., & Ma, K. (2018a). New pathways for the biodegradation of diethyl phthalate by Sphingobium yanoikuyae SHJ. Process Biochemistry, 71, 152–158. https://doi.org/10.1016/j.procbio.2018.05.010
Wang, Y., Liu, H., Peng, Y., Tong, L., Feng, L., & Ma, K. (2018b). Characterization of the diethyl phthalate-degrading bacterium Sphingobium yanoikuyae SHJ. Data in Brief, 20, 1758–1763. https://doi.org/10.1016/j.dib.2018.09.033
Zhang, L., Xu, D., Huang, Y., Zhu, X., Rui, M., Wan, T., Zheng, X., Shen, Y., Chen, X., Ma, K., & Gong, Y. (2017). Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Scientific Reports, 7(1), Article 1. https://doi.org/10.1038/srep42542
Shannon Majowicz
Bitzegeio, J., Majowicz, S., Matysiak-Klose, D., Sagebiel, D., & Werber, D. (2019). Estimating age-specific vaccine effectiveness using data from a large measles outbreak in Berlin, Germany, 2014/15: Evidence for waning immunity. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 24(17), 1800529. https://doi.org/10.2807/1560-7917.ES.2019.24.17.1800529
Côté, D., Durant, S., MacEachen, E., Majowicz, S., Meyer, S., Huynh, A.-T., Laberge, M., & Dubé, J. (2021). A rapid scoping review of COVID-19 and vulnerable workers: Intersecting occupational and public health issues. American Journal of Industrial Medicine, 64(7), 551–566. https://doi.org/10.1002/ajim.23256
Desta, B. N., Gobena, T., Macuamule, C., Fayemi, O. E., Ayolabi, C. I., Mmbaga, B. T., Thomas, K. M., Dodd, W., Pires, S. M., Majowicz, S. E., & Hald, T. (2022). Practicalities of implementing burden of disease research in Africa: Lessons from a population survey component of our multi-partner FOCAL research project. Emerging Themes in Epidemiology, 19(1), 4. https://doi.org/10.1186/s12982-022-00113-y
Devleesschauwer, B., Pires, S. M., Young, I., Gill, A., Majowicz, S. E., & study team. (2019). Associating sporadic, foodborne illness caused by Shiga toxin-producing Escherichia coli with specific foods: A systematic review and meta-analysis of case-control studies. Epidemiology and Infection, 147, e235. https://doi.org/10.1017/S0950268819001183
Diplock, K. J., Dubin, J. A., Leatherdale, S. T., Hammond, D., Jones-Bitton, A., & Majowicz, S. E. (2018). Observation of High School Students’ Food Handling Behaviors: Do They Improve following a Food Safety Education Intervention? Journal of Food Protection, 81(6), 917–925. https://doi.org/10.4315/0362-028X.JFP-17-441
Diplock, K. J., Leatherdale, S. T., & Majowicz, S. E. (2017). Diarrhea ain’t dope: Canada needs to consider the food safety implications of edible cannabis. Canadian Journal of Public Health = Revue Canadienne De Sante Publique, 108(4), e455. https://doi.org/10.17269/cjph.108.6362
Gohari, M. R., Taylor, M., MacKinnon, M. C., Panagiotoglou, D., Galanis, E., Kaplan, G. G., Cook, R. J., Patrick, D. M., Ethelberg, S., & Majowicz, S. E. (2022). Patterns of enteric infections in a population-wide cohort study of sequelae, British Columbia, Canada. Epidemiology and Infection, 151, e7. https://doi.org/10.1017/S0950268822001911
Graells, T., Lambraki, I. A., Cousins, M., Léger, A., Lillepold, K., Henriksson, P. J. G., Troell, M., Carson, C. A., Parmley, E. J., Majowicz, S. E., Wernli, D., & Jørgensen, P. S. (2022). Studying Factors Affecting Success of Antimicrobial Resistance Interventions through the Lens of Experience: A Thematic Analysis. Antibiotics (Basel, Switzerland), 11(5), 639. https://doi.org/10.3390/antibiotics11050639
Hopwood, P., MacEachen, E., Majowicz, S. E., Meyer, S. B., & Amoako, J. (2022). “We need to talk to each other”: Crossing traditional boundaries between public health and occupational health to address COVID-19. Frontiers in Public Health, 10, 1046628. https://doi.org/10.3389/fpubh.2022.1046628
John, P., Varga, C., Cooke, M., & Majowicz, S. E. (2022). Incidence, Demographic, and Seasonal Risk Factors of Infections Caused by Five Major Enteric Pathogens, Ontario, Canada, 2010-2017. Foodborne Pathogens and Disease, 19(4), 248–258. https://doi.org/10.1089/fpd.2021.0034
Lambraki, I. A., Chadag, M. V., Cousins, M., Graells, T., Léger, A., Henriksson, P. J. G., Troell, M. F., Harbarth, S., Wernli, D., Jørgensen, P. S., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2023). Factors impacting antimicrobial resistance in the South East Asian food system and potential places to intervene: A participatory, one health study. Frontiers in Microbiology, 13, 992507. https://doi.org/10.3389/fmicb.2022.992507
Lambraki, I. A., Cousins, M., Graells, T., Léger, A., Abdelrahman, S., Desbois, A. P., Gallagher, R., Staaf Larsson, B., Mattson, B., Henriksson, P., Troell, M., Søgaard Jørgensen, P., Wernli, D., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2022). Governing Antimicrobial Resistance (AMR) in a Changing Climate: A Participatory Scenario Planning Approach Applied to Sweden in 2050. Frontiers in Public Health, 10, 831097. https://doi.org/10.3389/fpubh.2022.831097
Lambraki, I. A., Cousins, M., Graells, T., Léger, A., Henriksson, P., Harbarth, S., Troell, M., Wernli, D., Søgaard Jørgensen, P., Desbois, A. P., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2022). Factors influencing antimicrobial resistance in the European food system and potential leverage points for intervention: A participatory, One Health study. PloS One, 17(2), e0263914. https://doi.org/10.1371/journal.pone.0263914
Lambraki, I. A., Majowicz, S. E., Parmley, E. J., Wernli, D., Léger, A., Graells, T., Cousins, M., Harbarth, S., Carson, C., Henriksson, P., Troell, M., & Jørgensen, P. S. (2021). Building Social-Ecological System Resilience to Tackle Antimicrobial Resistance Across the One Health Spectrum: Protocol for a Mixed Methods Study. JMIR Research Protocols, 10(6), e24378. https://doi.org/10.2196/24378
Léger, A., Lambraki, I., Graells, T., Cousins, M., Henriksson, P. J. G., Harbarth, S., Carson, C. A., Majowicz, S. E., Troell, M., Parmley, E. J., Jørgensen, P. S., & Wernli, D. (2021a). Characterizing social-ecological context and success factors of antimicrobial resistance interventions across the One Health spectrum: Analysis of 42 interventions targeting E. coli. BMC Infectious Diseases, 21(1), 873. https://doi.org/10.1186/s12879-021-06483-z
Léger, A., Lambraki, I., Graells, T., Cousins, M., Henriksson, P. J. G., Harbarth, S., Carson, C., Majowicz, S., Troell, M., Parmley, E. J., Jørgensen, P. S., & Wernli, D. (2021b). AMR-Intervene: A social-ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective. The Journal of Antimicrobial Chemotherapy, 76(1), 1–21. https://doi.org/10.1093/jac/dkaa394
Major, M., Majowicz, S. E., Oremus, M., Jimenez, L. J., Angulo, F. J., & Horton, S. (2022). Systematic literature review of SARS-CoV-2 seroprevalence surveys in Canada through April 2021. IJID Regions, 4, 157–164. https://doi.org/10.1016/j.ijregi.2022.07.010
Majowicz, S. E. (2020). Using Market Availability Data to Support Foodborne Disease Outbreak Investigations. American Journal of Public Health, 110(3), 278–280. https://doi.org/10.2105/AJPH.2019.305536
Majowicz, S. E., Hammond, D., Dubin, J. A., Diplock, K. J., Jones-Bitton, A., Rebellato, S., & Leatherdale, S. T. (2017). A longitudinal evaluation of food safety knowledge and attitudes among Ontario high school students following a food handler training program. Food Control, 76, 108–116. https://doi.org/10.1016/j.foodcont.2017.01.011
Majowicz, S. E., Parmley, E. J., Carson, C., & Pintar, K. (2018). Identifying non-traditional stakeholders with whom to engage, when mitigating antimicrobial resistance in foodborne pathogens (Canada). BMC Research Notes, 11(1), 170. https://doi.org/10.1186/s13104-018-3279-8
Pires, S. M., Desta, B. N., Mughini-Gras, L., Mmbaga, B. T., Fayemi, O. E., Salvador, E. M., Gobena, T., Majowicz, S. E., Hald, T., Hoejskov, P. S., Minato, Y., & Devleesschauwer, B. (2021). Burden of foodborne diseases: Think global, act local. Current Opinion in Food Science, 39, 152–159. https://doi.org/10.1016/j.cofs.2021.01.006
Pires, S. M., Majowicz, S., Gill, A., & Devleesschauwer, B. (2019). Global and regional source attribution of Shiga toxin-producing Escherichia coli infections using analysis of outbreak surveillance data. Epidemiology and Infection, 147, e236. https://doi.org/10.1017/S095026881900116X
Speed, K. A., Meyer, S. B., Hanning, R. M., & Majowicz, S. E. (2017). “Highly processed, highly packaged, very unhealthy. But they are low risk”: Exploring intersections between community food security and food safety. Health Promotion and Chronic Disease Prevention in Canada, 37(10), 323–332. https://doi.org/10.24095/hpcdp.37.10.02
Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2020). Spatial and space-time clustering and demographic characteristics of human nontyphoidal Salmonella infections with major serotypes in Toronto, Canada. PloS One, 15(7), e0235291. https://doi.org/10.1371/journal.pone.0235291
Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2021). Area-Level Clustering of Shiga Toxin-Producing Escherichia coli Infections and Their Socioeconomic and Demographic Factors in Ontario, Canada: An Ecological Study. Foodborne Pathogens and Disease, 18(7), 438–447. https://doi.org/10.1089/fpd.2020.2918
Wernli, D., Jørgensen, P. S., Parmley, E. J., Troell, M., Majowicz, S., Harbarth, S., Léger, A., Lambraki, I., Graells, T., Henriksson, P. J. G., Carson, C., Cousins, M., Skoog Ståhlgren, G., Mohan, C. V., Simpson, A. J. H., Wieland, B., Pedersen, K., Schneider, A., Chandy, S. J., … Pittet, D. (2020). Evidence for action: A One Health learning platform on interventions to tackle antimicrobial resistance. The Lancet. Infectious Diseases, 20(12), e307–e311. https://doi.org/10.1016/S1473-3099(20)30392-3
Brendan McConkey
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979–990. https://doi.org/10.1111/mmi.14588
Gromala, M., Neufeld, J. D., & McConkey, B. J. (2021). Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Applied and Environmental Microbiology, 87(7), e02914-20. https://doi.org/10.1128/AEM.02914-20
Logan, M., Rinas, K., McConkey, B., & Aucoin, M. G. (2022). Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. Scientific Reports, 12(1), Article 1. https://doi.org/10.1038/s41598-022-10221-z
Jenine McCutcheon
Lutz, S., McCutcheon, J., McQuaid, J. B., & Benning, L. G. (2018). The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping. Microbial Genomics, 4(3). https://doi.org/10.1099/mgen.0.000159
McCutcheon, J., Lutz, S., Williamson, C., Cook, J. M., Tedstone, A. J., Vanderstraeten, A., Wilson, S. A., Stockdale, A., Bonneville, S., Anesio, A. M., Yallop, M. L., McQuaid, J. B., Tranter, M., & Benning, L. G. (2021). Mineral phosphorus drives glacier algal blooms on the Greenland Ice Sheet. Nature Communications, 12(1). https://doi.org/10.1038/s41467-020-20627-w
McCutcheon, J., Nothdurft, L. D., Webb, G. E., Shuster, J., Nothdurft, L., Paterson, D., & Southam, G. (2017). Building biogenic beachrock: Visualizing microbially-mediated carbonate cement precipitation using XFM and a strontium tracer. Chemical Geology, 465, 21–34. https://doi.org/10.1016/j.chemgeo.2017.05.019
McCutcheon, J., Power, I. M., Shuster, J., Harrison, A. L., Dipple, G. M., & Southam, G. (2019). Carbon Sequestration in Biogenic Magnesite and Other Magnesium Carbonate Minerals. Environmental Science and Technology, 53(6), 3225–3237. https://doi.org/10.1021/acs.est.8b07055
McCutcheon, J., & Southam, G. (2018). Advanced biofilm staining techniques for TEM and SEM in geomicrobiology: Implications for visualizing EPS architecture, mineral nucleation, and microfossil generation. Chemical Geology, 498, 115–127. https://doi.org/10.1016/j.chemgeo.2018.09.016
McCutcheon, J., Turvey, C. C., Wilson, S. A., Hamilton, J. L., & Southam, G. (2017). Experimental deployment of microbial mineral carbonation at an asbestos mine: Potential applications to carbon storage and tailings stabilization. Minerals, 7(10). https://doi.org/10.3390/min7100191
Nicholes, M. J., Williamson, C. J., Tranter, M., Holland, A., Poniecka, E., Yallop, M. L., Anesio, A., Poniecka, E., Benning, L., McQuaid, J., Lutz, S., McCutcheon, J., Hodson, A., Hanna, E., Irvine-Fynn, T., Cook, J., Bamber, J., Tedstone, A., Box, J., … The Black & Bloom Group. (2019). Bacterial dynamics in supraglacial habitats of the Greenland ice sheet. Frontiers in Microbiology, 10(JUL). https://doi.org/10.3389/fmicb.2019.01366
Williamson, C. J., Cook, J., Tedstone, A., Yallop, M., McCutcheon, J., Poniecka, E., Campbell, D., Irvine-Fynn, T., McQuaid, J., Tranter, M., Perkins, R., & Anesio, A. (2020). Algal photophysiology drives darkening and melt of the Greenland Ice Sheet. Proceedings of the National Academy of Sciences of the United States of America, 117(11), 5694–5705. https://doi.org/10.1073/pnas.1918412117
Tizazu McKennon
Ogunsona, E. O., Muthuraj, R., Ojogbo, E., Valerio, O., & Mekonnen, T. H. (2020). Engineered nanomaterials for antimicrobial applications: A review. Applied Materials Today, 18, 100473. https://doi.org/10.1016/j.apmt.2019.100473
Ojogbo, E., Ward, V., & Mekonnen, T. H. (2020). Functionalized starch microparticles for contact-active antimicrobial polymer surfaces. Carbohydrate Polymers, 229, 115422. https://doi.org/10.1016/j.carbpol.2019.115422
Christine Moresoli
Khouri, J., Penlidis, A., & Moresoli, C. (2020). Heterogeneous method of chitosan film preparation: Effect of multifunctional acid on film properties. Journal of Applied Polymer Science, 137(18), 48648. https://doi.org/10.1002/app.48648
Le Goué, E., Gardrat, C., Romain, M., Rollini, M., Moresoli, C., & Coma, V. (2022). Effect of oleic acid on the release of tetrahydrocurcumin in chitosan-based films. Food Hydrocolloids, 124, 107202. https://doi.org/10.1016/j.foodhyd.2021.107202
Ranamukhaarachchi, S. A., Peiris, R. H., & Moresoli, C. (2017). Fluorescence spectroscopy and principal component analysis of soy protein hydrolysate fractions and the potential to assess their antioxidant capacity characteristics. Food Chemistry, 217, 469–475. https://doi.org/10.1016/j.foodchem.2016.08.029
Kirsten Müller
Cameron, E. S., Schmidt, P. J., Tremblay, B. J.-M., Emelko, M. B., & Müller, K. M. (2021). Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. Scientific Reports, 11(1), Article 1. https://doi.org/10.1038/s41598-021-01636-1
Müller, K. M., Chhun, A., Guildford, S. J., Yakobowski, S. J., & Jonlija, M. (2017). Molecular and ecological characterization of toxic cyanobacteria from the Bay of Quinte (Lake Ontario) and Maumee Bay (Lake Erie). Journal of Great Lakes Research, 43(6), 1067–1083. https://doi.org/10.1016/j.jglr.2017.03.021
Nema, M., Hanson, M. L., & Müller, K. M. (2019). Phylogeny of the egg-loving green alga Oophila amblystomatis (Chlamydomonadales) and its response to the herbicides atrazine and 2,4-D. Symbiosis, 77(1), 23–39. https://doi.org/10.1007/s13199-018-0564-1
Ross, A. A., Müller, K. M., Weese, J. S., & Neufeld, J. D. (2018). Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences, 115(25). https://doi.org/10.1073/pnas.1801302115
Schmidt, P. J., Cameron, E. S., Müller, K. M., & Emelko, M. B. (2022). Ensuring That Fundamentals of Quantitative Microbiology Are Reflected in Microbial Diversity Analyses Based on Next-Generation Sequencing. Frontiers in Microbiology, 13, 728146. https://doi.org/10.3389/fmicb.2022.728146
Josh Neufeld
Al-Ajeel, S., Spasov, E., Sauder, L. A., McKnight, M. M., & Neufeld, J. D. (2022). Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. Water Research X, 15. https://doi.org/10.1016/j.wroa.2022.100131
Bai, X., McKnight, M. M., Neufeld, J. D., & J Parker, W. (2023). Simultaneous nitrification, denitrification, and phosphorus removal from municipal wastewater at low temperature. Bioresource Technology, 368, 128261. https://doi.org/10.1016/j.biortech.2022.128261
Bai, X., McKnight, M. M., Neufeld, J. D., & Parker, W. J. (2022). Nitrogen removal pathways during simultaneous nitrification, denitrification, and phosphorus removal under low temperature and dissolved oxygen conditions. Bioresource Technology, 354, 127177. https://doi.org/10.1016/j.biortech.2022.127177
Beaver, R. C., Engel, K., Binns, W. J., & Neufeld, J. D. (2022). Microbiology of barrier component analogues of a deep geological repository. Canadian Journal of Microbiology, 68(2), 73–90. https://doi.org/10.1139/cjm-2021-0225
Bik, H. M., Alexiev, A., Aulakh, S. K., Bharadwaj, L., Flanagan, J., Haggerty, J. M., Hird, S. M., Jospin, G., Lang, J. M., Sauder, L. A., Neufeld, J. D., Shaver, A., Sethi, A., Eisen, J. A., & Coil, D. A. (2019). Microbial community succession and nutrient cycling responses following perturbations of experimental saltwater aquaria. MSphere, 4(1). https://doi.org/10.1128/mSphere.00043-19
Cavaco, M. A., St. Louis, V. L., Engel, K., St. Pierre, K. A., Schiff, S. L., Stibal, M., & Neufeld, J. D. (2019). Freshwater microbial community diversity in a rapidly changing High Arctic watershed. FEMS Microbiology Ecology, 95(11), fiz161. https://doi.org/10.1093/femsec/fiz161
Cheng, J., Lam, K. N., Engel, K., Hall, M., Neufeld, J. D., & Charles, T. C. (2017). Metagenomic cosmid libraries suitable for functional screening in proteobacteria. In Functional Metagenomics: Tools and Applications (pp. 1–11). https://doi.org/10.1007/978-3-319-61510-3_1
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545. https://doi.org/10.1371/journal.pone.0172545
Coyotzi, S., Doxey, A. C., Clark, I. D., Lapen, D. R., Van Cappellen, P., & Neufeld, J. D. (2017). Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environmental Microbiology, 19(3), 1189–1208. https://doi.org/10.1111/1462-2920.13643
De Palma, G., Lynch, M. D. J., Lu, J., Dang, V. T., Deng, Y., Jury, J., Umeh, G., Miranda, P. M., Pastor, M. P., Sidani, S., Pinto-Sanchez, M. I., Philip, V., McLean, P. G., Hagelsieb, M.-G., Surette, M. G., Bergonzelli, G. E., Verdu, E. F., Britz-McKibbin, P., Neufeld, J. D., … Bercik, P. (2017). Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice. Science Translational Medicine, 9(379). https://doi.org/10.1126/scitranslmed.aaf6397
Duguma, D., Hall, M. W., Smartt, C. T., Debboun, M., & Neufeld, J. D. (2019). Microbiota variations in Culex nigripalpus disease vector mosquito of west nile virus and saint louis encephalitis from different geographic origins. PeerJ, 2019(1). https://doi.org/10.7717/peerj.6168
Duguma, D., Hall, M. W., Smartt, C. T., & Neufeld, J. D. (2017a). Effects of organic amendments on microbiota associated with the Culex nigripalpus mosquito vector of the Saint Louis encephalitis and West Nile viruses. MSphere, 2(1). https://doi.org/10.1128/mSphere.00387-16
Duguma, D., Hall, M. W., Smartt, C. T., & Neufeld, J. D. (2017b). Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors. Microbial Ecology, 74(4), 979–989. https://doi.org/10.1007/s00248-017-0988-9
Element, G., Engel, K., Neufeld, J. D., Casselman, J. M., van Coeverden de Groot, P., Greer, C. W., & Walker, V. K. (2020). Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus). Environmental Microbiology, 22(8), 3112–3125. https://doi.org/10.1111/1462-2920.15049
Element, G., Engel, K., Neufeld, J. D., Casselman, J. M., Van Coeverden De Groot, P. J., & Walker, V. K. (2021). Distinct intestinal microbial communities of two sympatric anadromous arctic salmonids and the effects of migration and feeding. Arctic Science, 7(3), 634–654. https://doi.org/10.1139/as-2020-0011
Garcia, S. L., Mehrshad, M., Buck, M., Tsuji, J. M., Neufeld, J. D., McMahon, K. D., Bertilsson, S., Greening, C., & Peura, S. (2021). Freshwater chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations. MSystems, 6(3). https://doi.org/10.1128/mSystems.01196-20
Gromala, M., Neufeld, J. D., & McConkey, B. J. (2021). Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Applied and Environmental Microbiology, 87(7), e02914-20. https://doi.org/10.1128/AEM.02914-20
Gwak, J.-H., Jung, M.-Y., Hong, H., Kim, J.-G., Quan, Z.-X., Reinfelder, J. R., Spasov, E., Neufeld, J. D., Wagner, M., & Rhee, S.-K. (2020). Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. ISME Journal, 14(2), 335–346. https://doi.org/10.1038/s41396-019-0538-1
Hall, M. W., Singh, N., Ng, K. F., Lam, D. K., Goldberg, M. B., Tenenbaum, H. C., Neufeld, J. D., Beiko, R. G., & Senadheera, D. B. (2017). Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity. Npj Biofilms and Microbiomes, 3(1). https://doi.org/10.1038/s41522-016-0011-0
Hamilton, E. F., Element, G., van Coeverden de Groot, P., Engel, K., Neufeld, J. D., Shah, V., & Walker, V. K. (2019). Anadromous arctic char microbiomes: Bioprospecting in the high arctic. Frontiers in Bioengineering and Biotechnology, 7(FEB). https://doi.org/10.3389/fbioe.2019.00032
Hernández, M., Neufeld, J. D., & Dumont, M. G. (2017). Enhancing functional metagenomics of complex microbial communities using stable isotopes. In Functional Metagenomics: Tools and Applications (pp. 139–150). https://doi.org/10.1007/978-3-319-61510-3_8
Kvas, S., Rahn, J., Engel, K., Neufeld, J. D., Villeneuve, P. J., Trevors, J. T., Lee, H., Scroggins, R. P., & Beaudette, L. A. (2017). Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil. Journal of Microbiological Methods, 143, 66–77. https://doi.org/10.1016/j.mimet.2017.10.004
Liu, K., Schiff, S. L., Wu, L., Molot, L. A., Venkiteswaran, J. J., Paterson, M. J., Elgood, R. J., Tsuji, J. M., & Neufeld, J. D. (2022). Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes. Environmental Science and Technology, 56(20), 14840–14851. https://doi.org/10.1021/acs.est.2c04247
Lobb, B., Hodgson, R., Lynch, M. D. J., Mansfield, M. J., Cheng, J., Charles, T. C., Neufeld, J. D., Craig, P. M., & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2), e00145-20. https://doi.org/10.1128/mSystems.00145-20
Lu, X., Heal, K. R., Ingalls, A. E., Doxey, A. C., & Neufeld, J. D. (2020). Metagenomic and chemical characterization of soil cobalamin production. The ISME Journal, 14(1), 53–66. https://doi.org/10.1038/s41396-019-0502-0
Lu, X., Nicol, G. W., & Neufeld, J. D. (2018). Differential responses of soil ammonia-oxidizing archaea and bacteria to temperature and depth under two different land uses. Soil Biology and Biochemistry, 120, 272–282. https://doi.org/10.1016/j.soilbio.2018.02.017
Lu, X., Seuradge, B. J., & Neufeld, J. D. (2017). Biogeography of soil Thaumarchaeota in relation to soil depth and land usage. FEMS Microbiology Ecology, 93(2). https://doi.org/10.1093/femsec/fiw246
Lu, X., Taylor, A. E., Myrold, D. D., & Neufeld, J. D. (2020). Expanding perspectives of soil nitrification to include ammonia-oxidizing archaea and comammox bacteria. Soil Science Society of America Journal, 84(2), 287–302. https://doi.org/10.1002/saj2.20029
Min, D., Doxey, A. C., & Neufeld, J. D. (2021). AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology. GigaScience, 10(2). https://doi.org/10.1093/gigascience/giab006
Neufeld, J. D. (2023). Microbes ‘R’ us. Environmental Microbiology, 25(1), 177–178. https://doi.org/10.1111/1462-2920.16264
Pronk, G. J., Mellage, A., Milojevic, T., Smeaton, C. M., Engel, K., Neufeld, J. D., Rezanezhad, F., & Van Cappellen, P. (2020). Carbon turnover and microbial activity in an artificial soil under imposed cyclic drainage and imbibition. Vadose Zone Journal, 19(1). https://doi.org/10.1002/vzj2.20021
Ross, A. A., Doxey, A. C., & Neufeld, J. D. (2017). The Skin Microbiome of Cohabiting Couples. MSystems, 2(4). https://doi.org/10.1128/mSystems.00043-17
Ross, A. A., Müller, K. M., Weese, J. S., & Neufeld, J. D. (2018). Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences, 115(25). https://doi.org/10.1073/pnas.1801302115
Ross, A. A., Rodrigues Hoffmann, A., & Neufeld, J. D. (2019). The skin microbiome of vertebrates. Microbiome, 7(1). https://doi.org/10.1186/s40168-019-0694-6
Sauder, L. A., Albertsen, M., Engel, K., Schwarz, J., Nielsen, P. H., Wagner, M., & Neufeld, J. D. (2017). Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME Journal, 11(5), 1142–1157. https://doi.org/10.1038/ismej.2016.192
Sauder, L. A., Albertsen, M., Engel, K., Schwarz, J., Nielsen, P. H., Wagner, M., & Neufeld, J. D. (2020). Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system (The ISME Journal, (2017), 11, 5, (1142-1157), 10.1038/ismej.2016.192). ISME Journal, 14(9), 2366. https://doi.org/10.1038/s41396-020-0714-3
Sauder, L. A., Engel, K., Lo, C.-C., Chain, P., & Neufeld, J. D. (2018). Candidatus Nitrosotenuis aquarius," an ammonia-oxidizing archaeon from a freshwater aquarium biofilter. Applied and Environmental Microbiology, 84(19). https://doi.org/10.1128/AEM.01430-18
Schiff, S. L., Tsuji, J. M., Wu, L., Venkiteswaran, J. J., Molot, L. A., Elgood, R. J., Paterson, M. J., & Neufeld, J. D. (2017). Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry. Scientific Reports, 7(1), Article 1. https://doi.org/10.1038/srep46708
Seuradge, B. J., Oelbermann, M., & Neufeld, J. D. (2017). Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiology Ecology, 93(2). https://doi.org/10.1093/femsec/fiw239
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7. https://doi.org/10.1038/s41396-020-0650-2
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., … Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457–463. https://doi.org/10.1038/nature24621
Tsuji, J. M., Tran, N., Schiff, S. L., Venkiteswaran, J. J., Molot, L. A., Tank, M., Hanada, S., & Neufeld, J. D. (2020). Anoxygenic photosynthesis and iron–sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. The ISME Journal, 14(11), Article 11. https://doi.org/10.1038/s41396-020-0725-0
Tsuji, J., Shaw, N., Nagashima, S., Venkiteswaran, J., Schiff, S., Hanada, S., Tank, M., & Neufeld, J. (2020). Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota [Preprint]. Microbiology. https://doi.org/10.1101/2020.07.07.190934
Umbach, A. K., Stegelmeier, A. A., & Neufeld, J. D. (2021). Archaea are rare and uncommon members of the mammalian skin microbiome. MSystems, 6(4). https://doi.org/10.1128/mSystems.00642-21
Vachon, M. A., Engel, K., Beaver, R. C., Slater, G. F., Binns, W. J., & Neufeld, J. D. (2021). Fifteen shades of clay: Distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-01072-1
Jozef Nissimov
Johns, C. T., Grubb, A. R., Nissimov, J. I., Natale, F., Knapp, V., Mui, A., Fredricks, H. F., Van Mooy, B. A. S., & Bidle, K. D. (2019). The mutual interplay between calcification and coccolithovirus infection. Environmental Microbiology, 21(6), 1896–1915. https://doi.org/10.1111/1462-2920.14362
Knowles, B., Bonachela, J. A., Behrenfeld, M. J., Bondoc, K. G., Cael, B. B., Carlson, C. A., Cieslik, N., Diaz, B., Fuchs, H. L., Graff, J. R., Grasis, J. A., Halsey, K. H., Haramaty, L., Johns, C. T., Natale, F., Nissimov, J. I., Schieler, B., Thamatrakoln, K., Frede Thingstad, T., … Bidle, K. D. (2020). Temperate infection in a virus–host system previously known for virulent dynamics. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18078-4
Laber, C. P., Hunter, J. E., Carvalho, F., Collins, J. R., Hunter, E. J., Schieler, B. M., Boss, E., More, K., Frada, M., Thamatrakoln, K., Brown, C. M., Haramaty, L., Ossolinski, J., Fredricks, H., Nissimov, J. I., Vandzura, R., Sheyn, U., Lehahn, Y., Chant, R. J., … Bidle, K. D. (2018). Coccolithovirus facilitation of carbon export in the North Atlantic. Nature Microbiology, 3(5), 537–547. https://doi.org/10.1038/s41564-018-0128-4
Nissimov, J. I., & Bidle, K. D. (2017). Stress, death, and the biological glue of sinking matter. Journal of Phycology, 53(2), 241–244. https://doi.org/10.1111/jpy.12506
Nissimov, J. I., Campbell, C. N., Probert, I., & Wilson, W. H. (2022). Aquatic virus culture collection: An absent (but necessary) safety net for environmental microbiologists. Applied Phycology, 3(1), 211–225. https://doi.org/10.1080/26388081.2020.1770123
Nissimov, J. I., Pagarete, A., Ma, F., Cody, S., Dunigan, D. D., Kimmance, S. A., & Allen, M. J. (2017). Coccolithoviruses: A review of cross‐kingdom genomic thievery and metabolic thuggery. Viruses, 9(3). https://doi.org/10.3390/v9030052
Nissimov, J. I., Talmy, D., Haramaty, L., Fredricks, H. F., Zelzion, E., Knowles, B., Eren, A. M., Vandzura, R., Laber, C. P., Schieler, B. M., Johns, C. T., More, K. D., Coolen, M. J. L., Follows, M. J., Bhattacharya, D., Van Mooy, B. A. S., & Bidle, K. D. (2019). Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology, 21(6), 2182–2197. https://doi.org/10.1111/1462-2920.14633
Nissimov, J. I., Vandzura, R., Johns, C. T., Natale, F., Haramaty, L., & Bidle, K. D. (2018). Dynamics of transparent exopolymer particle production and aggregation during viral infection of the coccolithophore, Emiliania huxleyi. Environmental Microbiology, 20(8), 2880–2897. https://doi.org/10.1111/1462-2920.14261
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., … Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457–463. https://doi.org/10.1038/nature24621
Maren Oelbermann
Badewa, E. A., Yeung, C. C., Rezanezhad, F., Whalen, J. K., & Oelbermann, M. (2022). Spring Freeze–Thaw Stimulates Greenhouse Gas Emissions From Agricultural Soil. Frontiers in Environmental Science, 10. https://doi.org/10.3389/fenvs.2022.909683
Baskerville, M., Bazrgar, A., Reddy, N., Ofosu, E., Thevathasan, N., Gordon, A. M., & Oelbermann, M. (2021). Greenhouse gas emissions from riparian zones are related to vegetation type and environmental factors. Journal of Environmental Quality, 50(4), 847–857. https://doi.org/10.1002/jeq2.20250
Baskerville, M., Reddy, N., Ofosu, E., Thevathasan, N. V., & Oelbermann, M. (2021). Vegetation Type Does not Affect Nitrous Oxide Emissions from Riparian Zones in Agricultural Landscapes. Environmental Management, 67(2), 371–383. https://doi.org/10.1007/s00267-020-01419-w
Bichel, A., Oelbermann, M., & Echarte, L. (2017). Impact of residue addition on soil nitrogen dynamics in intercrop and sole crop agroecosystems. Geoderma, 304, 12–18. https://doi.org/10.1016/j.geoderma.2016.11.023
Buchanan, S. W., Baskerville, M., Oelbermann, M., Gordon, A. M., Thevathasan, N. V., & Isaac, M. E. (2020). Plant diversity and agroecosystem function in riparian agroforests: Providing ecosystem services and land-use transition. Sustainability (Switzerland), 12(2). https://doi.org/10.3390/su12020568
De Carlo, N. D., Oelbermann, M., & Gordon, A. M. (2019a). Carbon dioxide emissions: Spatiotemporal variation in a young and mature riparian forest. Ecological Engineering, 138, 353–361. https://doi.org/10.1016/j.ecoleng.2019.07.036
De Carlo, N. D., Oelbermann, M., & Gordon, A. M. (2019b). Spatial and temporal variation in soil nitrous oxide emissions from a rehabilitated and undisturbed riparian forest. Journal of Environmental Quality, 48(3), 624–633. https://doi.org/10.2134/jeq2018.10.0357
Jiang, R. W., Mechler, M. A. A., & Oelbermann, M. (2020). Softwood biochar and greenhouse gas emissions: A field study over three growing seasons on a temperate agricultural soil. Canadian Journal of Soil Science, 102(1), 197–211. https://doi.org/10.1139/cjss-2021-0160
Lévesque, V., Oelbermann, M., & Ziadi, N. (2020). Biochar in temperate soils: Opportunities and challenges. Canadian Journal of Soil Science, 102(1), 1–26. https://doi.org/10.1139/cjss-2021-0047
Lutes, K., Oelbermann, M., Thevathasan, N. V., & Gordon, A. M. (2019). Assessing the impact of fertilizer application on net soil-derived emission budgets from a temperate willow (Salix miyabeana) short rotation coppice system. Biomass and Bioenergy, 120, 135–143. https://doi.org/10.1016/j.biombioe.2018.11.010
Mafa-Attoye, T. G., Baskerville, M. A., Ofosu, E., Oelbermann, M., Thevathasan, N. V., & Dunfield, K. E. (2020). Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem. Science of the Total Environment, 724. https://doi.org/10.1016/j.scitotenv.2020.138148
McTavish, M. J., Cray, H. A., Murphy, S. D., Bauer, J. T., Havrilla, C. A., Oelbermann, M., & Sayer, E. J. (2020). Sustainable management of grassland soils. In Soils and Landscape Restoration (pp. 95–124). https://doi.org/10.1016/B978-0-12-813193-0.00004-7
Mechler, M. A. A., Jiang, R. W., Silverthorn, T. K., & Oelbermann, M. (2018). Impact of biochar on soil characteristics and temporal greenhouse gas emissions: A field study from southern Canada. Biomass and Bioenergy, 118, 154–162. https://doi.org/10.1016/j.biombioe.2018.08.019
Obregon, D., Mafa-Attoye, T. G., Baskerville, M., Mitter, E. K., de Souza, L. F., Oelbermann, M., Thevathasan, N. V., Tsai, S. M., & Dunfield, K. E. (2023). Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems. Science of the Total Environment, 870. https://doi.org/10.1016/j.scitotenv.2023.161921
Oelbermann, M., Echarte, L., Marroquin, L., Morgan, S., Regehr, A., Vachon, K. E., & Wilton, M. (2017). Estimating soil carbon dynamics in intercrop and sole crop agroecosystems using the Century model. Journal of Plant Nutrition and Soil Science, 180(2), 241–251. https://doi.org/10.1002/jpln.201600578
Oelbermann, M., Morgan, S., & Echarte, L. (2022). Elevated carbon dioxide and temperature effects on soil properties from sole crops and intercrops. Soil Use and Management, 38(1), 435–447. https://doi.org/10.1111/sum.12752
Seuradge, B. J., Oelbermann, M., & Neufeld, J. D. (2017). Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiology Ecology, 93(2). https://doi.org/10.1093/femsec/fiw239
Ziadi, N., Oelbermann, M., Price, G., & Whalen, J. (2020). Biochar amendments for sustainable soil management. Canadian Journal of Soil Science, 102(1), vii–viii. https://doi.org/10.1139/cjss-2022-0006
Wayne Parker
Bai, X., McKnight, M. M., Neufeld, J. D., & J Parker, W. (2023). Simultaneous nitrification, denitrification, and phosphorus removal from municipal wastewater at low temperature. Bioresource Technology, 368, 128261. https://doi.org/10.1016/j.biortech.2022.128261
Bai, X., McKnight, M. M., Neufeld, J. D., & Parker, W. J. (2022). Nitrogen removal pathways during simultaneous nitrification, denitrification, and phosphorus removal under low temperature and dissolved oxygen conditions. Bioresource Technology, 354, 127177. https://doi.org/10.1016/j.biortech.2022.127177
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7. https://doi.org/10.1038/s41396-020-0650-2
Sherry Schiff
Cavaco, M. A., St. Louis, V. L., Engel, K., St. Pierre, K. A., Schiff, S. L., Stibal, M., & Neufeld, J. D. (2019). Freshwater microbial community diversity in a rapidly changing High Arctic watershed. FEMS Microbiology Ecology, 95(11), fiz161. https://doi.org/10.1093/femsec/fiz161
Cejudo, E., Schiff, S., & Taylor, W. (2020). Epilithic algae from an urban river preferentially use ammonium over nitrate. International Aquatic Research, 12, 30–39. https://doi.org/10.22034/IAR(20).2020.671068
Schiff, S. L., Tsuji, J. M., Wu, L., Venkiteswaran, J. J., Molot, L. A., Elgood, R. J., Paterson, M. J., & Neufeld, J. D. (2017). Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry. Scientific Reports, 7(1), Article 1. https://doi.org/10.1038/srep46708
St. Pierre, K. A., St. Louis, V. L., Schiff, S. L., Lehnherr, I., Dainard, P. G., Gardner, A. S., Aukes, P. J. K., & Sharp, M. J. (2019). Proglacial freshwaters are significant and previously unrecognized sinks of atmospheric CO 2. Proceedings of the National Academy of Sciences, 116(36), 17690–17695. https://doi.org/10.1073/pnas.1904241116
Tsuji, J. M., Tran, N., Schiff, S. L., Venkiteswaran, J. J., Molot, L. A., Tank, M., Hanada, S., & Neufeld, J. D. (2020). Anoxygenic photosynthesis and iron–sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. The ISME Journal, 14(11), Article 11. https://doi.org/10.1038/s41396-020-0725-0
Tsuji, J., Shaw, N., Nagashima, S., Venkiteswaran, J., Schiff, S., Hanada, S., Tank, M., & Neufeld, J. (2020). Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota [Preprint]. Microbiology. https://doi.org/10.1101/2020.07.07.190934
Venkiteswaran, J. J., Schiff, S. L., & Ingalls, B. P. (2019). Quantifying the fate of wastewater nitrogen discharged to a Canadian river. FACETS, 4(1), 315–335. https://doi.org/10.1139/facets-2018-0028
Matthew Scott
Braniff, N., Scott, M., & Ingalls, B. (2019). Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design. Processes, 7(1), Article 1. https://doi.org/10.3390/pr7010052
Greulich, P., Doležal, J., Scott, M., Evans, M. R., & Allen, R. J. (2017). Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics. Physical Biology, 14(6), 065005. https://doi.org/10.1088/1478-3975/aa8001
Jaramillo‐Riveri, S., Broughton, J., McVey, A., Pilizota, T., Scott, M., & El Karoui, M. (2022). Growth‐dependent heterogeneity in the DNA damage response in Escherichia coli. Molecular Systems Biology, 18(5). https://doi.org/10.15252/msb.202110441
Jun, S., Si, F., Pugatch, R., & Scott, M. (2018). Fundamental principles in bacterial physiology—history, recent progress, and the future with focus on cell size control: A review. Reports on Progress in Physics, 81(5), 056601. https://doi.org/10.1088/1361-6633/aaa628
Scott, M. (2021). Metabolic models predict evolutionary dynamics. Nature Ecology & Evolution, 5(5), 560–561. https://doi.org/10.1038/s41559-021-01405-3
Scott, M., & Hwa, T. (2022). Shaping bacterial gene expression by physiological and proteome allocation constraints. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-022-00818-6
Maria Strack
Bieniada, A., & Strack, M. (2021). Steady and ebullitive methane fluxes from active, restored and unrestored horticultural peatlands. Ecological Engineering, 169, 106324. https://doi.org/10.1016/j.ecoleng.2021.106324
Bienida, A., Daté, V., Andersen, R., Nwaishi, F., Price, J., Mahmood, Md. S., & Strack, M. (2020). Methane emissions from fens in Alberta’s boreal region: Reference data for functional evaluation of restoration outcomes. Wetlands Ecology and Management, 28(4), 559–575. https://doi.org/10.1007/s11273-020-09715-2
Brown, C. M., Strack, M., & Price, J. S. (2017). The effects of water management on the CO2 uptake of Sphagnum moss in a reclaimed peatland. Mires and Peat, 20, 1–15. https://doi.org/10.19189/MaP.2016.OMB.258
Brummell, M., Lazcano, C., & Strack, M. (2017). The effects of Eriophorum vaginatum on N2O fluxes at a restored, extracted peatland. Ecological Engineering, 106, 287–295.
Clark, L. M., Strachan, I. B., Strack, M., Roulet, N. T., Knorr, K.-H., & Teickner, H. (2022). Years of extraction determines CO2 and CH4 emissions from an actively extracted peatland in eastern Québec, Canada. Biogeosciences Discussions, 1–38. https://doi.org/10.5194/bg-2022-156
Coulas, M., Parsons, C., Saraswati, S., & Strack, M. (2021). Organic matter decomposition at a constructed fen in the Athabasca Oil Sands region: Effect of substrate type and environmental conditions. Science of The Total Environment, 776, 145708. https://doi.org/10.1016/j.scitotenv.2021.145708
Davidson, S. J., Smith, M., Prystupa, E., Murray, K., Nwaishi, F. C., Petrone, R. M., & Strack, M. (2021). High sulfate concentrations maintain low methane emissions at a constructed fen over the first seven years of ecosystem development. The Science of the Total Environment, 789, 148014. https://doi.org/10.1016/j.scitotenv.2021.148014
Davidson, S. J., Strack, M., Bourbonniere, R. A., & Waddington, J. M. (2019). Controls on soil carbon dioxide and methane fluxes from a peat swamp vary by hydrogeomorphic setting. Ecohydrology, 12(8). https://doi.org/10.1002/eco.2162
Davidson, S. J., Van Beest, C., Petrone, R., & Strack, M. (2019). Wildfire overrides hydrological controls on boreal peatland methane emissions. Biogeosciences, 16(13), 2651–2660. https://doi.org/10.5194/bg-16-2651-2019
Engering, A., Davidson, S. J., Xu, B., Bird, M., Rochefort, L., & Strack, M. (2022). Restoration of a boreal peatland impacted by an in-situ oil sands well-pad 2: Greenhouse gas exchange dynamics. Restoration Ecology, 30(3), e13508. https://doi.org/10.1111/rec.13508
Gupta, P. K., Gharedaghloo, B., Lynch, M., Cheng, J., Strack, M., Charles, T. C., & Price, J. S. (2020). Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions. Environmental Research, 191, 110167. https://doi.org/10.1016/j.envres.2020.110167
Lazcano, C., Deol, A. S., Brummell, M. E., & Strack, M. (2020). Interactive effects of vegetation and water table depth on belowground C and N mobilization and greenhouse gas emissions in a restored peatland. Plant and Soil, 448(1), 299–313. https://doi.org/10.1007/s11104-020-04434-2
Lazcano, C., Robinson, C., Hassanpour, G., & Strack, M. (2018). Short-term effects of fen peatland restoration through the moss layer transfer technique on the soil CO2 and CH4 efflux. Ecological Engineering, 125, 149–158. https://doi.org/10.1016/j.ecoleng.2018.10.018
Lemmer, M., Rochefort, L., & Strack, M. (2020). Greenhouse Gas Emissions Dynamics in Restored Fens After In-Situ Oil Sands Well Pad Disturbances of Canadian Boreal Peatlands. Frontiers in Earth Science, 8. https://www.frontiersin.org/articles/10.3389/feart.2020.557943
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Munir, T., Khadka, B., Xu, B., & Strack, M. (2017). Partitioning Forest‐Floor Respiration into Source Based Emissions in a Boreal Forested Bog: Responses to Experimental Drought. Forests, 8(3), 75. https://doi.org/10.3390/f8030075
Munir, T. M., Khadka, B., Xu, B., & Strack, M. (2017). Mineral nitrogen and phosphorus pools affected by water table lowering and warming in a boreal forested peatland. Ecohydrology, 10(8), e1893. https://doi.org/10.1002/eco.1893
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Valerie Ward
Banerjee, A., & Ward, V. (2022). Production of recombinant and therapeutic proteins in microalgae. Current Opinion in Biotechnology, 78, 102784. https://doi.org/10.1016/j.copbio.2022.102784
Chatzivasileiou, A. O., Ward, V., Edgar, S. M., & Stephanopoulos, G. (2019). Two-step pathway for isoprenoid synthesis. Proceedings of the National Academy of Sciences, 116(2), 506–511. https://doi.org/10.1073/pnas.1812935116
Kabernick, D. C., Gostick, J. T., & Ward, V. C. A. (2022). Kinetic characterization and modeling of sequentially entrapped enzymes in 3D‐printed PMMA microfluidic reactors for the synthesis of amorphadiene via the isopentenol utilization pathway. Biotechnology and Bioengineering, 119(5), 1239–1251. https://doi.org/10.1002/bit.28046
Luo, Z., Liu, N., Lazar, Z., Chatzivasileiou, A., Ward, V., Chen, J., Zhou, J., & Stephanopoulos, G. (2020). Enhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicity. Metabolic Engineering, 61, 344–351. https://doi.org/10.1016/j.ymben.2020.07.010
Malekghasemi, S., Kariminia, H.-R., Plechkova, N. K., & Ward, V. C. A. (2021). Direct transesterification of wet microalgae to biodiesel using phosphonium carboxylate ionic liquid catalysts. Biomass and Bioenergy, 150, 106126. https://doi.org/10.1016/j.biombioe.2021.106126
Ojogbo, E., Ward, V., & Mekonnen, T. H. (2020). Functionalized starch microparticles for contact-active antimicrobial polymer surfaces. Carbohydrate Polymers, 229, 115422. https://doi.org/10.1016/j.carbpol.2019.115422
Palage, A. M., & Ward, V. C. (2022). Strategies for production of hydrophobic compounds. Current Opinion in Biotechnology, 75, 102681. https://doi.org/10.1016/j.copbio.2022.102681
Ward, V. C. A., Chatzivasileiou, A. O., & Stephanopoulos, G. (2018). Metabolic engineering of Escherichia coli for the production of isoprenoids. FEMS Microbiology Letters, 365(10). https://doi.org/10.1093/femsle/fny079
Ward, V. C. A., Chatzivasileiou, A. O., & Stephanopoulos, G. (2019). Cell free biosynthesis of isoprenoids from isopentenol. Biotechnology and Bioengineering, 116(12), 3269–3281. https://doi.org/10.1002/bit.27146
Ward, V. C. A., Munch, G., Cicek, N., & Rehmann, L. (2017). Direct Conversion of the Oleaginous Yeast Rhodosporidium diobovatum to Biodiesel Using the Ionic Liquid [C2mim][EtSO4]. ACS Sustainable Chemistry & Engineering, 5(6), 5562–5570. https://doi.org/10.1021/acssuschemeng.7b00976
Ward, V. C. A., & Rehmann, L. (2019). Fast media optimization for mixotrophic cultivation of Chlorella vulgaris. Scientific Reports, 9(1), 19262. https://doi.org/10.1038/s41598-019-55870-9
Zhang, Y., Ward, V., Dennis, D., Plechkova, N. V., Armenta, R., & Rehmann, L. (2018). Efficient Extraction of a Docosahexaenoic Acid (DHA)-Rich Lipid Fraction from Thraustochytrium sp. Using Ionic Liquids. Materials, 11(10), Article 10. https://doi.org/10.3390/ma11101986