Publications

Journal Articles

  1. S. L. Cheung, D. G. Allen, S. M. Short. 2019. Specific quantification of Scenedesmus obliquus and Chlorella vulgaris in mixed-species algal biofilms. Bioresource Technology, in press. (link coming soon)

  2. C. N. Palermo, R. R. Fulthorpe, R. Saati, S. M. Short. 2019. Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour. Viruses 11 (9): 792. https://www.mdpi.com/1999-4915/11/9/792

  3. J. M. A. Stough, N. Yutin, Y. V. Chaban, M. Moniruzzaman, E. R. Gann, H. L. Pound, M. M. Steffen, J. N. Black, E. V. Koonin, S. W. Wilhelm, S. M. Short. 2019. Genome and Environmental Activity of a Chrysochromulina parva Virus and its Virophages. Frontiers in Microbiology 10: 703. https://doi.org/10.3389/fmicb.2019.00703

  4. S. R. Coy, E. R. Gann, H. L. Pound, S. M. Short, S. W. Wilhelm. 2018. Viruses of eukaryotic algae: diversity, methods for detection, and future directions. Viruses 10, 487. https://doi.org/10.3390/v10090487

  5. A. M. Long, S. W. Wilhelm, S. M. Short. 2018. Algal viruses and cyanophages have distinct distributions in Lake Erie sediments. Aquatic Microbial Ecology 82: 161-175. https://www.int-res.com/abstracts/ame/v82/n2/p161-175/

  6. M. A. Staniewski, S. M. Short. 2018. Methodological Review and Meta-Analysis of Dilution Assays for Estimates of Virus- and Grazer-Mediated Phytoplankton Mortality. Limnology and Oceanography: Methods 16: 649-668. https://doi.org/10.1002/lom3.10273

  7. M. A. Staniewski, M. Fitzpatrick, I. F. Munawar, M. Munawar, S. M. Short. 2017. The influence of viruses on phytoplankton and bacterial productivity in Hamilton Harbour, an impaired embayment of Lake Ontario. Journal of Great Lakes Research 43: 1055–1066. https://doi.org/10.1016/j.jglr.2017.08.008

  8. A. M. Long, S. M Short. 2016. Seasonal determinations of algal virus decay rates reveal over-wintering in a temperate freshwater pond. The ISME Journal 10: 1602-1612. https://www.nature.com/articles/ismej2015240

  9. S.F. Mirza, M. A. Staniewski, C. M. Short, A.M Long, Y. V. Chaban, S. M. Short. 2015. Isolation and characterization of a virus infecting the freshwater algae Chrysochromulina parva. Virology 486: 105-115. https://doi.org/10.1016/j.virol.2015.09.005

  10. M. A. Staniewski, S. M. Short. 2014. Potential viral stimulation of primary production observed during experimental determinations of phytoplankton mortality. Aquatic Microbial Ecology 71: 239-256. https://doi.org/10.3354/ame01679

  11. R. M. Rozon, S. M. Short. 2013. Complex seasonality observed amongst diverse phytoplankton viruses in the Bay of Quinte, an embayment of Lake Ontario. Freshwater Biology 58: 2648-2663. https://doi.org/10.1111/fwb.12241

  12. M. A. Staniewski, C. M. Short, S. M. Short. 2012. Contrasting community versus population- based estimates of grazing and virus-induced mortality of phytoplankton. Microbial Ecology 64:25-38. https://doi.org/10.1007/s00248-012-0019-9

  13. S. M. Short. 2012. The ecology of viruses that infect eukaryotic algae. Environmental Microbiology 14: 2253-2271. https://doi.org/10.1111/j.1462-2920.2012.02706.x

  14. M. Andrew, R. Barua, S. M. Short, L. Kohn. 2012. Evidence for a common toolbox based on necrotrophy in a fungal lineage spanning necrotrophs, biotrophs, endophytes, host generalists and specialists. PLoS One 7: e29943. https://doi.org/10.1371/journal.pone.0029943

  15. E. D. de Araujo, J. Patel, C. de Araujo, S. P. Rogers, S. M. Short, D. A. Campbell, G. Espie. 2011. Physiological Characterization and Light Response of the CO2 Concentrating Mechanism in the Filamentous Cyanobacterium Leptolyngbya sp. CPCC 696. Photosynthesis Research 109: 85-101. https://doi.org/10.1007/s11120-011-9663-z

  16. M. G. Weinbauer, O. Bonilla-Findji, A. M. Chan, J. R. Dolan, S. M. Short, K. Simek, S. W. Wilhelm, C. A. Suttle. 2011. Synechococcus growth in the ocean may depend on the lysis of heterotrophic bacteria. Journal of Plankton Research 33: 1465-1476. https://doi.org/10.1093/plankt/fbr041

  17. C. M. Short, O. Rusanova, and S. M. Short. 2011. Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada. The ISME Journal 5: 810-821. https://doi.org/10.1038/ismej.2010.183

  18. S. M Short, O. Rusanova, M. A. Staniewski. 2011. Novel Phycodnavirus Genes Amplified from Canadian Freshwater Environments. Aquatic Microbial Ecology, 63: 61-67. https://doi.org/10.3354/ame01478

  19. S. M. Short, C. M. Short. 2009. Quantitative PCR reveals transient and persistent algal viruses in Lake Ontario, Canada. Environmental Microbiology 11: 2639-2648. https://doi.org/10.1111/j.1462-2920.2009.01988.x

  20. S. M. Short, C. M. Short. 2008. Diversity of algal viruses in various North American freshwater environments. Aquatic Microbial Ecology 51: 13-21. https://doi.org/10.3354/ame01183

  21. S. M. Short, J. P. Zehr. 2007. Nitrogenase gene expression in the Chesapeake Bay estuary. Environmental Microbiology 9: 1591-1596. https://doi.org/10.1111/j.1462-2920.2007.01258.x

  22. A. H. Gibson, B. D. Jenkins, F. P. Wilkerson, S. M. Short, J. P. Zehr. 2006. Characterization of cyanobacterial glnA gene diversity and gene expression in marine environments. FEMS Microbiology Ecology 55: 391-402. https://doi.org/10.1111/j.1574-6941.2005.00050.x

  23. S. M. Short, J. P. Zehr. 2005. Quantitative analysis of nifH genes and transcripts from aquatic environments. Methods in Enzymology 397: 380-394. https://doi.org/10.1016/S0076-6879(05)97023-7

  24. C. P. D. Brussaard, S. M. Short, C. M. Frederickson, C. A. Suttle. 2004. Isolation and phylogenetic analysis of novel viruses infecting the phytoplankter Phaeocystis globosa (Prymnesiophyceae). Applied and Environmental Microbiology 70: 3700-3705. https://doi.org/10.1128/AEM.70.6.3700-3705.2004

  25. S. M. Short, B. D. Jenkins, J. P. Zehr. 2004. Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay. Applied and Environmental Microbiology 70: 2186-2192. https://doi.org/10.1128/AEM.70.4.2186-2192.2004

  26. A. M. Comeau, S. M. Short, C. A. Suttle. 2004. The use of degenerate-primed random amplification of polymorphic DNA (DP-RAPD) for strain-typing and inferring the genetic similarity among closely related viruses. Journal of Virological Methods 118: 95-100. https://doi.org/10.1016/j.jviromet.2004.01.020

  27. B. D. Jenkins, G. F. Steward, S. M. Short, B. B. Ward, J. P. Zehr. 2004. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Applied and Environmental Microbiology 70: 1767-1776. https://doi.org/10.1128/AEM.70.3.1767-1776.2004

  28. C. M. Frederickson, S. M. Short, C. A. Suttle. 2003. The physical environment affects cyanophage communities in British Columbia inlets. Microbial Ecology 46: 348-357. https://doi.org/10.1007/s00248-003-1010-2

  29. J. P. Zehr, B. D. Jenkins, S. M. Short, G. F. Steward. 2003. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environmental Microbiology 5: 539-554. https://doi.org/10.1046/j.1462-2920.2003.00451.x

  30. S. M. Short, C. A. Suttle 2003. Temporal dynamics of natural communities of marine algal viruses and eukaryotes. Aquatic Microbial Ecology 32: 107-119. https://doi.org/10.3354/ame032107

  31. C. B. Nielsen, D. Cooper, S. M. Short, J. H. Myers, C. A. Suttle. 2002. DNA polymerase gene sequences suggest low divergence within Western and Forest Tent Caterpillar viruses. Journal of Invertebrate Pathology 81: 131-147. https://doi.org/10.1016/S0022-2011(02)00191-X

  32. S. M. Short, C. A. Suttle. 2002. Sequence analysis of marine virus communities reveals groups of related algal viruses are widely distributed in nature. Applied and Environmental Microbiology 68: 1290-1296. https://doi.org/10.1128/AEM.68.3.1290-1296.2002

  33. S. M. Short, C. A. Suttle. 2000. Denaturing gradient gel electrophoresis resolves virus sequences amplified with degenerate primers. BioTechniques 28: 20-26. https://doi.org/10.2144/00281bm02

  34. S. M. Short, C. A. Suttle. 1999. The use of polymerase chain reaction and denaturing gradient gel electrophoresis to study diversity in natural virus communities. Hydrobiologia 401: 19-32. https://doi.org/10.1023/A:1003711115967

  35. F. Chen, C. A. Suttle, S. M. Short. 1996. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Applied and Environmental Microbiology 62: 2869-2874. https://aem.asm.org/content/62/8/2869

Book Chapters

  1. S. M. Short, M. A. Staniewski, Y. Chaban, A. M. Long, and D. Wang. 2018. The Diversity of Viruses Infecting Eukaryotic Algae. In Viruses of Microorganisms: Diversity, Molecular Biology and Application, Eds. P. Hymen, and S. Abedon, Caister Academic Press, Norfolk, UK, 373 pp. https://www.caister.com/vom

  2. R.-A. Sandaa, S. M. Short, D. C. Schroeder. 2010. Fingerprinting aquatic virus communities, pp 9-18. In S.W. Wilhelm, M.G. Weinbauer, and C.A. Suttle [eds.] Manual of Aquatic Viral Ecology. Waco, TX: American Society of Limnology and Oceanography. https://www.aslo.org/page/manual-of-aquatic-viral-ecology

  3. S. M. Short, F. Chen, S. W. Wilhelm. 2010. The construction and analysis of marker gene Libraries, pp 82-91. In S.W. Wilhelm, M.G. Weinbauer, and C.A. Suttle [eds.] Manual of Aquatic Viral Ecology. Waco, TX: American Society of Limnology and Oceanography. https://www.aslo.org/page/manual-of-aquatic-viral-ecology