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Click here to find a full journal publiction list and the abstracts of published papers.

I am using Google scholar to organize my full publication record. Here I listed our recent publications. ​

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  1. Urakawa, H., Hancock, L. H., Kratz, M. A. & R. Armstrong (2021) QT-AMP: Quanti-Tray-based amplicon sequencing for simultaneous quantification and identification of enterococci for microbial source tracking Water Research (in review). (IF: 11.2, 2020)

  2. Urakawa, H., Ndungu, K, L., Hancock, L. T., Steele, J. H., & R. Bartleson (2021) Subtropical freshwater cyanobacterial blooms as hydrogen peroxide hotspots. Environmental Science & Technology Letters 8, 911-917. (IF: 7.7, 2020)

  3. Hancock, T. L., Blonder, S. L., Bury, A. A., Parsons, M. L., Robertson, A. & Urakawa, H.(2021) Succession pattern and phylotype analysis of microphytobenthic communities in a simulated oil spill seagrass mesocosm experiment. Science of the Total Environment 784. 147053. (IF: 8.0, 2020)

  4. Qin, W., Y. Zheng, F. Zhao, Y. Wang, H. Urakawa, W. Martens-Habbena, H. Liu, X. Huang, X. Zhang, T. Nakagawa, D. R. Mende, A. Bollmann, B. Wang, Y. Zhang, S. A. Amin, J. L. Nielsen, K. Mori, R. Takahashi, E. Virginia Armbrust, M.-K. H. Winkler, E. F. DeLong, M. Li, P.-H. Lee, J. Zhou, C. Zhang, T. Zhang, D. A. Stahl & A. E. Ingalls (2020) Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. The ISME Journal, 14, 2595-2609. (IF: 10.3, 2020).

  5. Harvey, N. J., ur Rehman, Z., Leiknes, T., Ghaffour, N., Urakawa, H., & Missimer, T. M. (2020). Organic compounds and microbial assessment of a seawater reverse osmosis facility at Tampa Bay Water, USA. Desalination, 496, 114735. (IF: 9.5, 2020)

  6. Urakawa, H., Hancock, T.L., Steele, J.H., Dahedl, E.K., Urakawa, H.E., Ndungu, L.K., Krausfeldt, L.E., Rosen, B.H. & Lopez, J.V. (2020) Complete genome sequence of Microcystis aeruginosa FD4, isolated from a subtropical river in southwest Florida. Microbiology Resource Announcements, 9(38). 10.1128/MRA.00813-20 (IF: 0.8, 2020)

  7. Urakawa, H., A. J. Sipos (2020) Application of the consortia of nitrifying archaea and bacteria for fish transportation may be beneficial for fish trading and aquaculture. Aquaculture Research 51(8): 3429-3442. (IF: 1.4, 2020)

  8. Hancock, T. L., Poulakis, G. R., Scharer, R. M., Urakawa, H. (2019) High-resolution molecular identification of smalltooth sawfish prey. Scientific Reports 9: 18307 doi: 10.1038/s41598-019-53931-7.

  9. Urakawa H., S. Rajan, M. E. Feeney, P. A. Sobecky and B. Mortazavi (2019) Ecological response of nitrification to oil spills and its impact on the nitrogen cycle. Environmental Microbiology 21(1):18-33.

  10. Ndungu, L. K., J. H. Steele, T. L. Hancock, R. D. Bartleson, E. C. Milbrandt, M. L. Parsons, H. Urakawa (2019) Hydrogen peroxide measurements in subtropical aquatic systems and their implications for cyanobacterial blooms. Ecological Engineering 138: 444-453.

  11. Lopardo C. R. and H. Urakawa (2019) Performance and microbial diversity of a closed recirculating aquaculture effluent treatment system using polycaprolactone and polyhydroxyalkanoate as carbon source and biofilm carrier. Aquaculture International 27(5):1251-1268.

  12. Sanchez, F. A., V. R. Vivian-Rogers, J. L. Bradfield and H. Urakawa (2019) Tilapia recirculating aquaculture systems as a source of plant growth-promoting bacteria. Aquaculture Research 50(8):2054-2065.

  13. Lopardo C. R., L. Zhang, W. J. Mitsch and H. Urakawa (2019) Comparison of nutrient retention efficiency between vertical-flow and floating treatment wetland mesocosms with and without biodegradable plastic. Ecological Engineering 131:120-130.

  14. Dohra, H., K. Arai, H. Urakawa and T. Fujiwara (2019) Draft genome sequence of Nitrosococcus oceani strain NS58, a marine ammonia-oxidizing gammaproteobacterium isolated from Tokyo Bay sediment. Microbiology Resource Announcements 8(35): e00923-19.

  15. Urakawa, H., J. Skutas and J. V. Lopez (2019) Draft genome sequence of Nitrosomonas sp. strain APG5, a betaproteobacterial ammonia-oxidizing bacterium isolated from beach sand. Microbiology Resource Announcements 8(21), e01573-18.

  16. Qin W., S. A Amin, R. A Lundeen, K. R Heal, W. Martens-Habbena, S. Turkarslan, H. Urakawa, K. C Costa, E. L Hendrickson, T. Wang, D. AC Beck, S. M Tiquia-Arashiro, F. Taub, A. D Holmes, N. Vajrala, P. M Berube, T. M Lowe, J. W Moffett, A. H Devol, N. S Baliga,D. J Arp, L. A Sayavedra-Soto, M. Hackett, E. V. Armbrust, A. E. Ingalls and D. A Stahl (2018) Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. The ISME Journal  12(2):508-519. (Nature Publications)

  17. Kucherenko A, J. E. Herman, E. M. Everham III and H. Urakawa (2018) Terrestrial snake environmental DNA accumulation and degradation dynamics and its environmental application. Herpetologica 74(1):38-49. (= most read articles in Herpetologica) (Tracking the elusive Burmese python—with DNA clues in the dirt March 2018 Science Posted in: Plants & Animals doi:10.1126/science.aat6441 by Erica Tennenhouse)

  18. Qin, W., K. R. Heal, R. Ramdasi, .J. N. Kobelt, W. Martens-Habbena, A. D. Bertagnolli, S. A. Amin, C. B. Walker, H. Urakawa, M. Könneke, A. H. Devol, J. W. Moffett, E. V. Armbrust, G. J. Jensen, A. E. Ingalls, D. A. Stahl (2017) Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminogenes gen. nov., sp. nov., Nitrosopumilus oxyclinae gen. nov., sp. nov., and Nitrosopumilus ureaphilus gen. nov., sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology 67: 5067-5079.

  19. Urakawa H. and A. E. Bernhard (2017) Wetland management using microbial indicators. Ecological Engineering 108:456-476. 

  20. Urakawa H., D. L. Dettmar and S. Thomas (2017) The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland. Ecological Engineering 108:573-580.

  21. Poulakis G., H. Urakawa, P. W. Stevens, J. A. DeAngelo, A. A. Timmers, R. D. Grubbs, A. T. Fisk. and J. A. Olin (2017) Sympatric elasmobranchs and fecal samples provide insight into the trophic ecology of the smalltooth sawfish. Endangered Species Research 32: 491-506.

  22. Sipos, A. and H. Urakawa (2016) Differential responses of nitrifying archaea and bacteria to methylene blue toxicity. Letters in Applied Microbiology 62:199-206. (Florida Sea Grant Extension Newsletters, Volume 6, Issue 3, July 27, 2016)

  23. Garcia C. J., R. D. J. Ketover, A. N. Loh, M. L. Parsons and H. Urakawa (2015) Influence of freshwater discharge in the microbial degradation processes of dissolved organic nitrogen in a subtropical estuary. Antonie van Leeuwenhoek 107:613-632.

  24. Martens-Habbena, W., W. Qin, R. E. A. Horak, H. Urakawa, A. J. Schauer, J. W. Moffette, E. V. Armbrust, A. E. Ingalls, A. H. Devol, and D. A. Stahl (2015) Nitric oxide metabolism in ammonia-oxidizing archaea and its significance to marine nitrification. Environmental Microbiology 17:2261-2274.

  25. Urakawa, H., J. C. Garcia, J. L. Nielsen, V.Q. Le, J. A. Kozlowski, L. Y. Stain, C. Kent Lim, A. Pommerening-Röser and M. G. Klotz (2015) Nitrosospira lacus sp. nov., a psychrotolerant ammonia-oxidizing bacterium from sandy lake sediment. International Journal of Systematic and Evolutionary Microbiology 65:242-250.

  26. Urakawa H. (2014) The family Moritellaceae.  In The Prokaryotes, 4th edition. Edited by Eugene Rosenberg, Edward F. DeLong, Fabiano Thompson, Stephen Lory and Erko Stackebrandt. Springer. NewYork. Gammaproteobacteria pp. 477-489.

  27. Qin, W, S. Amin, W. Martens-Habbena, C. B. Walker, H. Urakawa, A. H. Devol, A. E. Ingalls, J. W. Moffett, E. V. Armbrust and D. A. Stahl (2014) Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation.  Proceedings of the National Academy of Sciences of the USA 111 (34): 12504–12509.

  28. Urakawa, H., W. Martens-Habbena, C. Huguet, J. R. de la Torre, A. E. Ingalls, A. H. Devol, and D. A. Stahl (2014) Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary. Limnology and Oceanography 59 (4): 1321-1335.

  29. Urakawa H., J. Alli, R. D. J. Ketover, S. Talmage, J. Garcia, I. Campbell, A. N. Loh, and M. Parsons (2013) Shifts of bacterioplankton metabolic profiles along the salinity gradient in a subtropical estuary. ISRN Oceanography vol. 2013 Article ID 410814, doi:10.5402/2013/410814.

  30. Garcia, J. C., H. Urakawa, V. Q. Le, L. Y. Stein, M. G. Klotz and J. L. Nielsen (2013) Draft genome of Nitrosospira sp. strain APG3, a psychrotolerant ammonia-oxidizing bacterium isolated from sandy lake sediment. Genome Announcements 1(6) E00930-13.

  31. Urakawa H., J. C. Garcia, P. D. Barreto, G. A. Molina and J. C. Barreto (2012) A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria. Environmental Pollution 164:42-45.

  32. Urakawa, H., W. Martens-Habbena and D. A. Stahl (2011) Physiology and genomics of ammonia-oxidizing Archaea. In Nitrification. Edited by B. Ward, D. Arp & M. Klotz. ASM press. NewYork. pp. 117-155.

  33. Walker C.B., J.R. de la Torre, M.G. Klotz, H. Urakawa, N. Pinel, D. J. Arp, C. Brochier-Armanet, P. S. G. Chain, P. P. Chan, A. Gollabgir, J. Hemp, M. Hügler, E. A. Karr,M. Könneke, M. Shin, T. J. Lawton, T. Lowe, W. Martens-Habbena, L. A. Sayavedra-Soto, D. Lang, S. M. Sievert, A. C. Rosenzweig, G. Manning, and D. A. Stahl (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the USA 107:8818-8823.

  34. Huguet, C., H. Urakawa, W. Martens-Habbena, L. Truxal, D. A. Stahl and A. E. Ingalls (2010) Changes in intact membrane lipid content of archaeal cells as an indication of metabolic status. Organic Geochemistry 41:930-934.

  35. Urakawa H., W. Martine-Habbena and D. A. Stahl (2010) High abundance of ammonia-oxidizing archaea in coastal waters determined using a modified DNA extraction method. Applied and Environmental Microbiology 76:2129-2135.

  36. Huguet, C., W. Martens-Habbena, H. Urakawa, D. A. Stahl and A. E. Ingalls (2010) Comparison of extraction methods for quantitative analysis of core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs) in environmental samples. Limnology and Oceanography Methods 8:127-145.

  37. Iwai, S., F. Kurisu, H. Urakawa, O. Yagi and H. Furumai (2010) Characterization of monooxygenase gene diversity in benzene amended soils Letters in Applied Microbiology 50:138-145.

  38. Martens-Habbena, W., P. M. Berube, H. Urakawa, J. R. de la Torre and D. A. Stahl (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979.

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Toshi Urakawa, Professor of Environmental Science

Toshi Urakawa joined the Department of Marine and Ecological Sciences at FGCU in 2010. His fields of interest are environmental cleanup technology and biodiversity. After completing his doctoral degree with a study of cold-loving (psychrophilic/psychrotolerant) marine microorganisms and systematics of Vibrionaceae at the University of Tokyo, he continued his research as a postdoctoral researcher in Dave Stahl’s lab in Northwestern University and the University of Washington. In these places, he studied molecular microbial ecology. In his early professional carriers, he studied the nitrogen cycle and the problem of eutrophication and dead zone (i.e. oxygen depletion) at the National Institute for Environmental Studies (Japanese EPA) and the University of Tokyo in Japan. Before joining FGCU, he studied ammonia-oxidizing archaea and genomics in Dave Stahl’s lab at UW for a better understanding of the nitrogen cycle. At FGCU, he studies biogeochemical cycles in southwest Florida and biological and engineering water qualification technology as reducing means of human disturbance of aquatic environments. Recently he initiated conservation biology studies. Toshi teaches marine science classes, general ecology, and microbial ecology at FGCU.

hurakawa@fgcu.edu

Taylor Hancock, Post-Graduate Laboratory Assistant

Taylor graduated FGCU with a Bachelor’s degree in Biology in Fall 2016 and then with a Environmental Science Master’s degree in Spring of 2019 receiving distinction as FGCU's Graduate Student of the Year. His thesis work involved studying the feeding behavior and diet of smalltooth sawfish through genetic analysis to identify prey items at the species-level in hopes of furthering conservation efforts of this endangered ray. His current projects involve examining fish foragers of the Microcystis aeruginosa harmful algal bloom in the Caloosahatchee River using traditional and molecular methods as well as sequencing the genome of M. aeruginosa and other associated algal species. His research interests include molecular genetics, disturbance ecology, and evolutionary biology.

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thancock@fgcu.edu

Elizabeth Dahedl

Currently, Elizabeth studies picocyanobacteria, which are taxonomically identified as Synechococcus and Cyanobium. These cyanobacteria are abundant in our freshwater environments and may play key roles to control healthy phytoplankton communities. 

ekdahedl2130@eagle.fgcu.edu

Michael Kratz

Mike is mainly working on two bacteria source tracking studies. 

makratz5802@eagle.fgcu.edu

Former lab members

 Here is a list of former lab members.

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Graduate students

Megan Feeney (FGCU), Cristina Lopardo (FGCU-high school chemistry teacher, Orange County Public Schools), Alex Kucherenko (FGCU), Juan Garcia (FGCU-Environmental Chemist, Collier County), Irma Sanchez (FGCU), Rachel Smolinski (FGCU)

 

Undergraduates

Jacob Steele (FGCU), Julia Sereda (FGCU), Gabrianna Andrews (FGCU), Gregory Limardi II (FGCU), Jeffrey Mechanics (FGCU), Amy Murray (FGCU), Carissa Flaherty (FGCU), Elizabeth Schroeder (FGCU), Airea Williams (FGCU), Natalie Harvey (FGCU), Carissa Flaherty (FGCU), Max Pettit (FGCU), Irma Sanchez (FGCU), Kendall Karcher (FGCU), Anthony Bonacolta (University of Miami), Kaitlyn Wagner (FGCU), Kelsey Weissenhofer (FGCU), Francia Sanchez (FGCU), Nicole Jensen (FGCU-Environmental Specialist Solid & Hazardous Waste Management Division Collier County Public Utilities Department), Erika Kreuger (FGCU), Emma Fain (FGCU-UF), Leah Gexler (FGCU), Aaron Sipos (FGCU-UF), John Ciocca (FGCU), Derek Borgeson (FGCU), Anna Larson (FGCU), Dustin Chisum (FGCU), Isaac Holowell (FGCU-Algenol), Haruka Urakawa (FGCU -lab manager), Spencer Talmage (FGCU-Duke University), Erika Fulton (FGCU), Jonathan Maile (FGCU)

 

High school students

Natalie Staudacher (Gulf Coast High School &FGCU - Univ. of Michigan), Mariah Couglin (Fort Myers High School-Univ. of Central Florida), Lila Gutstein (Canterbury School-Pennsylvania State Univ.)

 

Middle school student

Esha Shah (Paul Laurence Dunbar Middle School-Fort Myers High School) 

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