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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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