Course:EOSC 475/ResearchProject/Ideas
28 January 2012: Please use UBC Connect course wiki pages!
Please sign up your name under the paper you are interested to critique. Only one person for each paper.
1. Ammerman,JW, Fuhrman, JA, Hagstrom, A, Azam, F. 1984. Bacterioplankton growth in seawater: Growth kinetics and cellular characteristics in seawater cultures. Marine Ecology Progress Series. 18:31-39.
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2. Angly, F. et al. 2006. The marine viromes of four oceanic regions. PLOS Biology 4: e368
Student name: Francesca Cusati
3. Azam, F, Fenchel, T, Field, JG, Gray, JS, Meyer-Reil, LA, Thingstad, F. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series. 10:257-263.
Student name: Rebecca Meng Qi Zhao
4. Beatty, J.T., et al. 2005. An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proceedings of the National Academy of Sciences. 102:9306-9310.
Student name: Cassandra Girdlestone
5. Beja, O et al. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Applied and Environmental Microbiology. 68:335-345.
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6. Beja,O, et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:1902-1906.
Student name: George Qi
7. Bergh,O, Borsheim, KY, Bratbak, G, Heldal, M 1989. High abundance of viruses found in aquatic environments. Nature. 340:467-468.
Student name: Bryant Rathbone
8. Boetius,A et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626.
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9. Brussaard CPD. 2004. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70: 1506-1513.
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10. Burns,BP, Goh, F, Allen, M, Neilan, BA. 2004. Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay,Australia. Environmental Microbiology. 6:1096-1101.
Student name: Rhonda Ko
11. Cerda-Cuellar, M, Jofre, J, Blanch AR. 2000. A selective medium and a specific probe for detection of Vibrio vulnificus. Appl. Environ.Microbiol 66:855-859.
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12. Choi,JW, Sherr, EB, Sherr, BF. 1996. Relation between presence-absence of a visible nucleoid and metabolic activity in bacterioplankton cells. Limnology and Oceanography. 41:1161-1168.
Student name: Meagan McKeen
13. Church, MJ, Hutchins, DA, Ducklow, HW. 2000. Limitation of bacterial growth by dissolved organic matter and iron in the Southern Ocean. Applied and Environmental Microbiology. 66:455-466.
Student name: Bailin Luo
14. Culley, AI, Lang, AS, Suttle, CA. 2003. High diversity of unknown picorna-like viruses in the sea. Nature. 424:1054-1057.
Student name: Jesse Kwan
15. Czyz,A, Jasiecki, J, Bogdan, A, Szpilewska, H, Wegrzyn, G. 2000. Genetically modified Vibrio harveyi strains as potential bioindicators of mutagenic pollution in marine environments. Applied and Environmental Microbiology. 66:599-605.
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15. Czyz, A, Wrobel, B, Wegrzyn G. 2000. Vibrio harveyi bioluminescence plays a role in stimulation of DNA repair Microbiology 146:283-288
Student name: Melissa Ng
16. Dang,H, Lovell CR. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ.Microbiol. 66:467-475
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17.Davis,PG, Sieburth, JM. 1984. Estuarine and oceanic microflagellate predation of actively growing bacteria: estimation by frequency of dividing-divided bacteria. Marine Ecology Progress Series. 19:237-246.
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18. DeLong,E.F. 1992. Archaea in coastal marine environments. PNAS 89: 5685-5689.
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19. DeLong,EF, et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311:496-503.
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20. Dinsdale,EA et al. 2007. Functional metagenomic profiling of nine biomes. Nature 452:629-32.
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21. Ducklow,HW, Hill, SM. 1985. The growth of heterotrophic bacteria in the surface waters of warm core rings. Limnology and Oceanography. 30:239-259.
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22.Fenchel, T, Finlay BJ. 2004. The ubiquity of small species: Patterns of local and global diversity. Bioscience 54: 777-784.
Student name: De Dong
23. Fuhrman,JA, McCallum K, Davis, AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 59:1294-1302.
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24.Fuhrman,JA, Noble RT. 1995. Viruses and protists cause similar bacterial mortality in coastal seawater. Limnol Oceaogr 40: 1236-1242
Student name: Rachel Lee
25. Fuhrman,JA et al. 2008. A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105: 7774-7778.
Student name: Ferdous Nawar
26. Ghai,R et al. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. The ISME Journal. 4:1154-1166.
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27. Giovannoni, SJ, Britschgi, TB, Moyer, CL. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 60-63.
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28. Giovannoni, SJ, et al. 2005. Genome Streamlining in a cosmopolitan oceanic bacterium.Science 309:1242-1245
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29. Gonzalez,JM, Sherr,, EB, Sherr, BF. 1990. Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56:583-589.
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30.Hallam,SJ et al. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science. 305:1457-1462.
Student name: Brandent Lam
31. Hewson,I. et al. 2009. Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat Limnol Oceanogr 54:1981-1994.
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32. Howard,EC et al. 2006. Bacterial taxa that limit sulfur flux from the ocean.Science 314: 649-652.
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33. Hutchinson,GE. 1961. The paradox of the plankton. American Naturalist. 95:137-145.
Student name: Takeshi Miyazaki"
34. Jedani,KE, Stroeher, UH, Manning, PA. 2000. Distribution of IS1358 and linkage to rfb-related genes in Vibrio anguillarum. Microbiology. 146:323-331.
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35. Jiang,SC, Matte, M, Matte, G, Huq, A, Colwell, RR. 2000. Genetic diversity of clinical and environmental isolates of Vibrio cholerae determined by amplified fragment length polymorphism fingerprinting. Applied and Environmental Microbiology. 66:148-153.
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36. Joint,I, Doney, SC, Karl, DM. 2011. Will ocean acidification affect marine microbes? The ISME Journal. 5:1-7.
Student name: Andrea Balba
37. Karaolis,DKR, et al. 1999. A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 300:375-379.
Student name: Katie Robbins
39. Karner, MB, DeLong, EF, Karl, DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. 2001. Nature. 409:507-510.
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40.Kuypers, MMM, et al. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:609-611.
Student name: SeoHyung Joo
41. La Scola, B, et al. 2003. A giant virus in amoebae. Science. 299:2033.
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42. LaMontagne,MG, Leifer, I, Bergmann, S, Van De Werfhorst, LC, Holden, PA. 2004.Bacterial diversity in marine hydrocarbon seep sediments. Environmental Microbiology. 6:799-808.
Student name: Jasper Tam
43. Li,WKW, et al. 1983. Autotrophic picoplankton in the tropical ocean. Science 219:292-295.
Student name: Brigid Wong
44. Martin,JH et al. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature. 371:123-129.
Student name: Valerie Tsang
45. Massana, R, Castresana, J, Balague, V, Guillou, L, Romari, K, Groisillier, A,Valentin, K, Pedros-Alio, C. 2004. Phylogenetic and ecological analysis of novel marine stramenopiles. Applied and Environmental Microbiology. 70:3528-3534.
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46. Moran,MA et al. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
Student name: Jonathan Mach
47. Moraru,C, Lam, P, Fuchs, PL, Kuypers, MMM, and Amann, R. 2010. GeneFISH- an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environmental Microbiology. 12:3057-3073.
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48. Morris, RM, Rappe, MS, Connon,SA, Vergin, KL, Siebold, WA, Carlson, CA, Giovannoni, SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature.420:806-810.
Student name: Xiaoxi Yu
49.Moisander, PH, et al. 2010. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science, 327:1512-1514.
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50. Mussmann,M et al. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PloS Biology 5:1923-1937.
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51. Nagasaki, K, Tarutani, K,Yamaguchi, M. 1999. Cluster analysis on algicidal activity of HaV clones and virus sensitivity of Heterosigma akashiwo (Raphidophyceae). Journal of Plankton Research. 21:2219-2226.
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52. Pomeroy,LR. 1974. The ocean's food web, a changing paradigm. Bioscience.24:499-504.
Student name: Lucy (Le) Ouyang
53. Riemann,L, Steward, GF, Azam, F, 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl.Environ.Microbiol 66, 578-587
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54. Rocap,G et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424:1042-1047.
Student name: Shawn Zhu
55. Rohwer,F, Seguritan, V, Azam, F, Knowlton, N. 2002. Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series. 243:1-10.
Student name: Melissa Jouen
56. Sharon,I et al. 2007. Viral photosynthetic reaction center genes and transcripts in the marine environment. The ISME Journal. 1:492-501.
Student name: Michael Medley
57. Short,CM, Suttle, CA. 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71:480-486
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58. Sogin, M.L. et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proceedings of the National Academy of Sciences USA 103:12115–12120.
Student name: Kate Broadley
59. Strzepek,RF, Maldonado, MT, Higgins, JL, Hall, J, Safi, K, Wilhelm, SW, Boyd, PW.2005. Spinning the “Ferrous Wheel”: the importance of the microbial community in an iron budget during the FeCycle experiment. Global Biogeochemical Cycles. 19.
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60.Venter,JC et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304:66-74.
Student name: Ryan Mar
61. Walsh,D et al. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 326:578-582.
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62. Wilson,KM, Schembri, MA, Baker, PD, Saint, CP. 2000. Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of species-specific PCR. Applied and Environmental Microbiology. 66:332-338.
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63. Wilson,WH, et al. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science. 309:1090-1092.
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64. Zehr,JP, et al. 2001. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature. 412:635-638.
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65. Zingone,A, Sarno, D, Forlani, G. 1999. Seasonal dynamics in the abundance of Micromonas pusilla (Prasinophyceae) and its viruses in the Gulf of Naples(Mediterranean Sea). Journal of Plankton Research. 21:2143-2159.
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66. Zweifel,UL, Hagstrom, A. 1995. Total counts of marine bacteria include a large fraction of non-nucleoid containg bacteria (ghosts). Applied and Environmental Microbiology. 61:2180-2185.
Student name: Yan Ko
67. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 105: 3805–3810.
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