C-MORE Contribution Series

1. Brix, H., N. Gruber, D.M. Karl and N.R. Bates. 2006. Interannual variability in the relationship between primary, net community, and export production in subtropical gyres. Deep-Sea Research II 53: 698–717.

2. DeLong, E.F., C.M. Preston, T. Mincer, V. Rich, S.J. Hallam, N.-U. Frigaard, A. Martinez, M.B. Sullivan, R. Edwards, B.R. Brito, S.W. Chisholm and D.M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean‘s interior. Science 311: 496–503.

3. Follows, M.S. Dutkiewicz, S. Grant, S.W. Chisholm. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315: 1843-1846

4. Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., Preston, C.M., de la Torre, J, Richardson, P.R. and DeLong, E.F. 2007. Genomic analysis of the uncultivated marine crenarchaeote, Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. USA 103: 18296–18301.

5. Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, C. Scholin. 2006. Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudonitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization. Limnology and Oceanography: Methods 4: 426–435.

6. Huisman, J., N.N.P. Thi, D.M. Karl and B. Sommeijer. 2006. Reduced mixing generates oscillations and chaos in the deep chlorophyll maximum. Nature 439: 322–325.

7. Rusch, D. et al. (including D.M. Karl). 2007. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLOS Biology 5: 0398–0431.

8. Martinez, A. , A. Bradley, J. Waldbauer, R. Summons and E. F. DeLong. 2007. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc. Natl. Acad. Sci. 104: 5590–5595.

9. Martiny, A.C., Coleman, M.L and S. W, Chisholm. 2006. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proc. Nat. Acad. Sci. USA 103 (33): 12552–12557

10. McAndrew, P.M., K.M. Bjorkman, M.J. Church, P.J. Morris, N. Jachowski, P.J. le B. Williams and D.M. Karl. 2007. Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Marine Ecology Progress Series 332: 63–75.

11. McCarren, J. and E.F. DeLong. 2007. Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla. Environ. Microbiol. 9: 846–858.

12. Mincer T.J., Church, M,J. , Taylor, L.T., Preston, C.M., Karl, D.M., and E.F. DeLong. 2007. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol., doi: 10.1111/j.1462-2920.2007.01239.x

13. Roman, B., C. Scholin, S. Jensen, E. Massion, R, Marin III, C. Preston, D. Greenfield, W. Jones, and K. Wheeler. 2007. Controlling a robotic marine water sampler with the Ruby scripting language. Journal of American Laboratory Automation 12: 56–61.

14. Rothstein, L.M., J.J. Cullen, M. Abbott, E. Chassignet, K. Denman, S. Doney, H. Ducklow, K. Fennel, M. Follows, D. Haidvogel, E. Hofmann, D. Karl, J. Kindle, I. Lima, M. Maltrud, C. McClain, D. McGillicuddy, J. Olascoaga, Y. Spitz, J. Wiggert and J. Yoder. 2006. Modeling ocean ecosystems: The PARADIGM program. Oceanography 19: 17–45.

15. Steglich, C. Futschik, M., Rector, T. and S.W. Chisholm. 2006. Genome-wide analysis of light sensing in Prochlorococcus. J. Bacteriol. 188: 7796–7806

16. Sullivan, M.B., D. Lindell, J.A. Lee, L. R. Thompson, J. P. Bielawski, and S.W. Chisholm. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLOS Biology 4 (8) 1345–1357.

17. Tolonen, A.C. Aach, J. Lindell, D., Johnson, Z.I., Rector, T. Steen, R., Church, G. M. and S.W. Chisholm (2006) Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Molecular Systems Biology. 3 October, Article 53. doi:10.1038/msb4100087.

18. White, A., Y. Spitz, D.M. Karl and R. M. Letelier. 2006. Flexible elemental stoichiometry in Trichodesmium spp. and its ecological implications. Limnology and Oceanography 51: 1777–1790.

19. Zehr, J. P., J. P. Montoya, C. Short, A. Hansen, B. D. Jenkins, M. J. Church and D. M. Karl. 2007. Nitrogenase gene expression in the North Pacific Subtropical Gyre. Limnology and Oceanography 52: 169–183.

20. Giovannoni, S.J., R.A. Foster, M.S. Rappé, and S. Epstein. 2007. New cultivation strategies bring more microbial plankton species into the laboratory. Oceanography 20: 24–30.

21. Karl, D., and L. Proctor, Editors. 2007. A Sea of Microbes, Oceanography 20 (2), special issue.

22. Karl, D., E. DeLong, and G. Rocap. 2007. Microbial Oceanography: Challenges and Opportunities, a report commissioned and published by The Agouron Institute, March 2007.

23. Becker, J.W., M.L. Brandon, and M.S. Rappé. Cultivating micro-organisms from dilute aquatic environments: melding traditional methodology with new cultivation techniques and molecular methods. Manual of Environmental Microbiology, 3rd Edition. ASM Press. In press

24. Brandon, M.L., J.W. Becker and M.S. Rappé. Isolation of aquatic microorganisms via high throughput cultivation methods. Molecular Microbial Ecology Manual, 3rd Edition. In press

25. Scholin, C.A., G.J. Doucette, and A.D. Cembella. Prospects for developing automated systems for in situ detection of harmful algae and their toxins. In: M. Babin, C.S. Roesler and J.J. Cullen (eds.) Real-Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms, UNESCO Publishing, Paris, France. In press

26. Zehr, J.P. and H.W. Paerl. Biological nitrogen fixation in the marine environment. In D. L. Kirchman (ed.) Microbial Ecology of the Oceans. 2nd Edition. Wiley-Liss, Inc. In press

27. Buesseler, K.O., C.H. Lamborg, P.W. Boyd, P.J. Lam, T.W. Trull, R.R. Bidigare, J.K.B. Bishop, K.L. Casciotti, F. Dehairs, M. Elskens, M. Honda, D.M. Karl, D. Siegel, M.W. Silver, D.K. Steinberg, J. Valdes, B. Van Mooy and S. Wilson. Revisiting carbon flux through the ocean’s twilight zone. Science. In press

28. Corno, G., D.M. Karl, M.J. Church, R.M Letelier, R. Lukas and M.R. Abbott. The impact of climate forcing on ecosystem processes in the North Pacific Subtropical Gyre. Journal of Geophysical Research. In press

29. Karl, D.M. 2007. Microbial nucleotide fingerprints in nature. In: C. A. Reddy, T. Beveridge, J. A. Breznak, S. Maloy, G. A. Marzluf, T.M. Schmidt (eds.). Methods for General and Molecular Microbiology, ASM Press, Washington, D.C. In press

30. Karl, D.M. The marine phosphorus cycle. 2007. In: Manual of Environmental Microbiology, Third Edition, ed. by J. L. Garland, American Society of Microbiology. In press

31. Karl, D.M., R.R. Bidigare, M.J. Church, J.E. Dore, R.M. Letelier, C. Mahaffey and J. Zehr. 2007. The nitrogen cycle in the North Pacific trades biome: An evolving paradigm. In: Nitrogen in the Marine Environment, ed. by D. Bronk, M. Mulholland, D. Capone and E. Carpenter, Academic Press. In press

32. Steward, G.F. and M.S. Rappé.  What’s the ”meta“ with metagenomics? The ISME Journal, 1:100-102. doi:10.1038/ismej.2007.25

33. Dhadwal, H.S., B. Mukherjee, P. Kemp, J. Aller, Y. Liu, and J. Radway. 2007. A dual detector Capillary Waveguide Sensor for detection and quantification of hybridized target species. Analytica Chimica Acta 598: 147–154.

34. Kolber, Z. 2007 Energy cycle in the ocean: Powering the microbial world. Oceanography 20, 79–88.

35. Saito, M.A. and D.L. Schneider. 2006. Examination of the precipitation chemistry and improvements in precision using the Mg(OH)₂ preconcentration ICP-MS method for high-throughput analysis of open-ocean Fe and Mn in seawater. Analytica Chimica Acta, 565, 222–233.

36. Bertrand, E.M., M.A. Saito, J.M. Rose, C.R. Riesselman, M.C. Lohan, A.E. Noble, P.A. Lee, G.R. DiTullio. 2007. Vitamin B12 and iron co-limitation of phytoplankton growth in the Ross Sea. Limnology and Oceanography 52: 1079–1093.

37. Saito, M.A. and T.J. Goepfert. 2008. Zinc-cobalt colimitation in Phaeocystis antarctica. Limnology and Oceanography. 53:266-275

38. Saito, M.A., T.J. Goepfert, and J.T. Ritt. 2008. Some thoughts on the concept of co-limitation: Three definitions and the importance of bioavailability. Limnology and Oceanography. 53:276-290

39. Moore, L.R., A. Coe, E.R. Zinser, M.A. Saito, M.B. Sullivan, D. Lindell, K. Frois-Moniz, J. Waterbury, and S. W. Chisholm. 2007. Culturing the marine cyanobacterium Prochlorococcus. Limnol. Oceanogr.: Methods. 5:353-362

40. Zinser, E.R.Z., I. Johnson, A. Coe, E. Karaca, D. Veneziano, and S.W. Chisholm. Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean. Limnol. Oceanogr. 52 (5): 2205-2220.

41. Lindell, D., J.D. Jaffe, M.l. Coleman, I.M. Axmann, T. Rector, G. Kettler, M.B. Sullivan, R. Steen, W.R. Hess, G.M. Church, and S. W. Chisholm. 2007. Genome-wide expression dynamics of a marine virus and host reveal features of coevolution. Nature 449: 83-86.

42. Culley, A.I. and Steward G.F. New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences. Appl. Environ. Microbiol. 73:5937-5944

43. D’Hondt, S., F. Inagaki, T. Ferdelman, B.B. Jørgensen, K. Kato, P. Kemp, P. Sobecky, M. Sogin and K. Takai. 2007. Exploring subseafloor life with the Integrated Ocean Drilling Program. Scientific Drilling 5: 58–69.

44. Kettler, G., A.C. Martiny, K. Huang, J. Zucker, M.L. Coleman, S. Rodrigue, F. Chen, A. Lapidus, S. Ferriera, J. Johnson, C. Steglich, G. Church, P. Richardson, and S.W. Chisholm. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus. PLoS Genetics 3:2515-2528

45. Aller, JY, Kemp, PF. Are Archaea inherently less diverse than Bacteria in the same environments? FEMS Microbiology Ecology In press.

46. Doney, S.C., Lima, I., Moore, J.K., Lindsay, K., Behrenfeld, M., Westberry, T.K., Mahowald, N., Glover, D.M., Takahashi T. Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data. J. Mar. Systems In Press.

47. Jin, X., Gruber, N., Frenzel, H., Doney, S.C., and McWilliams, J.C. 2008. The impact on atmospheric CO2 of iron fertilization induced changes in the ocean's biological pump. Biogeosciences 5:385-406

48. Frias-Lopez, J., Shi, Y., Tyson, G. W.,. Coleman, M.L., Schuster, S. C., Chisholm, S.W., DeLong, E. F. 2008. Microbial community gene expression in ocean surface waters. . Proc. Natl. Acad. Sci, U.S.A. 105:3805-3810

49. Woebken D., Teeling H., Wecker P., Dumitriu A., Kostadinov I., Delong E.F., Amann R., Glöckner F.O. 2007. Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes.. ISME J. 5:419-435

50. Rich, V. I., K. Konstantinidis, DeLong, E. F. 2008. . Design and testing of “genome-proxy” microarrays to profile marine microbial communities.. Environ. Microbiol. 10:506-521

51. Giaquinto L., Curmi P.M., Siddiqui K.S., Poljak A., DeLong E. F., Dassarma S., Cavicchioli R. 2007. Structure and function of cold shock proteins in archaea. J Bacteriol. 189:5738-5748

52. DeLong, E. F. 2007. Microbial domains in the ocean: A lesson from the Archaea. Oceanography 20:124-129

53. Follows, M.S., Dutkiewicz, Grant, S., Chisholm, S.W. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315:1843-1846

54. Coleman, M.L. and Chisholm, S.W. 2007. Code and Context: Prochlorococcus as a model for cross-scale biology. Trends in Microbiology 15:398-407

55. Dammeyer, T.S., Bagby, S.C., Sullivan, M.B., Chisholm, S.W., and Frankenberg-Dinkel, N. 2008. Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Current Biology 18:442-448

56. Noble, A.E., Saito, M.A., Maiti, K., Benitez-Nelson C. in press. Cobalt, manganese, and iron near the Hawaiian Islands: A potential concentrating mechanism for cobalt within a cyclonic eddy and implications for the hybrid-type trace metals. Deep-Sea Research II X:XX-XX

57. Pham, V., Konstantinidis, K. T., Palden, T., DeLong, E. F. in press. Phylogenetic Analyses of rDNA-containing Bacterioplankton Genome Fragments from a 4000-Metre Vertical Profile in the North Pacific Subtropical Gyre. . Environ. Microbiol. X:XX-XX

58. Falkowski, P.G., Fenchel, T. DeLong E. F. in press. The Microbial Engines that Drive Earth's Biogeochemical Cycles.. Science 319:XX-XX

59. Goebel, N. L., Edwards, C. A., Church, M. J., Zehr, J. P. 2007. Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA. . ISME Journal 1:606-619

60. Zehr, J. P., Bench, S., Mondragon, E., McCarren, J., DeLong, E. F. 2007. Low genomic diversity in tropical oceanic N2-fixing cyanobacteria. Proceedings PNAS 4:17808-17812

61. Hewson, I., Moisander, P. H., Morrison, A. E., Zehr, J. P. 2007. Diazotrophic bacterioplankton in a coral reef lagoon: Phylogeny, diel expression, and response to phosphate enrichment. ISME Journal 1:78-91

62. Moisander, P. H., Morrison, A. E., Ward, B. B., Jenkins, B. D., Zehr, J. P. 2007. Diazotrophic bacterioplankton in a coral reef lagoon: Phylogeny, diel expression, and response to phosphate enrichment.. Environmental Microbiology 9:1823-1835

63. Needoba, J. A., Foster, R.A., Sakamoto, C., Zehr, J. P., Johnson, K. S. 2007. Nitrogen fixation by unicellular diazotrophic cyanobacteria in the temperate, oligotrophic North Pacific Ocean. . Limnol. Oceanogr. 52:1317-1327

64. Rabouille, S., Edwards, C. A., Zehr, J. P. 2007. Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean. . Environmental Microbiology 9:2588-2602

65. Ward, B. B., Capone, D. G., Zehr, J. P. 2007. 2007. What's new in the nitrogen cycle?. Oceanography 20:101-109

66. Laney, S.R. and R.M. Letelier 2008. Artifacts in measurements of chlorophyll fluorescence transients, with specific application to fast repetition rate fluorometry. . Limnol. Oceanogr.: Methods 6:40-50

67. Dore, J.E., R.M. Letelier, M.J. Church, R.Lukas, and D.M. Karl 2008. Summer phytoplankton blooms in the oligotrophic North Pacific Subtropical Gyre: Historical perspective and recent observations. Progress in Oceanography 76:2-38

68. Desiderio, R., S. Laney, R. Letelier, and S. Giovannoni 2007. Using lasers to probe the transient light absorption by proteorhodopsin in marine bacterioplankton. Applied Optics 46:7329-7336

69. White, A.E., Y.H. Spitz, and R.M. Letelier 2007. What factors are driving summer phytoplankton blooms in the North Pacific subtropical gyre? J. Geophys. Res. 112(c2): :C12006-doi:10.1029/2007JC004129

70. Bane, J.M., Y.H. Spitz, R.M. Letelier, and W.T. Peterson 2007. Jet stream intraseasonal oscillations drive dominant ecosystem variations in Oregon’s summertime coastal upwelling system. Proc. Nat. Acad. Sci. 104:13,262-13,267

71. Corno, G., D.M. Karl, M.A. Abbott, M.J. Church, R. Lukas, and R.M. Letelier 2007. Impact of climate forcing on ecosystem processes in the North Pacific subtropical gyre. J. Geophys. Res 112:C04021-doi:10.1029/2006JC003730

72. Huyer, A., M. Kosro, R. Letelier, R.L. Smith, and P.A. Wheeler 2007. The Newport Line off Oregon: Studies in the North East Pacific. Progress in Oceanography 112: -, doi: 10.1016/j.pocean.2007.08.003

73. White, A. E., F.G. Prahl, R.M. Letelier, and B.N. Popp 2007. Summer surface waters in the Gulf of California: prime habitat for biological N2 fixation. Global Biogeochemical Cycles 21: GB2017-doi:10.1029/2006GBC002779

74. McAndrew, P., Bjorkman, K., Church, M., Morris, P., Jachowski, N., Williams, PJleB, Karl, D. 2007. The net metabolic balance of the open ocean: A test of the nutrient enrichment hypothesis. Marine Ecology Progress Series 332:63-75

75. Church, M.J., Bjorkman, K.M., Karl, D.M., Saito, M.A., Zehr, J.P. 2008. Regional distributions of nitrogen fixing bacteria in the Pacific Ocean. Limnology and Oceanography 53:63-77

76. Fong, A.A., Karl, D.M., Lukas, R., Letelier, R.M., Zehr, J.P., Church, M.J. 2008. Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean. ISME Journal doi:10.1038/ismej.2008.22:0-0

77. Church, M.J. in press. Resource control of bacterial dynamics in the sea. In: Kirchman, D.L. Microbial Ecology of the Oceans. pp 335–382. Wiley Liss

78. McAndrew, P. M., K. M. Bjorkman, M. J. Church, P. J. Morris, N. Jachowski, P. J. le B. Williams and D. M. Karl 2007. Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Marine Ecology Progress Series 332:63-75

79. Rusch, D. B., A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Rrmington, K. Beeson, B. Tran, H. Smith, H. Baden-Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews-Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y.-H. Rogers, L. I. Falcon, V. Souza, G. Bonilla-Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gal-lardo, G. Tamayo-Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier and J. C. Venter 2007. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. Public Library of Science (PLOS), Biology 5:0398-0431

80. Karl, D. M. and L. Proctor 2007. Foundations of microbial oceanography. Oceanography 20:16-27

81. Karl, D. M. 2007. Microbial oceanography: paradigms, processes and promise. Nature Reviews Microbiology 5:759-769

82. Buessler, K. O., S. C. Doney, D. M. Karl, P. W. Boyd, K. Caldiera, F. Chai, K. H. Coale, H. J. W. de Baar, P. G. Falkowski, K. S. Johnson, R. S. Lampitt, A. F. Michaels, S. W. A. Naqvi, V. Smetacek, S. Takeda and A. J. Watson 2008 Ocean iron fertilization – Moving forward in a sea of uncertainty. Science 319:162-162

83. Moutin, T., D. M. Karl, S. Duhamel, P. Rimmelin, P. Raimbault, B. A. S. Van Mooy and H. Claustre 2008. Phosphate availability and the ultimate control of new nitrogen input by nitrogen fixation in the tropical Pacific Ocean. Biogeosciences 5:95-109

84. Karl, D. M 2007. Plastics-irradiated-etched: The Nuclepore filter turns 45 years old. Limnology and Oceanography Bulletin 16:49-54

85. Paul, J., Scholin, C., van den Engh, G., Perry, M.J. 2007. In situ Instrumentation. Oceanography 20:58-66

86. Roman, B., Scholin, C., Jensen, S., Massion, E., Marin R. III, Preston, C., Greenfield, D., Jones, W., Wheeler, K. 2007. Controlling a Robotic Marine Water Sampler with the Ruby Scripting Language. Journal of American Laboratory Automation 12:56-61