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Marine Microbial Ecology Course

UCSC | Ocean Sciences |
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Marine Microbial Ecology

at UCSC (OCEA 118, 218, BIOL 171)
Spring 2008

Reading Material

Articles to read for student presentations (click here)

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The following is a library of relevant papers.

  • Bacterial Growth
    • Azam, F. and J. A. Fuhrman (1984). "Measurement of Bacterioplankton Growth in the Sea and its Regulation by Environmenal Conditions." Heterotrophic Activity In The Sea. J. E. Hobbie and P. J. L. Williams, Plenum Publishing Corporation. New York. pp. 179-196.
    • Grossart, H. P., T. Kiorboe, et al. (2003). "Bacterial colonization of particles: Growth and interactions." Applied And Environmental Microbiology 69(6): 3500-3509.

  • Biogeochemical Cycles (other than C & N)
    • Finster, K., W. Liesack, et al. (1998). "Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp nov, a new anaerobic bacterium isolated from marine surface sediment." Applied And Environmental Microbiology 64(1): 119-125.
    • Francis, C. A., E. M. Co, et al. (2001). "Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium." Applied And Environmental Microbiology 67(9): 4024-4029.
    • Gonzalez, J. M., R. P. Kiene, et al. (1999). "Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria." Applied and Environmental Microbiology 65(9): 3810-3819.
    • Guan, L. L., K. Kanoh, et al. (2001). "Effect of exogenous siderophores on iron uptake activity of marine bacteria under iron-limited conditions." Applied And Environmental Microbiology 67(4): 1710-1717.
    • Hagen, K. D. and D. C. Nelson (1997). "Use of reduced sulfur compounds by Beggiatoa spp.: Enzymology and physiology of marine and freshwater strains in homogeneous and gradient cultures." Applied And Environmental Microbiology 63(10): 3957-3964.
    • King, G. M. and M. A. Garey (1999). "Ferric iron reduction by bacteria associated with the roots of freshwater and marine macrophytes." Applied and Environmental Microbiology 65(10): 4393-4398.

  • Carbon Cycle
  • Chemotaxis
    • Gram, L., H. P. Grossart, et al. (2002). "Possible quorum sensing in marine snow bacteria: Production of acylated homoserine lactones by Roseobacter strains isolated from marine snow." Applied And Environmental Microbiology 68(8): 4111-4116.
    • Kiorboe, T., K. Tang, et al. (2003). "Dynamics of microbial communities on marine snow aggregates: Colonization, growth, detachment, and grazing mortality of attached bacteria." Applied And Environmental Microbiology 69(6): 3036-3047.
    • Mitchell, J. G., L. Pearson, et al. (1996). "Clustering of marine bacteria in seawater enrichments." Applied And Environmental Microbiology 62(10): 3716-3721.

  • Climate
    • Harvell, C. D., K. Kim, et al. (1999). "Review: Marine ecology - Emerging marine diseases - Climate links and anthropogenic factors." Science 285(5433): 1505-1510.
    • Ochs, C. A. and L. P. Eddy (1998). "Effects of UV-A (320 to 399 nanometers) on grazing pressure of a marine heterotrophic nanoflagellate on strains of the unicellular Cyanobacteria Synechococcus spp." Applied And Environmental Microbiology 64(1): 287-293.
    • Winter, C., M. M. Moeseneder, et al. (2001). "Impact of UV radiation on bacterioplankton community composition." Applied And Environmental Microbiology 67(2): 665-672.
    • Yoch, D. C. (2002). "Dimethylsulfoniopropionate: Its sources, role in the marine food web, and biological degradation to dimethylsulfide." Applied And Environmental Microbiology 68(12): 5804-5815.

  • Deep Sea
  • DOM
  • Fe
    • Crosa, J. H. (1997). "Signal transduction and transcriptional and posttranscriptional control of iron-regulated genes in bacteria." Microbiology And Molecular Biology Reviews 61(3): 319-&.
    • King, G. M. and M. A. Garey (1999). "Ferric iron reduction by bacteria associated with the roots of freshwater and marine macrophytes." Applied and Environmental Microbiology 65(10): 4393-4398.

  • Geomicrobiology
  • Growth Physiology
    • Binder, B. (2000). "Cell cycle regulation and the timing of chromosome replication in a marine Synechococcus (cyanobacteria) during light- and nitrogen-limited growth." Journal of Phycology 36(1): 120-126.
    • Burchard, R. P. and M. L. Sorongon (1998). "A gliding bacterium strain inhibits adhesion and motility of another gliding bacterium strain in a marine biofilm." Applied And Environmental Microbiology 64(10): 4079-4083.
    • Button, D. K. (1998). "Nutrient uptake by microorganisms according to kinetic parameters from theory as related to cytoarchitecture." Microbiology And Molecular Biology Reviews 62(3): 636-+.
    • Cottrell, M. T., J. A. Moore, et al. (1999). "Chitinases from uncultured marine microorganisms." Applied And Environmental Microbiology 65(6): 2553-2557.
    • Isaksen, M. F. and B. B. Jorgensen (1996). "Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments." Applied And Environmental Microbiology 62(2): 408-414.
    • Joux, F., P. Lebaron, et al. (1997). "Changes in cellular states of the marine bacterium Deleya aquamarina under starvation conditions." Applied And Environmental Microbiology 63(7): 2686-2694.
    • Knoblauch, C., B. B. Jorgensen, et al. (1999). "Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in Arctic marine sediments." Applied And Environmental Microbiology 65(9): 4230-4233.
    • Marie, D., F. Partensky, et al. (1997). "Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I." Applied And Environmental Microbiology 63(1): 186-193.
    • Mitchell, J. G., L. Pearson, et al. (1995). "Natural Assemblages Of Marine-Bacteria Exhibiting High-Speed Motility And Large Accelerations." Applied And Environmental Microbiology 61(12): 4436-4440.
    • Ostrowski, M., R. Cavicchioli, et al. (2001). "Specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium Sphingomonas alaskensis strain RB2256." Applied And Environmental Microbiology 67(3): 1292-1299.
    • Pernthaler, A., J. Pernthaler, et al. (2001). "Growth patterns of two marine isolates: Adaptations to substrate patchiness?" Applied And Environmental Microbiology 67(9): 4077-4083.
    • Simu, K. and A. Hagstrom (2004). "Oligotrophic bacterioplankton with a novel single-cell life strategy." Applied And Environmental Microbiology 70(4): 2445-2451.

  • Human Pollution
  • Marine Microbial Diversity
  • Methods: Molecular and Genomic
    • Amann, R. I., W. Ludwig, et al. (1995). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation." Microbiological Reviews 59(1): 143-169.
    • Brussaard, C. P. D. (2004). "Optimization of procedures for counting viruses by flow cytometry." Applied And Environmental Microbiology 70(3): 1506-1513.
    • DeLong, E. F., L. T. Taylor, et al. (1999). "Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization." Applied And Environmental Microbiology 65(12): 5554-5563.
    • Falkowski, P. G. and C. de Vargas (2004). "Shotgun sequencing in the sea: A blast from the past?" Science 304(5667): 58-60.
    • Hagstrom, A., T. Pommier, et al. (2002). "Use of 16S ribosomal DNA for delineation of marine bacterioplankton species." Applied And Environmental Microbiology 68(7): 3628-3633.
    • Pernthaler, J., A. Pernthaler, et al. (2003). "Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization." Applied And Environmental Microbiology 69(5): 2631-2637.
    • Sekar, R., B. M. Fuchs, et al. (2004). "Flow sorting of marine bacterioplankton after fluorescence in situ hybridization." Applied And Environmental Microbiology 70(10): 6210-6219.
    • Sharkey, F. H., I. M. Banat, et al. (2004). "Detection and quantification of gene expression in environmental bacteriology." Applied And Environmental Microbiology 70(7): 3795-3806.
    • Stoeck, T., W. H. Fowle, et al. (2003). "Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images." Applied And Environmental Microbiology 69(11): 6856-6863.
    • Stretton, S., S. Techkarnjanaruk, et al. (1998). "Use of green fluorescent protein to tag and investigate gene expression in marine bacteria." Applied And Environmental Microbiology 64(7): 2554-2559.
    • Teira, E., T. Reinthaler, et al. (2004). "Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean." Applied And Environmental Microbiology 70(7): 4411-4414.
    • Worden, A. Z., S. W. Chisholm, et al. (2000). "In situ hybridization of Prochlorococcus and Synechococcus (marine cyanobacteria) spp. with rRNA-targeted peptide nucleic acid probes." Applied and Environmental Microbiology 66(1): 284-289.

  • Methods: Physiology and Biochemistry
    • Bertone, S., M. Giacomini, et al. (1996). "Automated systems for identification of heterotrophic marine bacteria on the basis of their fatty acid composition." Applied And Environmental Microbiology 62(6): 2122-2132.
    • Fukuda, R., H. Ogawa, et al. (1998). "Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments." Applied and Environmental Microbiology 64(9): 3352-3358.
    • Gregori, G., S. Citterio, et al. (2001). "Resolution of viable and membrane-compromised bacteria in freshwater and marine waters based on analytical flow cytometry and nucleic acid double staining." Applied And Environmental Microbiology 67(10): 4662-4670.
    • Luna, G. M., E. Manini, et al. (2002). "Large fraction of dead and inactive bacteria in coastal marine sediments: Comparison of protocols for determination and ecological significance." Applied And Environmental Microbiology 68(7): 3509-3513.
    • Marie, D., D. Vaulot, et al. (1996). "Application of the novel nucleic acid dyes YOYO-1, YO-PRO-1, and PicoGreen for flow cytometric analysis of marine prokaryotes." Applied And Environmental Microbiology 62(5): 1649-1655.
    • Nielsen, M., L. H. Larsen, et al. (2004). "Bacterium-based NO2- biosensor for environmental applications." Applied And Environmental Microbiology 70(11): 6551-6558.
    • Schulz, H. N. and D. de Beer (2002). "Uptake rates of oxygen and sulfide measured with individual Thiomargarita namibiensis cells by using microelectrodes." Applied And Environmental Microbiology 68(11): 5746-5749.
    • Sieracki, M. E., T. L. Cucci, et al. (1999). "Flow cytometric analysis of 5-cyano-2,3-ditolyl tetrazolium chloride activity of marine bacterioplankton in dilution cultures." Applied and Environmental Microbiology 65(6): 2409-2417.
    • Zweifel, U. L. and A. Hagstrom (1995). "Total counts of marine bacteria include a large fraction of non-nucleoid-containing bacteria (ghosts)." Applied and Environmental Microbiology 61: 2180-2185.

  • Microbial Loop and Viruses
  • Nitrogen Cycle
    • Allen, A. E., M. G. Booth, et al. (2001). "Diversity and detection of nitrate assimilation genes in marine bacteria." Applied and Environmental Microbiology 67: 5343-5348.
    • Bano, N. and J. T. Hollibaugh (2000). "Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean." Applied And Environmental Microbiology 66(5): 1960-1969.
    • Capone, D. G., J. P. Zehr, et al. (1997). "Trichodesmium: a globally significant marine cyanobacterium." Science 276: 1221-1229.
    • Dalsgaard, T. and B. Thamdrup (2002). "Factors controlling anaerobic ammonium oxidation with nitrite in marine sediments." Applied And Environmental Microbiology 68(8): 3802-3808.
    • Freitag, T. E. and J. I. Prosser (2003). "Community structure of ammonia-oxidizing bacteria within anoxic marine sediments." Applied And Environmental Microbiology 69(3): 1359-1371.
    • Mazard, S. L., N. J. Fuller, et al. (2004). "PCR analysis of the distribution of unicellular cyanobacterial diazotrophs in the Arabian Sea." Applied And Environmental Microbiology 70(12): 7355-7364.
    • O'Mullan, G. D. and B. B. Ward (2005). "Relationship of temporal and spatial variabilities of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California." Applied And Environmental Microbiology 71(2): 697-705.
    • Thamdrup, B. and T. Dalsgaard (2002). "Production of N-2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments." Applied and Environmental Microbiology 68(3): 1312-1318.
    • Ward, B. B. and G. D. O'Mullan (2002). "Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by PCR and sequencing of 16S rRNA and amoA genes." Applied And Environmental Microbiology 68(8): 4153-4157.
    • Zehr, J. P. and B. B. Ward (2002). "Nitrogen cycling in the ocean: New perspectives on processes and paradigms." Applied and Environmental Microbiology 68(3): 1015-1024.

  • Pathogens
  • Phosphorus
  • Photosynthesis
    • Allgaier, M., H. Uphoff, et al. (2003). "Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats." Applied And Environmental Microbiology 69(9): 5051-5059.
    • Beja, O., M. T. Suzuki, et al. (2002). "Unsuspected diversity among marine aerobic anoxygenic phototrophs." Nature 415(6872): 630-633.
    • Fuller, N. J., D. Marie, et al. (2003). "Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea." Applied and Environmental Microbiology 69(5): 2430-2443.
    • Hess, W. R. (2004). "Genome analysis of marine photosynthetic microbes and their global role." Current Opinion In Biotechnology 15(3): 191-198.
    • Palenik, B. (2001). "Chromatic adaptation in marine Synechococcus strains." Applied and Environmental Microbiology 67(2): 991-994.
    • Partensky, F., W. R. Hess, et al. (1999). "Prochlorococcus, a marine photosynthetic prokaryote of global significance." Microbiology and Molecular Biology Reviews 63(1): 106-+.
    • Pradella, S., M. Allgaier, et al. (2004). "Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria." Applied And Environmental Microbiology 70(6): 3360-3369.
    • Rocap, G., D. L. Distel, et al. (2002). "Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences." Applied and Environmental Microbiology 68(3): 1180-1191.
    • Scanlan, D. J., N. J. Silman, et al. (1997). "An immunological approach to detect phosphate stress in populations and single cells of photosynthetic picoplankton." Applied and Environmental Microbiology 63(6): 2411-2420.
    • Scanlan, D. J. and N. J. West (2002). "Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus." Fems Microbiology Ecology 40(1): 1-12.
    • Wingard, L. L., S. R. Miller, et al. (2002). "Cyanophycin production in a phycoerythrin-containing marine Synechococcus strain of unusual phylogenetic affinity." Applied And Environmental Microbiology 68(4): 1772-1777.
    • Wyman, M., J. T. Davies, et al. (2000). "Molecular and physiological responses of two classes of marine chromophytic phytoplankton (diatoms and prymnesiophytes) during the development of nutrient-stimulated blooms." Applied And Environmental Microbiology 66(6): 2349-2357.
    • Yurkov, V. V. and J. T. Beatty (1998). "Aerobic anoxygenic phototrophic bacteria." Microbiology And Molecular Biology Reviews 62(3): 695-+.
    • Zubkov, M. V., B. M. Fuchs, et al. (2003). "High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters." Applied And Environmental Microbiology 69(2): 1299-1304.

  • Pollution
    • Nandakumar, K., H. Obika, et al. (2004). "In vitro laser ablation of natural marine biofilms." Applied And Environmental Microbiology 70(11): 6905-6908.
    • Kasai, Y., H. Kishira, et al. (2002). "Bacteria belonging to the genus Cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment." Applied And Environmental Microbiology 68(11): 5625-5633.

  • Sediment
    • Rontani, J. F., P. C. Bonin, et al. (1999). "Biodegradation of free phytol by bacterial communities isolated from marine sediments under aerobic and denitrifying conditions." Applied And Environmental Microbiology 65(12): 5484-5492.

  • Sulfur
  • Symbiosis