Overview of the marine Roseobacter lineage

Applied and Environmental Microbiology

Volumn 71, Issue 10, 2005, Pages 5665-5677

  Buchan, Alison ^a   González, José M ^b   Moran, Mary Ann ^c  

^a UNIVERSITY OF TENNESSEE   (United States)

^b UNIVERSIDAD DE LA LAGUNA   (Spain)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUND; CARBON DIOXIDE; RNA 16S;

MICROBIOLOGY;

ALGAL BLOOM; BACTERIAL METABOLISM; BACTERIOPLANKTON; CELL LINEAGE; CLADISTICS; ECOLOGY; ESTUARY; FLUORESCENCE IN SITU HYBRIDIZATION; GENOMICS; MARINE ENVIRONMENT; METABOLITE; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; ROSEOBACTER; SEA; SEASHORE; SHORT SURVEY; SYMBIOSIS;

DNA, BACTERIAL; ECOSYSTEM; PHYLOGENY; RNA, RIBOSOMAL, 16S; ROSEOBACTER; SEAWATER;

ALGAE; BACTERIA (MICROORGANISMS); ROSEOBACTER;

EID: 26844510681     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.10.5665-5677.2005     Document Type: Short Survey

References (125)

1. Acinas, S. G., J. Antón, and F. Rodríguez-Valera. 1999. Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65:514-522.
2. Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554.
3. Adachi, M., T. Kanno, R. Okamoto, S. Itakura, M. Yamaguchi, and T. Nishijima. 2003. Population structure of Alexandrium (Dinophyceae) cyst formation-promoting bacteria in Hiroshima Bay, Japan. Appl. Environ. Microbiol. 69:6560-6568.
4. Alavi, M., T. Miller, K. Erlandson, R. Schneider, and R. Belas. 2001. Bacterial community associated with Pfiesteria-like dinoflagellate cultures. Environ. Microbiol. 3:380-396.
5. Alavi, M. R. 2004. Predator/prey interaction between Pfiesteria piscicida and Rhodomonas mediated by a marine alpha proteobacterium. Microb. Ecol. 47:48-58.
6. Allgaier, M., H. Uphoff, A. Felske, and I. Wagner-Döbler. 2003. Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl. Environ. Microbiol. 69:5051-5059.
7. Althoff, K., R. Schütt, R. Steffen, R. Batel, and W. E. G. Müller. 1998. Evidence for a symbiosis between bacteria of the genus Rhodobacter and the bacteria of the marine sponge Halichondria panicea: harbor for putatively toxic bacteria? Mar. Biol. 130:529-536.
8. Ashen, J. B., and L. J. Goff. 2000. Molecular and ecological evidence for species specificity and coevolution in a group of marine algal-bacterial symbioses. Appl. Environ. Microbiol. 66:3024-3030.
9. Barbieri, E., B. J. Paster, D. Hughes, L. Zurek, D. P. Moser, A. Teske, and M. L. Sogin. 2001. Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda: Loliginidae). Environ. Microbiol. 3:151-167.
10. Béjà, O., E. V. Koonin, L. Aravind, L. T. Taylor, H. Seitz, J. L. Stein, D. C. Bensen, R. A. Feldman, R. V. Swanson, and E. F. DeLong. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68:335-345.
11. Benlloch, S., F. Rodríguez-Valera, and A. J. Martinez-Murcia. 1995. Bacterial diversity in two coastal lagoons deduced from 16S rDNA PCR amplification and partial sequencing. FEMS Microbiol. Ecol. 18:267-279.
12. Boettcher, K. J., B. J. Barber, and J. T. Singer. 2000. Additional evidence that juvenile oyster disease is caused by a member of the Roseobacter group and colonization of nonaffected animals by Stappia stellulata-like strains. Appl. Environ. Microbiol. 66:3924-3930.
13. Boettcher, K. J., B. J. Barber, and J. T. Singer. 1999. Use of antibacterial agents to elucidate the etiology of juvenile oyster disease (JOD) in Crassostrea virginica and numerical dominance of an α-Proteobacterium in JOD-affected animals. Appl. Environ. Microbiol. 65:2534-2539.
14. Bowman, J. P., and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl. Environ. Microbiol. 69:2463-2483.
15. Brinkhoff, T., G. Bach, T. Heidorn, L. F. Liang, A. Schlingloff, and M. Simon. 2004. Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates. Appl. Environ. Microbiol. 70:2560-2565.
16. Brinkmeyer, R., K. Knittel, J. Jürgens, H. Weyland, R. Amann, and E. Helmke. 2003. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl. Environ. Microbiol. 69:6610-6619.
17. Brown, M. V., and J. P. Bowman. 2001. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol. Ecol. 35:267-275.
18. Buchan, A., L. S. Collier, E. L. Neidle, and M. A. Moran. 2000. Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage. Appl. Environ. Microbiol. 66:4662-4672.
19. Buchan, A., E. L. Neidle, and M. A. Moran. 2001. Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community. Appl. Environ. Microbiol. 67:5801-5809.
20. Cho, J.-C., and S. J. Giovannoni. 2004. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate- producing marine bacteria in the order 'Rhodobacterales.' Int. J. Syst. Evol. Microbiol. 54:1129-1136.
21. Cooney, R. P., O. Pantos, M. D. A. L. Tissier, M. R. Barer, A. G. O'Donnell, and J. C. Bythell. 2002. Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques. Environ. Microbiol. 4:401-413.
22. Cottrell, M. T., D. N. Wood, L. Yu, and D. L. Kirchman. 2000. Selected chitinase genes in cultured and uncultured marine bacteria in the α- and γ-subclasses of the Proteobacteria. Appl. Environ. Microbiol. 66:1195-1201.
23. Crump, B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65:3192-3204.
24. Dang, H. Y., and C. R. Lovell. 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.
25. Dang, H. Y., and C. R. Lovell. 2002. Seasonal dynamics of particle-associated and free-living marine Proteobacteria in a salt marsh tidal creek as determined using fluorescence in situ hybridization. Environ. Microbiol. 4:287-295.
26. Delong, E. F., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
27. Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:3044-3051.
28. Eilers, H., J. Pernthaler, J. Peplies, F. O. Glöckner, G. Gerdts, and R. Amann. 2001. Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67:5134-5142.
29. Felsenstein, J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
30. Frias-Lopez, J., A. L. Zerkle, G. T. Bonheyo, and B. W. Fouke. 2002. Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl. Environ. Microbiol. 68:2214-2228.
31. Fuhrman, J. A., S. H. Lee, Y. Masuchi, A. A. Davis, and R. M. Wilcox. 1994. Characterization of marine prokaryotic communities via DNA and RNA. Microb. Ecol. 28:133-145.
32. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1294-1302.
33. Fuhrman, J. A., and C. C. Ouverney. 1998. Marine microbial diversity studied via rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes. Aquat. Ecol. 32:3-15.
34. Gallacher, S., K. Flynn, J. Franco, E. Brueggemann, and H. Hines. 1997. Evidence for production of paralytic shellfish toxins by bacteria associated with Alexandrium spp. (Dinophyta) in culture. Appl. Environ. Microbiol. 63:239-245.
35. Gescher, J., A. Zaar, M. Mohamed, H. Schägger, and G. Fuchs. 2002. Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J. Bacteriol. 184:6301-6315.
36. Giovannoni, S. J., and M. Rappé. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes, p. 47-84. In D. L. Kirchman (ed.), Microbial ecology of the oceans. John Wiley & Sons, Inc., New York, N.Y.
37. González, J., and M. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
38. González, J., W. Whitman, R. Hodson, and M. Moran. 1996. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl. Environ. Microbiol. 62:4433-4440.
39. González, J. M., J. S. Covert, W. B. Whitman, J. R. Henriksen, F. Mayer, B. Scharf, R. Schmitt, A. Buchan, J. A. Fuhrman, R. P. Kiene, and M. A. Moran. 2003. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int. J. Syst. Evol. Microbiol. 53:1261-1269.
40. González, J. M., R. P. Kiene, and M. A. Moran. 1999. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65:3810-3819.
41. González, J. M., F. Mayer, M. A. Moran, R. E. Hodson, and W. B. Whitman. 1997. Sagittula stellata gen. nov. sp. nov., a lignin-transforming bacterium from a coastal environment. Int. J. Syst. Evol. Microbiol. 47:773-780.
42. González, J. M., R. Simó, R. Massana, J. S. Covert, E. O. Casamayor, C. Pedrós-Alió, and M. A. Moran. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66:4237-4246.
43. Gosink, J. J., R. P. Herwig, and J. T. Staley. 1997. Octadecabacter arcticus gen. nov., sp. nov., and O. antarcticus, sp. nov., nonpigmented, psychrophilic gas vacuolate bacteria from polar sea ice and water. Syst. Appl. Microbiol. 20:356-365.
44. Gram, L., H. P. Grossart, A. Schlingloff, and T. Kiørboe. 2002. Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl. Environ. Microbiol. 68:4111-4116.
45. Green, D. H., L. E. Llewellyn, A. P. Negri, S. I. Blackburn, and C. J. S. Bolch. 2004. Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum. FEMS Microbiol. Ecol. 47:345-357.
46. Grigioni, S., R. Boucher-Rodoni, A. Demarta, M. Tonolla, and R. Peduzzi. 2000. Phylogenetic characterisation of bacterial symbionts in the accessory nidamental glands of the sepioid Sepia officinalis (Cephalopoda:Decapoda). Mar. Biol. 136:217-222.
47. Harder, T., S. C. K. Lau, S. Dobretsov, T. K. Fang, and P.-Y. Qian. 2003. A distinctive epibiotic bacterial community on the soft coral Dendronephthya sp. and antibacterial activity of coral tissue extracts suggest a chemical mechanism against bacterial epibiosis. FEMS Microbiol. Ecol. 43:337-347.
48. Henriques, I. S., A. Almeida, A. Cunha, and A. Correia. 2004. Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro. FEMS Microbiol. Ecol. 49:269-279.
49. Hjelm, M., O. Bergh, A. Riaza, J. Nielsen, J. Melchiorsen, S. Jensen, H. Duncan, P. Ahrens, T. H. Birkbeck, and L. Gram. 2004. Selection and identification of autochthonous potential probiotic bacteria from turbot larvae (Scophthalmus maximus) rearing units. Syst. Appl. Microbiol. 27:360-371.
50. Hold, G. L., E. A. Smith, M. S. Rappé, E. W. Maas, E. R. B. Moore, C. Stroempl, J. R. Stephen, J. I. Prosser, T. H. Birkheck, and S. Gallacher. 2001. Characterisation of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea. FEMS Microbiol. Ecol. 37:161-173.
51. Holmes, A. J., D. P. Kelly, S. C. Baker, A. S. Thompson, P. DeMarco, E. M. Kenna, and J. C. Murrell. 1997. Methylosulfonomonas methylovora gen. nov., sp. nov., and Marinosulfonomonas methylotropha gen. nov., sp. nov.: novel methylotrophs able to grow on methanesulfonic acid. Arch. Microbiol. 167:46-53.
52. Inagaki, F., M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, K. H. Nealson, and K. Horikoshi. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69:7224-7235.
53. Ivanova, E. P., N. M. Gorshkova, T. Sawabe, N. V. Zhukova, K. Hayashi, V. V. Kurilenko, Y. Alexeeva, V. Buljan, D. V. Nicolau, V. V. Mikhailov, and R. Christen. 2004. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int. J. Syst. Evol. Microbiol. 54:475-480.
54. Jonkers, H. M., and R. M. M. Abed. 2003. Identification of aerobic heterotrophic bacteria from the photic zone of a hypersaline microbial mat. Aquat. Microb. Ecol. 30:127-133.
55. Junge, K., F. Imhoff, T. Staley, and J. W. Deming. 2002. Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at sub-zero temperature. Microb. Ecol. 43:315-328.
56. Kelly, K. M., and A. Y. Chistoserdov. 2001. Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microb. Ecol. 35:85-95.
57. Kiene, R. P., and L. J. Linn. 2000. Distribution and turnover of dissolved DMSP and its relationship with bacterial production and dimethylsulfide in the Gulf of Mexico. Limnol. Oceanogr. 45:849-861.
58. King, G. M. 2003. Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. Appl. Environ. Microbiol. 69:7257-7265.
59. Kolber, M. K., C. L. Van Dover, R. A. Niederman, and P. G. Falkowski. 2000. Bacterial photosynthesis in surface waters of the open ocean. Nature 407:177-179.
60. Labrenz, M., M. D. Collins, P. A. Lawson, B. J. Tindall, G. Braker, and P. Hirsch. 1998. Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake. Int. J. Syst. Bacteriol. 48:1363-1372.
61. Lafay, B., R. Ruimy, C. R. Detraubenberg, V. Breittmayer, M. J. Gauthier, and R. Christen. 1995. Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. Int. J. Syst. Bacteriol. 45:290-296.
62. Lau, S. C. K., M. M. Y. Tsoi, X. Li, I. Plakhotnikova, M. Wu, P.-K. Wong, and P.-Y. Qian. 2004. Loktanella hongkongensis sp. nov., a novel member of the α-Proteobacteria originating from marine biofilms in Hong Kong waters. Int. J. Syst. Evol. Microbiol. 54:2281-2284.
63. Li, L., J. Guenzennec, P. Nichols, P. Henry, M. Yanagibayashi, and C. Kato. 1999. Microbial diversity in Nankai Trough sediments at a depth of 3,843 m. J. Oceanogr. 55:635-642.
64. López-Garcia, P., S. Duperron, P. Philippot, J. Foriel, J. Susini, and D. Moreira. 2003. Bacterial diversity in hydrothermal sediment and epsilon proteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5:961-976.
65. López-Garcia, P., A. López-López, D. Moreira, and F. Rodríguez-Valera. 2001. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol. Ecol. 36:193-202.
66. Madrid, V. M., J. Y. Aller, R. C. Aller, and A. Y. Chistoserdov. 2001. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisions. FEMS Microbiol. Ecol. 37:197-209.
67. Malmstrom, R. R., R. P. Kiene, and D. L. Kirchman. 2004. Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico. Limnol. Oceanogr. 49:597-606.
68. Martínez-Cánovas, M. J., E. Quesada, F. Martínez-Checa, A. del Moral, and V. Béjar. 2004. Salipiger mucescens gen. nov., sp. nov., a moderately halophilic, exopolysaccharide- producing bacterium isolated from hypersaline soil, belonging to the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 54:1735-1740.
69. Miller, T. R., and R. Belas. 2004. Dimethylsulfoniopropionate metabolism by Pfiesteria-associated Roseobacter spp. Appl. Environ. Microbiol. 70:3383-3391.
70. Mills, H. J., C. Hodges, K. Wilson, I. R. MacDonald, and P. A. Sobecky. 2003. Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol. Ecol. 46:39-52.
71. Mitova, M., G. Tommonaro, U. Hentschel, W. E. G. Muller, and S. De Rosa. 2004. Exocellular cyclic cipeptides from a Ruegeria strain associated with cell cultures of Suberites domuncula. Mar. Biotech. 6:95-103.
72. Moore, L. R., G. Rocap, and S. W. Chisholm. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464-467.
73. Moran, M. A., A. Buchan, J. M. González, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. John, B. Weaver, G. Pai, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D. A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, and N. Ward. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
74. Moran, M. A., J. M. González, and R. P. Kiene. 2003. Linking a bacterial taxon to sulfur cycling in the sea: studies of the marine Roseobacter group. Geomicrobiol. J. 20:375-388.
75. Moran, M. A., and R. E. Hodson. 1994. Dissolved humic substances of vascular plant-origin in a coastal marine-environment. Limnol. Oceanogr. 39:762-771.
76. Moune, S., P. Caumette, R. Matheron, and J. C. Willison. 2003. Molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in Mediterranean salterns. FEMS Microbiol. Ecol. 44:117-130.
77. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
78. O'Sullivan, L. A., K. E. Fuller, E. M. Thomas, C. M. Turley, J. C. Fry, and A. J. Weightman. 2004. Distribution and culturability of the uncultivated 'AGG58 cluster' of the Bacteroidetes phylum in aquatic environments. FEMS Microbiol. Ecol. 47:359-370.
79. Oz, A., G. Sabehi, M. Koblizek, R. Massana, and O. Béjà. 2005. Roseobacter-like bacteria in Red and Mediterranean Sea aerobic anoxygenic photosynthetic populations. Appl. Environ. Microbiol. 71:344-353.
80. Pantos, O., R. P. Cooney, M. D. A. Le Tissier, M. R. Barer, A. G. O'Donnell, and J. C. Bythell. 2003. The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis. Environ. Microbiol. 5:370-382.
81. Patel, P., M. E. Callow, I. Joint, and J. A. Callow. 2003. Specificity in the settlement-modifying response of bacterial biofilms towards zoospores of the marine alga Enteromorpha. Environ. Microbiol. 5:338-349.
82. Pernthaler, A., J. Pernthaler, M. Schattenhofer, and R. Amann. 2002. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl. Environ. Microbiol. 68:5728-5736.
83. Pinhassi, J., U. Zweifel, and A. Hagström. 1997. Dominant marine bacterioplankton species found among colony-forming bacteria. Appl. Environ. Microbiol. 63:3359-3366.
84. Powell, S. M., J. P. Bowman, I. Snape, and J. S. Stark. 2003. Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiol. Ecol. 45:135-145.
85. Pradella, S., M. Allgaier, C. Hoch, O. Päuker, E. Stackebrandt, and I. Wagner-Döbler. 2004. Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine alphaproteobacteria. Appl. Environ. Microbiol. 70:3360-3369.
86. Pukall, R., D. Buntefuss, A. Frühling, M. Rohde, R. Kroppenstedt, J. Burghardt, P. Lebaron, L. Bernard, and E. Stackebrandt. 1999. Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the α-Proteobacteria. Int. J. Syst. Bacteriol. 49:513-519.
87. Pukall, R., I. Kramer, M. Rohde, and E. Stackebrandt. 2002. Microbial diversity of cultivatable bacteria associated with the North Sea bryozoan Flustra foliacea. Syst. Appl. Microbiol. 24:623-633.
88. Rappé, M. S., P. F. Kemp, and S. J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42:811-826.
89. Rappé, M. S., K. Vergin, and S. J. Giovannoni. 2000. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol. Ecol. 33:219-232.
90. Riemann, L., G. F. Steward, and F. Azam. 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66:578-587.
91. Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser, and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042-1047.
92. Ruiz-Ponte, C., V. Cilia, C. Lambert, and J. L. Nicolas. 1998. Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. Int. J. Syst. Bacteriol. 48:537-542.
93. Sandaa, R.-A., T. Magnesen, L. Torkildsen, and Ø. Bergh. 2003. Characterisation of the bacterial community associated with early stages of great scallop (Pecten maximus), using denaturing gradient gel electrophoresis (DGGE). Syst. Appl. Microbiol. 26:302-311.
94. Schaefer, J. K., K. D. Goodwin, I. R. McDonald, J. C. Murrell, and R. S. Oremland. 2002. Leisingera methylohatidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int. J. Syst. Evol. Microbiol. 52:851-859.
95. Schäfer, H., B. Abbas, H. Witte, and G. Muyzer. 2002. Genetic diversity of 'satellite' bacteria present in cultures of marine diatoms. FEMS Microbiol. Ecol. 42:25-35.
96. Schmidt, T. M., E. F. Delong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S ribosomal RNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
97. Sekiguchi, H., H. Koshikawa, M. Hiroki, S. Murakami, K. Xu, M. Watanabe, M. Nakahara, M. Zhu, and H. Uchiyama. 2002. Bacterial distribution and phylogenetic diversity in the Changjiang Estuary before the construction of the Three Gorges Dam. Microb. Ecol. 43:82-91.
98. Selje, N., M. Simon, and T. Brinkhoff. 2004. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427:445-448.
99. Shiba, T. 1991. Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll-a. Syst. Appl. Microbiol. 14:140-145.
100. Shiba, T. 1984. Utilization of light energy by the strictly aerobic bacterium Erythrobacter sp. OCh 114. J. Gen. Appl. Microbiol. 30:239-244.
101. Shiba, T., U. Shimidu, and N. Taga. 1979. Distribution of aerobic bacteria which contain bacteriochlorophyll-a. Appl. Environ. Microbiol. 14:140-148.
102. Simu, K., and A. Hagström. 2004. Oligotrophic bacterioplankton with a novel single-cell life strategy. Appl. Environ. Microbiol. 70:2445-2451.
103. Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
104. Sorokin, D. Y. 1994. Influence of thiosulfate on the growth of sulfate-producing sulfur-oxidizing heterotrophic bacteria from the Black Sea in continuous culture. Microbiology 63:255-259.
105. Sorokin, D. Y. 1995. Sulfitobacter pontiacus gen. nov., sp. nov-a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Microbiology 64:295-305.
106. Sorokin, D. Y., and A. M. Lysenko. 1993. Heterotrophic bacteria from the Black Sea oxidizing reduced sulfur compounds to sulfate. Microbiology 62:594-602.
107. Suzuki, M., C. Preston, O. Béjà, J. de la Torre, G. Steward, and E. Delong. 2004. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 48:473-488.
108. Suzuki, M., M. Rappé, Z. Haimberger, H. Winfield, N. Adair, J. Ströbel, and S. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63:983-989.
109. Suzuki, M. T., C. M. Preston, F. P. Chavez, and E. F. DeLong. 2001. Quantitative mapping of bacterioplankton populations in seawater: field tests across an upwelling plume in Monterey Bay. Aquat. Microb. Ecol. 24:117-127.
110. Tanner, M. A., C. L. Everett, W. J. Coleman, M. M. Yang, and D. C. Youvan. 2000. Complex microbial communities inhabiting sulfide-rich black mud from marine coastal environments. Biotechnology et alia 8:1-16. [Online.] http://www.et-al.com.
111. Taylor, M. W., P. J. Schupp, I. Dahllöf, S. Kjelleberg, and P. D. Steinberg. 2004. Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity. Environ. Microbiol. 6:121-130.
112. Tolli, J. 2003. Identity and dynamics of the microbial community responsible for carbon monoxide oxidation in marine environments. Ph.D. thesis. Woods Hole Oceanographic Institution/Massachusetts Institute of Technology Joint Program, Woods Hole, Mass.
113. Urbance, J. W., B. J. Bratina, S. F. Stoddard, and T. M. Schmidt. 2001. Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid. Int. J. Syst. Evol. Microbiol. 51:1059-1070.
114. van Trappen, S., J. Mergaert, and J. Swings. 2004. Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int. J. Syst. Evol. Microbiol. 54:1263-1269.
115. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Y. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
116. Vetriani, C., H. V. Tran, and L. J. Kerkhof. 2003. Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Appl. Environ. Microbiol. 69:6481-6488.
117. Vila, M., R. Simó, R. P. Kiene, J. Pinhassi, J. M. González, M. A. Moran, and C. Pedrós-Alió. 2004. Use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incorporation by marine bacterioplankton taxa. Appl. Environ. Microbiol. 70:4648-4657.
118. Wagner-Döbler, I., H. Rheims, A. Felske, A. El-Ghezal, D. Flade-Schröder, H. Laatsch, S. Lang, R. Pukall, and B. J. Tindall. 2004. Oceanibulbus indolifex gen. nov., sp. nov., a North Sea α-proteobacterium that produces bioactive metabolites. Int. J. Syst. Evol. Microbiol. 54:1177-1184.
119. Webster, N. S., A. P. Negri, M. M. H. G. Munro, and C. N. Battershill. 2004. Diverse microbial communities inhabit Antarctic sponges. Environ. Microbiol. 6:288-300.
120. Weidner, S., W. Arnold, E. Stackebrandt, and A. Pühler. 2000. Phylogenetic analysis of bacterial communities associated with leaves of the seagrass Halophila stipulacea by a culture-independent small-subunit rRNA gene approach. Microb. Ecol. 39:22-31.
121. Yakimov, M. M., L. Giuliano, E. Crisafi, T. N. Chernikova, K. N. Timmis, and P. N. Golyshin. 2002. Microbial community of a saline mud volcano at San Biagio-Belpasso, Mt. Etna (Italy). Environ. Microbiol. 4:249-256.
122. Yoch, D. C. 2002. Dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide. Appl. Environ. Microbiol. 68:5804-5815.
123. Zafiriou, O. C., S. S. Andrews, and W. Wang. 2003. Concordant estimates of oceanic carbon monoxide source and sink processes in the Pacific yield a balanced global "blue-water" CO budget. Glob. Biogeochem. Cycl. 17:1015-1029.
124. Zhou, N.-Y, S. L. Fuenmayor, and P. A. Williams. 2001. nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 183:700-708.
125. Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2002. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep-Sea Res. II 49:3017-3038.