Growth and distribution patterns of Roseobacter/Rhodobacter, SAR11, and Bacteroidetes lineages in the Southern Ocean

Polar Biology

Volumn 36, Issue 5, 2013, Pages 691-704

  Tada, Yuya ^a   Makabe, Ryosuke ^b   Kasamatsu Takazawa, Nobue ^c   Taniguchi, Akito ^d   Hamasaki, Koji ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b HIROSHIMA UNIVERSITY   (Japan)

^c TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY   (Japan)

^d KINKI UNIVERSITY   (Japan)

Author keywords

Abundance; Bromodeoxyuridine; Fluorescence in situ hybridization; Growth; Marine bacteria; Southern Ocean

Indexed keywords

BACTERIUM; BIOMASS; CATALYSIS; CONCENTRATION (COMPOSITION); ENVIRONMENTAL GRADIENT; GENETIC ANALYSIS; GROWTH RATE; HYBRIDIZATION; ORGANIC MATTER; POPULATION DISTRIBUTION; TEMPERATURE EFFECT;

SOUTHERN OCEAN;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES;

EID: 84876107171     PISSN: 07224060     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00300-013-1294-8     Document Type: Article

References (72)

1. Abell GCJ, Bowman JP (2005) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51: 265-277.
2. Alonso-Saez L, Gasol JM (2007) Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in Northwestern Mediterranean coastal waters. Appl Environ Microbiol 73: 3528-3535.
3. Alonso-Saez L, Sanchez O, Gasol JM, Balague V, Pedros-Alio C (2008) Winter-to-summer changes in the composition and single-cell activity of near-surface Arctic prokaryotes. Environ Microbiol 10: 2444-2454.
4. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
5. Azam F (1998) Microbial control of oceanic carbon flux: the plot thickens. Science 280: 694-696.
6. Baldwin AJ, Moss JA, Pakulski JD, Catala P, Joux F, Jeffrey WH (2005) Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic Circles. Aquat Microb Ecol 41: 91-102.
7. Bjørnsen PK, Kuparinen J (1991) Determination of bacterioplankton biomass, net production and growth efficiency in the Southern Ocean. Mar Ecol Prog Ser 71: 185-194.
8. Bowman JP, McCammon SA, Brown MV, Nichols DS, McMeekin TA (1997a) Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microbiol 63: 3068-3078.
9. Bowman JP, McCammon SA, Brown JL, Nichols PD, McMeekin TA (1997b) Psychroserpens burtonensis gen. nov., sp. nov. and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from Antarctic lacustrine and sea ice habitats. Int J Syst Bacteriol 47: 670-677.
10. Brown SL, Landry MR (2001) Mesoscale variability in biological community structure and biomass in the Antarctic Polar Front region at 170 degrees W during austral spring 1997. J Geophys Res Oceans 106: 13917-13930.
11. Campbell BJ, Kirchman DL (2012) Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J 7: 210-220.
12. Campbell BJ, Yu L, Heidelberg JF, Kirchman DL (2011) Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci USA 108: 12776-12781.
13. Church MJ, Hutchins DA, Ducklow HW (2000) Limitation of bacterial growth by dissolved organic matter and iron in the Southern Ocean. Appl Environ Microbiol 66: 455-466.
14. Church MJ, DeLong EF, Ducklow HW, Karner MB, Preston CM, Karl DM (2003) Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula. Limnol Oceanogr 48: 1893-1902.
15. Cottrell MT, Kirchman DL (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular weight dissolved organic matter. Appl Environ Microbiol 66: 1692-1697.
16. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 38: 924-934.
17. Ducklow HW, Dickson ML, Kirchman DL, Steward G, Ochardo J, Marra J, Azam F (2000) Constraining bacterial production conversion efficiency and respiration in the Ross Sea, Antarctica, January-February, 1997. Deep-Sea Res II 47: 3227-3248.
18. Ducklow HW, Carlson C, Church M, Kirchman D, Smith D, Steward G (2001) The seasonal development of the bacterioplankton bloom in the Ross Sea, Antarctica, 1994-1997. Deep-Sea Res II 48: 4199-4221.
19. Ducklow HW, Schofield O, Vernet M, Stammerjohn S, Erickson M (2012) Multiscale control of bacterial production by phytoplankton dynamics and sea ice along the western Antarctic Peninsula: a regional and decadal investigation. J Mar Syst 98-99: 26-39.
20. Elifantz H, Dittell AI, Cottrell MT, Kirchman DL (2007) Dissolved organic matter assimilation by heterotrophic bacterial groups in the western Arctic Ocean. Aquat Microb Ecol 50: 39-49.
21. Fandino LB, Riemann L, Steward GF, Long RA, Azam F (2001) Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquat Microb Ecol 23: 119-130.
22. Fazi S, Amalfitano S, Piccini C, Zoppini A, Puddu A, Pernthaler J (2008) Colonization of overlaying water by bacteria from dry river sediments. Environ Microbiol 10: 2760-2772.
23. Giebel HA, Brinkhoff T, Zwisler W, Selje N, Simon M (2009) Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean. Environ Microbiol 11: 2164-2178.
24. Giovannoni SJ, Rappé M (2000) Evolution, diversity, and molecular ecology of marine prokaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, pp 47-84.
25. Giuliano L, De Domenico M, De Domenico E, Höfle MG, Yakimov MM (1999) Identification of culturable oligotrophic bacteria within naturally occurring bacterioplankton communities of the Ligurian Sea by 16S rRNA sequencing and probing. Microb Ecol 37: 77-85.
26. Glöckner FO, Fuchs BM, Amann R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65: 3721-3726.
27. Gosink JJ, Woese CR, Staley JT (1998) Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov., and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of "Flectobacillus glomeratus" as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 48: 223-235.
28. Hagström Å, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68: 3628-3633.
29. Hamasaki K, Long R, Azam F (2004) Individual cell growth rates of marine bacteria, measured by bromodeoxyuridine incorporation. Aquat Microb Ecol 35: 217-227.
30. Hamasaki K, Taniguchi A, Tada Y, Long RA, Azam F (2007) Actively growing bacteria in the Inland Sea of Japan identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis. Appl Environ Microbiol 73: 2787-2798.
31. Holm-Hansen O, Lorenzen CJ, Holmes RW, Strickland JDH (1965) Fluorometric determination of chlorophyll. J Cons Perm Int Explor Mer 30: 3-15.
32. Kirchman DL, Morán XAG, Ducklow H (2009) Microbial growth in the polar oceans-role of temperature and potential impact of climate change. Nat Rev 7: 451-459.
33. Lami R, Cottrell MT, Ras J, Ulloa O, Obernosterer I, Claustre H, Lebaron P (2007) High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean. Appl Environ Microbiol 73: 4198-4205.
34. Lochte K, Bjonrsen PK, Giesenhagen H, Weber A (1997) Bacterial standing stock and production and their relationship to phytoplankton in the Southern Ocean. Deep-Sea Res II 44(1-2): 321-340.
35. Malmstrom RR, Cottrell MT, Elifantz H, Kirchman DL (2005) Biomass production and dissolved organic matter assimilation by SAR11 bacteria in the Northwest Atlantic Ocean. Appl Environ Microbiol 71: 2979-2986.
36. Malmstrom RR, Straza TRA, Cottrell MT, Kirchman DL (2007) Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean. Aquat Microb Ecol 47: 45-55.
37. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer KH (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142: 1097-1106.
38. Marr D, Hildreth M (1980) Theory of edge detection. Proc R Soc Lond B 207: 187-217.
39. Maruyama A, Sunamura M (2000) Simultaneous direct counting of total and specific microbial cells in seawater, using a deep-sea microbe as target. Appl Environ Microbiol 66: 2211-2215.
40. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
41. Murray AE, Grzymski JJ (2007) Diversity and genomics of Antarctic marine micro-organisms. Philos Trans R Soc Lond B 362: 2259-2271.
42. Orsi AH, Whitworth T III, Nowlin DN Jr (1995) On the meridional extent and fronts of the Antarctic Circumpolar Current. Deep-Sea Res I 42: 641-673.
43. Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3: 537-546.
44. Pernthaler A, Pernthaler J, Amann R (2002a) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Ecol 68: 3094-3101.
45. Pernthaler A, Penthaler J, Schattenhofer M, Amann R (2002b) Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microb 68: 5728-5736.
46. Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol Ò, Malits A, Marrasé C (2004) Changes in bacterioplankton composition under different phytoplankton regimens. Appl Environ Microbiol 70: 6753-6766.
47. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström A (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16: 867-880.
48. Rappé MS, Connon SA, Vergin KL, Giovanni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
49. Rath J, Wu KY, Herndl GJ, DeLong EF (1998) High phylogenetic diversity in a marine-snow-associated bacterial assemblage. Aquat Microb Ecol 14: 262-269.
50. 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.
51. Selje N, Simon M, Brinkhoff T (2004) A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427: 445-448.
52. Sieracki ME, Reichenbach SE, Webb KL (1989) Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis. Appl Environ Microbiol 55: 2762-2772.
53. Simon M, Azam F (1989) Protein content and protein synthesis rates of planktonic marine bacteria. Mar Ecol Prog Ser 51: 201-213.
54. Simon M, Glöckner FO, Amann R (1999) Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat Microb Ecol 18: 275-284.
55. Smith EM, del Giorgio PA (2003) Low fractions of active bacteria in natural aquatic communities? Aquat Microb Ecol 31: 203-208.
56. Steward GF, Azam F (1999) Bromodeoxyuridine as an alternative to H-3-thymidine for measuring bacterial productivity in aquatic samples. Aquat Microb Ecol 19: 57-66.
57. Straza TRA, Cottrell MT, Ducklow HW, Kirchman DL (2009) Geographic and phylogenetic variation in bacterial biovolume using protein and nucleic acid staining. Appl Environ Microbiol 75: 4028-4034.
58. Straza TRA, Ducklow HW, Murray AE, Kirchman DL (2010) Abundance and single-cell activity of bacterial groups in Antarctic coastal waters. Limnol Oceanogr 55: 2526-2536.
59. Suttle CA (2007) Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 5: 801-812.
60. Suzuki R, Ishimaru T (1990) An improved method for the determination of phytoplankton chlorophyll using N, N-dimethylformamide. J Oceanogr 46: 190-194.
61. Tada Y, Taniguchi A, Hamasaki K (2009) Phylotype-specific productivity of marine bacterial populations in eutrophic seawater, as revealed by bromodeoxyuridine immunocytochemistry combined with fluorescence in situ hybridization. Microb Environ 24: 315-321.
62. Tada Y, Taniguchi A, Hamasaki K (2010) Phylotype-specific growth rates of marine bacteria measured by bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization. Aquat Microb Ecol 59: 229-238.
63. Tada Y, Taniguchi A, Nagao I, Miki T, Uematsu M, Tsuda A, Hamasaki K (2011) Differing growth responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean. Appl Environ Microbiol 77: 4055-4065.
64. Taniguchi A, Hamasaki K (2008) Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific. Environ Microbiol 10: 1007-1017.
65. Teira E, Mouriño-Carballido B, Martínez-García S, Sobrino C, Ameneiro J, Hernández-León S, Vázquez E (2012) Primary production and bacterial carbon metabolism around South Shetland Islands in the Southern Ocean. Deep-Sea Res I 69: 70-81.
66. Topping JN, Heywood JL, Ward P, Zubkov MV (2006) Bacterioplankton composition in the Scotia Sea, Antarctica, during the austral summer of 2003. Aquat Microb Ecol 45: 229-235.
67. Urbach E, Vergin KL, Giovanoni SJ (1999) Immunochemical detection and isolation of DNA from metabolically active bacteria. Appl Environ Microbiol 65: 1207-1213.
68. Vila-Costa M, Simó R, Alonso-Sáez L, Pedrós-Alió C (2008) Number and phylogenetic affiliation of bacteria assimilating dimethylsulfoniopropionate and leucine in the ice-covered coastal Arctic Ocean. J Mar Syst 74: 957-963.
69. Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14: 136-143.
70. Warnecke F, Sommaruga R, Sekar R, Hofer J, Pernthaler J (2005) Abundances, identity and growth of Actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol 71: 5551-5559.
71. West NJ, Obernosterer I, Zemb O, Lebaron P (2008) Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean. Environ Microbiol 10: 738-756.
72. Zeder M, Peter S, Shabarova T, Pernthaler J (2009) A small population of planktonic Flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake. Environ Microbiol 11: 2676-2686.