Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater

FEMS Microbiology Ecology

Volumn 53, Issue 3, 2005, Pages 379-391

  Abell, G C J ^a,b   Bowman, John P ^a  

^a UNIVERSITY OF TASMANIA   (Australia)

^b CSIRO   (Australia)

Author keywords

Biogeography; Cytophaga Flavobacterium Bacteroides group; DGGE; Flavobacteria; Psychrophilic bacteria; Seawater; Southern Ocean

Indexed keywords

ICE; ORGANIC MATTER; RNA 16S; SEA WATER;

COMMUNITY DYNAMICS; MESOCOSM; SECONDARY PRODUCTION;

ALPHAPROTEOBACTERIA; ANTARCTICA; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL FLORA; BACTERIOPLANKTON; COMMUNITY ECOLOGY; COMPREHENSION; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DETRITUS; DIATOM; EUKARYOTE; FLAVOBACTERIA; GAMMAPROTEOBACTERIA; INCUBATION TIME; MARINE ENVIRONMENT; MESOCOSM; MICROBIAL POPULATION DYNAMICS; MICROPORE FILTER; MOLECULAR CLONING; MOLECULAR STABILITY; NONHUMAN; OBSERVATION; PARTICLE RESUSPENSION; PARTICULATE MATTER; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SAMPLE; SEA; SPECIES COMPOSITION; SPECIES DIVERSITY;

DIATOMS; DNA, BACTERIAL; ELECTROPHORESIS; FLAVOBACTERIUM; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SILICON DIOXIDE; WATER MICROBIOLOGY;

OCEANIC REGIONS; SOUTHERN OCEAN; WORLD;

ALPHAPROTEOBACTERIA; BACILLARIOPHYTA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); CYTOPHAGA; EUKARYOTA; FLAVOBACTERIA; FLAVOBACTERIUM; GAMMAPROTEOBACTERIA; NITZSCHIA ALBA; NITZSCHIA CLOSTERIUM;

EID: 22044458597     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2005.01.008     Document Type: Article

References (54)

1. D.M. Karl Microbial processes in the Southern Oceans Antarctic microbiology 1992 Wiley-Liss New York 1 63
2. E.E. Kopczynska, F. Dehairs, M. Elskens, and S. Wright Phytoplankton and microzooplankton variability between the Subtropical and Polar Fronts south of Australia: Thriving under regenerative and new production in late summer J. Geophys. Res.-Oceans 106 2001 31597 31609
3. J.J Cole, S. Findlay, and M.L. Pace Bacterial production in fresh and saltwater ecosystems - a cross-system overview Mar. Ecol. Prog. Ser. 43 1988 1 10
4. H.W. Paerl, and T.F. Steppe Scaling up: the next challenge in environmental microbiology Environ. Microbiol. 5 2003 1025 1038
5. K.D. Bidle, and F. Azam Accelerated dissolution of diatom silica by marine bacterial assemblages Nature 397 1999 508 512
6. K.D. Bidle, and F. Azam Bacterial control of silicon regeneration from diatom detritus: significance of bacterial ectohydrolases and species identity Limnol. Oceanogr. 46 2001 1606 1623
7. K.D. Bidle, M.A. Brzezinski, R.A. Long, J.L. Jones, and F. Azam Diminished efficiency in the oceanic silica pump caused by bacteria-mediated silica dissolution Limnol. Oceanogr. 48 2003 1855 1868
8. L. Riemann, G.F. Steward, and F. Azam Dynamics of bacterial community composition and activity during a mesocosm diatom bloom Appl. Environ. Microbiol. 66 2000 578 587
9. L. Prieto, J. Ruiz, F. Echevarria, C.M. Garcia, A. Bartual, J.A. Galvez, A. Corzo, and D. Macias Scales and processes in the aggregation of diatom blooms: high time resolution and wide size range records in a mesocosm study Deep-Sea Res. I. 49 2002 1233 1253
10. P. Lebaron, P. Servais, M. Troussellier, C. Courties, J. Vives-Rego, G. Muyzer, L. Bernard, T. Guindulain, H. Schafer, and E. Stackebrandt Changes in bacterial community structure in seawater mesocosms differing in their nutrient status Aquat. Microb. Ecol. 19 1999 255 267
11. J. Pinhassi, F. Azam, J. Hemphala, R.A. Long, J. Martinez, U.L. Zweifel, and Å. Hagstrom Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation Aquat. Microb. Ecol. 17 1999 13 26
12. H. Schafer, L. Bernard, C. Courties, P. Lebaron, P. Servais, R. Pukall, E. Stackebrandt, M. Trousellier, T. Guindulain, J. Vives-Rego, and G. Muyzer Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations FEMS Microbiol. Ecol. 34 2001 243 253
13. I. Joint, P. Henriksen, G.A. Fonnes, D. Bourne, T.F. Thingstad, and B. Riemann Competition for inorganic nutrients between phytoplankton and bacterioplankton in nutrient manipulated mesocosms Aquat. Microb. Ecol. 29 2002 145 159
14. H.P. Grossart, L. Riemann, and F. Azam Bacterial motility in the sea and its ecological implications Aquat. Microb. Ecol. 25 2001 247 258
15. H. Heukelekian, and A. Heller Relation between food concentration and surface for bacterial growth J. Bacteriol. 40 1940 547 558
16. F.O. Glöckner, B.M. Fuchs, and R. Amann Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization Appl. Environ. Microbiol. 65 1999 3721 3726
17. M. Simon, F.O. Glöckner, and R. Amann Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean Aquat. Microb. Ecol. 18 1999 275 284
18. M.V. Brown, and J.P. Bowman A molecular phylogenetic survey of sea-ice microbial communities (SIMCO) FEMS Microbiol. Ecol. 35 2001 267 275
19. R. Brinkmeyer, K. Knittel, J. Jurgens, H. Weyland, R. Amann, and E. Helmke Diversity and structure of bacterial communities in Arctic versus Antarctic Pack Ice Appl. Environ. Microbiol. 69 2003 6610 6619
20. G.C.J. Abell, and J.P. Bowman Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean FEMS Microbiol. Ecol. 51 2005 265 277
21. J. Rath, K.Y. Wo, G.J. Herndl, and E.F. DeLong High phylogenetic diversity in a marine-snow-associated bacterial assemblage Aquat. Microb. Ecol. 14 1998 261 269
22. L.A. O'Sullivan, K.E. Fuller, E.M. Thomas, C.M. Turley, J.C. Fry, and A.J. Weightman Distribution and culturability of the uncultivated 'AGG58 cluster' of the Bacteroidetes phylum in aquatic environments FEMS Microbiol. Ecol. 47 2004 359 370
23. L.B. Fandino, L. Riemann, G.F. Steward, R.A. Long, and F. Azam Variations in bacterial community structure during a dinoflagellate bloom analysed by DGGE and 16S rDNA sequencing Aquat. Microb. Ecol. 23 2001 119 130
24. J. Pinhassi, M.M. Sala, H. Havskum, P. Fransesc, O. Guadayol, A. Malits, and C. Marrasé Changes in bacterioplankton composition under different phytoplankton regimes Appl. Environ. Microbiol. 70 2004 6753 6766
25. M.T. Cottrell, and D.L. Kirchman 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 2000 1692 1697
26. I. Janse, G. Zwart, M.J.E.C. van de Maarel, and J.C. Gottschal Composition of the bacterial community degrading Phaeocystis mucopolysaccharides in enrichment cultures Aquat. Microb. Ecol. 22 2001 119 133
27. J.S. Covert, and M.A. Moran Molecular characterization of estuarine bacterial communities that use high- and low-molecular weight fractions of dissolved organic carbon Aquat Microb. Ecol. 25 2001 127 139
28. J.P. Bowman, C.A. Mancuso Nichols, and J.A.E. Gibson Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats Int. J. Syst. Evol. Microbiol. 53 2003 1343 1355
29. D.L. Kirchman, L. Yu, and M.T. Cottrell Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary Appl. Environ. Microbiol. 69 2003 6587 6596
30. E.F. DeLong, D.G. Franks, and A.L. Alldredge Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages Limnol. Oceanogr. 38 1993 924 934
31. K. Graßhoff On the determination of silica in seawater Deep Sea Res. 11 1964 597 604
32. R. Weller, F.O. Glöckner, and R. Amann 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides Syst. Appl. Microbiol. 23 2000 107 114
33. J.A. Fuhrman, D.E. Comeau, Å. Hagstrom, and A.M. Chan Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies Appl. Environ. Microbiol. 54 1988 1426 1429
34. D.J. Lane 16S/23S rRNA sequencing E. Stackebrandt M. Goodfellow Nucleic acid techniques in bacterial systematics 1991 John Wiley & Sons New York 115 175
35. M.J. Ferris, G. Muyzer, and D.M. Ward Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community Appl. Environ. Microbiol. 62 1996 340 346
36. S.M. Powell, J.P. Bowman, I. Snape, and J.S. Stark Microbial community variation in pristine and polluted nearshore Antarctic sediments FEMS Microbiol. Ecol. 45 2003 135 145
37. M.S. Rappé, S.A. Connon, K.L. Vergin, and S.J. Giovannoni Cultivation of the ubiquitous SAR11 marine bacterioplankton clade Nature 418 2002 630 633
38. J. Marmur, and P. Doty Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature J. Mol. Biol. 5 1962 109 118
39. T.A. Hall A user-friendly biological sequence alignment editor for Windows 95/98/NT Nucl. Acids Symp. Ser. 41 1999 95 98
40. Felsenstein, J. PHYLIP, phylogenetic inference package. 1993. Available from: http://evolution.genetics._washington.edu/phylip.html
41. Bowman, J.P., Nichols, D.S. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium gen. nov, Subsaxibacter gen. nov., Lacinutrix gen. nov., and new species of the genera Biziolla, Gelidibacter and Gillisia. Int. J. Syst. Evol. Microbiol., DOI: 10.1099/ijs.0.63527-0, in press
42. L. Riemann, G.F. Steward, L.B. Fandino, L. Campbell, M.R. Landry, and F. Azam Bacterial community composition during two consecutive NE monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes Deep Sea Res. II 46 1999 1791 1811
43. E.O. Casamayor, H. Schafer, L. Baneras, C. Pedros-Alio, and G. Muyzer Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis Appl. Environ. Microbiol. 66 2000 499 508
44. Kan, J., Wang, K., Chen, F. Are 5000 bacterial cells per ml the detection threshold for PCR-DGGE annalysis? in: 10th International Symposium on Microbial Ecology, Cancun, Mexico, August 22-27, 2004, p. 266
45. M. Gleitz, S. Grossmann, R. Scharek, and V. Smetacek Ecology of diatom and bacterial assemblages in water associated with melting summer sea ice in the Weddell Sea, Antarctica Antarctic Sci. 8 1996 135 146
46. F. Azam Microbial control of oceanic carbon flux: The plot thickens Science 280 1998 694 696
47. D.A. Ratkowsky, J. Olley, and T. Ross Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins J. Theoret. Biol. 233 2005 351 362
48. T. Kiorboe, and G.A. Jackson Marine snow, organic solute plumes, and optimal chemosensory behavior of bacteria Limnol. Oceanogr. 46 2001 1309 1318
49. H.P. Grossart, T. Kiorboe, K. Tang, and H. Ploug Bacterial colonization of particles: Growth and interactions Appl. Environ. Microbiol. 69 6 2003 3500 3509
50. K. Meiners, R. Brinkmeyer, M.A. Granskog, and A. Lindfors Abundance, size distribution and bacterial colonization of exopolymer particles in Antarctic sea ice (Bellingshausen Sea) Aquat. Microbiol. Ecol. 35 2004 283 296
51. R.A. Long, and F. Azam Antagonistic interactions among marine pelagic bacteria Appl. Environ. Microbiol. 67 2001 4975 4983
52. P. Chesson, S.W. Pacala, and C. Neuhauser Environmental niches and ecosystem functioning A.P. Kinzig S.W. Pacala D. Tilman The functional consequences of biodiversity: empirical progress and theoretical extensions 2002 Princeton University, Press Princeton, NJ 213 245
53. M.W. Hahn, P. Stadler, Q.L. Wu, and M. Pockl The filtration- acclimatization method for isolation of an important fraction of the not readily cultivable bacteria J. Microbiol. Meth. 57 2004 379 390
54. T. Kaeberlein, K. Lewis, and S.S. Epstein Isolating " uncultivable" microorganisms in pure culture in a simulated natural environment Science 296 2002 1127 1129