Colonization of overlaying water by bacteria from dry river sediments

Environmental Microbiology

Volumn 10, Issue 10, 2008, Pages 2760-2772

  Fazi, Stefano ^a   Amalfitano, Stefano ^a   Piccini, Claudia ^b   Zoppini, Annamaria ^a   Puddu, Alberto ^a   Pernthaler, Jakob ^c  

^a WATER RESEARCH INSTITUTE   (Italy)

^b INSTITUTO DE INVESTIGACIONES BIOLÓGICAS CLEMENTE ESTABLE   (Uruguay)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALINE PHOSPHATASE; AMINOPEPTIDASE; BACTERIAL DNA; LEUCINE; RIBOSOME DNA; RNA 16S; THYMIDINE; TRITIUM;

ARTICLE; BACTERIAL COUNT; BACTERIUM; BIODIVERSITY; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; ITALY; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RIVER; SEDIMENT;

ALKALINE PHOSPHATASE; AMINOPEPTIDASES; BACTERIA; BIODIVERSITY; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; ITALY; LEUCINE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; THYMIDINE; TRITIUM;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACILLI (CLASS); BACILLUS (BACTERIUM); BACILLUS SP.; BACTERIA (MICROORGANISMS); BREVUNDIMONAS; CAULOBACTER; CYTOPHAGA; FLAVOBACTERIA; PROTEOBACTERIA; PROTISTA;

EID: 51649106623     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01695.x     Document Type: Article

References (77)

1. Abu-Ashour, J. Lee, H. (2000) Transport of bacteria on sloping soil surfaces by runoff. Environ Toxicol 15 : 149 153.
2. Abu-Ashour, J., Joy, D.M., Lee, H., Whiteley, H.R. Zelin, S. (1994) Transport of microorganisms through soil. Water Air Soil Pollut 75 : 141 158.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
4. Amalfitano, S., Fazi, S., Zoppini, A., Barra Caracciolo, A., Grenni, P. Puddu, A. (2008) Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers. Microb Ecol 55 : 270 279.
5. Amann, R., Ludwig, W. Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59 : 143 169.
6. st edn. Eaton, A.D., Clesceri, L.S., Rice, E.W. Greenberg, A.E. (eds). Washington, DC, USA : American Public Health Association, pp. 8/7 8/14.
7. Bär, M., von Hardenberg, J., Meron, E. Provenzale, A. (2002) Modeling the survival of bacteria in drylands: the advantage of being dormant. Proc R Soc Lond B 269 : 937 942.
8. Bell, R.T. (1993) Estimating production of heterotrophic bacterioplankton via incorporation of tritiated thymidine. In Handbook of Methods in Aquatic Microbial Ecology. Kemp, P.F., Sherr, B.F., Sherr, E.B. Cole, J.J. (eds). Boca Raton, FL, USA : Lewis Publisher, pp. 495 503.
9. Boenigk, J., Stadler, P., Wiedlroither, A. Hahn, M.W. (2004) Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the polynucleobacter cluster. Appl Environ Microbiol 70 : 5787 5793.
10. Buesing, N. Gessner, M.O. (2006) Benthic bacterial and fungal productivity and carbon turnover in a freshwater marsh. Appl Environ Microbiol 72 : 596 605.
11. Campbell Rehmann, L.L., Welty, C. Harvey, R.W. (1999) Stochastic analysis of virus transport in aquifers. Water Resour Res 35 : 1987 2006.
12. Camper, A.K., Hayes, J.T., Sturman, P.J., Jones, W.L. Cunningham, A.B. (1993) Effects of motility and adsorption rate coefficient on transport of bacteria through saturated porous media. Appl Environ Microbiol 59 : 3455 3462.
13. Chrost, R.J. (1990) Microbial ectoenzymes in aquatic environments. In Aquatic Microbial Ecology: Biochemical and Molecular Approaches. Overbeck, J. Chrost, R.J. (eds). New York, USA : Springer-Verlag, pp. 47 78.
14. Cole, J. (1999) Aquatic microbiology for ecosystem scientists: new and recycled paradigms in ecological microbiology. Ecosystems 2 : 215 225.
15. Daims, H., Bruhl, A., Amann, R., Schleifer, K.H. Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22 : 434 444.
16. De Weaver, A., Muylaert, K., Van der Gucht, K., Pirlot, S., Cocquyt, C., Descy, J.P., et al. (2005) Bacterial community composition in Lake Tanganyika: vertical and horizontal heterogeneity. Appl Environ Microbiol 71 : 5029 5037.
17. DeFlaun, M.F., Oppenheimer, S.R., Streger, S., Condee, C.W. Fletcher, M. (1999) Alterations in adhesion, transport, and membrane characteristics in an adhesion-deficient pseudomonad. App Environ Microbial 65 : 759 765.
18. Ducklow, H.W. Carlson, C.A. (1992) Oceanic bacterial production. Adv Microb Ecol 12 : 113 181.
19. Fazi, S., Amalfitano, S., Pernthaler, J. Puddu, A. (2005) Bacterial communities associated with benthic organic matter in headwater stream microhabitats. Environ Microbiol 7 : 1633 1640.
20. Fazi, S., Amalfitano, S., Pizzetti, I. Pernthaler, J. (2007) Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content. Syst Appl Microbiol 30 : 463 470.
21. Felske, A., Wolterink, A., van Lis, R., de Vos, W.M. Akkermans. A.D. (2000) Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66 : 3998 4003.
22. Fierer, N. Schimel, J.P. (2002) Effects of drying-rewetting frequency on soil carbon and nitrogen transformations. Soil Biol Biochem 34 : 777 787.
23. Fierer, N. Schimel, J.P. (2003) A proposed mechanism for the pulse in carbon dioxide production commonly observed following the rapid rewetting of a dry soil. Soil Sci Soc Am J 67 : 798 805.
24. Fierer, N., Schimel, J.P. Holden, P.A. (2003) Influence of drying-rewetting frequency on soil bacterial community structure. Microbial Ecol 45 : 63 71.
25. Fierer, N., Bradford, M.A. Jackson, R.B. (2007) Toward an ecological classification of soil bacteria. Ecology 88 : 1354 1364.
26. Fischer, H. Pusch, M. (2001) Comparison of bacterial production in sediments, epiphyton, and the pelegiac zone of a lowland river. Freshwater Biol 46 : 1335 1348.
27. Fritz, K.M. Dodds, W.K. (2004) Resistance and resilience of macroinvertebrate assemblages to drying and flood in a tallgrass prairie stream system. Hydrobiologia 527 : 99 112.
28. del Giorgio, P.A., Pace, M.L. Fischer, D. (2006) Relationship of bacterial growth efficiency to spatial variation in bacterial activity in the Hudson River. Aquat Microb Ecol 45 : 55 67.
29. Griebler, C., Mindl, B., Slezak, D. Geiger-Kaiser, M. (2002) Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat Microb Ecol 28 : 117 129.
30. Hamasaki, K., Long, R.A. Azam, F. (2004) Individual cell growth rates of marine bacteria, measured by bromodeoxyuridine incorporation. Aquat Microb Ecol 35 : 217 227.
31. Hoppe, H.G. (1993) Use of fluorogenic model substrates for extracellular enzyme activity measurement of bacteria. In Handbook of Methods in Aquatic Microbial Ecology. Kemp, P.F., Sherr, B.F., Sherr, E.B. Cole, J.J. (eds). Boca Raton, FL, USA : Lewis Publisher, pp. 423 431.
32. Hugenholtz, P., Goebel, B.M. Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180 : 4765 4774.
33. Hullar, M.A.J., Kaplan, L.A. Stahl, D.A. (2006) Recurring seasonal dynamics of microbial communities in stream habitats. Appl Environ Microbiol 72 : 713 722.
34. Iuga, M., Awram, P., Nomellini, J.F. Smit, J. (2004) Comparison of S-layer secretion genes in freshwater caulobacters. Can J Microbiol 50 : 751 766.
35. Jackson, E.F., Echlin, H.L. Jackson, C.R. (2006) Changes in the phyllosphere communityof the resurrectionfern, Polypodium polypodioides, associated with rainfall and wetting. FEMS Microbiol Ecol 58 : 236 246.
36. Jackson, R.B., Fierer, N. Schimel, J.P. (2007) New directions in microbial ecology. Ecology 88 : 1343 1344.
37. Janssen, P.H. (2006) Identifying the dominant soil bacterial taxa in libraries of 16s rRNA and 16s rRNA genes. Appl Environ Microbiol 72 : 1719 1728.
38. Kane, M.D., Poulsen, L.K. Stahl, D.A. (1993) Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl Environ Microbiol 59 : 682 686.
39. Kim, S.B. (2006) Numerical analysis of bacterial transport in saturated porous media. Hydrol Process 20 : 1177 1186.
40. Kirchman, D.L. (2001) Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. In Methods in Microbiology. Paul, J.H. (ed.). San Diego, CA, USA : Academic Press, 227 237.
41. Kirchman, D.L. (2002) The ecology of Cytophaga-Flavobacteria in aquatic environment. FEMS Microbiol Ecol 39 : 91 100.
42. Kirchman, D.L., Yu, L., Fuchs, B.M. Amann, R. (2001) Structure of bacterial communities in aquatic systems as revealed by filter PCR. Aquat Microb Ecol 26 : 13 22.
43. Koval, S.F. Hynes, S.H. (1991) Effect of paracrystalline protein surface layers on predation by Bdellovibrio bacteriovorus. J Bacteriol 173 : 2244 2249.
44. Lake, P.S. (2000) Disturbance, patchiness, and diversity in streams. J N Am Benthol Soc 19 : 573 592.
45. Lake, P.S., Palmer, M.A., Biro, P., Cole, J., Covich, A.P., Dahm, C., et al. (2000) Global change and the biodiversity of freshwater ecosystems: impacts on linkages between above-sediment and sediment biota. Bioscience 50 : 1099 1107.
46. Longnecker, K., Sherr, B.F. Sherr, E.B. (2006) Variation in cell-specific rates of leucine and thymidine incorporation by marine bacteria with high and with low nucleic acid content off the Oregon coast. Aquat Microb Ecol 43 : 113 125.
47. Loy, A., Horn, M. Wagner, M. (2003) ProbeBase - an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31 : 514 516.
48. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
49. Marxsen, J. Witzel, K.P. (1990) Significance of extracellular enzymes for organic matter degradation and nutrient regeneration in small streams. In Microbial Ectoenzymes in Aquatic Environments. Chrost, R.J. (ed.). New York, USA : Springer-Verlag, pp. 270 285.
50. Massana, R., Gasol, J.M., Bjørnsen, P.K., Blackburn, N.T., Hagström, Å., Hietanen, S., et al. (1997) Measurement of bacterial size via image analysis of epifluorescence preparations: description of an inexpensive system and solutions to some of the most common problems. Sci March 61 : 397 407.
51. Meier, H., Amann, R., Ludwig, W. Schleifer, K.H. (1999) Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G+C content. Syst Appl Microbiol 22 : 186 196.
52. Mikulík, K., Bobek, J., Bezousková, S., Benada, O. Kofronová, O. (2002) Expression of proteins and protein kinase activity during germination of aerial spores of Streptomyces granaticolor. Biochem Biophys Res Commun 299 : 335 342.
53. Miller, A.E., Schimel, J.P., Meixner, T., Sickman, J.O. Melack, J.M. (2005) Episodic rewetting enhances carbon and nitrogen release from chaparral soils. Soil Biol Biochem 37 : 2195 2204.
54. Muyzer, G., Hottenträger, S., Teske, A. Wawer, C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA: a new molecular approach to analyse the genetic diversity of mixed microbial communities. In Molecular Microbial Ecology Manual, vol. 3. Akkermans, A.D.L., Van Elsas, J.D. De Bruijn, F.J. (eds). Dordrecht, the Netherlands : Kluwer Academic Publishers, pp. 4.4.1 4. 4.23.
55. Onyenwoke, R.U., Brill, J.A., Farahi, K. Wiegel, J. (2004) Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes). Arch Microbiol 182 : 182 192.
56. Overpeck, J.T. Cole, J.E. (2006) Abrupt change in earth's climate system. Annu Rev Environ Res 31 : 1 31.
57. Pernthaler, J. (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3 : 537 546.
58. Pernthaler, A. Pernthaler, J. (2005) Diurnal variation of cells proliferation in three bacterial taxa from coastal North Sea waters. Appl Environ Microbiol 71 : 4638 4644.
59. Pernthaler, A., Pernthaler, J., Schattenhofen, M. Amann, R. (2002a) Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microbiol 68 : 5728 5736.
60. Pernthaler, A., Pernthaler, J. Amann, R. (2002b) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68 : 3094 3101.
61. Piccini, C., Conde, D., Alonso, C., Sommaruga, R. Pernthaler, J. (2006) Blooms of single bacterial species in a coastal lagoon of the Southwestern Atlantic Ocean. Appl Environ Microbiol 72 : 6560 6568.
62. Porter, K.G. Feig, Y.S. (1980) The use of DAPI for identifying and counting acquatic microflora. Limnol Oceanogr 25 : 943 948.
63. Potts, M. (1994) Desiccation tolerance of prokaryotes. Microbiol Rev 58 : 755 805.
64. Puddu, A., Zoppini, A., Fazi, S., Rosati, M., Amalfitano, S. Maialetti, E. (2003) Bacterial uptake of DOM released from P-limited phytoplankton. FEMS Microbiol Ecol 46 : 257 268.
65. Rees, G.N., Watson, G.O., Baldwin, D.S. Mitchell, A.M. (2006) Variability in sediment microbial communities in a semipermanent stream: impact of drought. J N Am Benthol Soc 25 : 370 378.
66. Sahoo, P.K., Soltani, S., Wong, K.C. Chen, Y.C. (1988) A survey of thresholding techniques. Comput Vis Graph Image Process 41 : 233 260.
67. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., et al. (1988) Primer-directed enzymatic amplification of DNA with thermostable DNA Polymerase. Science 239 : 487 491.
68. Salcher, M.M., Pernthaler, J., Psenner, R. Posch, T. (2005) Succession of bacterial grazing defense mechanisms against protistan predators in an experimental microbial community. Aquat Microb Ecol 38 : 215 229.
69. Sanger, F., Nicklen, S. Coulsen, A.R. (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci 74 : 5457 5463.
70. Schimel, J., Balser, T.C. Wallenstein, M. (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88 : 1386 1394.
71. Siegle, D.A. Kolter, R. (1992) Life after log. J Bacteriol 174 : 345 348.
72. Sirová, D., Vrba, J. Rejmánková, E. (2006) Extracellular enzyme activities in benthic cyanobacterial mats: comparison between nutrientenriched and control sites in marshes of northern Belize. Aquat Microb Ecol 44 : 11 20.
73. Suzuki, M.T. Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of rRNA genes by PCR. Appl Environ Microbiol 62 : 625 630.
74. Warnecke, F., Sommaruga, R., Sekar, R., Hofer, J. Pernthaler, J. (2005) Abundances, identity, and growth state of actinobacteria in mountain lakes of different UV transparency. Appl Environ Microbiol 71 : 5551 5559.
75. Wilczek, S., Fischer, H. Pusch, M.T. (2005) Regulation and seasonal dynamics of extracellular enzyme activities in the sediments of a large lowland river. Microb Ecol 50 : 253 267.
76. Williams, V. Fletcher, M. (1996) Pseudomonas fluorescens adhesion and transport through porous media are affected by lipopolysaccharide composition. Appl Environ Microbiol 62 : 100 104.
77. Yung, P.T., Shafaat, H.S., Connon, S.A. Ponce, A. (2007) Quantification of viable endospores from a Greenland ice core. FEMS Microbiol Ecol 59 : 300 306.