Stability and change in estuarine biofilm bacterial community diversity

Applied and Environmental Microbiology

Volumn 72, Issue 9, 2006, Pages 5679-5688

  Moss, Joseph A ^a   Nocker, Andreas ^a   Lepo, Joe E ^a   Snyder, Richard A ^a  

^a UNIVERSITY OF WEST FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; ECOSYSTEMS; ESTUARIES; GENETIC ENGINEERING; MICROORGANISMS; SALINITY MEASUREMENT;

AQUATIC ECOSYSTEM; BIOFOULING COMMUNITIES; GLASS SLIDES; POLYMORPHISM;

BIOFILMS;

DISSOLVED OXYGEN; RNA 16S;

AQUATIC ECOSYSTEM; BIOFILM; BIOFOULING; BIOGEOCHEMICAL CYCLE; ESTUARINE ECOSYSTEM; GENE EXPRESSION; MICROBIAL COMMUNITY; PHYLOGENETICS; POLYMORPHISM; RNA; SPECIES DIVERSITY;

AQUATIC ENVIRONMENT; ARTICLE; BENTHOS; BIOFILM; BIOGEOCHEMICAL CYCLING; ESTUARY; LIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT AVAILABILITY; PHYLOGENY; RIBOTYPING; SALINITY; SEASONAL VARIATION; TEMPERATURE;

BACTERIA; BACTERIAL PHYSIOLOGY; BASE SEQUENCE; BIOFILMS; BIOMASS; ECOSYSTEM; FLORIDA; GENES, BACTERIAL; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEASONS; WATER MICROBIOLOGY;

FLORIDA [UNITED STATES]; LITTLE SABINE BAY; NORTH AMERICA; UNITED STATES;

BACTERIA (MICROORGANISMS);

EID: 33748801965     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02773-05     Document Type: Article

References (48)

1. Allison, D. G., and P. Gilbert. 1992. Bacterial biofilms. Sci. Prog. 76:305-321.
2. Anwar, H., J. L. Strap., and J. W. Costerton. 1992. Establishment of aging biofilms: a possible mechanism of bacterial resistance to antimicrobial therapy. Antimicrob. Agents Chemother. 36:1347-1351.
3. Araya, R., K. Tani, T. Takagi, N. Yamaguchi, and M. Nasu. 2003. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol. Ecol. 43:111-119.
4. Boivin, J., and J. W. Costerton. 1991. Biofilms and biodeteriation, p. 53-62. In H. W. Rossmore (ed.), Biodeterioration and biodegradation. Elsevier Applied Science, London, England.
5. Bowman, J. P., S. A. McCammon, M. V. Brown, D. S. Nichols, and T. A. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:3068-3078.
6. Brummer, I. H. M., W. Fehr, and I. Wagner-Dobler. 2000. Biofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. Appl. Environ. Microbiol. 66:3078-3082.
7. Brunk, C. F., A. Aghajani, and C. A. Brunk. 1996. A complete analysis of primer and probe hybridization potential with bacterial small sub-unit sequences. Appl. Environ. Microbiol. 12:872-879.
8. Busscher, H. J., and H. C. Van der Mei. 1995. Use of flow chamber devices and image analysis methods to study microbial adhesion. Methods Enzymol. 253:455-476.
9. Clarke, K. R., and R. M. Warwick. 1998. A taxonomic distinctness index and its statistical properties. J. Appl. Ecol. 35:423-531.
10. Clarke, K. R., and R. M. Warwick. 1999. The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Mar. Ecol. Prog. Ser. 184:21-29.
11. Clarke, K. R., and R. M. Warwick. 2001. A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar. Ecol. Prog. Ser. 216:265-278.
12. Costerton, J. W., Z. Lewandowski, D. E. Caldwell, D. R. Korber, and H. M. Lappin-Scott. 1995. Microbial biofilms. Annu. Rev. Microbiol. 49:711-745.
13. Davies, D. G., A. M. Chakrabarty, and G. G. Geesey. 1993. Exopolysaccharide production in biofilms: substratum activation of alginate gene expression by Pseudomonas aeruginosa. Appl. Environ. Microbiol. 59:1181-1186.
14. Farrelly, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
15. Felsenstein, J. 1989. PHYLIP-Phylogenetic Inference Package (version 3.2). Cladistics 5:164-166.
16. Gupta, R. S. 2000. The phylogeny of proteobacteria: relationships to other cubacterial phyla and eukaryotes. FEMS Microbiol. Rev. 24:367-402.
17. Hamilton, W. A. 1985. Sulfate-reducing bacteria and anaerobic corrosion. Annu. Rev. Microbiol. 39:195-217.
18. Harper, J. L, and D. L. Hawksworth. 1994. Biodiversity: measurement and estimation. Phil. Trans. R. Soc. Lond. Ser. 345:5-12.
19. Huber, J. A., D. A. Butterfield, and J. A. Baross. 2004. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol. Ecol. 43:393-409.
20. Jackson, S. M., and E. B. G. Jones. 1991. Interactions within biofilms: the disruption of biofilm structure by protozoa. Kiel. Meeresforsch. Sonderh. 8:264-268.
21. Keith-Roach, M. J., N. D. Bryan, R. D. Bardgett, and F. R. Livens. 2002. Seasonal changes in the microbial community of a salt marsh, measured by phospholipid fatty acid analysis. Biogeochemistry 60:77-96.
22. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, N.Y.
23. Lawrence, J. R., P. J. Delaquis, D. R. Korber, and D. E. Caldwell. 1989. Behaviour of Pseudomonas fluorescens in the hydrodynamic boundary layer of surface microenvironments. Microb. Ecol. 14:1-14.
24. Lewis, M. A., D. A. Weber, L. R. Goodman, R. S. Stanley, G. Craven, J. M. Patrick, R. L. Quarles, T. H. Roush, and J. M. Macauley. 2000. Periphyton and sediment bioassessment in North Florida Bay. Environ. Monit. Assess. 65:503-522.
25. Liesack, W., H. Weyland, and E. Stackebrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21:191-198.
26. Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
27. Ludemann, H., I. Arth, and W. Liesack. 2000. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66:754-762.
28. Lukow, T., P. F. Dunfield, and W. Liesack. 2000. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol. Ecol. 32:241-247.
29. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, P. R. Saxman, J. M. Stredwick, G. M. Garrity, B. Li, G. J. Olsen, S. Pramanik, T. M. Schmidt, and J. M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:173-174.
30. Manz, W., K. Wendt-Potthoff, T. R. Neu, U. Szewyck, and J. R. Lawrence. 1999. Phylogenetic composition, spatial structure, and dynamics of lotie bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. Microb. Ecol. 37:225-237.
31. Marchesi, J. R., S. Takuichi, A. J. Weightman, T. A. Martin, J. C. Fry, S. J. Hiom, and G. M. Wade. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64:795-799.
32. Marshall, K. C. 1992. Biofilms: an overview of bacterial adhesion, activity, and control at surfaces. ASM News 58:202-207.
33. Michaud, L., F. Di Cello, M. Brilli, R. Fani, A. L. Giudice, and V. Bruni. 2004. Biodiversity of cultivable psychrotrophic marine bacteria from Terra Nova Bay (Ross Sea, Antarctica). FEMS Microbiol. Lett. 230:63-71.
34. Millie, D. F., H. J. Carrick, P. H. Doering, and K. A. Steidinger. 2004. Intra-annual variability of water quality of phytoplankton in the North Fork of the St. Lucie River Estuary, Florida (USA): a quantitative assessment. Estuar. Coast. Shelf Sci. 61:137-149.
35. Mummey, D. L., and P. Stahl. 2003. Spatial and temporal variability of bacterial 16S rDNA-based T-RFLP patterns derived from soil of two Wyoming grassland ecosystems. FEMS Microbiol. Ecol. 46:113-120.
36. Murrell, M. C., and E. M. Lores. 2004. Phytoplankton and Zooplankton seasonal dynamics in a subtropical estuary: importance of cyanobacteria. J. Plankton Res. 26:371-382.
37. Schmalenberger, A., F. Schwieger, and C. C. Tebbe. 2001. Effect of primers hybridizing to different evolutionary conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl. Environ. Microbiol. 67:3557-3563.
38. Shirtliff, M. E., J. T. Mader, and A. K. Camper. 2002. Molecular interactions in biofilms. Chem. Biol. 9:859-871.
39. Smit, E., P. Leeflang, and K. Wernars. 1997. Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol. Ecol. 23:249-261.
40. Smit, E., P. Leeflang, S. Gommans, J. van der Broek, S. van Mil, and K. Warners. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67:2284-2291.
41. Smith, N. R., Z. Yu, and W. W. Mohn. 2003. Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown. Water Res. 37:4873-4884.
42. Snyder, R. A., M. A. Lewis, A. Nocker, and J. E. Lepo. 2005. Microbial biofilms as integrative sensors of environmental quality, p. 111-122. In S. A. Bortone (ed.), Estuarine indicators. CRC Press, Boca Raton, Fla.
43. Soares, A., B. Guieysse, O. Delgado, and B. Mattiasson. 2003. Aerobic biodegradation of nonylphenol by cold-adapted bacteria. Biotechnol. Lett. 25:731-738.
44. van den Heuvael, J. C. 1992. Mass transfer in and around biofilms, p. 239-250. In L. F. Melo, T. R. Bott, M. Fletcher, and B. Capdeville (ed.), Biofilms: science and technology. Kluwer, Dordrecht, The Netherlands.
45. Viera, M. J., L. F. Melo., and M. M. Pinheiro. 1993. Biofilm formation: hydrodynamic effects on internal diffusion and structure. Biofouling 7:67-80.
46. Warwick, R. M., and K. R. Clarke. 1995. New "biodiversity" measures reveal a decrease in taxonomic distinctness with increasing stress. Mar. Ecol. Prog. Ser. 129:301-305.
47. Warwick, R. M., and K. R. Clarke. 1998. Taxonomic distinctness and environmental assessment. J. Appl. Ecol. 35:532-543.
48. Wolsing, M., and A. Prieme. 2004. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiol. Ecol. 48:261-271.