Influence of particle size on bacterial community structure in aquatic sediments as revealed by 16S rRNA gene sequence analysis

Applied and Environmental Microbiology

Volumn 74, Issue 16, 2008, Pages 5237-5240

  Jackson, Colin R ^a   Weeks, Andrew Q ^a  

^a UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; 16S RRNA GENE SEQUENCE; AQUATIC SEDIMENTS; BACTERIAL ASSEMBLAGES; BACTERIAL COMMUNITIES; BACTERIAL COMMUNITY STRUCTURE; COMMUNITY STRUCTURES; DENATURING GRADIENT GEL ELECTROPHORESIS; PLANCTOMYCETES; SEDIMENT PARTICLES;

BACTERIOLOGY; COLLOIDS; ELECTROPHORESIS; GELATION; GRAIN SIZE AND SHAPE; PARTICLE SIZE; SEDIMENTATION; SEDIMENTOLOGY; SEDIMENTS; WASTEWATER TREATMENT;

PARTICLE SIZE ANALYSIS;

RNA 16S;

BACTERIUM; COMMUNITY STRUCTURE; ELECTROKINESIS; GEL; GENETIC ANALYSIS; MICROBIAL COMMUNITY; PARTICLE SIZE; POLYMERASE CHAIN REACTION; RNA;

ARTICLE; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; GENE SEQUENCE; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTICLE SIZE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

BACTERIA; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENE LIBRARY; GENES, RRNA; GEOLOGIC SEDIMENTS; MISSISSIPPI; MOLECULAR SEQUENCE DATA; PARTICLE SIZE; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVERS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); PLANCTOMYCETES; VERRUCOMICROBIA;

EID: 50049102997     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00923-08     Document Type: Article

References (21)

1. Allgaier, M., and H.-P. Grossart. 2006. Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany. Aquat. Microb. Ecol. 45:115-128.
2. Beier, S., K.-P. Witzel, and J. Marxsen. 2008. Bacterial community composition in central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes. Appl. Environ. Microbiol. 74:188-199.
3. Besemer, K., M. M. Moeseneder, J. M. Arrieta, G. J. Herndl, and P. Peduzzi. 2005. Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Appl. Environ. Microbiol. 71:609-620.
4. 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.
5. DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
6. DeSantis, T. Z., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394-W399.
7. Jackson, C. R., H. W. Langner, J. Donahoe-Christiansen, W. P. Inskeep, and T. R. McDermott. 2001. Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring. Environ. Microbiol. 3:532-542.
8. Jackson, E. F., H. L. Echlin, and C. R. Jackson. 2006. Changes in the phyllosphere community of the resurrection fern, Polypodium polypodioides, associated with rainfall and wetting. FEMS Microbiol. Ecol. 58:236-246.
9. 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.
10. Lozupone, C. A., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
11. Lozupone, C. A., M. Hamady, and R. Knight. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371.
12. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
13. Lyautey, E., C. R. Jackson, J. Cayrou, J.-L. Rols, and F. Garabétian. 2005. Bacterial community succession in natural river biofilm assemblages. Microb. Ecol. 50:589-601.
14. Nold, S. C., and G. Zwart. 1998. Patterns and governing forces in aquatic microbial communities. Aquat. Ecol. 32:17-35.
15. Rappe, M. S., and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369-394.
16. Santmire, J. A., and L. G. Leff. 2007. The influence of stream sediment particle size on bacterial abundance and community composition. Aquat. Ecol. 41:153-160.
17. Sessitsch, A., A. Weilharter, M. H. Gerzabek, H. Kirchmann, and E. Kandeler. 2001. Microbial population structures in soil particle size fraction of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67:4215-4224.
18. Sinsabaugh, R. L., T. Weiland, T., and A. E. Linkins. 1992. Enzymic and molecular analysis of microbial communities associated with lotie particulate organic matter. Freshw. Biol. 28:393-404.
19. Smart, K. A., H. L. Smart, and C. R. Jackson. 2008. The effects of fine scale environmental variation on microbial community structure and function in aquatic environments, p. 167-190. In G. V. Kurladze (ed.), Environmental microbiology research trends. Nova Science Publishers, Hauppauge, NY.
20. Wagner, M., and M. Horn. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17:241-249.
21. Yeager, P. E., and R. L. Sinsabaugh. 1998. Microbial diversity along a sediment dctrital particle size gradient. Aquat. Ecol. 32:281-289.