Serial analysis of ribosomal sequence tags (SARST): A high-throughput method for profiling complex microbial communities

Environmental Microbiology

Volumn 6, Issue 2, 2004, Pages 131-144

  Neufeld, Josh D ^a   Yu, Zhongtang ^b   Lam, Wan ^c   Mohn, William W ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b OHIO STATE UNIVERSITY   (United States)

^c BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA;

ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; RNA GENE;

BACTERIA; BACTERIAL PHYSIOLOGY; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 1142306022     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00547.x     Document Type: Article

References (54)

1. Angelastro, J.M., Ryu, E.J., Törõcsik, B., Fiske, B.K., and Greene, L.A. (2002) Blue-white selection step enhances the yield of SAGE concatemers. Biotechniques 32: 486.
2. Axelrood, P.E., Chow, M.L., Radomski, C.C., McDermott, J.M., and Davies, J. (2002) Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can J Microbiol 48: 655-674.
3. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A., and Wheeler, D.L. (2000) Genbank. Nucleic Acids Res 28: 15-18.
4. Bertilsson, S., Cavanaugh, C.M., and Polz, M.F. (2002) Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers. Appl Environ Microbiol 68: 6077-6086.
5. Borneman, J., Skroch, P.W., O'Sullivan, K.M., Palus, J.A., Rumjanek, N.G., Jansen, J.L., et al. (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62: 1935-1943.
6. Borneman, J., Austin, S., and Triplett, E.W. (1997) Method development to assess microbial diversity in soil. In Biotechnology Risk Assessment Symposium. Levin, M., Grim, C. and Angle, J.S., (eds). Maryland, USA: University of Maryland Biotechnology Institute, pp. 10-16.
7. Chao, A. (1984) Non-parametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
8. Chow, M.L., Radomski, C.C., McDermott, J.M., Davies, J., and Axelrood, P.E. (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42: 347-357.
9. Clayton, R., Sutton, G., Hinkle, P. Jr, Bult, C., and Fields, C. (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45: 595-599.
10. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
11. Crosby, L.D., and Criddle, C.S. (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-802.
12. Dunbar, J., Takala, S., Barns, S.M., Davis, J.A., and Kuske, C.R. (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65: 1662-1669.
13. Dunbar, J., Barns, S.M., Ticknor, L.O., and Kuske, C.R. (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68: 3035-3045.
14. Dunn, J.J., McCorkle, S.R., Praissman, L.A., Hind, G., Van Der Lelie, D., Bahou, W.F., et al. (2002) Genomic signature tags (GSTs): a system for profiling genomic DNA. Genome Res 12: 1756-1765.
15. Farrelly, V., Rainey, F., and Stackebrandt, E. (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.
16. Fogel, G.B., Collins, C.R., Li, J., and Brunk, C.F. (1999) Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microbiol Ecol 38: 93-113.
17. Fox, G., Wisotzkey, J., and Jurtshuk, P. Jr (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42: 166-170.
18. Hill, T.C.J., Walsh, K.A., Harris, J.A., and Moffett, B.F. (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43: 1-11.
19. Hobbie, J.E., Daley, R.J., and Jasper, S. (1977) Use of nucleopore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33: 1225-1228.
20. Hugenholtz, P., and Huber, T. (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53: 289-293.
21. Hughes, J.B., Hellmann, J.J., Ricketts, T.H., and Bohannan, B.J.M. (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
22. Kenzelmann, M., and Mühlemann, K. (1999) Substantially enhanced cloning efficiency of SAGE (Serial Analysis of Gene Expression) by adding a heating step to the original protocol. Nucleic Acids Res 27: 917-918.
23. Klappenbach, J.A., Dunbar, J.M., and Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
24. Koehl, A., Friauf, E., and Nothwang, H.G. (2003) Efficient cloning of SAGE tags by blunt-end ligation of polished concatemers. Biotechniques 34: 692-694.
25. Kopczynski, E.D., Bateson, M.M., and Ward, D.M. (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60: 746-748.
26. Kroes, I., Lepp, P.W., and Relman, D.A. (1999) Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci USA 96: 14547-14552.
27. Lee, C., Grasso, C., and Sharlow, M.F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18: 452-464.
28. Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Saxman, P.R., Farris, R.J., et al. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 173-174.
29. McCaig, A.E., Glover, L.A., and Prosser, J.I. (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65: 1721-1730.
30. McCaig, A.E., Glover, L.A., and Prosser, J.I. (2001a) Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol 67: 4554-4559.
31. McCaig, A.E., Grayston, S.J., Prosser, J.I., and Glover, L.A. (2001b) Impact of cultivation on characterisation of species composition of soil bacterial communities. FEMS Microbiol Ecol 35: 37-48.
32. Neufeld, J.D., and Mohn, W.W. (2002a) Alignment Scanner vs. 1.0. [WWW document] URL http://www.microbiology. ubc.ca/Mohn/SARST.
33. Neufeld, J.D., and Mohn, W.W. (2002b) SARSTeditor vs. 1.0. In [WWW document] URL http://www.microbiology.ubc.ca/ Mohn/SARST.
34. Nogales, B., Moore, E.R., Abraham, W.R., and Timmis, K.N. (1999) Identification of the metabolically active members of a bacterial community in the polychlorinated biphenyl-polluted moorland soil. Environ Microbiol 1: 199-212.
35. Nogales, B., Moore, E.R., Llobet-Brossa, E., Rossello-Mora, R., Amann, R., and Timmis, K.N. (2001) Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67: 1874-1884.
36. Pace, N.R., Stahl, D.A., Lane, D.J., and Olsen, G.J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microbial Ecol 9: 1-55.
37. Qiu, X., Wu, L., Huang, H., McDonel, P.E., Palumbo, A.V., Tiedje, J.M., and Zhou, J. (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67: 880-887.
38. Ravenschlag, K., Sahm, K., Pernthaler, J., and Amann, R. (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65: 3982-3989.
39. Rossello-Mora, R., and Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39-67.
40. Sambrook, J., and Russel, D.W. (2001) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
41. Seguritan, V., and Rohwer, F. (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences. BMC Bioinformatics 2: 9.
42. Smit, E., Leeflang, P., Gommans, S., van den Broek, J., van Mil, S., and Wernars, K. (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.
43. Snaidr, J., Amann, R., Huber, I., Ludwig, W., and Schleifer, K.-H. (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63: 2884-2896.
44. Speksnijder, A.G.C.L., Kowalchuk, G.A., De Jong, S., Kline, E., Stephen, J.R., and Laanbroek, H.J. (2001) Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 67: 469-472.
45. Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D., and Doré, J. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65: 4799-4807.
46. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
47. Tiedje, J.M., Asuming-Brempong, S., Nüsslein, K., Marsh, T.L., and Flynn, S.J. (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13: 109-122.
48. Valinsky, L., Della Vedova, G., Scupham, A.J., Alvey, S., Figueroa, A., Yin, B., et al. (2002) Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 68: 3243-3250.
49. Van de Peer, Y., and De Wachter, R. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10: 569-570.
50. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. (1995) Serial analysis of gene expression. Science 270: 484-487.
51. Wang, G.C., and Wang, Y. (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiol 142: 1107-1114.
52. Wang, G., and Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63: 4645-4650.
53. Wintzingerode, F.V., Göbel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
54. Yu, Z., and Mohn, W.W. (2001) Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analysis and 16S ribosomal DNA sequencing. Appl Environ Microbiol 67: 1565-1574.