Characterization of several synthetic and environmental microbial samples by quantitative hybridization

Abstract

Abstract: Limitations of traditional techniques based on selective enrichment and pure culture isolation make it difficult to precisely characterize the natural microbial ecosystems. Molecular techniques are now being developed and used to address these limitations. Group specific 16SrRNAs targeted oligonucleotide probes of different phylogenetic levels are increasingly used to identify and quantify the microbial members in complex environmental samples. Two domain specific probes were used in this study to elementarily characterize the defined mixtures of RNAs extracted from pure culture (synthetic samples) and a RNAsample obtained from landfill leachate (environmental sample). The results demonstrated that 16SrRNAquantitative hybridization provided an excellent estimation of domain level community composition of these samples, and thus, had a huge potential of usefulness in microbial ecology studies.

Key words: 16S rRNA, Oligonucleotide probes, Quantitative hybridization, Microbial ecology, MTCLIM model, net primary productivity, topographic factor., 3PGS model, fire severity

CLC Number:

HUANG Linan, CHEN Yueqin, ZHOU Hui, QU Lianghu . Characterization of several synthetic and environmental microbial samples by quantitative hybridization[J]. Chinese Journal of Applied Ecology, 2003, (3): 405-408.

References

[1] Alm EW, Oerther DB, Larsen N,et al. 1996. The oligonucleotide probe database.Appl Environ Microbiol, 62:3557～3559
[2] Amann RI, Krumholz L,Stahl DA. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology.J Bacteriol,172:762～770
[3] Amann RI, Ludwig W,Schleifer KH. 1995. Phologenetic identification and in situ detection of individual microbial cells without cultivation.Microbiol Rev,59:143～169
[4] Atlas RM.1983.Use of microbial diversity measurements to assess environmental stress. In: Klug MJ and Reddy CA,eds. Current Perspectives in Microbial Ecology.Washington, D.C.:American Society for Microbiology.540～545
[5] Kogure K, Simidu U,Taga N. 1980. Distribution of viable marine bacterial in netrtic seawater around Japan.Can J Microbiol,26:318～323
[6] Raskin L,Capman WC, Sharp R,et al.1997. Molecular ecology of gastrointestinal ecosystems.In:Mackie RI, White BA, Issacson RE, eds. Gastrointestinal Microbiology 2.Gastrointestinal Microbes and Host Interactions.New York:Chanpman & Hall,243～298
[7] Raskin L, Poulse LK, Noguera DR,et al. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization.Appl Environ Microbiol,60:1241～1248
[8] Raskin L, Stromley JM, Rittmann BE,et al. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens.Appl Environ Microbiol,60:1232～1240
[9] Sambrook J, Fritsch EF Maniatis T. 1989. Molecular Cloning, A Laboratory Manual.2nd ed.New York: Cold Spring Harbor Laboratory Press.
[10] Stahl DA, Flesher B, Mansfield HR,et al. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology.Appl Environ Microbiol,54:1079～1084
[11] Staley JT,Konopka A. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats.Annu Rev Microbiiol,39:321～346
[12] Wagner M, Amann R, Lemmer H,et al. 1993. Probing activated sludge with proteobacteria-specific oligonucleotides:Inadequacy of culture-dependent methodsfor describing microbial community structure.Appl Environ Microbiol,59:1520～1525
[13] Ward DM, Bateson MM, Weller R,et al.1992.Ribosomal RNA analysis of microorganisms as they occur in nature. In: Marshall KC ed. Advances in Microbial Ecology.12. New York:Plenum Press. 219～286
[14] Woese CR,Fox GE. 1977. Phylogenetic structure of the prokaryotic domain:The primary kingdoms.Proc Natl Acad Sci USA,74:5088～5090
[15] Zheng D, Alm EW, Stahl DA,et al. 1996. Characterization of universal small subunit rRNA hybridization probes for quantitative molecular microbial studies.Appl Environ Microbiol,62:4504～4513