Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques - PubMed (original) (raw)

Comparative Study

Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques

Hideyuki Tamaki et al. Appl Environ Microbiol. 2005 Apr.

Abstract

Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

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Figures

FIG. 1.

Effects of medium composition, pH conditions, and gelling reagents on viable counts after 11 weeks of incubation under aerobic (a) and anaerobic (b) conditions. White and black bars represent CFU counts from agar-based (A) and gellan gum-based (G) media, respectively. The vertical bars indicate 1 SD from the mean.

FIG. 2.

Effects of gelling reagents (agar [a] and gellan gum [b]) on the phylogenetic distribution of microbes cultivated from freshwater sediment with PE03 medium (pH 7.0) over various bacterial lineages on the basis of 16S rRNA gene analysis.

FIG. 3.

Effects of gelling reagents in PE03 medium (pH 7.0) on the cultivation of novel microbes from freshwater sediment under aerobic conditions. The similarity percentages shown are the 16S rRNA gene sequence similarities between the cultivated microbes and their closest relatives in the GenBank database.

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References

1. 1. Altmann, D., P. Stief, R. Amann, D. De Beer, and A. Schramm. 2003. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ. Microbiol. 5:798-803. - PubMed
2. 1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. - PubMed
3. 1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169. - PMC - PubMed
4. 1. Brummer, I. H., A. Felske, and I. Wagner-Dobler. 2003. Diversity and seasonal variability of beta-proteobacteria in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning. Appl. Environ. Microbiol. 69:4463-4473. - PMC - PubMed
5. 1. Bruns, A., H. Cypionka, and J. Overmann. 2002. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68:3978-3987. - PMC - PubMed

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