Abstract
The combination of molecular-genetic techniques used in the study is applied to investigate microorganisms associated with macrophytes. The method of enzymatic lysis with phenol-chloroform extraction is optimal for the total bacterial DNA isolation from both periphyton organisms and enriched cultures. Amplifying the total DNA on conservative primers at the two-step PCR regime is recommended. An analysis of the taxonomic diversity of the microbial community from biofilm on the reed grass and in the enriched cultures propagated on various growth media has been carried out. The results have revealed a high diversity of periphyton microorganisms associated with reed grass, including representatives of such phylogenetic lines as proteobacteria (α, β, γ, and δ subgroups), Bacteroidetes/Chlorobi, Chlamydiae/Verrucomicrobia, and cyanobacteria. The low diversity of sequences in enriched cultures is represented by dominating genotypes of Cellvibrio with a high percentage of homology and uncultivated bacilla.
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References
Bel’kova, N.L., Parfenova, V.V., Kostornova, T.Ya., et al., Microbial Biodiversity in the Water of Lake Baikal, Mikrobiologiya, 2003, vol. 72, no. 2, pp. 239–249.
Bel’kova, N.L., Dzyuba, E.V., Sukhanova, E.V., and Khanaeva, T.A., Adaptations of Methods of Molecular-Genetic Analysis for Study of Microorganisms Associated with Fish, Biol. Vnutr. Vod, 2008, no. 2, pp. 91–94.
Bel’kova, N.L., Khanaeva, T.A., and Dzyuba, E.V., Study of the Microflora of the Gastrointestinal Tract of Fish from Lake Baikal: Development of Efficient Methods for Isolating Total DNA, in Povyshenie effektivnost ispol’zovaniya vodnykh biologicheskikh resursov. Mater. Konf. (Improving the Efficiency of the Use of Water Biological Resources) (Proc. Conf.), Moscow, 2006, pp. 132–133.
Grachev, M.A., Kuznetsova, S.Yu., and Shcherbakova, T.A., A Method of Isolation of Highly Purified DNA to Be Used in Polymerase Chain Reaction, Mol. Biol. (Moscow), 2006, vol. 40, no. 1, pp. 180–183.
Denisova, L.Ya., Bel’kova, N.L., Tulokhonov, I.I., and Zaichikov, E.F., Bacterial Biodiversity at Different Depths of the South Trough of Lake Baikal Detected by 16S rRNA Sequences, Mikrobiologiya, 1999, vol. 68, no. 4, pp. 475–483.
Kudryavtsev, V.M., Bacteria in Foulings of Higher Water Plants, Gidrobiol. Zh., 1983, vol. 19, no. 3, pp. 60–65.
Rybakova, I.V., Microflora of Periphyton of Macrophytes of the Volga Stretch of the Rybinsk Reservoir, Biol. Vnutr. Vod, 2006, no. 2, pp. 13–18.
Yakushin, V.M., The Role of Bacterioplankton in the Destruction of Organic Matter in Lothic Ecosystems, Extended Abstract of Cand. Sci. (Biol.) Dissertation, Kiev, 1997.
Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., et al., Fine-Scale Phylogenetic Architecture of a Complex Bacterial Community, Nature (G. Brit.), 2004, vol. 430, no. 6999, pp. 551–554.
Ait Tayeb, L., Ageron, E., Grimont, F., and Grimont, P.A., Molecular Phylogeny of the Genus Pseudomonas Based on RpoB Sequences and Application for the Identification of Isolates, Res. Microbiol., 2005, vol. 156, nos. 5–6, pp. 763–773.
Amann, R.I., Ludwig, W., and Schleifer, K.-H., Phylogenetic Identification and in Situ Detection of Individual Microbial Cell without Cultivation, Microbiol. Rev., 1995, vol. 59, no. 1, pp. 143–169.
Anzai, Y., Kim, H., Park, J.-Y., et al., Phylogenetic Affiliation of the Pseudomonads Based on 16S RRNA Sequence, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, pp. 1563–1589.
Costello, A.M. and Lidstrom, M.E., Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments, Appl. Environ. Microbiol., 1999, vol. 65, no. 11, pp. 5066–5074.
Dauga, C., Evolution of the GyrB Gene and the Molecular Phylogeny of Enterobacteriaceae: A Model Molecule for Molecular Systematic Studies, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, no. 2, pp. 531–547.
Goebel, B.M. and Stackebrandt, E., Cultural and Phylogenetic Analysis of Mixed Microbial Populations Found in Natural and Commercial Bioleaching Environments, Appl. Environ. Microbiol., 1994, vol. 60, no. 5, pp. 1614–1621.
Masayasu, Y., Hiroshi, M., Aya, T., et al., Bacterial Flora in the Biofilm Formed on the Submerged Surface of the Reed Phragmites australis, Microb. Environ., 2005, vol. 20, no. 1, pp. 14–24.
Roggenkamp, A., Phylogenetic Analysis of Enteric Species of the Family Enterobacteriaceae using the OriCLocus, Syst. Appl. Microbiol., 2007, vol. 30, no. 3, pp. 180–188.
Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Coning: A Laboratory Manual,. New York: Cold Spring Harbor Laboratory Press, 1989, vol. 2.
Zhou, J., Bruns, M.A., and Tiede, J.M., DNA Recovery from Soils for Diverse Composition, Appl. Environ. Microbiol., 1996, vol. 62, no. 2, pp. 316–322.
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Original Russian Text © I.V. Rybakova, N.L. Bel’kova, N.A. Lapteva, E.V. Sukhanova, 2009, published in Biologiya Vnutrennikh Vod, No. 1, 2009, pp. 102–110.
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Rybakova, I.V., Bel’kova, N.L., Lapteva, N.A. et al. Adapting molecular-genetic methods for studying the taxonomic diversity of microbial communities associated with macrophytes. Inland Water Biol 2, 96–103 (2009). https://doi.org/10.1134/S1995082909010155
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DOI: https://doi.org/10.1134/S1995082909010155