OJE  Vol.4 No.8 , May 2014
Antarctic Cyanobacteria Biodiversity Based on ITS and TrnL Sequencing and Its Ecological Implication

Antarctic cyanobacteria biodiversity was investigated by simultaneous sequencing of the nuclear ribosomal internal transcribed spacer (ITS flanked by partial 16S and 23S), and Chloroplast tRNALeu UAA intron (TrnL), exploring whether such morphotypes constitute distinct species and explaining their current distribution. We identified Nostocales, Chrococcales and Oscillatoriales species, collected in different habitats (soil, algal mats, lake sediments, ice-water) after their growth in cultures. By comparative sequence analyses available in Genbank, our results proved to be mostly in agreement with both TrnL and ITS, in the identification of the strains, particularly for Nostocales. Although ITS demonstrated more usefully than TrnL did in identifying Oscillatoriales and Chroococcales, due to the frequent lack of the intron in these groups, our results lead us to support an independent phylogenetic dataset of ITS and TrnL (the latter based on conserved regions) producing not only concordant clusters but also a secondary structure. Specific assignments of the secondary structure evidenced by different cyanobacteria groups, especially the D1-D1’ region of ITS and the P6b region of TrnL. For the latter region, the sequences analyzed for Nostoc species could be divided into the two classes previously identified, on the basis of different heptanucleotide repeats in P6b which were not foun

Cite this paper: Micheli, C. , Cianchi, R. , Paperi, R. , Belmonte, A. and Pushparaj, B. (2014) Antarctic Cyanobacteria Biodiversity Based on ITS and TrnL Sequencing and Its Ecological Implication. Open Journal of Ecology, 4, 456-467. doi: 10.4236/oje.2014.48039.

[1]   Warwick, F.V. (2000) Evolutionary Origins of Antarctic Microbiota: Invasion, Selection and Endemism. Antarctic Science, 12, 374-385.

[2]   Trenberth, K.E. (2009) An Imperative for Climate Change Planning: Tracking Earth’s Global Energy. Current Opinion in Environmental Sustainability, 1, 19-27.

[3]   Smetacek, V. and Nicol, S. (2005) Polar Ocean Ecosystems in a Changing World. Nature, 437, 362-368.

[4]   Graham, L.E. and Wilcox, L.W. (2000) Algae. Prentice Hall, Upper Saddle River, 640.

[5]   Honda, D., Yokota, A. and Sugiyava, J. (1998) Detection of Seven Major Evolutionary Lineages in Cyanobacteria Based on the 16S tRNA Gene Sequence Analysis with New Sequences of Five Marine Synecococcus Strains. Journal of Molecular Evolution, 48, 723-739.

[6]   Oksanen, I., Lohtander, K., Sivonen, K. and Rikkinen, J. (2004) Repeat-Type Distribution in TrnL Intron Does Not Correspond with Species Phylogeny; Comparison of the Genetic Markers 16S rRNA and TrnL Intron in Heterocystous Cyanobacteria. International Journal of Systematic and Evolutionary Microbiology, 54, 765-772.

[7]   Komárek, J. and Anagnostidis, K. (2005) Cyanoprokaryota 2.Teil: Oscillatoriales. Elsevier GmbH, Munchen, 759 p.

[8]   Komarek, J. and Anagnostic, K. (1989) Modern Approach to the Classification System of Cyanophites 4-Nostocales. Algological Studies/Archiv für Hydrobiologie, 56, 247-345.

[9]   Hoffmann, L., Komárek, J. and Kastovsky, J. (2005) System of Cyanoprokaryotes (Cyanobacteria)—State 2004. Algological Studies, 117, 95-115.

[10]   Anagnostidis, K. and Komárek, J. (1985) Modern Approach to the Classification System of Cyanophytes 1—Introduction. Archiv für Hydrobiologie, Supplement, 71, 291-302.

[11]   Rippka, R, Deruelles, J., Waterbury, J.B., Herdmann, M. and Stanier, R.Y. (1979) Generic Assignments, Strain Histories and Properties of Pure Coltures of Cyanobacteria. Journal of General Microbiology, 3, 1-61.

[12]   Wirtz, N., Lumbsch, H.T., Gree, T.G.A., Turk, R., Pindado, A., Sancho, L. and Schroeter, B. (2003) Lichen Fungi Have Low Cyanobiont Selectivity in Maritime Antarctica. New Phytologist, 160, 177-183.

[13]   Wilmotte, A. (1994) Molecular Evolution and Taxonomy of Cyanobacteria. In: Bryant, D.A., Ed., The Molecular Biology of Cyanobacteria, Kluwer, Dordrecht, 1-25.

[14]   Caroppo, C., Albertano, P., Bruno, L., Montinari, M., Rizzi, M., Vigliotta, G. and Pagliara, P. (2012) Identification and Characterization of a New Halomicronema Species (Cyanobacteria) Isolated from the Mediterranean Marine Sponge Petrosia ficiformis (Porifera) Fottea. Olomouc, 12, 315-326.

[15]   Iteman, I., Rippka, R., de Marsac, N.T. and Herdman, M. (2001) Comparison of Conserved Structural and Regulatory Domains within Divergent 16S rRNA-23S rRNA Spacer Sequences of Cyanobacteria. Microbiology, 146, 1275-1286.

[16]   Taberlet, P., Gielly, L., Pautou, G. and Bouvet, J. (1991) University Primers for Amplification of Three Non-Coding Regions of Chloroplast DNA. Plant Molecular Biology, 17, 1105-1109.

[17]   Ferris, C., Oliver, R.P, Davy, A.J. and Hewitt, G.M. (1993) Native Oak Chloroplast Reveals an Ancient Divide across Europe. Molecular Ecology, 2, 337-344.

[18]   Gielly, L. and Taberlet, P. (1994) The Use of Chloroplast DNA to Resolve Plant Phylogenies: Noncoding versus rbcL Sequences. Molecular Biology and Evolution, 11, 769-777.

[19]   Paquin, B., Kathe, S.D., Nierzwick-Bauer, S.A. and Shub, D.A. (1997) Origin and Evolution of Group I Introns in Cyanobacterial tRNA Genes. Journal of Bacteriology, 179, 6798-6806.

[20]   Kuhsel, M.G., Strickland, R. and Palmer, J.D. (1990) An Ancient Group I Intron Shared by Eubacteria and Chloroplasts. Science, 250, 1570-1573.

[21]   Xu, E.M., Kathe, S.D., Goodrich-Blair, H., Nierzwicki-Bauer, S.A. and Shub, D.A. (1990) Bacterial Origin of a Chloroplast Intron: Conserved Self-Splicing Group I Introns in Cyanobacteria. Science, 250, 1570-1573.

[22]   Amoutzias, G.D., Van de Peer, Y. and Mossialos, D. (2008) Evolution and Taxonomic Distribution of Noribosomal Peptide and Polyketide Synthases. Future Microbiology, 3, 361-370.

[23]   Zhao, J., Yang, N. and Zeng, R. (2008) Phylogenetic Analysis of Type I Polyketide Synthase and Non-Ribosomal Peptide Synthetase Genes in Antarctic Sediment. Extremophiles, 12, 97-105.

[24]   Pushparaj, B., Buccioni, A., Paperi, R., Piccardi, R., Ena, A., Carrozzi, P. and Sili, C. (2008) Fatty Acid Composition of Antarctic Cyanobacteria. Phycologia, 47, 430-434.

[25]   Dembitsky, V.M. and Rezanka, T. (2005) Metabolites Produced by Nitrogen Fixing Nostoc Species. Folia Microbiologica, 50, 363-391.

[26]   Paulsrud, P. and Lindblad, P. (1997) Sequence Variation of the tRNA(Leu) Intron as a Marker for Genetic Diversity and Specificity of Symbiotic Cyanobacteria in Some Lichens. Applied and Environmental Microbiology, 64, 310-315.

[27]   Paulsrud, P., Rikkinen, J. and Lindblad, P. (1998) Cyanobiont Specificity in Some Nostoc-Containing Lichens and in a Peltigera aphthosa Photosymbiodeme. New Phytologist, 139, 517-524.

[28]   Costa, J.L., Paulsrud, P., Rikkinen, J. and Lindblad, P. (2001) Genetic Diversity of Nostoc Symbionts Endophytically Associated with Two Bryophyte Species. Applied and Environmental Microbiology, 67, 4393-4396.

[29]   Costa, J.L., Paulsrud, P. and Lindblad, P. (2002) The Cyanobacterial tRNALeu (UAA) Intron: Evolutionary Patterns in a Genetic Marker. Molecular Biology and Evolution, 19, 850-857.

[30]   Hoshina, R. and Imamura, N. (2008) Eu-Chlorella Large Subunit rDNA Sequences and Group I Intron in Ribosomal DNA of the Paramecian Symbiotic Alga NC64A. Phycological Research, 56, 21-32.

[31]   Micheli, C., Spinosa, F., Paperi, R., Buccioni, A. and Pushparaj, B. (2007) Biodiversity and Fatty Acid Production in Cyanobacteria. Rapports et Proces-Verbaux des Rèunions Commission Internationale pour l’Exploration Scientifique de la Mer Méditerranée, 38, 380.

[32]   Galtier, N., Gouy, M. and Gautier, C. (1996) SEAVIEW and PHYLO_WIN: Two Graphic Tools for Sequence Alignment and Molecular Phylogeny. Computer Applications in the Biosciences, 12, 543-548.

[33]   Edgar, R.C. (2004) MUSCLE: Multiple Sequence Alignment with High Accuracy and High throughput. Nucleic Acids Research, 32, 1792-1797.

[34]   Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution, 24, 1596-1599.

[35]   Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004) Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure. Proceedings of the National Academy of Sciences of the United States of America, 101, 7287-7292.

[36]   Taton, A., Grubisic, S., Balthasart, P., Hodgson, D.A., Laybourn-Parry, Wilmotte, A. (2006) Biogeographycal Distribution and Ecological Ranges of Benthic Cyanobacteria in East Antarctica Lakes. FEMS Microbiology Ecology, 57, 272-289.

[37]   Condon, C., Squires, C. and Squires, C.L. (1995) Control of rRNA Transcription in Escherichia coli. Microbiological Reviews, 59, 623-645.

[38]   Reháková, K., Johansen, J.R., Casamatta, D.A., Li, X.S. and Vincent, J. (2007) Morphological and Molecular Characterization of Selected Desert Soil Cyanobacteria: Three Species New to Science Including Mojavia pulchra Gen. et sp. Nov. Phycologia, 46, 481-502.

[39]   Johansen, J.R., Olsen, C.E., Lowe, R.L., Fucíková, K. and Casamatta, D.A. (2008) Leptolyngbya Species from Selected Seep Walls in the Great Smoky Mountains National Park. Algological Studies, 126, 21-36.

[40]   Cech, T.R., Damberger, S.H. and Gutell, R.R. (1994) Representation of the Secondary and Tertiary Structures of Group I Introns. Nature Structural Biology, 1, 273-280.

[41]   Taton, A., Grubisic, S., Brambilla, B., De Vit, R. and Wilmotte, A. (2003) Cyanobacterial Diversity in Natural and Artificial Microbial Mats of Lake Fryxell (McMurdo Dry Valley, Antarctica): A Morphological and Molecular Approach. Applied and Environmental Microbiology, 69, 5157-5169.