Cyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo dry valleys, Antarctica): A morphological and molecular approach
Taton, A.; Grubisic, Stana; Brambilla, E.et al.
2003 • In Applied and Environmental Microbiology, 69 (9), p. 5157-5169
cyanobacteria; ribosomal RNA; diversity; lake Fryxell; endemism
Abstract :
[en] Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria in a field microbial mat sample from Lake Fryxell and in an artificial cold-adapted sample cultured in a benthic gradient chamber (BGC) by using an inoculum from the same mat. Light microscopy and molecular tools, including 16S rRNA gene clone libraries, denaturing gradient gel electrophoresis, and sequencing, were used. For the first time in the study of cyanobacterial diversity of environmental samples, internal transcribed spacer (ITS) sequences were retrieved and analyzed to complement the information obtained from the 16S rRNA gene. Microscopy allowed eight morphotypes to be identified, only one of which is likely to be an Antarctic endemic morphotype. Molecular analysis, however, revealed an entirely different pattern. A much higher number of phylotypes (15 phylotypes) was found, but no sequences from Nodularia and Hydrocoryne, as observed by microscopy, were retrieved. The 16S rRNA gene sequences determined in this study were distributed in 11 phylogenetic lineages, 3 of which were exclusively Antarctic and 2 of which were novel. Collectively, these Antarctic sequences together with all the other polar sequences were distributed in 22 lineages, 9 of which were exclusively Antarctic, including the 2 novel lineages observed in this study. The cultured BGC mat had lower diversity than the field mat. However, the two samples shared three morphotypes and three phylotypes. Moreover, the BGC mat allowed enrichment of one additional phylotype. ITS sequence analysis revealed a complex signal that was difficult to interpret. Finally, this study provided evidence of molecular diversity of cyanobacteria in Antarctica that is much greater than the diversity currently known based on traditional microscopic analysis. Furthermore, Antarctic endemic species were more abundant than was estimated on the basis of morphological features. Decisive arguments concerning the global geographic distribution of cyanobacteria should therefore incorporate data obtained with the molecular tools described here.
Grubisic, Stana ; Université de Liège - ULiège > Services administratifs généraux > Protection et hygiène du travail (SUPHT)
Brambilla, E.
De Wit, R.
Wilmotte, Annick ; Université de Liège - ULiège > Département des sciences de la vie > Enzymologie
Language :
English
Title :
Cyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo dry valleys, Antarctica): A morphological and molecular approach
Publication date :
September 2003
Journal title :
Applied and Environmental Microbiology
ISSN :
0099-2240
eISSN :
1098-5336
Publisher :
Amer Soc Microbiology, Washington, United States - Washington
Amann, R. I., W. Ludwig, and K. H. Schleifer. 11995. Phylogenic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
Anagnostidis, K., and J. Komárek. 1988. Modern approach to the classification system of cyanophytes. 3. Oscillatoriales. Arch. Hydrobiol. 50/ 53(Suppl. 80):327-472.
Baurain, D., L. Renquin, S. Grubisic, and P. Scheldeman. 2002. Remarkable conservation of internally transcribed spacer sequences of Arthrospira ("Spirulina") (Cyanophyceae, Cyanobacteria) strains from four continents and of recent and 30-year-old dried samples from Africa. J. Phycol. 38:384-393.
Bebout, B. M., and F. Garcia-Pichel. 1995. UV B-induced vertical migrations of cyanobacteria in a microbial mat. Appl. Environ. Microbiol. 61:4215-4222.
Benlloch, S., S. G. Acinas, J. Anton, L. Lopez, S. P. Luz, and F. Rodiguez-Valera. 2001. Archeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microb. Ecol. 41:12-19.
Bowman, J. P., S. M. Rea, S. A. MeCammon, and T. A. McMeekin. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environ. Microbiol. 2:227-237.
Boyer, S. L., J. R. Johansen, V. R. Flechtner, and G. L. Howard. 2002. Phylogeny and genetic variance in terrestrial Microcoleus (Cyanophyceae) species based on sequence analysis of the 16S rRNA gene and associated 16S-23S ITS region. J. Phycol. 38:1222-1235.
Brambilla, E., H. Hippe, A. Hagelstein, B. J. Tindall, and E. Stackebrandt. 2001. 16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antarctica. Extremophiles 5:23-33.
Broady, P. A. 1982. Taxonomy and ecology of algae in a freshwater stream in Taylor Valley, Victoria Land, Antarctica. Arch. Hydrobiol. 32:331-349.
Broady, P. A., and A. L. Kibblewhite. 1991. Morphological characterization of Oscillatoriales (eyanobacteria) from Ross Island and southern Victoria Land, Antarctica. Antarct. Sci. 3:35-45.
Buffan-Dubau, E., O. Pringault, and R. de Wit. 2001. Artificial cold-adaptated microbial mats cultured from Antarctic lake samples. I. Formation and structure. Aquat. Microb. Ecol. 26:115-125.
Christner, B. C., B. H. Kvitko II, and J. N. Reeve. 2003. Molecular identification of bacteria and eukarya inhabiting an Antarctic cryoconite hole. Extremophiles 7:177-183.
Ernst, A., S. Becker, U. I. A. Wollenzien, and C. Postius. 2003. Ecosystem-dependent adaptive radiations of picocyanobacteria inferred from 16S rRNA and ITS-1 sequence analysis. Microbiology 149:217-228.
Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-346.
Furhman, J. A., and L. Campbell. 1998. Microbial microdiversity. Nature 393:410-411.
Garcia-Pichel, F., A. López-Cortés, and U. Nübel. 2001. Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado Plateau. Appl. Environ. Microbiol. 67:1902-1910.
Garcia-Pichel, F., L. Prufert-Bebout, and G. Muyzer. 1996. Phenotypic and phylogenetic analyses show Microcoleus chtlionoplastes to be a cosmopolitan cyanobacterium. Appl. Environ. Microbiol. 62:3284-3291.
Geitler, L. 1932. Cyanophyceae. Rabenhorst's Kryptogamen-Flora von Deutschland, Österreich und der Schweiz. Akademische Verlagsgesellsehaft, Leipzig, Germany.
Good, I. J. 1953. The population frequencies of species and the estimation to the population parameters. Biometrika 40:237-264.
Gordon, D. A., J. Priscu, and S. Giovannoni. 2000. Origin and phylogeny of microbes living in permanent Antarctic lake ice. Microb. Ecol. 36:197-202.
Hodgson, D. A., W. Vyverman, and K. Sabbe. 2001. Limnology and biology of saline lakes in the Rauer Islands, eastern Antarctica. Antarct. Sci. 13:255-270.
Howsley, R., and H. W. Pearson. 1979. pH dependent sulfide toxicity to oxygenic photosynthesis in cyanobacteria. FEMS Microbiol. Lett. 6:287-292.
lshida, T., M. M. Watanabe, J. Sugiyama, and A. Yokota. 2001. Evidence for polyphyletic origin of the members of Oscillatoriales and Pleurocapsales as determined by 16S rDNA analysis. FEMS Microbiol. Lett. 201:79-82.
Iteman, I., R. Rippka, N. Tandeau de Marsac, and M. Herdman. 2000. Comparison of conserved structural and regulatory domains within divergent 16S rRNA-23S rRNA spacer sequences of cyanobacteria. Microbiology 146:1275-1286.
Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
Komárek, J., and K. Anagnostidis. 1989. Modern approach to the classification system of cyanophytes. 4. Nostocales. Arch. Hydrobiol. 56(Suppl. 82/3):247-345.
Komárek, J. 1999. Diversity of cyanoprokaryotes (cyanobacteria) of King George Island, maritime Antarctica-a survey, Arch. Hydrobiol. 94:181-193.
Lepère, C., A. Wilmotte, and B. Meyer. 2000. Molecular diversity of Microcystis strains (Cyanophyceae, Chroococcales) based on 16S rDNA sequences. Syst. Geogr. Plants 70:275-283.
Ludwig, W., O. Strunk, S. Klubauer, M. Weizeneger, J. Neumaier, M. Bachleitner, and K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-11 (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
Margalef, R. 1958. Information theory in ecology. Gen. Syst. 3:36-71.
May, R. M. 1975. Patterns of species abundance and diversity, p. 81-120. In M. L. Cody and J. M. Diamond (ed.), Ecology and evolution of communities. Harvard University Press, Cambridge, Mass.
McKnight, D. M., A. Alger, C. M. Tate, G. Shupe, and S. A. Spaulding. 1998. Longitudinal patterns in algal abundance and species distribution in melt-water streams in Taylor Valley, southern Victoria Land, Antarctica, p. 109-127. In J. C. Priscu (ed.), Ecosystem dynamics in a polar desert: the McMurdo Dry Valleys, Antarctica. American Geophysical Union, Washington, D.C.
McKnight, D. M., B. L. Howes, C. D. Taylor, and D. D. Goehringer. 2000. Phytoplankton dynamics in a stability stratified Antarctic lake during winter darkness. J. Phycol. 36:852-861.
Miller, S. R., and R. W. Castenholz. 2001. Ecological physiology of Synechococcus sp. strain SH-94-5, a naturally occurring cyanobacterium deficient in nitrate assimilation. Appl. Environ. Microbiol. 67:3002-3009.
Nadeau, T. L., C. Howard Williams, and R. W. Castenholz. 1999. Effects of solar UV and visible irradiance on photosynthesis and vertical migration of Oscillatoria sp. (cyanobacteria) in an Antarctic microbial mat. Aquat. Microb. Ecol. 20:231-243.
Nadeau, T. L., E. C. Milbrandt, and R. W. Castenholz. 2001. Evolutionary relationships of cultivated Antarctic oscillatoriaceans (cyanobacteria). J. Phycol. 37:650-654.
Nelissen, B., R. De Baere, A. Wilmotte, and R. De Wachter. 1996. Phylogenetic relationships of nonaxenic filamentous cyanobacterial strains based on 16S rRNA sequence analysis. J. Mol. Evol. 42:194-200.
Normand, P., C. Ponsonnet, X. Nesme, M. Neyra, and P. Simonet. 1996, ITS analysis of prokaryotes, 3.4.5, p. 1-12. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Nübel, U., F. Garcia-Pichel, and G. Muyzer. 1997. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol 63:3327-3332.
O'Sullivan, L. A., A. J. Weigthman, and J. C. Fry. 2002. New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. Appl. Environ. Microbiol. 68:201-210.
Prescott, G. W. 1979. A contribution to a bibliography of Antarctic and subantarctic algae, p. 1-312. In J. Cramer (ed.), Bibliotheca phycologica. A. R. Gantner Verlag, Vaduz, Liechtenstein.
Pringault, O., E. Buffan-Dubau, and R. de Wit. 2001. Artificial cold-adapted microbial mats cultured from Antarctic lake sample. 2. Short-term temperature effects on oxygen turn-over. Aquat. Microb. Ecol. 26:127-138.
Priscu, J. C., C. H. Fristen, E. E. Adams, S. J. Giovannoni, H. W. Paerl, C. P. McKay, P. T. Doran, D. A. Gordon, B. D. Lanoil, and J. L. Pinckney. 1998. Perennial Antarctic lake ice: an oasis for life in a polar desert. Science 280:2095-2098.
Qiu, X., L. Wu, H. Huang, P. E. McDonel, A. V. Palumbo, J. M. Tiedje, and J. Zou. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67:880-887.
Redfield, E., S. M. Barns, J. Belnap, L. L. Daane, and C. R. Kuske. 2002. Comparative diversity and composition of cyanobacteria in three predominant soil crusts of Colorado Plateau. FEMS Microbiol. Ecol. 4:55-63.
Rudi, K., O. M. Skulberg, F. Larsen, and K. S. Jakobsen. 1997. Strain characterization and classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from the variable regions V6, V7, and V8. Appl. Environ. Microbiol. 63:2593-2599.
Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
Scheldeman, P., D. Baurain, R. Bouhy, M. Scott, M. Mühling, B. A. Whitton, A. Belay, and A. Wilmotte. 1999. Arthrospira ('Spirulina') strains from four continents are resolved into only two clusters, based on amplified ribosomal DNA restriction analysis of the internally transcribed spacer. FEMS Microbiol. Lett. 172:213-222.
Simmons, G. M., Jr., J. R. Vestal, and R. A. Wharton, Jr. 1993. Environmental regulators of microbial activity in continental Antarctic lakes, p. 491-541. In W. J. Green and E. 1. Freidmann (ed.), Physical and biogeochemical processes in Antarctic lakes. American Geopbysical Union, Washington, D.C.
Smalla, K., N. Cresswell, L. C. Mendoca-Hagler, A. Wolters, and J. D. van Elsas. 1993. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:78-85.
Smith, M. C., J. P. Bowman, F. J. Scott, and M. A. Line. 2000. Sublithic bacteria associated with Antarctic quartz stones. Antarct. Sci. 12:177-184.
Spaulding, S. A., D. M. McKnight, R. L. Smith, and R. Dufford. 1994. Phytoplankton population dynamics in perennially ice-covered Lake Fryxell, Antarctica. J. Plankton Res. 16:527-541.
Speksnijder, A. G. C. L., G. A. Kowalchuk, S. De Jong, E. Kline, J. R. Stephen, and H. J. Laanbroek. 2001. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl. Environ. Microbiol. 67:469-472.
Spigel, R. H., and J. C. Priscu. 1998. Physical limnology of the McMurdo Dry Valleys lakes, p. 153-188. In J. C. Priscu (ed.), Ecosystem dynamics in a polar desert: the McMurdo Dry Valleys, Antarctica. American Geophysical Union, Washington, D.C.
Stackebrandt, E., and B. M. Göbel. 1994. A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
Stougaard, P., F. Jorgensen, M. G. Johnsen, and O. C. Hansen. 2002. Microbial diversity in ikaite tufa columns: an alkaline, cold ecological niche in Greenland. Environ. Microbiol. 4:487-493.
Tang, E. P. Y., R. Tremblay, and W. F. Vincent. 1997. Cyanobacterial dominance of polar freshwater ecosystems: are high-latitude mat-formers adapted to low temperature? J. Phycol. 33:171-181.
Tindall, B. J., E. Brambilla, M. Steffen, R. Neumann, R. Pukall, R. M. Kroppensted, and E. Stackebrandt. 2000. Cultivable microbial biodiversity: gnawing at the Gordian knot. Environ. Microbiol. 2:310-318.
Van de Peer, Y., and R. De Wachter. 1997. Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Applic. Biosci. 13:227-230.
Van Trappen S., J. Mergaert, S. Van Eygen, P. Dawyndt, M. C. Cnockaert, and J. Swings. Diversity of 746 heterotrophic bacteria isolated from microbial mats in Antarctic lakes. Syst. Appl. Microbiol. 25:603-610.
Vincent, W. F. 2000. Cyanobacterial dominance in the polar regions, p. 321-340. In B. A. Whitton and M. Potts (ed.), The ecology of cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Vincent, W. F. 2000. Evolutionary origins of Antarctic microbiota: invasion, selection and endemism. Antarct. Sci. 12:374-385.
Vincent, W. F., J. P. Bowman, L. M. Rankin, and T. A. McMeekin. 2000. Phylogenetic diversity of picocyanobacteria in Arctic and Antarctic ecosystems, p. 317-322. In R. Bell, C. M. Brylinsky, and M. Johnson-Green (ed.), Microbial biosystems: new frontiers. Proceedings of the 8th International Symposium on Microbial Ecology, Halifax Canada. Atlantic Canada Society for Microbial Ecology, Halifax, Canada.
Ward, D. M., M. J. Ferris, S. C. Nold, and M. M. Bateson. 1998. A natural view of microbial diversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62:1353-1370.
Wharton, R. A., Jr., C. B. Parker, and G. M. Simmons, Jr. 1983. Distribution, species composition and morphology of algal mats in Antarctic Dry Valley lakes. Phycologia 22:355-365.
Wilmotte, A., and M. Herdman. 2001. Phylogenetic relationships among cyanobacteria based on 16S rRNA sequences, p. 487-493. In D. R. Boone and R. W. Castenholz (ed.), Bergey's manual of systematic bacteriology, vol. 1. Springer, New York, N.Y.
Wilmotte, A. 1988. Growth and morphological variability of six strains of Phormidium cf. ectocarpi (Cyanophyeae) cultivated under different temperatures and light intensities Arch. Hydrobiol. 50/53(Suppl. 80):35-46.
Wilmotte, A. 1994. Molecular evolution and taxonomy of the cyanobacteria, p. 1-25. In A. Bryant (ed.), The molecular biology of cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Wilmotte, A., C. Demonceau, A. Goffart, J.-H. Hecq, V. Demoulin, and A. C. Crossley. 2002. Molecular and pigment studies of the picophytoplankton in a region of Southern Ocean (42-54°S, 141-144°E) in March 1998. Deep-Sea Res. II 49:3351-3363.
Wilmotte, A., G. Van der Auwera, and R. De Wachter. 1993. Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenic analysis. FEMS Lett. 317:96-100.
Wilmotte, A., J.-M. Neefs, and R. De Wachter. 1994. Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis. Microbiology 140:2159-2164.
