Quantifying microbial diversity: Morphotypes, 16s rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats

Applied and Environmental Microbiology

Volumn 65, Issue 2, 1999, Pages 422-430

  Nübel, Ulrich ^a   Garcia Pichel, Ferran ^a   Kühl, Michael ^a,b   Muyzer, Gerard ^a,c  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CAROTENOID;

ESTIMATION METHOD; HYPERSALINE ENVIRONMENT; MICROBIAL MAT; SPECIES DIVERSITY;

ARTICLE; DIAGNOSTIC IMAGING; ECOSYSTEM; ELECTROPHORESIS; EXTRACTION; GENE EXPRESSION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IMAGE ANALYSIS; PHOTOTROPHIC BACTERIUM; PLASTID; POLYMERASE CHAIN REACTION;

ALGAE; CYANOBACTERIA; EUKARYOTA; PHOTOBACTERIA;

EID: 2542509415     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.2.422-430.1999     Document Type: Article

References (69)

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.
2. Anagnostidis, K., and J. Komárek. 1985. Modern approach to the classification system of cyanophytes. 1. Introduction. Arch. Hydrobiol. (Suppl.) 71:291-302.
3. Begon, M., J. L. Harper, and C. R. Townsend. 1990. Ecology - individuals, populations, communities. Blackwell Scientific Publications, Oxford, United Kingdom.
4. Birky, C. W., Jr., and J. B. Walsh. 1992. Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes. Genetics 130:677-683.
5. Brosius, M., T. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
6. Castenholz, R. W. 1992. Species usage, concept, and evolution in the Cyanobacteria (blue-green algae). J. Phycol. 28:737-745.
7. Castenholz, R. W., and J. B. Waterbury. 1989. Oxygenic phototrophic bacteria, group I. Cyanobacteria, p. 1710-1728. In M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology. The Williams and Wilkins Co., Baltimore, Md.
8. Claridge, M. F., H. A. Dawah, and M. R. Wilson. 1997. Practical approaches to species concepts for living organisms, p. 1-15. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman and Hall, London, United Kingdom.
9. Des Marais, D. J. 1995. The biogeochemistry of hypersaline microbial mats. Adv. Microb. Ecol. 14:251-274.
10. Embley, T. M., and E. Stackebrandt. 1997. Species in practice: exploring uncultured prokaryote diversity in natural samples, p. 1-15. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman and Hall, London, United Kingdom.
11. Ferris, M. J., A. L. Ruff Roberts, E. D. Kopczynski, M. M. Bateson, and D. M. Ward. 1996. Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat. Appl. Environ. Microbiol. 62:1045-1050.
12. Ferris, M. J., and D. M. Ward. 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 43:1375-1381.
13. Garcia-Pichel, F., L. Prufert-Bebout, and G. Muyzer. 1996. Phenotypic and phylogenetic analyses show Microcoleus chthonoplastes to be a cosmopolitan cyanobacterium. Appl. Environ. Microbiol. 62:3284-3291.
14. Garcia-Pichel, F., M. Kühl, U. Nübel, and G. Muyzer. Salinity-dependent limitation of photosynthesis and oxygen exchange in microbial mats. J. Phycol., in press.
15. Garcia-Pichel, F., M. Mechling, and R. W. Castenholz. 1994. Diel migrations of microorganisms within a benthic, hypersaline mat community. Appl. Environ. Microbiol. 60:1500-1511.
16. Garcia-Pichel, F., U. Nübel, and G. Muyzer. 1998. The phylogeny of unicellular, extremely halotolerant cyanobacteria. Arch. Microbiol. 169:469-482.
17. Garcia-Pichel, F., U. Nübel, G. Muyzer, and M. Kühl. On cyanobacterial community diversity and its quantification. In C. Bell (ed.), Trends in microbial ecology, in press.
18. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
19. Goodwin, T. W. 1981. The biochemistry of carotenoids, 2nd ed., vol. 1. Chapman and Hall, London, United Kingdom.
20. Hanski, I. 1997. Be diverse, be predictable. Nature 390:440-441.
21. Holben, W. E., J. K. Jansson, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
22. Javor, B. 1989. Hypersaline environments. Springer-Verlag, Berlin, Germany.
23. Jordan, T. L., and J. T. Staley. 1976. Electron microscopic study of succession in the periphyton community of Lake Washington. Microb. Ecol. 2:241-251.
24. Karsten, U., and F. Garcia Pichel. 1996. Carotenoids and mycosporine-like amino acid compounds in members of the genus Microcoleus (cyanobacteria): a chemosystematic study. Syst. Appl. Microbiol. 19:285-294.
25. Klug, M. J., and J. M. Tiedje. 1993. Response of microbial communities to changing environmental conditions: chemical and physiological approaches, p. 371-374. In R. Guerrero and C. Pedrós-Alió (ed.), Trends in microbial ecology. Spanish Society for Microbiology, Madrid, Spain.
26. Kolasa, J., and E. Biesiadka. 1984. Diversity concept in ecology. Acta Biotheoretica 33:145-162.
27. Komárek, J. 1996. Towards a combined approach for the taxonomy and species delimitation of picoplanktic cyanoprokaryotes. Arch. Hydrobiol. Suppl. 117:377-401.
28. Lanoil, B. D., and S. J. Giovannoni. 1997. Identification of bacterial cells by chromosomal painting. Appl. Environ. Microbiol. 63:1118-1123.
29. Legendre, L., and P. Legendre. 1982. Numerical ecology. Elsevier, Amsterdam, The Netherlands.
30. Ludwig, J. A., and J. F. Reynolds. 1988. Statistical ecology. John Wiley and Sons, New York, N.Y.
31. May, R. 1995. Conceptual aspects of the quantification of the extent of biological diversity, p. 13-20. In D. L. Hawksworth (ed.), Biodiversity -measurement and estimation. Chapman and Hall, London, United Kingdom.
32. Mayden, R. 1997. A hierarchy of species concepts: the denouement in the saga of the species problem, p. 381-424. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman and Hall, London, United Kingdom.
33. McNaughton, S. J. 1993. Biodiversity and function of grazing ecosystems, p. 361-382. In E. D. Schulze and H. A. Mooney (ed.), Biodiversity and ecosystem function. Springer-Verlag, Berlin, Germany.
34. Medlin, L. K. 1995. Can molecular techniques change our ideas about the species concept? p. 133-152. In I. Joint (ed.), Molecular ecology of aquatic microbes, vol. G38. Springer-Verlag, Berlin, Germany.
35. Medlin, L. K., W. H. C. F. Kooistra, R. Gersonde, and U. Wellbrock. 1996. Evolution of the diatoms (Bacillariophyta). II. Nuclear-encoded small-subunit rRNA sequence comparisons confirm a paraphyletic origin for the centric diatoms. Mol. Biol. Evol. 13:67-75.
36. Muyzer, G., E. D. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
37. Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig, and H. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.
38. Nübel, U., F. Garcia Pichel, and G. Muyzer. 1997. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63:3327-3332.
39. O'Donnell, A. G., M. Goodfellow, and D. L. Hawksworth. 1995. Theoretical and practical aspects of the quantification of biodiversity among microorganisms, p. 65-73. In D. L. Hawksworth (ed.), Biodiversity - measurement and estimation. Chapman and Hall, London, United Kingdom.
40. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
41. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
42. Paerl, H. W. 1984. Cyanobacterial carotenoids: their roles in maintaining optimal photosynthetic production among aquatic bloom-forming genera. Oecologia 61:143-149.
43. Palys, T., L. K. Nakamura, and F. M. Cohan. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47:1145-1156.
44. Pielou, E. C. 1966. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13:131-144.
45. Pierson, B. K., D. Valdez, M. Larsen, E. Morgan, and E. E. Mack. 1994. Chloroflexus-like organisms from marine and hypersaline environments: distribution and diversity. Photosynth. Res. 41:35-52.
46. Pinevich, A. V., S. G. Averina, and N. V. Velichko. 1997. Another view on the role of photosynthetic pigments in taxonomy of oxygenic-phototrophic bacteria: proposed rejection of the order Prochlorales Florenzano, Balloni, and Materassi 1986 (Emend. Burger-Wiersma, Stal, and Mur 1989), the family Prochloraceae Florenzano, Balloni, and Materassi 1986, and the family Prochlorotrichaceae Burger-Wiersma, Stal, and Mur 1989. Int. J. Syst. Bacteriol. 47:1264-1267.
47. Pinhassi, J., U. L. Zweifel, and A. Hagström. 1997. Dominant marine bacterioplanklon species found among colony-forming bacteria. Appl. Environ. Microbiol. 63:3359-3366.
48. Revsbech, N. P., and B. B. Jørgensen. 1986. Microelectrodes: their use in microbial ecology. Adv. Microb. Ecol. 9:293-352.
49. Round, F. E., R. M. Crawford, and D. G. Mann. 1990. The diatoms: morphology and biology of the genera. Cambridge University Press, Cambridge, United Kingdom.
50. Sardelli, A. D. 1993. Plateau effect - understanding PCR limitations. Amplifications 9:1-3.
51. Schulze, E. D., and H. A. Mooney. 1993. Ecosystem function and biodiversity: a summary, p. 497-510. In E. D. Schulze and H. A. Mooney (ed.), Biodiversity and ecosystem function. Springer-Verlag, Berlin, Germany.
52. Shannon, C. E., and W. Weaver. 1949. The mathematical theory of communication. University of Illinois Press, Urbana, Ill.
53. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
54. Staley, J. T. 1997. Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8:340-345.
55. Steinberg, C. E. W., and W. Geller. 1993. Biodiversity and interactions within pelagic nutrient cycling and productivity, p. 497-510. In E. D. Schulze and H. A. Mooney (ed.), Biodiversity and ecosystem function. Springer-Verlag, Berlin, Germany.
56. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
57. Tiedje, J. M. 1995. Approaches to the comprehensive evaluation of prokaryote diversity of a habitat, p. 73-87. In D. Allsopp, R. R. Colwell, and D. L. Hawksworth (ed.), Microbial diversity and ecosystem function. CAB International, Oxon, United Kingdom.
58. Tilman, D., and J. A. Downing. 1994. Biodiversity and stability in grasslands. Nature 367:363-365.
59. Tilman, D., J. Knops, D. Wedin, P. Reich, M. Ritchie, and E. Siemann. 1997. The influence of functional diversity and composition on ecosystem processes. Science 277:1300-1302.
60. Tinnberg, L. 1979. Phytoplankton diversity in Lake Norvikken 1961-1975. Holarctic Ecol. 2:150-159.
61. Von Wintzingerode, F., U. B. Goebel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
62. Wagner, R. 1994. The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch. Microbiol. 161:100-109.
63. Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1:271-277.
64. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rihosomal RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
65. Washington, H. G. 1984. Diversity, biotic and similarity indices. Water Res. 18:653-694.
66. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-464.
67. Wilmotte, A. 1995. 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.
68. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
69. Wood, A. M., and T. Leatham. 1992. The species concept in phytoplankton ecology. J. Phycol. 28:723-729.