Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat

Applied and Environmental Microbiology

Volumn 77, Issue 4, 2011, Pages 1359-1367

  Melendrez, Melanie C ^a   Lange, Rachel K ^a   Cohan, Frederick M ^b   Ward, David M ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; 16S RRNA GENE; ECOLOGICAL DIVERSITY; FLOW CHANNELS; HOT SPRING MICROBIAL MATS; INTERNAL TRANSCRIBED SPACERS; MOLECULAR RESOLUTION; SEQUENCE ANALYSIS; SEQUENCE VARIATIONS; SYNECHOCOCCUS; YELLOWSTONE NATIONAL PARKS;

ENCODING (SYMBOLS); GENES; HOT SPRINGS; MICROORGANISMS; PARKS; RNA; TRANSCRIPTION;

PLANTS (BOTANY);

BACTERIAL PROTEIN; RNA 16S; RNA 23S; SILICON DIOXIDE;

ALGORITHM; ALKALINITY; BACTERIUM; ECOTYPE; MICROBIAL MAT; POLYMERASE CHAIN REACTION; PROTEIN; SILICEOUS DEPOSIT; THERMAL SPRING;

ARTICLE; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; GENE LOCUS; GENETIC VARIABILITY; GENETICS; GENOTYPE; HEAT; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYNECHOCOCCUS; THERMAL SPRING;

BACTERIAL PROTEINS; BASE SEQUENCE; BIODIVERSITY; GENETIC LOCI; GENETIC VARIATION; GENOTYPE; HOT SPRINGS; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SILICON DIOXIDE; SYNECHOCOCCUS;

UNITED STATES; YELLOWSTONE NATIONAL PARK;

BASIDIOMYCOTA; SYNECHOCOCCUS;

EID: 79953186115     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02032-10     Document Type: Article

References (58)

1. Allewalt, J. P., M. M. Bateson, N. P. Revsbech, K. Slack, and D. M. Ward. 2006. Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in Octopus Spring microbial mat community of Yellowstone National Park. Appl. Environ. Microbiol. 72:544-550.
2. 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. http://blast.ncbi.nlm.nih.gov.
3. Bhaya, D., et al. 2007. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analysis. ISME J. 1:703-713.
4. Boni, M. F., D. Posada, and M. W. Feldman. 2007. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047.
5. Chao, A. and T.-J. Shen. 2003. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ. Ecol. Stat. 10:429-443.
6. Chao, A. 1984. Nonparametric estimation of the number of classes in a population. Scand. Stat. Theory Appl. 11:265-270.
7. Chare, E. R., E. A. Gould, and E. C. Holmes. 2003. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 84:2691-2703.
8. Cohan, F. M., and A. F. Koeppel. 2008. The origins of ecological diversity in prokaryotes. Curr. Biol. 18:R1024-R1034.
9. Cohan, F. M., and E. B. Perry. 2007. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 17:R373-R386.
10. Cohan, F. M., A. Koeppel, and D. Krizanc. 2006. Sequence-based discovery of ecological diversity within Legionella, p. 367-376. In N. P. Cianciotto et al. (ed.), Legionella: state of the art 30 years after its recognition. ASM Press, Washington, DC.
11. Colwell, R. K., and J. A. Coddington. 1994. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 345:101-118.
12. Connor, N., et al. 2010. The ecology of speciation in Bacillus. Appl. Environ. Microbiol. 76:1349-1358.
13. Denef, V. J., et al. 2010. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. U. S. A. 107:2383-2390.
14. Feil, E. J., B. C. Li, D. M. Aanensen, W. P. Hanage, and B. G. Spratt. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186:1518-1530.
15. Feil, E. J., J. Maynard-Smith, M. C. Enright, and B. G. Spratt. 2000. Estimating recombination parameters in Streptococcus pneumoniae from multi-locus sequence typing data. Genetics 154:1439-1450.
16. Ferris, M. J., M. Kühl, A. Wieland, and D. M. Ward. 2003. Cyanobacterial ecotypes in different optical microenvironments of a 68°C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation. Appl. Environ. Microbiol. 69:2893-2898.
17. Ferris, M. J., and D. M. Ward. 1997. Season distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1375-1381.
18. 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.
19. Fuhrman, J. A., and L. Campbell. 1998. Microbial microdiversity. Nature 393:410-411.
20. Goodfellow, M., G. P. Manfio, and J. Chun. 1997. Towards a practical species concept for cultivable bacteria, p. 25-59. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman & Hall, London, United Kingdom.
21. Hanage, W. P., W. Fraser, and B. G. Spratt. 2006. Sequences, sequence clusters and bacterial species. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:1917-1927.
22. Hunt, D. E., et al. 2008. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320:1081-1085.
23. Johnson, J. L. 1973. Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria. Int. J. Syst. Bacteriol. 23:308-315.
24. Kettle, G. C., et al. 2007. Patterns and implications of gene gain and loss in the evolution of Procholorococcus. PLoS Genet. 3:2515-2528.
25. Koeppel, A., et al. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl. Acad. Sci. U. S. A. 105:2504-2509.
26. Konstantinidis, K. T., and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102: 2567-2572.
27. Librado, P., and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
28. Manning, S. D., et al. 2008. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Natl. Acad. Sci. U. S. A. 105:4868-4873.
29. Martiny, A. C., A. P. K. Tai, D. Veneziano, F. Primeau, and S. W. Chisholm. 2009. Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ. Microbiol. 11:823-832.
30. Miller, S. R., and R. W. Castenholz. 2000. Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Appl. Environ. Microbiol. 66:4222-4229.
31. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
32. 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.
33. Papke, R. T., et al. 2007. Searching for species in Haloarchaea. Proc. Natl. Acad. Sci. U. S. A. 104:14092-14097.
34. Peary, J. A., and R. W. Castenholz. 1964. Temperature strains of a thermophilic blue-green alga. Nature 202:720-721.
35. Perriere, G., and M. Gouy. 1996. WWW-Query: an online retrieval system for biological sequence banks. Biochimie 78:364-369.
36. Ramsing, N. B., M. J. Ferris, and D. M. Ward. 2000. Highly ordered vertical structure of Synechococcus population within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66:1038-1049.
37. Salerno, A., et al. 2007. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing. J. Bacteriol. 189:7808-7818.
38. Schloss, P. D., and J. Handelsman. 2006. Introducing SONS, a tool for OTU-based comparisons of membership and structure between microbial communities. Appl. Environ. Microbiol. 72:6773-6779.
39. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
40. Schloss, P. D., B. R. Larget, and J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70:5485-5492.
41. Sikorski, J., and E. Nevo. 2007. Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of 'Evolution Canyons' I and II, Israel. Environ. Microbiol. 9:716-726.
42. Smith, N. H., S. V. Gordon, R. de la Rua-Domenech, R. S. Clifton-Hadley, and R. G. Hewinson. 2006. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat. Rev. Microbiol. 4:670-681.
43. Soyer, Y., R. H. Orsi, L. D. Rodriguez-Rivera, Q. Sun, and M. Wiedmann. 2009. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol. Biol. 9:264.
44. Stackenbrandt, E., and J. Ebers. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today November:153-155.
45. Stackenbrandt, E., and B. M. Goebel. 1994. Taxonomic note: 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.
46. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
47. Van Valen, L. 1976. Ecological species, multispecies, and oaks. Taxon 25: 233-239.
48. Venter, J. C., et al. 2004. Environmental shotgun sequencing of the Sargasso Sea. Science 304:66-74.
49. Vitorino, L. R., et al. 2008. Fine-scale phylogeographic structure of Borrelia lusitaniae revealed by multilocus sequence typing. PLoS One 3:1-13.
50. Walk, S. T., et al. 2009. Cryptic lineages of the genus Escherichia. Appl. Environ. Microbiol. 75:6534-6544.
51. Walk, S. T., E. W. Alm, L. M. Calhoun, J. M. Mladonicky, and T. S. Whittam. 2007. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ. Microbiol. 9:2274-2288.
52. Ward, D. M., et al. 2008. Genomes, environmental genomics and the issue of microbial species. Heredity 100:207-219.
53. Ward, D. M., et al. 2006. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:1997-2008.
54. Ward, D. M., and F. M. Cohan. 2005. Microbial diversity in hot spring cyanobacterial mats: pattern and prediction, p. 185-201. In B. Inskeep and T. McDermott (ed.), Geothermal biology and geochemistry in Yellowstone National Park. Thermal Biology Institute, Bozeman, MT.
55. Ward, D. M. 1998. A natural species concept for prokaryotes Curr. Opin. Microbiol. 1:271-277.
56. Wayne, L. G., et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-464.
57. Whitaker, R. J., and J. F. Banfield. 2005. Population dynamics through the lens of extreme environments. Rev. Mineral. Geochem. 59:259-277.
58. Zhou, D. S., et al. 2004. DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation. J. Bacteriol. 186:5138-5146.