An Overview of Biodiversity—Estimating the Scale

Alan T. Bull; James Ε. M. Stach

doi:10.1128/9781555817770.ch2

Chapter 2 : An Overview of Biodiversity—Estimating the Scale

Authors: Alan T. Bull¹, James Ε. M. Stach¹

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Affiliations: 1: Research School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom

Content Type: Monograph

Publication Year: 2004

Category: Environmental Microbiology; Applied and Industrial Microbiology

Book DOI: 10.1128/9781555817770

Chapter DOI: 10.1128/9781555817770.ch2

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Abstract:

The term "biological diversity" was introduced by Elliot Norse and colleagues to define diversity at three levels of complexity: (i) genetic (intraspecies diversity), (ii) species (numbers of species), and (iii) ecological (community diversity), but subsequently the contracted expression "biodiversity" has become the common parlance. An exciting opportunity for extending the knowledge of global biodiversity is presented by little-studied habitats, the most expansive of which are marine habitats, and the least explored of which are the deep seas. At the same time that Wilson was publishing his exuberant account of biodiversity, Gaston and May were evaluating the state of the taxonomic workforce in Australia, the United States, and the United Kingdom. This innovation has led to the discovery of numerous novel microbial taxa, from species to division status, and is discussed in detail. Bioprospecting of deep-sea sediments by the combined application of methods described allows to conclude that the differing sections of the core profile contained significantly different actinomycete populations, both in terms of species richness and phylogenetic diversity; thus, each section represents a unique environment for biotechnological exploitation.

Citation: Bull A, Stach J. 2004. An Overview of Biodiversity—Estimating the Scale, p 15-28. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch2

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References

/content/book/10.1128/9781555817770.chap2

1. Andersen, R. A. 1998. What to do with Protists? Austr. Syst. Bot. 11: 185– 201.

2. Andersen, R. A.,, G. W. Saunders,, M. P. Paskind,, and J. Sexton. 1993. Ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. and sp. nov. and the description of a new algal class, the Pelageophyceae classis nov. J. Phycol. 29: 701– 715.

3. Andre, H. M.,, M. I. Noti,, and P. Lebrun. 1994. The soil fauna: the other last biotic frontier. Biodiver. Conserv. 3: 45– 56.

4. Arnold, A. E.,, Z. Maynard,, and G. S. Gilbert. 2001. Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity. Mycol. Res. 105: 1502– 1507.

5. Bakken, L. R. 1995. Separation and purification of bacteria from soil. Appl. Environ. Microbiol. 49: 143– 169.

6. Barnes, S. M.,, S. L. Takala,, and C. R. Kuske. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65: 1731– 1737.

7. Beja, O.,, E. V. Koonin,, L. Aravind,, L. T. Taylor,, H. Seitz,, J. L. Stern,, D. C. Bensen,, R. A. Feldman,, R. V. Swanson,, and E. F. DeLong. 2002. Comparative genomic analysis of archaeal geno-typic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68: 335– 345.

8. Boucher, Y.,, C. L. Nesbo,, and W. F. Doolittle. 2001. Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4: 285– 289.

9. Bull, A. T.,, A. C. Ward,, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64: 573– 606.

10. Busse, H.-J.,, E. B. M. Denner,, and W. Lubitz. 1996. Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J. Biotechnol. 47: 3– 38.

11. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11: 265– 270.

12. Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783– 791.

13. Chao, A.,, and S.-M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87: 210– 217.

14. Colwell, R. K.,, and J. A. Coddington,. 1995. Estimating terrestrial biodiversity through extrapolation, p. 101– 118. In D. L. Hawksworth (ed.), Biodiversity, Measurement and Estimation. Chapman & Hall, London, United Kingdom.

15. Coomans, A. 2000. Nematode systematics: past, present and future. Hematology 2: 3– 7.

16. Curtis, T. P.,, W. T. Sloan,, and J. W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99: 10494– 10499.

17. Dauga, C. 2002. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52: 531– 547.

18. Dawson, S. C.,, and N. R. Pace. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99: 8324– 8329.

19. DeLong, E. F.,, and N. R. Pace. 2001. Environmental diversity of bacteria and archaea. Syst. Biol. 50: 1– 9.

20. Dojka, M. A.,, J. K. Harris,, and N. R. Pace. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66: 1617– 1621.

21. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124– 2128.

22. Dunbar, J.,, S. M. Barns,, L. O. Ticknor,, and C. R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68: 3035– 3045.

23. Eardly, B. D.,, F. S. Wang,, and P. vanBerkum. 1996. Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies. Plant Soil 186: 69– 74.

24. Edgcomb, V. P.,, D. T. Kysela,, A. Teske,, A. de Vera Gomez,, and M. L. Sogin. 2002. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad. Sci. USA 99: 7658– 7662.

25. Erwin, T. L. 1982. Tropical forests: their richness in Coleoptera and other arthropd species. Coleopt Bull. 36: 74– 75.

26. Fox, G.,, J. D. Wisotskey,, and P. Jurtshuk. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166– 170.

27. Froese, R.,, and F. A. Bisby (ed.). 2002. Species 2000 & ITIS Catalogue of Life: Indexing the World's Known Species. CD-ROM. Species 2000, Los Banos, Philippines.

28. Galvez, A.,, M. Maqueda,, M. Martinez-Bueno,, and E. Valdivia. 1998. Publication rates reveal trends in microbiological research. ASM News 64: 269– 275.

29. Gaston, K. J.,, and R. M. May. 1992. Taxonomy of taxonomists. Nature 356: 281– 282.

30. 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.

31. Grassle, J. F.,, and N.J. Maciolek. 1992. Deep-sea species richness: regional and local diversity estimates from quantitative bottom samples. Am. Nat. 139: 313– 341.

32. Guillou, L.,, M. J. Chretiennot-Dinet,, L. K. Medlin,, H. Claustre,, S. Loisseaux-de Goer,, and D. Vaulot. 1999. Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). J. Phycol. 35: 368– 381.

33. Hackstein, J. H. P. 1997. Eukaryotic molecular biodiversity: systematic approaches for the assessment of symbiotic associations. Antonie Leeuwenhoek 72: 63– 76.

34. Hamamoto, M.,, and T. Nakase,. 2000. Phylogenetic relationships among fungi inferred from small subunit ribosomal RNA gene sequences, p. 57– 71. In F. G. Priest, and M. Goodfellow (ed.), Applied Microbial Systematics. Kluwer Academic Publishers, Dordrecht, The Netherlands.

35. Hammond, P. M., 1992. Species inventory, p. 17– 39. In B. Groom-bridge (ed.), Global Biodiversity, Status of the Earth's Living Resources. Chapman & Hall, London, United Kingdom.

36. Hammond, P. M., 1995a. Described and estimated species numbers: an objective assessment of current knowledge, p. 29– 71. In D. Allsopp,, R. R. Colwell,, and D. L. Hawksworth. (ed.), Microbial Diversity and Ecosystem Function. CAB International, Wallingford, United Kingdom.

37. Hammond, P. M., 1995b. The current magnitude of biodiversity, p. 113– 138. In V. H. Heywood (ed.), Global Biodiversity Assessment. Cambridge University Press, Cambridge, United Kingdom.

38. Harper, J. L.,, and D. L. Hawksworth,. 1995. Preface, p. 5– 12. In D. L. Hawksworth (ed.), Biodiversity, Measurement and Estimation. Chapman & Hall, London, United Kingdom.>

39. Hawksworth, D. L. 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res. 95: 641– 655.

40. Hawksworth, D. L. 2001. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol. Res. 105: 1422– 1432.

41. Heywood, V. H.,, and R. T. Watson (ed.). 1995. Global Biodiversity Assessment. Cambridge University Press, Cambridge, United Kingdom.

42. Hughes, J. B.,, J. J. Hellmann,, J. H. Ricketts,, and B. J. M. Bohan-nan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67: 4399– 4406.

43. Hyde, K. D. 2001. Where are the missing fungi? Does Hong Kong have any answers? Mycol. Res. 105: 1514– 1518.

44. Karner, M. B.,, E. F. DeLong,, and D. M. Karl. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507– 509.

45. Kristensen, R. M. 1983. Loricifera, a new phylum with Aschelminthes characters from the meiobenthos. Z. Zoo J. Syst. Evol. 21: 163– 180.

46. Kroes, I.,, P. W. Lepp,, and D. A. Relman. 1999. Bacterial diversity within the human subgingival crevice. Proc. Natl. Acad. Sci. USA 96: 14547– 14552.

47. Lambshead, P. J. D. 1993. Recent developments in marine benthic research. Oceanis 19: 5– 24.

48. Lan, R.,, and P. R. Reeves. 2000. Intraspecies variation in bacterial genomes: the need for species genome concept. Trends Microbiol. 8: 396– 401.

49. Lande, R.,, P. J. DeVries,, and T. R. Walla. 2000. When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 89: 601– 605.

50. Lawler, A. 2001. Up for the count. Science 294: 769– 770.

51. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50: 470– 496.

52. Lopez-Garcia, P.,, F. Rodriguez-Valera,, C. Pedros-Alio,, and D. Moreira. 2001. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603– 607.

53. Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68: 3673– 3682.

54. Martin, W.,, and F. Salamini. 2000. A meeting at the gene. Biodiversity and natural history. EMBO Rep. 1: 208– 210.

55. Massana, R.,, L. Guillou,, B. Diez,, and C. Pedro-Alio. 2002. Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl. Environ. Microbiol. 68: 4554– 4558.

56. May, R. M. 1988. How many species are there on Earth? Science 241: 1441– 1449.

57. May, R. M. 1992. How many species inhabit the Earth? Sci. Am. 267: 42– 48.

58. May, R. M., 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 & Hall, London, United Kingdom.

59. McCaig, A. E.,, L. A. Glover,, and J. I. Prosser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65: 1721– 1730.

60. Minelli, A. 1993. Biological Systematics. The State of the Art. Chapman & Hall, London, United Kingdom.

61. Moreira, D.,, and P. Lopez-Garcia. 2002. The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol. 10: 266– 267.

62. Ødegaard, F. 2000. How many species of arthropods? Erwin's estimate revisited. Biol. J. Linn. Soc. 71: 583– 597.

63. Overmann, J. 2001. Diversity and ecology of phototrophic sulfur bacteria. Microbiol. Today 28: 116– 118.

64. Patterson, D. J. 1999. The diversity of eukaryotes. Am. Nat. 65: S96– S124.

65. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grofbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch,, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529– 533.

66. Polz, M. F.,, J. A. Ott,, M. Bright,, and C. M. Cavanaugh. 2000. When bacteria hitch a ride. ASM News 66: 531– 539.

67. Prance, G. T. 2001. Discovering the plant world. Taxon 50: 345– 359.

68. Preston, F. W. 1962. The canonical distribution of commonness and rarity, Parts I and II. Ecology 43: 185- 215, 410– 432.

69. Purvis, A.,, and A. Hector. 2000. Getting the measure of biodiversity. Nature 405: 212– 219.

70. Quicke, D. L. J. 1993. Principles and Techniques of Contemporary Taxonomy . Blackie Academic & Professional, London, United Kingdom.

71. Rabinowitz, D.,, S. Cairns,, and T. Dillin,. 1986. Seven forms of rarity and their frequency in the flora of the British Isles, p. 182– 204. In M. Soule (ed.), Conservation Biology: The Science of Scarcity and Diversity. Sinauer Associates, Sunderland, Mass..

72. Rainey, F. A.,, and N. Ward-Rainey,. 2000. Prokaryotic diversity, p. 31– 42. In J. Seckbach (ed.), Journey to Diverse Worlds. Adaptation to Exotic Environments. Kluwer Academic Publishers, Dordrecht, The Netherlands.

73. Reaka-Kudla, M. L., 1997. The global diversity of coral reefs: a comparison with rain forests, p. 83– 108. In M. L. Reaka-Kudla,, D. E. Wilson,, and E. O. Wilson (ed.), Biodiversity II: Understanding and Protecting Our Biological Resources. Joseph Henry Press, Washington, D.C..

74. Singleton, D. R.,, M. A. Furlong,, S. L. Rathbun,, and W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67: 4374– 4376.

75. Sipman, H. J. M.,, and A. Aptroot. 2001. Where are the missing lichens? Mycol. Res. 105: 1433– 1439.

76. Soberon, J.,, and J. Llorente. 1993. The use of species accumulation functions for the prediction of species richness. Conserv. Biol. 7: 480– 488.

77. Stach, J. E. M.,, and R. G. Burns. 2002. Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities. Environ. Microbiol. 4: 169– 182.

78. Stach, J. E. M.,, L. A. Maldonado,, A. C. Ward,, M. Goodfellow,, and A. T. Bull. New primers for Actinobacteria: application to marine and terrestrial environments. Environ. Microbiol., in press.

79. Stackebrandt, E.,, and B. M. Gobel. 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.

80. Tilman, D.,, and C. Lehman,. 2001. Biodiversity, composition, and ecosystem processes: theory and concepts, p. 9– 41. In A. P. Kinzig,, S. W. Pacala,, and D. Tilman (ed.), The Functional Consequences of Biodiversity. Empirical and Theoretical Extensions. Monographs in Population Biology 33. Princeton University Press, Princeton, N. J..

81. Torsvik, V.,, J. Goksoyr,, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782– 787.

82. Torsvik, V.,, F. L. Daae,, R. A. Sandaa,, and L. 0vreas,. 2000. Molecular biology and genetic diversity of microorganisms, p. 45– 57. In J. Seckbach (ed.), Journey to Diverse Worlds. Adaptation to Exotic Environments. Kluwer Academic Publishers, Dordrecht, The Netherlands.

83. Valdecasas, A. G.,, and A. I. Camacho. 2003. Conservation to the rescue of taxonomy. Biodiver. Conserv. 12: 1113– 1117.

84. van Hoek, A. H. A. M.,, T. A. van Alen,, V. S. I. Sprakel,, J. A. M. Leunissen,, T. Brigge,, G. D. Vogels,, and J. H. Hackstein. 2000. Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates. Mol. Biol. Evol. 17: 251– 258.

85. von Wintzingerode, F.,, U. B. Gobel,, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21: 213– 229.

86. Weir, A.,, and P. M. Hammond. 1997. Laboulbeniales on beetles: host utilization patterns and species richness of the parasites. Biodiver. Conserv. 5: 701– 719.

87. Whitman, W. B.,, D. C. Coleman,, and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad Sci. USA 95: 6578– 6583.

88. Wilson, E. O. 1992. The Diversity of Life. Allen Lane. The Penguin Press, London, United Kingdom.

89. Wilson, E. O.,, and F. M. Peter (ed.). 1988. Biodiversity. National Academy Press, Washington, D.C..

90. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221– 271.

91. Woese, C. R. 2002. On the evolution of cells. Proc. Natl. Acad. Sci. USA 99: 8742– 8747.

92. Wolf, Y. I.,, I. B. Rogozin,, N. V. Grishin,, R. L. Tatusov,, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1: 1– 38.

Tables

An Overview of Biodiversity—Estimating the Scale

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Table 1

Described and estimated species numbers a

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10.1128/9781555817770/tab2-1.gif

Table 1

Described and estimated species numbers a