Chapter 7 : How To Look, Where To Look

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

How To Look, Where To Look, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap07-2.gif


A distinctive feature of microbial communities is that their diversity can be extraordinarily high, not infrequently orders of magnitude greater that the diversity of macrobial ecosystems. The state of "supersaturated coexistence" that defines the coexisting species-limiting resource paradox may be maintained by competition for such resources such that nonequilibrium conditions are generated. The challenge now is to design experiments that can discriminate between these models for supersaturated coexistence, or enable more realistic ones to be formulated. It is increasingly clear that scale effects, both spatial and temporal, are principal determinants of species richness and need to be recognized when attempting to quantify microbial diversity, when addressing basic problems in microbial ecology and microbiogeography, and when maximizing returns from biotechnology search and discovery programs. All too frequently insufficient attention is paid to the design of environment sampling strategies and to evaluating the sampling effort. Despite the spectacular advances in the molecular detection and circumscription of microorganisms and functional genomics, organisms in culture are essential for providing an understanding of microbial interactions, pathogenesis, phenotypic variability, and, in the present context, for delivering biotechnological innovation. Three approaches are presented here: habitat simulation, technological innovation, and taxonomic databases. The success of the molecular detection strategy depends on the quality of the DNA extracted from the environment.

Citation: Bull A. 2004. How To Look, Where To Look, p 71-79. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch7

Key Concept Ranking

Microbial Ecology
Microbial Communities in Environment
Atomic Force Microscopy
Single-Strand Conformation Polymorphism
Atomic Force Microscopy
16s rRNA Sequencing
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Achenbach, L. A.,, and J. D. Coates. 2000. Disparity between bacterial phylogeny and physiology. ASM News 66:714715.
2. Akkermans, A. D. L.,, J. D. van Elsas,, and F. J. de Bruijn (ed.). 1995. Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
3. Alef, K.,, and P. Nannipieri (ed.). 1995. Quality Control and Quality Assurance in Applied Soil Microbiology and Biochemistry. Academic Press Ltd., London, United Kingdom.
4. Atalan, E.,, G. P. Manfio,, A. C. Ward,, R. M. Kroppenstedt,, and M. Goodfellow. 2000. Biosystematic studies on novel streptomycetes from soil. Antonie Leeuwenhoek 77:337353.
5. Boyd, R. D.,, J. Verran,, M. V. Jones,, and M. Bhakoo. 2002. Use of the atomic force microscope to determine the effect of substratum surface topography on bacterial adhesion. Langmuir 18:23422346.
6. Brady, S. F.,, M. M. Wagenaar,, M. P. Singh,, J. E. Janso,, and J. Clardy. 2000. The cytosporones, new octaketide antibiotics isolated from an endophytic fungus. Org. Lett. 2:40434046.
7. Brandao, P. F. B.,, M. Torimura,, R. Kurane,, and A. T. Bull. 2002. Dereplication for biotechnology screening: PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes. Appl. Microbiol. Biotechnol. 58:7783.
8. Bull, A. T., 1983. Continuous culture for production, p. 405437. In A. Hollaender,, A. I. Laskin,, and P. Rogers (ed.), Basic Biology of New Developments in Biotechnology. Plenum Press, New York, N.Y..
9. Bull, A. T.,, M. Goodfellow,, and J. H. Slater. 1992. Biodiversity as a source of innovation in biotechnology. Annu. Rev. Microbiol. 42:219257.
10. Bull, A. T.,, A. C. Ward,, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64:573606.
11. Bussmann, I.,, B. Philipp,, and B. Schink. 2001. Factors influencing the cultivability of lake water bacteria. J. Microbiol. Methods 47:4150.
12. Button, D. K.,, F. Schut,, P. Quang,, R. Martin,, and B. R. Robinson.1993. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl. Environ. Microbiol. 59:881891.
13. Button, D. K.,, B. R. Robertson,, P. W. Lepp,, and T. M. Schmidt. 1998. A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in sea water. Appl. Environ. Microbiol. 64:44674476.
14. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, N. Honore,, T. Gamier,, C. Churcha,, D. Harris et al. 2001. Massive gene decay in the leprosy bacillus. Nature 409:10071011.
15. Colquhoun, J. A.,, J. Mexson,, M. Goodfellow,, A. C. Ward,, K. Horikoshi,, and A. T. Bull. 1998. Novel rhodococci and other mycolate actinomycetes from the deep sea. Antonie Leeuwenhoek 74:2740.
16. Colquhoun, J. A.,, J. Zulu,, M. Goodfellow,, K. Horikoshi,, A. C. Ward,, and A. T. Bull. 2000. Rapid characterisation of deep-sea actinomycetes for biotechnological screening programmes. Antonie Leeuwenhoek 77:359367.
17. Courtois, S.,, A. Frostegard,, P. Göransson,, G. Depret,, P. Jeannin,, and P. Simonet. 2001. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3:341439.
18. Czaran, T.,, R. F. Hoekstra,, and L. Pagie. 2002. Chemical warfare between microbes promotes biodiversity. Proc. Natl. Acad. Sci. USA 99:786790.
19. Eder, W.,, L. L. Jahnke,, M. Schmidt,, and R. Huber. 2001. Microbial diversity of the brine-seawater interface of the Kebrit Deep, Red Sea, studied via 16S rRNA gene sequences and cultivation methods. Appl. Environ. Microbiol. 67:30773085.
20. Eguchi, M.,, M. Ostrowski,, F. Fegatella,, J. Bowman,, D. Nichols,, T. Nishino,, and R. Cavicchioli. 2001. Sphingomonas alaskensis strain AF01, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl. Environ. Microbiol. 67:49454954.
21. Hengstmann, U.,, K.-J. Chin,, P. H. Janssen,, and W. Liesack. 1999. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Appl. Environ. Microbiol. 65:50505058.
22. Hildebrandt, U.,, K. Janetta,, and H. Bothe. 2002. Towards growth of arbuscular mycorrhizal fungi independent of a plant host. Appl Environ. Microbiol. 68:19191924.
23. Hooper, J. N. A.,, J. A. Kennedy,, and R. J. Quinn. 2002. Biodiversity "hotspots," patterns of richness and endemism, and taxonomic affinities of tropical Australian sponges (Porifera). Biodivers. Conserv. 11:851885.
24. Hopkins, D. W.,, S. J. MacNaughton,, and A. G. O'Donnell. 1991. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol. Biochem. 23:217225.
25. Huisman, J.,, and F. J. Weissing. 1999. Biodiversity of plankton by species oscillations and chaos. Nature 402:407410
26. Huisman, J.,, A. M. Johansson,, E. O. Folmer,, and F. J. Weissing. 2001. Towards a solution of the plankton paradox: the importance of physiology and life history. Ecol. Lett. 4:408411.
27. Hutchinson, G. E. 1961. The paradox of the plankton. Am. Nat. 95:137145.
28. Inagaki, F.,, K. Takai,, T. Komatsu,, T. Kanamatsu,, K. Fujioka,, and K. Horikoshi. 2001. Archaeology of Archaea: geomicrobiological record of Pleistocene events in a deep-sea subseafloor environment. Extremophiles 5:385392.
29. Inagaki, F.,, Y. Sakihama,, A. Inoue,, C. Kato,, and K. Horikoshi. 2002. Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments. Environ. Microbiol. 4:277286.
30. Janssen, P. H.,, P. S. Yates,, B. E. Grinton,, P. M. Taylor,, and M. Sait. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68:23912396.
31. Jaspers, E.,, K. Nauhaus,, H. Cypionka,, and J. Overmann. 2001. Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol. Ecol. 36:153164.
32. Kaeberlein, T.,, K. Lewis,, and S. S. Epstein. 2002. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296:11271129.
33. Kursar, T. A.,, T. L. Capson,, P. D. Coley,, D. G. Corley,, M. B. Gupta,, L. A. Harrison,, E. Ortega-Barria,, and D. M. Windsor. 1999. Ecologically guided bioprospecting in Panama. Pharmaceut. Biol. 37:114126.
34. Lee, D. H.,, Y. G. Zo,, and S. J. Kim. 1996. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl. Environ. Microbiol. 62:31123120.
35. Leser, T. D.,, J. Z. Amenuvor,, T. K. Jensen,, R. H. Lindecrona,, M. Boye,, and K. Moller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisted. Appl. Environ. Microbiol. 68:673690.
36. Levin, L. A.,, R. J. Etter,, M. A. Rex,, A. J. Gooday,, C. R. Smith,, J. Pineda,, C. T. Stuart,, R. R. Hessler,, and D. Pawson. 2001. Environmental influences on regional deep-sea species diversity. Annu. Rev. Ecol. Syst. 32:5193.
37. Li, L.,, C. Kato,, and K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodiver. Conserv. 8:659677.
38. Lilburn, T. G.,, T. M. Schmidt,, and J. A. Breznak. 1999. Phylogenetic diversity of termite gut spirochaetes. Environ. Microbiol. 1:331345.
39. MacNaughton, S. J.,, and A. G. O'Donnell. 1994. Tuberculostearic acid as a means of estimating the recovery (using dispersion and differential centrifugation) of actinomycetes from soil. J. Microbiol. Methods 20:6977.
40. Mexson, J. 2001. Selective isolation and taxonomic analysis of the genus Micromonospora. Ph.D. thesis. University of Kent at Canterbury, United Kingdom.
41. Morishima, K.,, F. Arai,, T. Fukuda,, and H. Matsuura. 1998. Screening of single Escherichia coli in a microchannel system by electric field and laser tweezers. Anal. Chim. Acta 365:273278.
42. Muyzer, G.,, E. C. de Waal,, and A. G. Uitterlinden. 1993. Profile of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl. Environ. Microbiol. 59: 695700.
43. Myers, N. 1988. Threatened biotas: "hotspots" in tropical forests. Environmentalist 8:120.
44. Myers, N.,, R. A. Mittermeier,, C. G. Mittermeier,, G. A. B. da Fonseca,, and J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403:853858.
45. Noti, M.-I,, H. M., André,, X. Ducarme,, and P. Lebrun. 2003. Diversity of soil oribatid mites (Acari: Oribatida) from high Katanga (Dem. Rep. Congo): a multiscale and multifactor approach. Biodivers. Conserv. 12:767785.
46. Osterhage, C.,, M. Schwibbe,, G. M. König,, and A. D. Wright. 2000. Differences between marine and terrestrial Phoma species as determined by HPLC-DAD and HPLC-MS. Phytochem. Anal. 11:288294.
47. Pace, N. R. 2000. Community interactions: towards a natural history of the microbial world. Environ. Microbiol. 2:78.
48. Pace, N. R.,, D. A. Stahl,, D. J. Lane,, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Microb. Ecol. 9:156.
49. Rainey, P. 2000. An organism is more than its genotype. Environ. Microbiol. 2:89.
50. Roberts, C. M.,, C. J. McClean,, J. E. N. Veron,, J. P. Hawkins,, G. R. Allen,, D. E. McAllister,, C. G. Mittermeir,, F. W. Schueler,, M. Spalding,, F. Wells,, C. Vynne,, and T. B. Werner. 2002. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295:12801284.
51. Schippers, P.,, A. M. Verschoor,, M. Vos,, and W. M. Mooij. 2001. Does "supersaturated coexistence" resolve the "paradox of the plankton"? Ecol. Lett. 4:404407.
52. Schut, F.,, J. C. Gottschal,, and R. A. Prins. 1997. Isolation and characterisation of the marine ultramicrobacterium Sphingomonas sp. strain RB2256. FEMS Microbiol. Rev. 20:363369.
53. Seguritan, V.,, and F. Rohwer. 2001. FastGroup: a program to dereplicate libraries of 16S rDNA sequences. BMC Bioinformatics 2:9.
54. Smalla, K.,, G. Wieland,, A. Buchner,, A. Zock,, J. Parzy,, S. Kaiser,, N. Roskot,, H. Heuer,, and G. Berg. 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl. Environ. Microbiol. 67:47424751.
55. Smit, E.,, P. Leeflang,, S. Gommans,, J. van den Broek,, S. van Mil,, and K. Wernars. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl. Environ. Microbiol. 67:22842291.
56. 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. 4:169182.
57. Stahl, D. A.,, D. J. Lane,, G. J. Olsen,, and N. R. Pace. 1984. Analysis of hydrothermal vent-associated symbionts by ribosomal-RNA sequences. Science 224:409411.
58. Steinberg, C. E. W.,, and W. Geller,. 1993. Biodiversity and interactions within pelagic nutrient cycling and productivity, p. 4364. In E.-D. Schulze, and H. A. Mooney (ed.), Biodiversity and Ecosystem Function. Springer-Verlag, Berlin, Germany.
59. Strous, M.,, J. A. Fuerst,, E. H. M. Kramer,, S. Logemann,, G. Muyzer,, K. T. Van de Pas-Schooner,, R. Webb,, J. Gijs Kuenen,, and M. S. M. Jeiten. 1999. Missing lithotroph identified as a new planctomycete. Nature 400:446449.
60. Suau, A.,, R. Bonnet,, M. Sutren,, J. J. Godon,, G. R. Gibson,, M. D. Collins,, and J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65: 47994807.
61. Taberlet, P. 1998. Biodiversity at the intraspecific level: the comparative phylogeographic approach. J. Biotechnol. 64:91100.
62. Tankéré, S. P. C.,, D. G. Bourne,, F. L. L. Muller,, and V. Torsvik. 2002. Microenvironments and microbial community structure in sediments. Environ. Microbiol. 4:97105.
63. Tiedje, J. M., 1995. Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat, p. 7387. In D. Allsopp,, R. R. Colwell,, and D. L. Hawksworth. (ed.), Microbial Diversity and Ecosystem Function. CABI Publishing, Wallingford, United Kingdom.
64. Tiedje, J. M.,, J. C. Cho,, A. Murray,, D. Treves,, B. Xia,, and J. Zhou,. 1999. Soil teeming with life: new frontiers for soil science, p. 393412. In R. M. Rees,, B. C. Ball,, C. D. Campbell,, and C. A. Watson (ed.), Sustainable Management of Soil Organic Matter. CABI Publishing, Wallingford, United Kingdom.
65. Torsvik, V.,, L. Øvreas,, and T. F. Thingstad. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:10641066.
66. Totsche, K., 1995. Quality-project design-spatial sampling, p. 551. In K. Alef,, and P. Nannnipieri. (ed.), Quality Control and Quality Assurance in Applied Soil Microbiology and Biochemistry. Academic Press Ltd., London, United Kingdom.
67. Urakawa, H.,, K. Kita-Tsukamoto,, and K. Ohwada. 1999. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145:33053315.
68. Vandermeer, J.,, M. A. Evans,, P. Foster,, T. Hook,, M. Reiskind,, and M. Wund. 2002. Increased competition may promote species coexistence. Proc. Natl. Acad. Sci. USA 99:87318736.
69. Veldkamp, H. 1977. Ecological studies with the chemostat. Adv. Microbial Ecol. 1:5994.
70. Wagner, M.,, and A. Loy. 2002. Bacterial community composition and function in sewage treatment systems. Curr. Opin. Biotechnol. 13:218227.
71. Willis, K. J.,, and R. J. Whittaker. 2002. Species diversity—scale matters. Science 295:12451248.
72. Xia, B. C,, D. S. Treves,, J. Z. Zhou,, and J. M. Tiedje. 2001. Soil microbial community diversity and driving mechanisms. Prog. Nat. Sci. 11:818824.
73. Yang, C.-H.,, D. E. Crowley,, J. Borneman,, and N. T. Keen. 2001. Microbial phyllosphere populations are more complex than previously realized. Proc. Natl. Acad. Sci. USA 98:38893894.
74. Zhou, J.,, and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13: 204207.
75. Zhou, J. Z.,, M. E. Davey,, J. B. Figueras,, E. Rivkina,, D. Gilichinsky,, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:39133919.
76. Zhou, J. Z.,, B. C. Xia,, D. S. Treves,, L.-Y. Wu,, T. L. Marsh,, R. V. O'Neill,, A. V. Palumbo,, and J. M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326334.
77. Zinder, S. H. 2002. The future for culturing environmental organisms: a golden era ahead? Environ. Microbiol. 4:1415.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error