Using ecological diversity measures with bacterial communities

FEMS Microbiology Ecology

Volumn 43, Issue 1, 2003, Pages 1-11

  Hill, Tom C J ^a   Walsh, Kerry A ^a   Harris, James A ^a,b   Moffett, Bruce F ^a  

^a UNIVERSITY OF EAST LONDON   (United Kingdom)

^b CRANFIELD UNIVERSITY   (United Kingdom)

Author keywords

Abundance model; Bacterial diversity; Diversity index; Evenness; Extrapolation; Heavy metal; Shannon

Indexed keywords

ZINC;

BACTERIUM; ECOLOGICAL MODELING; MICROBIAL COMMUNITY; SOIL POLLUTION; SPECIES DIVERSITY;

AMPLIFIED RIBOSOMAL DNA RESTRICTION ANALYSIS; BACTERIAL FLORA; CONTAMINATION; GENETIC ANALYSIS; MICROBIAL BIOMASS; MICROBIAL DIVERSITY; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; REVIEW; SOIL POLLUTION; SPECIES DISTRIBUTION; SPECIES RICHNESS; STATISTICAL ANALYSIS; TAXONOMY; TERRITORIALITY; THEORY;

BACTERIA (MICROORGANISMS); OTUS;

EID: 0037314132     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(02)00449-X     Document Type: Article

References (42)

1. Godon J.-J., Zumstein E., Dabert P., Habouzit F., Moletta R. Microbial 16S rDNA diversity in an anaerobic digester. Water Sci. Technol. 36:1997;49-55.
2. Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1999;1662-1669.
3. Torsvik V., Sørheim R., Goksøyr J. Total bacterial diversity in soil and sediment communities - a review. J. Ind. Microbiol. 17:1996;170-178.
4. Cho J.-C., Kim S.-J. Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl. Environ. Microbiol. 66:2000;956-965.
5. McCaig A.E., Glover L.A., Prosser J.I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65:1999;1721-1730.
6. Hughes J.B., Hellmann J.J., Ricketts T.H., Bohannan B.J.M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:2001;4399-4406.
7. Curtis T.P., Sloan W.T., Scannell J.W. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA. 99:2002;10494-10499.
8. Krebs, C.J. (1989) Ecological Methodology, 654 pp. Harper Collins Inc., New York.
9. Usher M.B. Species diversity: a comment on a paper by W.B. Yapp. Field Stud. 5:1983;825-832.
10. Shannon, C.E. and Weaver, W. (1949) The Mathematical Theory of Communication, 117 pp. University of Illinois Press, Urbana, IL.
11. Wiener, N. (1948) Cybernetics: or Control and Communication in the Animal and Machine, 194 pp. John Wiley and Sons, New York.
12. Wilde, O. (1893) The Importance of Being Earnest: A Trivial Comedy for Serious People, 52 pp. Samuel French, London.
13. Magurran, A.E. (1988) Ecological Diversity and its Measurement, 179 pp. Chapman and Hall, London.
14. Moffett, B.F., Nicholson, F.A., Uwakwe, N.C., Chambers, B.J., Harris, J.A. and Hill, T.C.J. (2003) Zinc contamination decreases the bacterial diversity of agricultural soil. FEMS Microbiol. Ecol. this issue, S0168(02)00448-8 .
15. Steffan R.J., Goksøyr J., Bej A.K., Atlas R.M. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:1988;2908-2915.
16. Zhou J., Bruns M.A., Tiedje J.M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:1996;316-322.
17. Sessitsch A., Weilharter A., Gerzabek M.H., Kirchmann H., Kandeler E. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67:2001;4215-4224.
18. Chao A. Non-parametric estimation of the number of classes in a population. Scan. J. Stat. 11:1984;265-270.
19. Colwell R.K., Coddington J.A. Estimating terrestrial biodiversity through extrapolation. Philos. Trans. R. Soc. Lond. B. 345:1994;101-118.
20. Lloyd M., Ghelardi R.J. A table for calculating the 'equitability' component of species diversity. J. Anim. Ecol. 33:1964;217-255.
21. Pielou, E.C. (1975) Ecological Diversity, 165 pp. John Wiley and Sons, New York.
22. Pielou E.C., Arnason A.N. Correction to one of MacArthur's species-abundance formulas. Science. 151:1965;592.
23. MacArthur R.H. On the relative abundance of bird species. Proc. Natl. Acad. Sci. USA. 43:1957;293-295.
24. May, R.M. (1975) Patterns of species abundance and diversity. In: Ecology and Evolution of Communities (Cody, M.L. and Diamond, J.M., Eds.), pp. 81-120. Harvard University Press, Cambridge, MA.
25. Gotelli N.J., Colwell R.K. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4:2001;379-391.
26. Chazdon, R.L., Colwell, R.K., Denslow, J.S. and Guariguata, M.R. (1998) Statistical methods for estimating species richness of woody regeneration in primary and secondary rain forests of northeastern Costa Rica. In: Forest Biodiversity Research, Monitoring and Modelling Conceptual Background and Old World Case Studies (Dallmeier, F. and Comiskey, J.A., Eds.), pp. 285-304. Unesco and The Parthenon Publishing Group, Paris.
27. Odum E.P. Trends expected in stressed ecosystems. BioScience. 35:1985;419-422.
28. Margalef, R. (1981) Stress in ecosystems: a future approach. In: Stress Effects on Natural Ecosystems (Barrett, G.W. and Rosenberg, R., Eds.), pp. 281-289. John Wiley and Sons, New York.
29. Burkhardt C., Insam H., Hutchinson T.C., Reber H.H. Impact of heavy metals on the degradative capabilities of soil bacterial communities. Biol. Fert. Soils. 16:1993;154-156.
30. Watve M.G., Gangal R.M. Problems in measuring bacterial diversity and a possible solution. Appl. Environ. Microbiol. 62:1996;4299-4301.
31. Hill M.O. Diversity and evenness: a unifying notation and its consequences. Ecology. 54:1973;427-431.
32. Peet R.K. The measurement of species diversity. Annu. Rev. Ecol. Syst. 5:1974;285-307.
33. Bulla L. An index of evenness and its associated diversity measure. Oikos. 70:1994;167-171.
34. Harte J., Kinzig A., Green J. Self-similarity in the distribution and abundance of species. Science. 284:1999;334-336.
35. Izsák J., Papp L. A link between ecological diversity indices and measures of biodiversity. Ecol. Model. 130:2000;151-156.
36. Horn M.E.T., Faith D.P., Walker P.A. The phylogenetic moment - a new diversity measure, with procedures for measurement and optimisation. Environ. Plan. A. 28:1996;2139-2154.
37. Faith D.P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1992;1-10.
38. Hurlbert S.H. The nonconcept of species diversity: a critique and alternative parameters. Ecology. 52:1971;577-586.
39. Sugihara G. Minimal community structure: an explanation of species abundance patterns. Am. Nat. 116:1980;770-787.
40. Tokeshi M. Niche apportionment or random assortment: species abundance patterns revisited. J. Anim. Ecol. 59:1990;1129-1146.
41. Tokeshi M. Species abundance patterns and community structure. Adv. Ecol. Res. 24:1993;111-186.
42. Bengtsson J. Which species? What kind of diversity? Which ecosystem function? Some problems in studies of relations between biodiversity and ecosystem function. Appl. Soil Ecol. 10:1998;191-199.