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Chapter 38 : What Is the Evidence for the Loss of Microbial Diversity?
Author:
James Borneman1
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Affiliations:
1: Department of Plant Pathology, University of California, Riverside, CA 92521
Content Type: Monograph
Publication Year:
2004
Category: Environmental Microbiology; Applied and Industrial Microbiology
Book DOI:
10.1128/9781555817770
Chapter DOI:
10.1128/9781555817770.ch38
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What Is the Evidence for the Loss of Microbial Diversity?, Page 1 of 2
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Abstract:
This chapter examines the effects of anthropogenic activities on microbial species richness and diversity. This is a challenging area of study because current investigative methods do not allow accurate assessment of species composition and diversity. Although this limitation, among others, does not allow firm conclusions to be made, an examination of the literature showed that most reports identified a negative relationship between anthropogenic activities and microbial species richness and diversity. This chapter reviews these studies, discusses the importance of the findings, and describes some of the challenges for future investigations. Agricultural practices including deforestation, the use of herbicides, fish farming, sewage sludge amendments, and copper amendments have all been shown to lower microbial diversity. Several reports described anthropogenic activities that have increased microbial diversity. The chapter addresses the relationship between microbial diversity and ecosystem functioning.
Citation:
Borneman J.
2004.
What Is the Evidence for the Loss of Microbial Diversity?,
p 421-425.
In
Bull A (ed),
Microbial Diversity and Bioprospecting.
ASM Press, Washington, DC.
doi: 10.1128/9781555817770.ch38
References
/content/book/10.1128/9781555817770.chap38
1.
Andren, O.,, J. Bengtsson,, and M. Clarholm,. 1995. Biodiversity and species redundancy among litter decomposers, p. 141– 151. In H. P. Collins (ed.), The Significance and Regulation of Soil Biodiversity. Kluwer Academic Publisher, Dondrecht, The Netherlands.
2.
Arnold, A. E.,, Z. Maynard,, G. S. Gilbert,, P. D. Coley,, and T. A. Kursar. 2000. Are tropical fungal endophytes hyperdiverse? Ecol. Lett. 3: 267– 274.
3.
Arnolds, E. 1988. The changing macromycete flora in the Netherlands. Trans. Br. Mycol. Soc. 90: 391– 406.
4.
Barkay, T.,, S. C. Tripp,, and B. H. Olson. 1985. Effect of metal-rich sewage sludge application on the bacterial communities of grasslands. Appl. Environ. Microbiol. 49: 333– 337.
5.
Behr, T.,, C. Koob,, M. Schedl,, A. Mehlen,, H. Meier,, D. Knopp,, E. Frahm,, U. Obst,, K. H. Schleifer,, R. Niessner,, and W. Ludwig. 2000. A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization. Syst. Appl. Microbiol. 23: 563– 572.
6.
Bej, A. K.,, M. Perlin,, and R. M. Atlas. 1991. Effect of introducing genetically engineered microorganisms on soil microbial community diversity. FEMS Microbiol. Ecol. 86: 169– 175.
7.
Colwell, R. R. 1997. Microbial diversity: the importance of exploration and conservation. J. Ind. Microbiol. Biotechnol. 18: 302– 307.
8.
Dean-Ross, D.,, and A. L. Mills. 1989. Bacterial community structure and function along a heavy metal gradient. Appl. Environ. Microbiol. 55: 2002– 2009.
9.
Diltz, M. S.,, C. E. Hepfer,, E. Hartz,, and K. H. Baker. 1992. Recovery of heterotrophic soil bacterial guilds from transient gasoline pollution. Hazard. Waste Hazard. Mater. 9: 267– 273.
10.
Eichner, C. A.,, R. W. Erb,, K. N. Timmis,, and I. Wagner-Dobler. 1999. Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community. Appl. Environ. Microbiol. 65: 102– 109.
11.
Fenchel, T.,, G. F. Esteban,, and B. J. Finlay. 1997. Local versus global diversity of microorganisms: cryptic diversity of ciliated protozoa. Oikos 80: 220– 225.
12.
Fulthorpe, R. R.,, A. N. Rhodes,, and J. M. Tiedje. 1998. High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl. Environ. Microbiol. 64: 1620– 1627.
13.
Giller, K. E.,, E. Witter,, and S. P. McGrath. 1998. Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol. Biochem. 30: 1389– 1414.
14.
Griffiths, B. S.,, K. Ritz,, R. D. Bardgett,, R. Cook,, S. Christensen,, F. Ekelund,, S. J. Sorensen,, E. Baath,, J. Bloom,, P. C. de Ruiter,, J. Dolfing,, and B. Nicolardot. 2000. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90: 279– 294.
15.
Guschin, D. Y.,, B. K. Mobarry,, D. Proudnikov,, D. A. Stahl,, B. E. Rittmann,, and A. D. Mirzaberkov. 1997. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63: 2397– 2402.
16.
Hawksworth, D. L. 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res. 95: 641– 655.
17.
Hiroki, M. 1993. Effect of arsenic pollution on soil microbial population. Soil Sci. Plant Nutr. 39: 227– 235.
18.
Hood, M. A.,, W. S. Bishop,, F. W. Bishop,, S. P. Meyers,, and T. Whelan. 1975. Microbial indicators of oil-rich salt marsh sediments. Appl. Microbiol. 30: 982– 987.
19.
Houston, A. P. C.,, S. Visser,, and R. A. Lautenschlager. 1998. Microbial processes and fungal community structure in soils from clear-cut and unharvested areas of two mixedwood forests. Can. J. Bot. 76: 630– 640.
20.
Hughes, J. B.,, and O. L. Petchey. 2001. Merging perspectives on biodiversity and ecosystem functioning. Trends Ecol. Evol. 16: 222– 223.
21.
Jaenike, J. 1991. Mass extinction of European fungi. Trends Ecol. Evol. 6: 174– 175.
22.
Jonsson, L. M.,, M. C. Nilsson,, D. A. Wardle,, and O. Zackrisson. 2001. Context dependent effects of ectomycorrhizal species richness on tree seedling productivity. Oikos 93: 353– 364.
23.
Maltby, L.,, and R. Booth. 1991. The effect of coal-mine effluent on fungal assemblages and leaf breakdown. Water Res. 25: 247– 250.
24.
Naeem, S.,, and S. Li. 1997. Biodiversity enhances ecosystem reliability. Nature 390: 507– 509.
25.
Nelson, J. H.,, D. L. Stoneburner,, E. S. Evans,, N. E. Pennington,, and M. V. Meisch. 1976. Diatom diversity as a function of insecticidal treatment with a controlled-release formulation of chlorpyrifos. Bull. Environ. Contam. Toxicol. 15: 630– 634.
26.
Ovreas, L.,, S. Jensen,, F. L. Daae,, and V. Torsvik. 1998. Microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. Appl. Environ. Microbiol. 64: 2739– 2742.
27.
Palm, M. E.,, and I. H. Chapela,. 1997. Mycology in sustainable development: expanding concepts, vanishing borders. In M. E. Palm, and I. H. Chapela (ed.), Mycology in Sustainable Development: Expanding Concepts, Vanishing Borders. Parkway Publishers, Boone, N.C.
28.
Persiani, A. M.,, O. Maggi,, M. A. Casado,, and F. D. Pineda. 1998. Diversity and variability in soil fungi from a disturbed tropical rain forest. Mycologia 90: 206– 214.
29.
Porter, N.,, and F. M. Fox. 1993. Diversity of microbial products: discovery and application. Pestic. Sci. 39: 161– 168.
30.
Robinson, C. H.,, J. Dighton,, J. C. Frankland,, and P. A. Coward. 1993. Nutrient and carbon dioxide release by interacting species of straw-decomposing fungi. Plant Soil 151: 139– 142.
31.
Rudi, K.,, O. M. Skulberg,, R. Skulberg,, and K. S. Jakobsen. 2000. Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl. Eyiviron. Microbiol. 66: 4004– 4011.
32.
Sandaa, R. A.,, V. Torsvik,, O. Enger,, F. L. Daae,, T. Castberg,, and D. Hahn. 1999. Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution. FEMS Microbiol. Ecol. 30: 237– 251.
33.
Segal, W.,, and R. L. Mancinelli. 1987. Extent of regeneration of the microbial community in reclaimed spent oil shale land. J. Environ. Qual. 16: 44– 48.
34.
Seghers, D. 2001. Do conventionally and biologically cultivated soils differ in bacterial diversity and community structure? Meded. Fac. Landbouwkd. Toegep. Biol. Wet. Univ. Gent 66: 381– 388.
35.
Small, J.,, D. R. Call,, F. J. Broekman,, T. M. Straub,, and D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microassays. Appl. Environ. Microbiol. 67: 4708– 4716.
36.
Smit, E.,, P. Leeflang,, and K. Wernars. 1997. Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol. Ecol. 23: 249– 261.
37.
Staley, J. T. 1997. Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8: 340– 345.
38.
Stevenson, R. J.,, and E. F. Stoermer. 1982. Abundance patterns of diatoms on Cladophora in Lake Huron with respect to a point source of wastewater treatment plant effluent. J. Great Lakes Res. 8: 184– 195.
39.
Tannock, G. W. 1999. Probiotics: A Critical Review. Horizon Scientific Press, Norfolk, England.
40.
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. CABI Publishing, Wallingford, United Kingdom.
41.
Torsvik, V.,, J. Goksoyr,, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782– 787.
42.
Torsvik, V.,, J. Goksoyr,, F. L. Daae,, R. Sorheim,, J. Michaelsen,, and K. Salte,. 1993. Diversity of microbial communities determined by DNA reassociation technique, p. 375– 378. In R. Guerrero, and C. Pedros-Alio (ed.), Trends in Microbial Ecology. Spanish Society for Microbiology, Barcelona.
43.
Torsvik, V.,, R. Sorheim,, and J. Goksoyr. 1996. Total bacterial diversity in soil and sediment communities—a review. J. Ind. Microbiol 17: 170– 178.
44.
Urakawa, H.,, P. A. Noble,, S. El Fantroussi,, J. J. Kelly,, and D. A. Stahl. 2002. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl. Environ. Microbiol. 68: 235– 244.
45.
Valinsky, L.,, G. D. Vedova,, A. J. Scupham,, S. Alvey,, A. Figueroa,, B. Yin,, R. J. Hartin,, M. Chrobak,, D. E. Crowley,, T. Jiang,, and J. Borneman. 2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68: 3243– 3250.
46.
van der Heijden, M. G. A.,, J. N. Klironomos,, M. Ursic,, P. Moutoglis,, R. Steriwolf-Engel,, T. Boller,, A. Wiemken,, and I. R. Sanders. 1998. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396: 69– 72.
47.
von Canstein, H.,, S. Kelly,, Y. Li,, and I. Wagner-Dobler. 2002. Species diversity improves the efficiency of mercury-reducing biofilms under changing environmental conditions. Appl. Environ. Microbiol. 68: 2829– 2837.
48.
Wassel, R. A.,, and A. L. Mills. 1983. Changes in water and sediment bacterial community structure in a lake receiving acid mine drainage. Microb. Ecol. 9: 155– 169.