Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-cd9895bd7-mkpzs Total loading time: 0 Render date: 2024-12-26T01:21:24.508Z Has data issue: false hasContentIssue false

7 - Biodiversity scaling relationships: are microorganisms fundamentally different?

Published online by Cambridge University Press:  05 August 2012

By
Jessica Green  and
Brendan J. M. Bohannan
Edited by
David Storch ,
Pablo Marquet  and
James Brown
Jessica Green
Affiliation:
University of California, Merced
Brendan J. M. Bohannan
Affiliation:
University of Oregon
David Storch
Affiliation:
Charles University, Prague
Pablo Marquet
Affiliation:
Pontificia Universidad Catolica de Chile
James Brown
Affiliation:
University of New Mexico
Get access

Summary

Introduction

One of the key goals of ecology is to understand the spatial scaling of species diversity. Spatial patterns of species diversity provide important clues about the underlying mechanisms that regulate biodiversity and are central in the development of biodiversity theory (MacArthur & Wilson, 1967; Rosenzweig, 1995; Brown, 1995; Gaston & Blackburn, 2000; Hubbell, 2001; Holyoak, Leibold & Holt, 2005). Assumptions regarding the spatial scaling of biodiversity are a fundamental component of conservation biology and are frequently used to identify local- and global-scale priority conservation areas (Ferrier et al., 2004; Desmet & Cowling, 2004) and to predict extinction risk due to climate change (Thomas et al., 2004) and habitat loss (Gaston, Blackburn & Goldewijk, 2003). Although scaling patterns have been documented in hundreds of studies of plant and animal diversity, such patterns in microbial species (i.e. bacteria, archaea, and single-celled eukarya) have not been well documented. This is a serious omission, given that microorganisms may comprise much of Earth's biodiversity (Whitman, Coleman & Wiebe, 1998; Torsvik, Ovreas & Thingstad, 2002) and play critical roles in biogeochemical cycling and ecosystem functioning (Balser, 2000; Wardle, 2002; Morin & McGrady-Steed, 2004). Furthermore, microbial biodiversity is a major source of novel pharmaceuticals and other compounds of industrial importance, and an understanding of the scaling of microbial biodiversity is crucial to the search for such compounds (Bull, 2004).

Type
Chapter
Information
Scaling Biodiversity , pp. 129 - 149
Publisher: Cambridge University Press
Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amann, R. I., Ludwig, W., Schleifer, K. H., Torsvik, V. & Goksoyr, J. (1995). Phylogenetic identification and in situ detection of individual microbial-cells without cultivation. Microbiological Reviews, 59, 2019–2027.Google ScholarPubMed
Arrhenius, O. (1921). Species and area. Journal of Ecology, 9, 95–99.CrossRefGoogle Scholar
Azovksy, A. I. (2002). Size-dependent species-area relationships in benthos: is the world more diverse for microbes?Ecography, 25, 273–282.Google Scholar
Balser, T. C. (2000). Linking Microbial Communities and Ecosystem Functioning. Berkeley: University of California.Google Scholar
Bass-Becking, L. G. M. (1934). Geobiologie of Inleiding to de Milieukunde, The Hague: W. P van Stockum & Zoon N. V.Google Scholar
Bell, T., Ager, D., Song, J.-I., et al. (2005). Larger islands house more bacterial taxa. Science, 308, 1884.CrossRefGoogle ScholarPubMed
Bohannan, B. J. M. & Hughes, J. (2003). New approaches to analyzing microbial biodiversity data. Current Opinion in Microbiology, 6, 282–287.CrossRefGoogle ScholarPubMed
Brandao, P. F. B., Clapp, J. P. & Bull, A. T. (2002). Discrimination and taxonomy of geographically diverse strains of nitrile-metabolizing actinomycetes using chemometric and molecular sequencing techniques. Environmental Microbiology, 4, 262–276.CrossRefGoogle ScholarPubMed
Brown, J. H. (1995). Macroecology, Chicago: University of Chicago Press.Google Scholar
Bull, A. T. (2004). How to look, where to look. In Microbial Diversity and Bioprospecting, ed. Bull, A. T., Washington D.C.: American Society for Microbial Press.CrossRefGoogle Scholar
Cam, E., Nichols, J. D., Hines, J. E., Sauer, J. R., Alpizar-Jara, R. & Flather, C. H. (2002). Disentangling sampling and ecological explanations underlying species-area relationships. Ecology, 83, 1118–1130.Google Scholar
Cho, J.-C. & Tiedje, J. M. (2000). Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Applied and Environmental Microbiology, 66, 5448–5456.CrossRefGoogle ScholarPubMed
Cohan, F. M. (2001). Bacterial species and speciation. Systematic Biology, 50, 513–524.CrossRefGoogle ScholarPubMed
Cohan, F. M. (2002). What are bacterial species?Annual Review of Microbiology, 56, 457–487.CrossRefGoogle ScholarPubMed
Coleman, A. W., Finlay, B. J. & Fenchel, T. (2002). Microbial eukaryote species. Science, 297, 337.CrossRefGoogle ScholarPubMed
Condit, R., Pitman, N., Leigh, E. G. Jr., et al. (2002). Beta-diversity in tropical forest trees. Science, 295, 666–669.CrossRefGoogle ScholarPubMed
Connor, E. F. & McCoy, E. D. (1979). The statistics and biology of the species-area relationship. American Naturalist, 113, 791–833.CrossRefGoogle Scholar
Curtis, T. P., Sloan, W. T. & Scannell, J. W. (2002). Estimating prokaryotic diversity and its limits. Proceedings of the National Academy of Sciences of the United States of America, 99, 10494–10499.CrossRefGoogle ScholarPubMed
DeCandolle, A. (1855). Géographie Botanique Raisonnée; ou exposition des faits principaux et des lois concernant la distribution géograhique des plates de l'époque actuelle. Paris: Maisson.Google Scholar
Desmet, P. & Cowling, R. (2004). Using the species-area relationship to set baseline targets for conservation. Ecology and Society, 9, 11.CrossRefGoogle Scholar
Dunbar, J., Barns, S. M., Ticknor, L. O. & Kuske, C. R. (2002). Empirical and theoretical bacterial diversity in four Arizona soils. Applied and Environmental Microbiology, 68, 3035–3045.CrossRefGoogle ScholarPubMed
Dykhuizen, D. E. (1998). Santa Rosalia revisited: Why are there so many species of bacteria?Antonie van Leeuwenhoek, 73, 25–33.CrossRefGoogle Scholar
Fenchel, T. & Finlay, B. J. (2004). The ubiquity of small species: patterns of local and global diversity. BioScience, 54, 777–784.CrossRefGoogle Scholar
Ferrier, S., Powell, G. V. N., Richardson, K. S., et al. (2004). Mapping more of terrestrial biodiversity for global conservation assessment. BioScience, 54, 1101–1109.CrossRefGoogle Scholar
Finlay, B. J. (2002). Global dispersal of free-living microbial eukaryote species. Science, 296, 1061–1063.CrossRefGoogle ScholarPubMed
Finlay, B. J. & Clarke, K. J. (1999). Ubiquitous dispersal of microbial species. Nature, 400, 828.CrossRefGoogle Scholar
Finlay, B. J. & Esteban, G. (2004). Ubiquitous dispersal of free-living microorganisms. In Microbial Diversity and Bioprospecting, ed. Bull, A. T., Washington D.C.: American Society for Microbiology Press.CrossRefGoogle Scholar
Finlay, B. J. & Fenchel, T. (2004). Cosmopolitan metapopulations of free-living microbial eukaryotes. Protist, 55, 237–244.CrossRefGoogle Scholar
Finlay, B. J., Corliss, J. O., Esteban, G. & Fenchel, T. (1996). Biodiversity at the microbial level: the number of free-living ciliates in the biosphere. Quarterly Review of Biology, 71, 221–237.CrossRefGoogle Scholar
Finlay, B. J., Esteban, G. V. & Fenchel, T. (1998). Protozoan diversity: converging estimates of the global number of free-living ciliate species. Protist, 149, 29–37.CrossRefGoogle ScholarPubMed
Foissner, W. (1997). Global scale ciliate (Protozoa, Ciliophora) diversity: a probability-based approach using large sample collections from Africa, Australia and Antartica. Biodiversity and Conservation, 6, 1627–1638.CrossRefGoogle Scholar
Foissner, W. (1999). Protist diversity: estimates of the near-imponderable. Protist, 150, 363–368.CrossRefGoogle ScholarPubMed
Franklin, R. B. & Mills, A. L. (2003). Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiology Ecology, 44, 335–346.CrossRefGoogle Scholar
Fuhrman, J. & Campbell, L. (1998). Microbial microdiversity. Nature, 393, 410–411.CrossRefGoogle Scholar
Fulthorpe, R. R., Rhodes, A. N. & Tiedje, J. M. (1998). High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Applied and Environmental Microbiology, 64, 1620–1627.Google ScholarPubMed
Gage, S. H., Isard, S. A. & Colunga, G. M. (1999). Ecological scaling of aerobiological dispersal processes. Agricultural and Forestry Meteorology, 30, 249–261.CrossRefGoogle Scholar
Gaston, K. & Blackburn, T. (2000). Pattern and Process in Macroecology, Oxford: Blackwell Science.CrossRefGoogle Scholar
Gaston, K. J., Blackburn, T. M. & Goldewijk, K. K. (2003). Habitat conversion and global avian biodiversity loss. Proceedings of the Royal Society of London: Biological Sciences, 270, 1293–1300.CrossRefGoogle ScholarPubMed
Gleason, H. A. (1922). On the relation between species and area. Ecology, 71, 213–225.Google Scholar
Glöckner, F. O., Zaichikov, E., Belkova, N., et al. (2000). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Applied and Environmental Microbiology, 66, 5053–5065.CrossRefGoogle ScholarPubMed
Gogarten, J. P. (2003). Gene transfer: gene swapping craze reaches eukaryotes. Current Biology, 13, R53–R54.CrossRefGoogle ScholarPubMed
Green, J. L., Holmes, A. J., Westoby, M., et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature, 432, 747–750.CrossRefGoogle ScholarPubMed
Green, J. L., Hastings, A., Arzberger, P., et al. (2005). Complexity in ecology and conservation: mathematical, statistical, and computational challenges. Bioscience, 55, 501–510.CrossRefGoogle Scholar
Hagstrom, A., Pinhassi, J. & Zweifel, U. L. (2000). Biogeographical diversity among marine bacterioplankton. Aquatic Microbial Ecology, 21, 231–244.CrossRefGoogle Scholar
He, F. & Legendre, P. (1996). On species-area relations. American Naturalist, 148, 719–737.CrossRefGoogle Scholar
Head, I. M., Saunders, J. R. & Pickup, R. W. (1998). Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated organisms. Microbial Ecology, 35, 1–21.CrossRefGoogle Scholar
Hedlund, B. P. & Staley, J. T. (2004). Microbial endemism and biogeography. In Microbial Biodiversity and Bioprospecting, ed. Bull, A. T., Washington D.C.: ASM Press.Google Scholar
Hillebrand, H., Watermann, F., Karez, R. & Berninger, U. (2001). Differences in species richness patterns between unicellular and multicellular organisms. Oecologia, 126, 114–124.CrossRefGoogle ScholarPubMed
Holyoak, M., Leibold, M. A. & Holt, R. D. (2005). Metacommunities: Spatial Dynamics and Ecological Communities, Chicago: University of Chicago Press.Google Scholar
Horner-Devine, M., Lage, M., Hughes, J. & Bohannan, B. (2004a). A taxa-area relationship for bacteria. Nature, 432, 750–753.CrossRefGoogle Scholar
Horner-Devine, M. C., Carney, K. M. & Bohannan, B. J. M. (2004b). An ecological perspective on bacterial biodiversity. Proceedings of the Royal Society of London, Series B, 271, 113–122.CrossRefGoogle Scholar
Hubbell, S. P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton: Princeton University Press.Google Scholar
Krishnamani, R., Kumar, A. & Harte, J. (2004). Estimating species richness at large spatial scales using data from small discrete plots. Ecography, 27, 637–642.CrossRefGoogle Scholar
Leff, L. G., McArthur, J. V. & Shimkets, L. J. (1998). Persistence and dissemination of introduced bacteria in freshwater microcosms. Microbial Ecology, 36, 202–211.CrossRefGoogle ScholarPubMed
Lighthart, B. (1997). The ecology of bacteria in the alfresco atmosphere. FEMS Microbiology Ecology, 23, 263–274.CrossRefGoogle Scholar
MacArthur, R. H. & Wilson, E. O. (1967). The Theory of Island Biogeography. Princeton: Princeton University Press.Google Scholar
Magurran, A. E. (2004). Measuring Biological Diversity. Malden, MA: Blackwell Science.Google Scholar
Martiny, J. B. H., Bohannan, B. J. M., Brown, J. H., et al. (2006). Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology, 4, 102–112.CrossRefGoogle Scholar
May, R. M. (1975). Patterns of species abundance and diversity. In Ecology and Evolution of Communities, ed. Cody, M. L. & Diamond, J. M.. Cambridge: Harvard University Press.Google Scholar
McNair, J. N., Newbold, J. D. & Hart, D. D. (1997). Turbulent transport of suspended particles and dispersing benthic organisms: how long to hit bottom?Journal of Theoretical Biology, 188, 29–52.CrossRefGoogle Scholar
Mlot, C. (2004). Microbial diversity unbound: what DNA-based techniques are revealing about the planet's hidden biodiversity. Bioscience, 54, 1064–1068.
Moore, L. R., Rocap, G. & Chisholm, S. W. (1998). Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature, 393, 464–467.CrossRefGoogle ScholarPubMed
Morin, P. J. & McGrady-Steed, J. (2004). Biodiversity and ecosystem functioning in aquatic microbial systems: a new analysis of temporal variation and species richness-predictability relations. Oikos, 104, 458–466.CrossRefGoogle Scholar
Nekola, J. C. & White, P. S. (1999). The distance decay of similarity in biogeography and ecology. Journal of Biogeography, 26, 867–878.CrossRefGoogle Scholar
Noguez, A. M., Arita, H. T., Escalante, A. E., Forney, L. J., Garcia-Oliva, F. & Souza, V. (2005). Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Global Ecology and Biogeography, 14, 241–248.CrossRefGoogle Scholar
Ochman, H., Lawrence, J. G. & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299–304.CrossRefGoogle ScholarPubMed
O'Donnell, A. G., Goodfellow, G. & Hawksworth, D. L. (1994). Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Philosophical Transactions of the Royal Society of London, Series B, 345, 65–73.CrossRefGoogle ScholarPubMed
Papke, R. T. & Ward, D. M. (2004). The importance of physical isolation to microbial diversification. FEMS Microbiology Ecology, 48, 293.CrossRefGoogle ScholarPubMed
Papke, R. T., Ramsing, N. B., Bateson, M. M. & Ward, D. M. (2003). Geographical isolation in hot spring cyanobacteria. Environmental Microbiology, 5, 650–659.CrossRefGoogle ScholarPubMed
Qian, H., Ricklefs, R. E. & White, P. S. (2005). Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America. Ecology Letters, 8, 1–15.Google Scholar
Reche, I., Pulido-Villena, E., Morales-Baquero, R. & Casamayor, E. O. (2005). Does ecosystem size determine aquatic bacterial richness?Ecology, 86, 1715–1722.CrossRefGoogle Scholar
Roberts, M. S. & Cohan, F. M. (1995). Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution, 49, 1081–1094.CrossRefGoogle ScholarPubMed
Rosenzweig, M. L. (1995). Species Diversity in Space and Time. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Smith, V. H., Foster, B. L., Grover, J. P., Holt, R. D., Leibold, M. A. & Denoyelles, F. (2005). Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans. Proceedings of the National Academy of Sciences of the United States of America, 102, 4393–4396.CrossRefGoogle ScholarPubMed
Stackebrandt, E. & Rainey, F. A. (1995). Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In Molecular Microbial Ecology Manual, ed. Akkermans, A. D. L., Elsas, J. D. & Bruijn, F. J.. Dordrecht: Kluwer Academic Publishers.CrossRefGoogle Scholar
Staley, J. T. (1997). Biodiversity: are microbial species threatened? Commentary. Current Opinion in Biotechnology, 8, 340.CrossRefGoogle Scholar
Staley, J. T. & Gosink, J. J. (1999). Poles apart: biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology, 53, 189–215.CrossRefGoogle ScholarPubMed
Thomas, C. D., Cameron, A., Green, R. E., et al. (2004). Climate change and extinction risk. Nature, 427, 145–148.CrossRefGoogle ScholarPubMed
Tiedje, J. (1993). Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat. In Microbial Diversity and Ecosystem Function, ed. Allksopp, D., Colwell, R. R. & Hawksworth, D. L.. Wallingford, UK: CAB International.Google Scholar
Torsvik, V., Ovreas, L. & Thingstad, T. F. (2002). Prokaryotic diversity – magnitude, dynamics, and controlling factors. Science, 296, 1064–1066.CrossRefGoogle ScholarPubMed
Tuomisto, H., Ruokolainen, K. & Yli-Halla, M. (2003). Dispersal, environment, and floristic variation of western Amazonian forests. Science, 999, 241–244.CrossRefGoogle Scholar
Gast, C. J., Lilley, A. K., Ager, D. & Thompson, I. P. (2005). Island size and bacterial diversity in an archipelago of engineering machines. Environmental Microbiology, 7, 1220–1226.CrossRefGoogle Scholar
Ward, B. B. & O'Mullan, G. D. (2002). Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing {gamma}-proteobacterium, detected by PCR and sequencing of 16 S rRNA and amoA genes. Applied and Environmental Microbiology, 68, 4153–4157.CrossRefGoogle Scholar
Ward, D. M., Ferris, M. J., Nold, S. C. & Bateson, M. M. (1998). A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiology and Molecular Biology Reviews, 62, 1353–1370.Google ScholarPubMed
Wardle, D. A. (2002). Communities and Ecosystems: Linking Aboveground and Belowground Components. Princeton: Princeton University Press.Google Scholar
Whitaker, R. J., Grogan, D. W. & Taylor, J. W. (2003). Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science, 301, 976–978.CrossRefGoogle ScholarPubMed
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. (1998). Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences of the United States of America, 95, 6578–6583.CrossRefGoogle ScholarPubMed
Wilkinson, D. M. (2001). What is the upper size limit for cosmopolitan distribution in free-living microorganisms?Journal of Biogeography, 28, 285–291.CrossRefGoogle Scholar
Wintzingerode, F. V., Göbel, U. B. & Stackebrandt, E. (1997). Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews, 21, 213–229.CrossRefGoogle Scholar
Yannarell, A. C. & Triplett, E. W. (2005). Geographic and environmental sources of variation in lake bacterial community composition. Applied and Environmental Microbiology, 71, 227–239.CrossRefGoogle ScholarPubMed
Zhou, J., Xia, B., Treves, D. S., et al. (2002). Spatial and resource factors influencing high microbial diversity in soil. Applied and Environmental Microbiology, 68, 326–334.CrossRefGoogle ScholarPubMed
Zwart, G., Crump, B. C., Agterveld, M. P. K. V., Hagen, F. & Han, S. K. (2002). Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquatic Microbial Ecology, 28, 141–155.CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×