Microbial biogeography: putting microorganisms on the map (original) (raw)
References
Brown, J. H. & Lomolino, M. V. Biogeography (Sinauer, Sunderland, 1998). A definitive textbook on the biogeography of macroorganisms; has just been updated in a 2005 edition. Google Scholar
Ward, D. M., Weller, R. & Bateson, M. M. 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature345, 63–65 (1990). CASPubMed Google Scholar
Øvreås, L. Population and community level approaches for analysing microbial diversity in natural environments. Ecol. Lett.3, 236–251 (2000). Google Scholar
Floyd, M. M., Tang, J., Kane, M. & Emerson, D. Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the American type culture collection. Appl. Environ. Microbiol.71, 2813–2823 (2005). CASPubMedPubMed Central Google Scholar
Schloss, P. D. & Handelsman, J. Status of the microbial census. Microbiol. Mol. Biol. Rev.68, 686–691 (2004). PubMedPubMed Central Google Scholar
Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science304, 66–74 (2004). ArticleCASPubMed Google Scholar
Fenchel, T., Esteban, G. F. & Finlay, B. J. Local versus global diversity of microorganisms: cryptic diversity of ciliated protozoa. Oikos80, 220–225 (1997). Google Scholar
Staley, J. T. Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol.8, 340–345 (1997). CASPubMed Google Scholar
Finlay, B. J. Global dispersal of free-living microbial eukaryote species. Science296, 1061–1063 (2002). A summary of the arguments for why microbial eukaryotes might not be restricted by geographic barriers. CASPubMed Google Scholar
Hedlund, B. P. & Staley, J. T. Microbial endemism and biogeography. In Microbial Diversity and Bioprospecting (ed. Bull, A. T.) (ASM, Washington DC, 2003). Google Scholar
Anagnostakis, S. Chestnut blight: the classical problem of an introduced pathogen. Mycologia 79, 23–27 (1987).
Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585 (2003).
Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol.13, 278–284 (2005). CASPubMed Google Scholar
de Candolle, A. P. Essai Elementaire de Geographie Botanique (F. G. Levrault, Paris, 1820). Google Scholar
Beijerinck, M. W. De infusies en de ontdekking der backteriën. In Jaarboek van de Koninklijke Akademie van Wetenschappen (Müller, Amsterdam, 1913). Google Scholar
Baas-Becking, L. G. M. Geobiologie of Inleiding Tot de Milieukunde (Van Stockkum & Zoon, The Hague, 1934). Google Scholar
Zhang, N. & Blackwell, M. Population structure of dogwood anthracnose fungus. Phytopathology92, 1276–1283 (2002). CASPubMed Google Scholar
Bala, A., Murphy, P. & Giller, K. E. Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics. Mol. Ecol.12, 917–929 (2003). CASPubMed Google Scholar
Papke, R. T. & Ward, D M. The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol.48, 293–303 (2004). A recent review discussing how physical isolation might affect prokaryote evolution. CASPubMed Google Scholar
Cho, J. C. & Tiedje, J. M. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol.66, 5448–5456 (2000). One of the first examples of relating the genetic similarity of a free-living bacterial assemblage with geographic distance, using fluorescentPseudomonasisolates. CASPubMedPubMed Central Google Scholar
Oda, Y., Star, B., Huisman, L. A., Gottschal, J. C. & Forney, L. J. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl. Environ. Microbiol.69, 5186–5191 (2003). CASPubMedPubMed Central Google Scholar
Crump, B. C., Hopkinson, C. S., Sogin, M. L. & Hobbie, J. E. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl. Environ. Microbiol.70, 1494–1505 (2004). CASPubMedPubMed Central Google Scholar
Øvreås, L., Forney, L., Daae, R. L. & Torsvik, V. Distribution of bacterioplankton in meromictic Lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol.63, 3367–3373 (1997). PubMedPubMed Central Google Scholar
Schwalbach, M. S., Hewson, I. & Fuhrman, J. A. Viral effects on bacterial community composition in marine plankton microcosms. Aquat. Microb. Ecol.34, 117–127 (2004). Google Scholar
Rosenzweig, M. L. Species Diversity in Space and Time. (Cambridge University Press, Cambridge, 1995). Google Scholar
Green, J. L. et al. Spatial scaling of microbial eukaryote diversity. Nature432, 747–750 (2004). Along with reference 27, this study uses distance–decay curves to demonstrate non-random bacterial-assemblage distributions; the studies then test whether the non-random distributions are due to isolation by distance and/or local environmental conditions. CASPubMed Google Scholar
Horner-Devine, M. C., Lage, M., Hughes, J. B. & Bohannan, B. J. M. A taxa–area relationship for bacteria. Nature432, 750–753 (2004). CASPubMed Google Scholar
Noguez, A. M. et al. Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Glob. Ecol. Biogeogr.14, 241–248 (2005). Google Scholar
Bell, T. et al. Larger islands house more bacterial taxa. Science308, 1884 (2005).
Smith, V. H. et al. Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans. Proc. Natl Acad. Sci. USA102, 4393–4396 (2005). CASPubMedPubMed Central Google Scholar
Cam, E. et al. Disentangling sampling and ecological explanations underlying species–area relationships. Ecology84, 1118–1130 (2002). Google Scholar
Colwell, R. K., Mao, C. X. & Chang, J. Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology85, 2717–2727 (2004). Google Scholar
Kuske, C. R. et al. Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl. Environ. Microbiol.68, 1854–1863 (2002). CASPubMedPubMed Central Google Scholar
Yannarell, A. C. & Triplett, E. W. Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales. Appl. Environ. Microbiol.70, 214–223 (2004). CASPubMedPubMed Central Google Scholar
Legendre, P. & Legendre, L. Numerical Ecology 2nd edn (Elsevier, Amsterdam, 1998). Google Scholar
Papke, R. T., Ramsing, N. B., Bateson, M. M. & Ward, D. M. Geographical isolation in hot spring cyanobacteria. Environ. Microbiol.5, 650–659 (2003). CASPubMed Google Scholar
Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science301, 976–978 (2003). Already a classic microbial biogeography study, it considers both the effects of spatial isolation and contemporary environmental parameters on hotspringSulfolobusassemblages within and across continents. CASPubMed Google Scholar
Reche, I., Pulido-Villena, E., Morales-Baquero, R. & Casamayor, E. O. Does ecosystem size determine aquatic bacterial richness? Ecology86, 1715–1722 (2005). Google Scholar
Brown, J. H., West, G. B. & Enquist, B. J. Scaling in biology: patterns and processes, causes and consequences. In Scaling in Biology (eds Brown, J. H. & West, G. B.) 1–24 (Oxford University Press, Oxford, 2000). A comprehensive introduction to allometric patterns in biology. Google Scholar
Bell, G. The distribution of abundance in neutral communities. Am. Nat.155, 606–617 (2000). PubMed Google Scholar
Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (Princeton University Press, Princeton, 2001). Google Scholar
Clark, J. S., Silman, M., Kern, R., Macklin, E. & HilleRisLambers, J. Seed dispersal near and far: patterns across temperate and tropical forests. Ecology80, 1475–1494 (1999). Google Scholar
Brown, J. H. & Maurer, B. A. Evolution of species assemblages: effects of energetic constraints and species dynamics on the diversification of the North American avifauna. Am. Nat.130, 1–17 (1987). Google Scholar
Morse, D. R., Stork, N. E. & Lawton, J. H. Species number, species abundance and body length relationships of arboreal beetles in Bornean lowland rain forest trees. Ecol. Entomol.13, 25–37 (1988). Google Scholar
Lawton, J. H. Species richness and population dynamics of animal assemblages. Patterns in body size: abundance space. Philos. Trans. R. Soc. Lond. B Biol. Sci.330, 283–291 (1990). Google Scholar
Siemann, E., Tilman, D. & Haarstad, J. Insect species diversity, abundance and body size relationships. Nature380, 704–706 (1996). CAS Google Scholar
Brown, J. H. Macroecology (Chicago University Press, Chicago, 1995). Google Scholar
Li, W. K. W. Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean. Nature419, 154–157 (2002). CASPubMed Google Scholar
Roberts, M. S. & Cohan, F. M. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution49, 1081–1094 (1995). PubMed Google Scholar
Stanley, S. M. Macroevolution: Pattern and Process (W. H. Freeman, San Francisco, 1979). Google Scholar
Paradis, E. Statistical analysis of diversification with species traits. Evolution59, 1–12 (2005). PubMed Google Scholar
Lenski, R. E. & Travisano, M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial-populations. Proc. Natl Acad. Sci. USA91, 6808–6814 (1994). CASPubMedPubMed Central Google Scholar
Rainey, P. B. & Travisano, M. Adaptive radiation in a heterogeneous environment. Nature394, 69–72 (1998). CASPubMed Google Scholar
Manne, L. L., Brooks, T. M. & Pimm, S. L. Relative risk of extinction of passerine birds on continents and islands. Nature399, 258–261 (1999). CAS Google Scholar
Purvis, A., Gittleman, J. L., Cowlishaw, G. & Mace, G. M. Predicting extinction risk in declining species. Proc. R. Soc. Lond. B Biol. Sci.267, 1947–1952 (2000). CAS Google Scholar
Lawton, J. H. Range, Population abundance and conservation. Trends Ecol. Evol.8, 409–413 (1993). CASPubMed Google Scholar
Silva, M. & Downing, J. A. Allometric scaling of minimal mammal densities. Conserv. Biol.8, 732–743 (1994). Google Scholar
Meretsky, V. J., Snyder, N. F. R., Beissinger, S. R., Clendenen, D. A. & Wiley, J. W. Demography of the California condor: implications for reestablishment. Conserv. Biol.14, 957–967 (2000). Google Scholar
Finlay, B. J. & Clarke, K. J. Apparent global ubiquity of species in the protist genus Paraphysomonas. Protist150, 419–430 (1999). CASPubMed Google Scholar
Massana, R., DeLong, E. F. & Pedrós-Alió, C. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol.66, 1777–1787 (2000). CASPubMedPubMed Central Google Scholar
Lindström, E. S. & Leskinen, E. Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions. Microb. Ecol.44, 1–9 (2002). PubMed Google Scholar
Brown, J. H., Stevens, G. C. & Kaufman, D. M. The geographic range: size, shape, boundaries, and internal structure. Annu. Rev. Ecol. Syst.27, 597–623 (1996). Google Scholar
May, R. M. How many species are there on Earth? Science241, 1441–1449 (1988). CASPubMed Google Scholar
Gaston, K. J., Chown, S. L. & Mercer, R. D. The animal species-body size distribution of Marion Island. Proc. Natl Acad. Sci. USA98, 14493–14496 (2001). CASPubMedPubMed Central Google Scholar
Dykhuizen, D. E. Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek73, 25–33 (1998). CASPubMed Google Scholar
Avise, J. C. & Aquadro, C. F. A comparative summary of genetic distances in the vertebrates. Evol. Biol.15, 151–185 (1982). Google Scholar
de Vargas, C., Norris, R., Zaninetti, L., Gibb, S. W. & Pawlowski, J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc. Natl Acad. Sci. USA96, 2864–2868 (1999). CASPubMedPubMed Central Google Scholar
Cohan, F. M. What are bacterial species? Annu. Rev. Microbiol.56, 457–487 (2002). CASPubMed Google Scholar
Coyne, J. A., Orr, H. A. & Futuyma, D. J. Do we need a new species concept? Syst. Zool.37, 190–200 (1988). Google Scholar
Green, J. L. & Bohannan, B. J. M. Spatial scaling of microbial biodiversity in Scaling Biodiversity (eds Storch, D. & Marquet, P. A. & Brown, J. H.) (Cambridge University Press, Cambridge, 2006). Google Scholar
Martiny, J. B. H. & Field, D. Ecological perspectives on the sequenced genome collection. Ecol. Lett. (in the press).
Naeem, S., Thompson, L. J., Lawler, S. P., Lawton, J. H. & Woodfin, R. M. Declining biodiversity can alter the performance of ecosystems. Nature368, 734–737 (1994). Google Scholar
Hooper, D. U. &. Vitousek, P. M. The effects of plant composition and diversity on ecosystem processes. Science277, 1302–1305 (1997). CAS Google Scholar
Dukes, J. S. Biodiversity and invasibility in grassland microcosms. Oecologia126, 563–568 (2001). PubMed Google Scholar
Treseder, K. K. & Vitousek, P. M. Potential ecosystem-level effects of genetic variation among populations of Metrosideros polymorpha from a soil fertility gradient in Hawaii. Oecologia126, 266–275 (2001). PubMed Google Scholar
McGrady-Steed, J., Harris, P. M. & Morin, P. J. Biodiversity regulates ecosystem predictability. Nature390, 162–165 (1997). CAS Google Scholar
Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & Lilley, A. K. The contribution of species richness and composition to bacterial services. Nature436, 1157–1160 (2005). CASPubMed Google Scholar
Naeem, S. & Li, S. B. Biodiversity enhances ecosystem reliability. Nature390, 507–509 (1997). CAS Google Scholar
van der Heijden, M. G. A. et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature396, 69–72 (1998). CAS Google Scholar
Cavigelli, M. A. & Robertson, G. P. The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology81, 1402–1414 (2000). Google Scholar
Horz, H. -P., Barbrook, A., Field, C. B. & Bohannan, B. J. M. Ammonia-oxidizing bacteria respond to multifactorial global change. Proc. Natl Acad. Sci. USA101, 15136–15141 (2004). CASPubMedPubMed Central Google Scholar
Bull, A. T., ed. Microbial Diversity and Bioprospecting. (ASM Press, Washington DC, 2003). Google Scholar
Finlay, B. J., Esteban, G. F., Olmo, J. L. & Tyler, P. A. Global distribution of free-living microbial species. Ecography22, 138–144 (1999). Google Scholar
Magurran, A. E. Ecological Diversity and Its Measurement (Princeton University Press, Princeton, 1988). Google Scholar
Chao, A., Chazdon, R. L., Colwell, R. K. & Shen, T. J. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett.8, 148–159 (2005). Google Scholar
Ricketts, T. H. The matrix matters: effective isolation in fragmented landscapes. Am. Nat.158, 87–99 (2001). CASPubMed Google Scholar
Mantel, N. The detection of disease clustering and a generalized regression approach. Cancer Res.27, 209–220 (1967). CASPubMed Google Scholar
Borcard, D., Legendre, P. & Drapeau, P. Partialling out the spatial component of ecological variation. Ecology73, 1045–1055 (1992). Google Scholar
Smouse, P. E., Long, J. C. & Sokal, R. R. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst. Zool.35, 627–632 (1986). Google Scholar
Fulthorpe, R. R., Rhodes, A. N. & Tiedje, J. M. High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl. Environ. Microbiol.64, 1620–1627 (1998). CASPubMedPubMed Central Google Scholar
Schwalbach, M. S. & Fuhrman, J. A. Wide-ranging abundances of aerobic anoxygenic phototrophic bacteria in the world ocean revealed by epifluorescence microscopy and quantitative PCR. Limnol. Oceanogr.50, 620–628 (2005). CAS Google Scholar
Garcia-Martinez, J. & Rodriguez-Valera, F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol. Ecol.9, 935–948 (2000). CASPubMed Google Scholar
Glaeser, J. & Overmann, J. Biogeography, evolution, and diversity of epibionts in phototrophic consortia. Appl. Environ. Microbiol.70, 4821–4830 (2004). CASPubMedPubMed Central Google Scholar
Yeager, C. M. et al. Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Appl. Environ. Microbiol.70, 973–983 (2004). CASPubMedPubMed Central Google Scholar
Sliwinski, M. K. & Goodman, R. M. Spatial heterogeneity of Crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling. Appl. Environ. Microbiol.70, 1811–1820 (2004). CASPubMedPubMed Central Google Scholar
Sliwinski, M. K. & Goodman, R. M. Comparison of Crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl. Environ. Microbiol.70, 1821–1826 (2004). CASPubMedPubMed Central Google Scholar
Riemann, L. & Middelboe, M. Stability of bacterial and viral community compositions in Danish coastal waters as depicted by DNA fingerprinting techniques. Aquat. Microb. Ecol.27, 219–232 (2002). Google Scholar
Pinhassi, J. et al. Spatial variability in bacterioplankton community composition at the Skagerrak–Kattegat Front. Mar. Ecol. Prog. Ser.255, 1–13 (2003). CAS Google Scholar
Troussellier, M. et al. Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat. Microb. Ecol.28, 13–24 (2002). Google Scholar
Casamayor, E. O. et al. Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ. Microbiol.4, 338–348 (2002). PubMed Google Scholar
McArthur, J. V., Kovacic, D. A. & Smith, M. H. Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc. Natl Acad. Sci. USA85, 9621–9624 (1988). CASPubMedPubMed Central Google Scholar
Buckley, D. H. & Schmidt, T. M. Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ. Microbiol.5, 441–452 (2003). PubMed Google Scholar
Staddon, W. J., Trevors, J. T., Duchesne, L. C. & Colombo, C. A. Soil microbial diversity and community structure across a climatic gradient in western Canada. Biodivers. Conserv.7, 1081–1092 (1998). Google Scholar
Franklin, R. B., Taylor, D. R. & Mills, A. L. The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer. Microb. Ecol.38, 377–386 (1999). CASPubMed Google Scholar
Franklin, R. B. & Mills, A. L. Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol. Ecol.44, 335–346 (2003). CASPubMed Google Scholar
Martiny, A. C., Jorgensen, T. M., Albrechtsen, H. J., Arvin, E. & Molin, S. Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl. Environ. Microbiol.69, 6899–6907 (2003). CASPubMedPubMed Central Google Scholar
Franklin, R. B., Blum, L. K., McComb, A. C. & Mills, A. L. A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments. FEMS Microbiol. Ecol.42, 71–80 (2002). CASPubMed Google Scholar
Rohwer, F., Seguritan, V., Azam, F. & Knowlton, N. Diversity and distribution of coral-associated bacteria. Mar. Ecol. Prog. Ser.243, 1–10 (2002). Google Scholar
Yannarell, A. C. & Triplett, E. W. Geographic and environmental sources of variation in lake bacterial community composition. Appl. Environ. Microbiol.71, 227–239 (2005). CASPubMedPubMed Central Google Scholar
Hewson, I. & Fuhrman, J. A. Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl. Environ. Microbiol.70, 3425–3433 (2004). CASPubMedPubMed Central Google Scholar