Drivers of bacterial β-diversity depend on spatial scale

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 19, 2011, Pages 7850-7854

  Martiny, Jennifer B H ^a   Eisen, Jonathan A ^b   Penn, Kevin ^c   Allison, Steven D ^a   Horner Devine, M Claire ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Distance decay; Ecological drift; Microbial composition; Nitrosomonadales

Indexed keywords

RNA 16S;

AMMONIA OXIDIZING BACTERIA; ARTICLE; BACTERIUM; BIODIVERSITY; CONTROLLED STUDY; EVOLUTIONARY ADAPTATION; GEOGRAPHIC DISTRIBUTION; MICROBIAL COMMUNITY; NONHUMAN; PRIORITY JOURNAL; SALT MARSH;

AMMONIA; BACTERIA; BETAPROTEOBACTERIA; BIODIVERSITY; ECOSYSTEM; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS); NITROSOMONADALES;

EID: 79956366900     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1016308108     Document Type: Article

References (49)

1. Daily GC (1997) Nature's Services: Societal Dependence on Natural Ecosystems (Island Press, Washington, D.C.).
2. Nekola JC, White PS (1999) The distance decay of similarity in biogeography and ecology. J Biogeogr 26:867-878. (Pubitemid 30030997)
3. Green JL, et al. (2004) Spatial scaling of microbial eukaryote diversity. Nature 432:747-750. (Pubitemid 39656292)
4. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJ (2004) A taxa-area relationship for bacteria. Nature 432:750-753. (Pubitemid 39656293)
5. Buckley LB, Jetz W (2008) Linking global turnover of species and environments. Proc Natl Acad Sci USA 105:17836-17841.
6. Ramette A, Tiedje JM (2007) Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci USA 104:2761-2766. (Pubitemid 46327953)
7. Tuomisto H, Ruokolainen K, Yli-Halla M (2003) Dispersal, environment, and floristic variation of western Amazonian forests. Science 299:241-244. (Pubitemid 36125208)
8. Condit R, et al. (2002) Beta-diversity in tropical forest trees. Science 295:666-669. (Pubitemid 34111822)
9. Bell T (2010) Experimental tests of the bacterial distance-decay relationship. ISME J 4:1357-1365.
10. Baas Becking LGM (1934) Geobiology or Introduction to Environmental Science (Translated from Dutch). (W.P. Van Stockum & Zoon, The Hague, The Nethelands).
11. Bell G (2001) Neutral macroecology. Science 293:2413-2418.
12. Rosenzweig ML (1995) Species Diversity in Space and Time (Cambridge University Press, Cambridge).
13. Preston FW (1960) Time and space and the variation of species. Ecology 41:611-627.
14. Leininger S, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809. (Pubitemid 44258909)
15. Martiny JBH, et al. (2006) Microbial biogeography: Putting microorganisms on the map. Nat Rev Microbiol 4(2):102-112. (Pubitemid 43158153)
16. Fridley JD, Peet RK, Wentworth TR, White PS (2005) Connecting fine- and broad-scale species-area relationships of Southeastern US Flora. Ecology 86:1172-1177. (Pubitemid 40641190)
17. Kowalchuk GA, et al. (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63:1489-1497. (Pubitemid 27174859)
18. McCaig AE, Embley TM, Prosser JI (1994) Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett 120:363-367. (Pubitemid 124012209)
19. Sahan E, Muyzer G (2008) Diversity and spatio-temporal distribution of ammoniaoxidizing Archaea and Bacteria in sediments of the Westerschelde estuary. FEMS Microbiol Ecol 64(2):175-186. (Pubitemid 351533424)
20. Purkhold U, Wagner M, Timmermann G, Pommerening-Röser A, Koops HP (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammoniaoxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53:1485-1494. (Pubitemid 37184980)
21. Chao A, Chazdon RL, Colwell RK, Shen TJ (2005) A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol Lett 8:148-159. (Pubitemid 40218100)
22. Legendre P, Lapointe FJ, Casgrain P (1994) Modeling brain evolution from behavior: A permutational regression approach. Evolution 48:1487-1499.
23. Primeau F (2005) Characterizing transport between the surface mixed layer and the ocean interior with a forward and adjoint global ocean transport model. J Phys Oceanogr 35:545-564.
24. Martiny AC, Tai APK, Veneziano D, Primeau F, Chisholm SW (2009) Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11:823-832.
25. Avrahami S, Liesack W, Conrad R (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ Microbiol 5:691-705. (Pubitemid 36953530)
26. Fierer N, Carney KM, Horner-Devine MC, Megonigal JP (2009) The biogeography of ammonia-oxidizing bacterial communities in soil. Microb Ecol 58:435-445.
27. Bertness MD (1999) The Ecology of Atlantic Shorelines (Sinauer, Sunderland, MA).
28. Young WR, Roberts AJ, Stuhne G (2001) Reproductive pair correlations and the clustering of organisms. Nature 412:328-331. (Pubitemid 32691845)
29. Morlon H, et al. (2008) A general framework for the distance-decay of similarity in ecological communities. Ecol Lett 11:904-917.
30. Chase JM (2007) Drought mediates the importance of stochastic community assembly. Proc Natl Acad Sci USA 104:17430-17434.
31. Cho JC, Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66:5448-5456.
32. Schauer R, Bienhold C, Ramette A, Harder J (2010) Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4:159-170.
33. Langenheder S, Ragnarsson H (2007) The role of environmental and spatial factors for the composition of aquatic bacterial communities. Ecology 88:2154-2161. (Pubitemid 351345125)
34. Heino J, et al. (2010) Geographical patterns of micro-organismal community structure: Are diatoms ubiquitously distributed across boreal streams? Oikos 119(1):129-137.
35. Wang JJ, et al. (2008) High beta diversity of bacteria in the shallow terrestrial subsurface. Environ Microbiol 10:2537-2549.
36. Wiens JA (1989) Spatial scaling in ecology. Funct Ecol 3:385-397.
37. Levin SA (1992) The problem of pattern and scale in ecology. Ecology 73:1943-1967.
38. Ludwig W, et al. (2004) ARB: A software environment for sequence data. Nucleic Acids Res 32:1363-1371. (Pubitemid 38854737)
39. Pruesse E, et al. (2007) SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196.
40. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319. (Pubitemid 39341624)
41. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734-5741. (Pubitemid 44414595)
42. Maidak BL, et al. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27(1):171-173. (Pubitemid 29209430)
43. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6 (Distributed by the author, Department of Genome Sciences, University of Washington, Seattle).
44. Schloss PD, et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-7541.
45. Magurran AE (1988) Ecological Diversity and Its Measurement (Princeton University, Princeton).
46. R Development Core Team (2008) R: A language and environment for statistical computing. (R Foundation for Statistical Computing, Vienna, Austria), ISBN 3-900051-07-0, http://www.R-project.org). Accessed March 11, 2010.
47. Goslee SC, Urban DL (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22(7):1-19.
48. Clarke KR, Warwick RM (2001) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation (PRIMER-E, Plymouth).
49. Harrell JFE (2001) Regression Modeling Strategies with Applications to Linear Models, Logistic Regression, and Survival Analysis (Springer, New York).