Phylogenetic beta diversity in bacterial assemblages across ecosystems: Deterministic versus stochastic processes

ISME Journal

Volumn 7, Issue 7, 2013, Pages 1310-1321

  Wang, Jianjun ^a,b   Shen, Ji ^a   Wu, Yucheng ^c   Tu, Chen ^d   Soininen, Janne ^e   Stegen, James C ^f   He, Jizheng ^b   Liu, Xingqi ^a   Zhang, Lu ^a   Zhang, Enlou ^a  

^a NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

^b RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^d YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

^e UNIVERSITY OF HELSINKI   (Finland)

^f PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

bacteria; community composition; distance decay relationship; evolutionary niche conservatism; neutral theory; phylogenetic beta diversity

Indexed keywords

RNA 16S;

BACTERIUM; BIOFILM; HABITAT TYPE; LACUSTRINE DEPOSIT; LAKE WATER; MICROBIAL COMMUNITY; PHYLOGENETICS; SPATIAL DISTRIBUTION; SPECIALIZATION; STREAM; SUBTERRANEAN ENVIRONMENT;

ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; STATISTICS;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIODIVERSITY; ECOSYSTEM; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; STOCHASTIC PROCESSES; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 84880919285     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.30     Document Type: Article

References (53)

1. Anderson MJ. (2001). A new method for non parametric multivariate analysis of variance. Austral Ecol 26: 32-46
2. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, Freestone AL et al. (2011). Navigating the multiple meanings of b diversity: A roadmap for the practicing ecologist. Ecol Lett 14: 19-28
3. Andersson AF, Riemann L, Bertilsson S. (2010). Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities. ISME J 4: 171-181
4. Besemer K, Peter H, Logue JB, Langenheder S, Lindstrom ES, Tranvik LJ et al. (2012). Unraveling assembly of stream biofilm communities. ISME J 6: 1459-1468
5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335-336
6. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW. (2009). The merging of community ecology and phylogenetic biology. Ecol Lett 12: 693-715
7. Chase JM, Myers JA. (2011). Disentangling the importance of ecological niches from stochastic processes across scales. Phil Trans R Soc B 366: 2351-2363
8. Cottenie K. (2005). Integrating environmental and spatial processes in ecological community dynamics. Ecol Lett 8: 1175-1182
9. C. Darwin, On the Origin of Species (John Murray, London, UK, 1859)
10. Delmont TO, Malandain C, Prestat E, Larose C, Monier J-M, Simonet P et al. (2011). Metagenomic mining for microbiologists. ISME J 5: 1837-1843.
11. Diniz-Filho JAF, Terribile LC, da Cruz MJR, Vieira LCG. (2010). Hidden patterns of phylogenetic non-stationarity overwhelm comparative analyses of niche conservatism and divergence. Glob Ecol Biogeogr 19: 916-926
12. Duan H, Ma R, Xu X, Kong F, Zhang S, Kong W et al. (2009). Two-decade reconstruction of algal blooms in China's Lake Taihu. Environ Sci Technol 43: 3522-3528
13. L. Fan, D. Reynolds, M. Liu, M. Stark, S. Kjelleberg, N. S. Webster et al., , 1887 (2012)
14. Fierer N, Jackson RB. (2006). The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631
15. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL et al. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109: 21390-21395
16. Fine PVA, Kembel SW. (2011). Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography 34: 552-565
17. Graham CH, Fine PVA. (2008). Phylogenetic beta diversity: Linking ecological and evolutionary processes across space in time. Ecol Lett 11: 1265-1277
18. Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. (2012). Beyond biogeographic patterns: Processes shaping the microbial landscape. Nat Rev Microbiol 10: 497-506
19. Hardy OJ. (2008). Testing the spatial phylogenetic structure of local communities: Statistical performances of different null models and test statistics on a locally neutral community. J Ecol 96: 914-926
20. S. P. Hubbell, The Unified Neutral Theory of Biodiversity and Biogeography (Princeton University Press, 2001)
21. A. J. King, K. R. Freeman, K. F. McCormick, R. C. Lynch, C. Lozupone, R. Knight et al., Nat Commun 1, 53 (2010)
22. P. Legendre and L. Legendre, Numerical Ecology (Elsevier, New York, NY, 1998)
23. Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF et al. (2004). The metacommunity concept: A framework for multi-scale community ecology. Ecol Lett 7: 601-613
24. Lindström ES, Langenheder S. (2012). Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep 4: 1-9
25. Liu X, Dong H, Yang X, Herzschuh U, Zhang E, Stuut J-BW et al. (2009). Late Holocene forcing of the Asian winter and summer monsoon as evidenced by proxy records from the northern Qinghai-Tibetan Plateau. Earth Planet Sci Lett 280: 276-284
26. Losos JB. (2008). Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett 11: 995-1003
27. Lozupone C, Knight R. (2005). UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235
28. Lozupone CA, Knight R. (2007). Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104: 11436-11440
29. Martiny AC, Tai APK, Veneziano D, Primeau F, Chisholm SW. (2009). Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11: 823-832
30. Martiny AC, Treseder K, Pusch G. (2012). Phylogenetic conservatism of functional traits in microorganisms. ISME J; e-pub ahead of print 13 December 2012 doi:10.1038/ismej.2012.160
31. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL et al. (2006). Microbial biogeography: Putting microorganisms on the map. Nat Rev Microbiol 4: 102-112
32. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. (2011). Drivers of bacterial b-diversity depend on spatial scale. Proc Natl Acad Sci USA 108: 7850-7854
33. M. W. McKnight, P. S. White, R. I. McDonald, J. F. Lamoreux, W. Sechrest, R. S. Ridgely et al., PLoS Biol. 5, e272 (2007)
34. V. Merhej, M. Royer-Carenzi, P. Pontarotti, and D. Raoult, Biol. Direct 4, 13 (2009)
35. Morlon H, Chuyong G, Condit R, Hubbell S, Kenfack D, Thomas D et al. (2008). A general framework for the distance-decay of similarity in ecological communities. Ecol Lett 11: 904-917
36. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK et al. (2011). Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13: 135-144
37. Newton RJ, Jones SE, Helmus MR, McMahon KD. (2007). Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73: 7169-7176
38. Oden NL, Sokal RR. (1986). Directional autocorrelation: An extension of spatial correlograms to two dimensions. Syst Biol 35: 608-617
39. Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA et al. (2010). Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107: 15345-15350
40. Philippot L, Andersson SGE, Battin TJ, Prosser JI, Schimel JP, Whitman WB et al. (2010). The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529
41. Popa O, Dagan T. (2011). Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol 14: 615-623
42. J. C. Stegen and A. H. Hurlbert, PLoS ONE 6, e20906 (2011)
43. Stegen JC, Lin X, Konopka AE, Fredrickson JK. (2012). Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6: 1653-1664
44. Tuomisto H, Ruokolainen K. (2006). Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis. Ecology 87: 2697-2708
45. Vellend M. (2010). Conceptual synthesis in community ecology. Q Rev Biol 85: 183-206
46. Wang J, Soininen J, He J, Shen J. (2012a). Phylogenetic clustering increases with elevation for microbes. Environ Microbiol Rep 4: 217-226
47. Wang J, Soininen J, Zhang Y,Wang B, Yang X, Shen J. (2011). Contrasting patterns in elevational diversity between microorganisms and macroorganisms. J Biogeogr 38: 595-603
48. Wang J, Soininen J, Zhang Y, Wang B, Yang X, Shen J. (2012b). Patterns of elevational beta diversity in microand macroorganisms. Glob Ecol Biogeogr 21: 743-750
49. Wang J, Wu Y, Jiang H, Li C, Dong H, Wu Q et al. (2008). High beta diversity of bacteria in the shallow terrestrial subsurface. Environ Microbiol 10: 2537-2549
50. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. (2002). Phylogenies and community ecology. Annu Rev Ecol Syst 33: 475-505
51. Wiedenbeck J, Cohan FM. (2011). Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35: 957-976
52. Xiong J, Liu Y, Lin X, Zhang H, Zeng J, Hou J et al. (2012). Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau. Environ Microbiol 14: 2457-2466
53. L. Zinger, L. A. Amaral-Zettler, J. A. Fuhrman, M. C. Horner-Devine, S. M. Huse, D. B. M. Welch et al., PLoS ONE 6, e24570 (2011)