Soil bacterial communities are shaped by temporal and environmental filtering: Evidence from a long-term chronosequence

Environmental Microbiology

Volumn 17, Issue 9, 2015, Pages 3208-3218

  Freedman, Zachary ^a   Zak, Donald R ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; NITROGEN; SOIL;

BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; ENVIRONMENT; GENETICS; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY; PHYLOGENY; SOIL;

BACTERIA; BIODIVERSITY; CARBON; ENVIRONMENT; MICROBIAL CONSORTIA; NITROGEN; PHYLOGENY; SOIL; SOIL MICROBIOLOGY;

EID: 84932197643     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12762     Document Type: Article

References (66)

1. Anderson, M.J. (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.
2. Anderson, M.J. (2004) PERMDISP: A FORTRAN Computer Program for Permutational Analysis of Multivariate Dispersions (For Any Two-Factor ANOVA design) Using PERMUTATION tests. Auckland, New Zealand: Department of Statistics, University of Auckland.
3. Batten, K.M., Scow, K.M., Davies, K.F., and Harrison, S.P. (2006) Two invasive plants alter soil microbial community composition in serpentine grasslands. Biol Invasions 8: 217-230.
4. Braun, E.L. (1950) Deciduous Forests of Eastern North America. New York, NY, USA: Macmillan Publishing.
5. Brown, S.P., and Jumpponen, A. (2014) Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils. Mol Ecol 23: 481-497.
6. Burton, A.J., Ramm, C.W., Pregitzer, K.S., and Reed, D.D. (1991) Use of multivariate methods in forest research site selection. Can J For Res 21: 1573-1580.
7. Castro, H.F., Classen, A.T., Austin, E.E., Norby, R.J., and Schadt, C.W. (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76: 999-1007.
8. Chao, A. (1984) Nonparametricestimation of the number of classes in a population. Scand J Stat 11: 265-270.
9. Cho, J.C., and Tiedje, J.M. (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66: 5448-5456.
10. Clarke, K.R., and Ainsworth, M. (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol Prog Ser 92: 205-219.
11. Cline, L.C., and Zak, D.R. (2014) Dispersal limitation structures fungal community assembly in a long-term glacial chronosequence. Environ Microbiol 16: 1538-1548.
12. Davis, M.B. (1983) Quaternary history of deciduous forests of eastern North-America and Europe. Ann Mo Bot Gard 70: 550-563.
13. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
14. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., etal. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323: 133-138.
15. Eisenlord, S.D., Zak, D.R., and Upchurch, R.A. (2012) Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence. Ecol Evol 2: 538-549.
16. Evenson, E.B., Farragund, W.R., Eschman, D.F., Mickelson, D.M., and Maher, L.J. (1976) Greatlakean substage: a replacement for Valderan substage in the Lake Michigan basin. Quaternary Res 6: 411-424.
17. Favet, J., Lapanje, A., Giongo, A., Kennedy, S., Aung, Y.Y., Cattaneo, A., etal. (2013) Microbial hitchhikers on intercontinental dust: catching a lift in Chad. ISME J 7: 850-867.
18. Ferrenberg, S., O'Neill, S.P., Knelman, J.E., Todd, B., Duggan, S., Bradley, D., etal. (2013) Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J 7: 1102-1111.
19. Fichot, E.B., and Norman, R.S. (2013) Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome 1: 10-14.
20. Fierer, N., and Jackson, R.B. (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
21. Freedman, Z., and Zak, D.R. (2014) Atmospheric N deposition increases bacterial laccase-like multicopper oxidases: implications for organic matter decay. Appl Environ Microbiol 80: 4460-4468.
22. Freedman, Z., Eisenlord, S.D., Zak, D.R., Xue, K., He, Z., and Zhou, J. (2013) Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol Biochem 66: 130-138.
23. Fukami, T., Dickie, I.A., Wilkie, J.P., Paulus, B.C., Park, D., Roberts, A., etal. (2010) Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol Lett 13: 675-684.
24. Garbeva, P., and de Boer, W. (2009) Inter-specific interactions between carbon-limited soil Bacteria affect behavior and gene expression. Microb Ecol 58: 36-46.
25. Green, S.J., Inbar, E., Michel, F.C., Jr, Hadar, Y., and Minz, D. (2006) Succession of bacterial communities during early plant development: transition from seed to root and effect of compost amendment. Appl Environ Microbiol 72: 3975-3983.
26. Hanson, C.A., Fuhrman, J.A., Horner-Devine, M.C., and Martiny, J.B.H. (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10: 497-506.
27. van der Heijden, M.G.A., Bardgett, R.D., and van Straalen, N.M. (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310.
28. Keddy, P.A. (1992) Assembly and response rules - 2 goals for predictive community ecology. J Veg Sci 3: 157-164.
29. Knelman, J.E., Legg, T.M., O'Neill, S.P., Washenberger, C.L., Gonzalez, A., Cleveland, C.C., and Nemergut, D.R. (2012) Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biol Biochem 46: 172-180.
30. Kuo, C.H., Moran, N.A., and Ochman, H. (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 1450-1454.
31. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). New York, NY, USA: Wiley, pp. 115-175.
32. Lauber, C.L., Strickland, M.S., Bradford, M.A., and Fierer, N. (2008) The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 40: 2407-2415.
33. Legendre, P., and Legendre, L. (1998) Numerical Ecology. Amsterdam, The Netherlands: Elsevier.
34. Loreau, M., Naeem, S., Inchausti, P., Bengtsson, J., Grime, J.P., Hector, A., etal. (2001) Ecology - biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804-808.
35. Lozupone, C., and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
36. Ludwig, R.A. (1984) Rhizobium free-living nitrogen-fixation occurs in specialized nongrowing cells. Proc Natl Acad Sci USA 81: 1566-1569.
37. Macdonald, N.W., Burton, A.J., Jurgensen, M.F., McLaughlin, J.W., and Mroz, G.D. (1991) Variation in forest soil properties along a great-lakes air-pollution gradient. Soil Sci Soc Am J 55: 1709-1715.
38. Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
39. Marshall, C.W., Ross, D.E., Fichot, E.B., Norman, R.S., and May, H.D. (2012) Electrosynthesis of commodity chemicals by an autotrophic microbial community. Appl Environ Microbiol 78: 8412-8420.
40. Martiny, A.C., Tai, A.P., Veneziano, D., Primeau, F., and Chisholm, S.W. (2009) Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11: 823-832.
41. Martiny, J.B., Eisen, J.A., Penn, K., Allison, S.D., and Horner-Devine, M.C. (2011) Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci USA 108: 7850-7854.
42. Martiny, J.B.H., Bohannan, B.J.M., Brown, J.H., Colwell, R.K., Fuhrman, J.A., Green, J.L., etal. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-112.
43. Needleman, S.B., and Wunsch, C.D. (1970) A general method applicable to search for similarities in amino acid sequence of 2 proteins. J Mol Biol 48: 443-453.
44. Nemergut, D.R., Schmidt, S.K., Fukami, T., O'Neill, S.P., Bilinski, T.M., Stanish, L.F., etal. (2013) Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev 77: 342-356.
45. Ostman, O., Drakare, S., Kritzberg, E.S., Langenheder, S., Logue, J.B., and Lindstrom, E.S. (2010) Regional invariance among microbial communities. Ecol Lett 13: 118-127.
46. Papke, R.T., and Ward, D.M. (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol Ecol 48: 293-303.
47. Pearce, D.A., Bridge, P.D., Hughes, K.A., Sattler, B., Psenner, R., and Russell, N.J. (2009) Microorganisms in the atmosphere over Antarctica. FEMS Microbiol Ecol 69: 143-157.
48. Pietikainen, J., Pettersson, M., and Baath, E. (2005) Comparison of temperature effects on soil respiration and bacterial and fungal growth rates. FEMS Microbiol Ecol 52: 49-58.
49. Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
50. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., etal. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-D596.
51. Ramirez, K.S., Craine, J.M., and Fierer, N. (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Change Biol 18: 1918-1927.
52. Schadt, E.E., Turner, S., and Kasarskis, A. (2010) A window into third-generation sequencing. Hum Mol Genet 19: R227-R240.
53. Schauer, R., Bienhold, C., Ramette, A., and Harder, J. (2010) Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4: 159-170.
54. Schlaeppi, K., Dombrowski, N., Oter, R.G., van Themaat, E.V.L., and Schulze-Lefert, P. (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA 111: 585-592.
55. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., etal. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
56. Shannon, C.E., and Weaver, W. (1963) The Mathematical Theory of Communication. Champaign, IL, USA: University of Illinois Press.
57. Stegen, J.C., Lin, X.J., Fredrickson, J.K., Chen, X.Y., Kennedy, D.W., Murray, C.J., etal. (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7: 2069-2079.
58. Talbot, J.M., Bruns, T.D., Taylor, J.W., Smith, D.P., Branco, S., Glassman, S.I., etal. (2014) Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci USA 111: 6341-6346.
59. Taylor, C.R., Hardiman, E.M., Ahmad, M., Sainsbury, P.D., Norris, P.R., and Bugg, T.D. (2012) Isolation of bacterial strains able to metabolize lignin from screening of environmental samples. J Appl Microbiol 113: 521-530.
60. Travers, K.J., Chin, C.S., Rank, D.R., Eid, J.S., and Turner, S.W. (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 38: e159.
61. Vellend, M. (2010) Conceptual synthesis in community ecology. Q Rev Biol 85: 183-206.
62. Wang, Q., Garrity, G.M., Tiedje, J.M., and Cole, J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
63. Whitaker, R.J., Grogan, D.W., and Taylor, J.W. (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
64. Wohl, D.L., and McArthur, J.V. (1998) Actinomycete flora associated with submersed freshwater macrophytes. FEMS Microbiol Ecol 26: 135-140.
65. - deposition increases soil organic matter by slowing decomposition. Ecol Appl 18: 2016-2027.
66. Zimmermann, W. (1990) Degradation of lignin by bacteria. J Biotechnol 13: 119-130.