Metacommunity organization of soil microorganisms depends on habitat defined by presence of Lobelia siphilitica plants

Ecology

Volumn 92, Issue 1, 2011, Pages 57-65

  Hovatter, Stephanie R ^a   Dejelo, Chris ^a   Case, Andrea L ^a   Blackwood, Christopher B ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

Habitat type; Lobelia siphilitica; Metacommunity; Microbial biogeography; Plant microbe interactions; Soil microorganisms; Terminal restriction fragment length polymorphism

Indexed keywords

BACTERIUM; BIOGEOGRAPHY; COMMUNITY COMPOSITION; DISPERSAL; FUNGUS; HABITAT TYPE; MICROBIAL COMMUNITY; SOIL MICROORGANISM;

ARTICLE; DEMOGRAPHY; ECOSYSTEM; LOBELIA; MICROBIOLOGY; PHYSIOLOGY; UNITED STATES;

DEMOGRAPHY; ECOSYSTEM; LOBELIA; OHIO; SOIL MICROBIOLOGY; WEST VIRGINIA;

OHIO; UNITED STATES; WEST VIRGINIA;

BACTERIA (MICROORGANISMS); LOBELIA SIPHILITICA;

EID: 79955549446     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/10-0332.1     Document Type: Article

References (59)

1. American Society for Testing and Materials Standards. 2002. Standard test method for particle size analysis of soils, D422-63. American Society for Testing and Materials Standards, Conshohocken, Pennsylvania, USA.
2. Baxter, C. V., K. D. Fausch, and W. C. Saunders. 2005. Tangled webs: reciprocal flows of invertebrate prey link streams and riparian zones. Freshwater Biology 50:201-220. (Pubitemid 40210694)
3. Berg, G., and K. Smalla. 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology 68:1-13.
4. Bever, J. D. 2003. Soil community feedback and the oexistence of competitors: conceptual frameworks and empirical tests. New Phytologist 157:465-473. (Pubitemid 36333207)
5. Blackwood, C. B., T. Marsh, S.-H. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Applied and Environmental Microbiology 69:926-932. (Pubitemid 36204820)
6. Blackwood, C. B., A. Oaks, and J. S. Buyer. 2005. Phylum- and class-specific PCR primers for general microbial community analysis. Applied and Environmental Microbiology 71:6193-6198. (Pubitemid 41456918)
7. Blanchet, F. G., P. Legendre, and D. Borcard. 2008. Forward selection of explanatory variables. Ecology 89:2623-2632.
8. Boddy, L. 2000. Interspecific combative interactions between wood-decay basidiomycetes. FEMS Microbiology Ecology 31:185-194. (Pubitemid 30136209)
9. Chase, J. M. 2007. Drought mediates the importance of stochastic community assembly. Proceedings of the National Academy of Sciences USA 104:17430-17434. (Pubitemid 350219855)
10. Chase, J. M., P. Amarasekare, K. Cottenie, A. Gonzalez, R. D. Holt, M. Holyoak, M. F. Hoopes, M. A. Leibold, M. Loreau, N. Mouquet, J. B. Shurin, and D. Tilman. 2005. Competing theories for competitive metacommunities. 335-353 in M. Holyoak, M. A. Leibold, and R. D. Holt, editors. Metacommunities: spatial dynamics and ecological communities. University of Chicago Press, Chicago, Illinois, USA.
11. Costa, R., M. Gotz, N. Mrotzek, J. Lottman, G. Berg, and K. Smalla. 2006. Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiology Ecology 56:236-249.
12. Cottenie, K. 2005. Integrating environmental and spatial processes in ecological community dynamics. Ecology Letters 8:1175-1182. (Pubitemid 41532401)
13. Crutsinger, G. M., M. W. Cadotte, and N. J. Sanders. 2009. Plant genetics shapes inquiline community structure across spatial scales. Ecology Letters 12:285-292.
14. Curtin, D., C. E. Wright, M. H. Beare, and F. M. McCallum. 2006. Hot water-extractable nitrogen as an indicator of soil nitrogen availability. Soil Science Society of America Journal 70:1512-1521. (Pubitemid 44373279)
15. Daims, H., A. Bruhl, R. Amann, K. H. Schleifer, and M. Wagner. 1999. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology 22:434-444. (Pubitemid 29485930)
16. DeAngelis, K. M., E. L. Brodie, T. Z. DeSantis, G. L. Andersen, S. E. Lindow, and M. K. Firestone. 2009. Selective progressive response of soil microbial community to wild oat roots. ISME Journal 3:168-178.
17. Ellwood, M. D., F. A. Manica, and W. A. Foster. 2009. Stochastic and deterministic processes jointly structure tropical arthropod communities. Ecology Letters 12:277-284.
18. Fierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences USA 103:626-631. (Pubitemid 43153076)
19. Fierer, N., J. L. Morse, S. T. Berthrong, E. S. Bernhardt, and R. B. Jackson. 2007. Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88:2162-2173. (Pubitemid 351345126)
20. Garbeva, P., J. A. van Veen, and J. D. van Elsas. 2004. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology 42:243-270. (Pubitemid 39308513)
21. Garbeva, P., J. A. van Veen, and J. D. van Elsas. 2008. Rhizosphere microbial community and its response to plant species and soil history. Plant and Soil 302:19-32.
22. Gilbert, B., and M. J. Lechowicz. 2004. Neutrality, niches, and dispersal in a temperate forest understory. Proceedings of the National Academy of Sciences USA 101:7651-7656. (Pubitemid 38658084)
23. Graham, M. H. 2003. Confronting multicollinearity in ecological multiple regression. Ecology 84:2809-2815. (Pubitemid 38261430)
24. Green, J. L., A. J. Holmes, M. Westoby, I. Oliver, D. Briscoe, M. Dangerfield, M. Gillings, and A. J. Beattie. 2004. Spatial scaling of microbial eukaryote diversity. Nature 432:747-750. (Pubitemid 39656292)
25. Hartmann, M., and F. Widmer. 2008. Reliability for detecting composition and changes of microbial communities by TRFLP genetic profiling. FEMS Microbiology Ecology 63: 249-260.
26. Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, New Jersey, USA.
27. Jesus, E. C., T. L. Marsh, J. M. Tiedje, and F. M. S. Moreira. 2009. Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME Journal 3: 1004-1011.
28. Johnson, M. J., K. Y. Lee, and K. M. Scow. 2003. DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114:279-303. (Pubitemid 36524271)
29. Johnston, M. O. 1991. Pollen limitation of female reproduction in Lobelia cardinalis and L. siphilitica. Ecology 72:1500-1503.
30. Keeney, D. R., and J. M. Bremner. 1966. Comparison and evaluation of laboratory methods of obtaining an index of soil nitrogen availability. Agronomy Journal 58:498-503.
31. Kowalchuk, G. A., D. S. Buma, W. de Boer, P. G. L. Klinkhamer, and J. A. Van Veen. 2002. Effects of aboveground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie van Leeuwenhoek 81:509-520. (Pubitemid 35314634)
32. Kuske, C. R., L. O. Ticknor, M. E. Miller, J. M. Dunbar, J. A. Davis, S. M. Barns, and J. Belnap. 2002. Comparison of soil bacterial communities in rhizopsheres of three plant species and the interspaces in an arid grassland. Applied and Environmental Microbiology 68:1854-1863. (Pubitemid 34279994)
33. Lauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75:5111-5120.
34. Legendre, P., D. Borcard, and P. R. Peres-Neto. 2005. Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecological Monographs 75: 435-450. (Pubitemid 41476777)
35. Legendre, P., D. Borcard, and P. R. Peres-Neto. 2008. Analyzing or explaining beta diversity? Comment. Ecology 89:3238-3244.
36. Legendre, P., and E. D. Gallagher. 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129:271-280. (Pubitemid 32996572)
37. Legendre, P., and L. Legendre. 1998. Numerical ecology. Second edition. Elsevier, Amsterdam, The Netherlands.
38. Leibold, M. A., M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase, M. F. Hoopes, R. D. Holt, J. B. Shurin, R. Law, D. Tilman, M. Loreau, and A. Gonzalez. 2004. The metacommunity concept: a framework for multi-scale ecology. Ecology Letters 7:601-613. (Pubitemid 38847749)
39. Lekberg, Y., R. T. Koide, J. R. Rohr, L. Aldrich-Wolfe, and J. B. Morton. 2007. Role of niche restrictions and dispersal in the composition of arbuscular mycorrhizal fugal communities. Journal of Ecology 95:95-105. (Pubitemid 44952301)
40. Macdonald, L. M., E. Paterson, L. A. Dawson, and A. J. S. McDonald. 2006. Defoliation and fertilizer influences on the soil microbial community associated with two contrasting Lolium perenne cultivars. Soil Biology and Biochemistry 38: 674-682.
41. Martin, K. J., and P. T. Rygiewicz. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiology 5:1-11.
42. Martiny, J. B. H., et al. 2006. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4:102-112. (Pubitemid 43158153)
43. Mougel, C., P. Offre, L. Ranjard, T. Corberand, E. Gamalero, C. Robin, and P. Lemanceau. 2006. Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytologist 170:165-175. (Pubitemid 43327227)
44. Peres-Neto, P. R., P. Legendre, S. Dray, and D. Borcard. 2006. Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87:2614-2625. (Pubitemid 44885972)
45. Ranjard, L., D. P. H. Lejon, C. Mougel, L. Schehrer, D. Merdinoglu, and R. Chaussod. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environmental Microbiology 5:1111-1120. (Pubitemid 37417783)
46. Rantalainen, M. L., J. Haimi, H. Fritze, T. Pennanen, and H. Setälä. 2008. Soil decomposer community as a model system in studying the effects of habitat fragmentation and habitat corridors. Soil Biology and Biochemistry 40:861-871.
47. Reche, I., E. Pulido-Villena, R. Morales-Baquero, and E. O. Casamayor. 2005. Does ecosystem size determine aquatic bacterial richness? Ecology 86:1715-1722. (Pubitemid 40938772)
48. Reinhart, K. O., A. Packer, W. H. Van der Putten, and K. Clay. 2003. Plant-soil biota interactions and spatial distribution of black cherry in its native and invasive ranges. Ecology Letters 6:1046-1050. (Pubitemid 37537824)
49. SAS Institute. 2004. SAS version 9.1. SAS Institute, Cary, North Carolina, USA.
50. Schweitzer, J. A., J. K. Bailey, D. G. Fischer, C. J. LeRoy, E. V. Lonsdorf, T. G. Whitham, and S. C. Hart. 2008. Plant-soil-microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology 89:773-781. (Pubitemid 351550010)
51. Sumner, M. E., and W. P. Miller. 1996. Cation exchange capacity and exchange coefficients. 1201-1229 in D. L. Sparks, editor. Methods of soil analysis part 3: chemical methods. Soil Science Society of America, Madison, Wisconsin, USA.
52. Tscharntke, T., C. H. Sekercioglu, T. V. Dietsch, N. S. Sodhi, P. Hoehn, and J. M. Tylianakis. 2008. Landscape constraints on functional diversity of birds and insects in tropical agroecosystems. Ecology 89:944-951. (Pubitemid 351620059)
53. Tuomisto, H., and K. Ruokolainen. 2006. Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis. Ecology 87:2697-2708. (Pubitemid 44904855)
54. Tuomisto, H., and K. Ruokolainen. 2008. Analyzing or explaining beta diversity? Reply. Ecology 89:3244-3256.
55. Tuomisto, H., K. Ruokolainen, and M. Yli-Halla. 2003. Dispersal, environment, and floristic variation of western Amazonian forests. Science 299:241-244. (Pubitemid 36125208)
56. Ulrich, A., and R. Becker. 2006. Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiology Ecology 56:430-443. (Pubitemid 43725598)
57. Van der Gucht, K., et al. 2007. The power of species sorting: local factors drive bacterial community composition over a wide range of scales. Proceedings of the National Academy of Sciences USA 104:20404-20409.
58. Wakelin, S. A., L. M. Macdonald, S. L. Rogers, A. L. Gregg, T. P. Bolger, and J. A. Baldock. 2008. Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biology and Biochemistry 40:803-813.
59. Whitham, T. G., W. P. Young, G. D. Martinsen, C. A. Gehring, J. A. Schweitzer, S. M. Shuster, G. M. Wimp, D. G. Fischer, J. K. Bailey, R. L. Lindroth, S. Woolbright, and C. R. Kuske. 2003. Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84:559-573. (Pubitemid 36893039)