Advertisement

Plant and Soil

, Volume 333, Issue 1–2, pp 417–430 | Cite as

Is vegetation composition or soil chemistry the best predictor of the soil microbial community?

  • Ruth J. Mitchell
  • Alison J. Hester
  • Colin D. Campbell
  • Stephen J. Chapman
  • Clare M. Cameron
  • Richard L. Hewison
  • Jackie M. Potts
Regular Article

Abstract

With the species composition and/or functioning of many ecosystems currently changing due to anthropogenic drivers it is important to understand and, ideally, predict how changes in one part of the ecosystem will affect another. Here we assess if vegetation composition or soil chemistry best predicts the soil microbial community. The above and below-ground communities and soil chemical properties along a successional gradient from dwarf shrubland (moorland) to deciduous woodland (Betula dominated) were studied. The vegetation and soil chemistry were recorded and the soil microbial community (SMC) assessed using Phospholipid Fatty Acid Extraction (PLFA) and Multiplex Terminal Restriction Fragment Length Polymorphism (M-TRFLP). Vegetation composition and soil chemistry were used to predict the SMC using Co-Correspondence analysis and Canonical Correspondence Analysis and the predictive power of the two analyses compared. The vegetation composition predicted the soil microbial community at least as well as the soil chemical data. Removing rare plant species from the data set did not improve the predictive power of the vegetation data. The predictive power of the soil chemistry improved when only selected soil variables were used, but which soil variables gave the best prediction varied between the different soil microbial communities being studied (PLFA or bacterial/fungal/archaeal TRFLP). Vegetation composition may represent a more stable ‘summary’ of the effects of multiple drivers over time and may thus be a better predictor of the soil microbial community than one-off measurements of soil properties.

Keywords

Co-correspondence analysis Ecosystem engineer Succession Moorland TRFLP PLFA 

Notes

Acknowledgements

We are grateful to the late John Miles who identified these chronosequences. We would like to thank Angela Fraser and Tara Breedon for technical assistance. This work was funded by the Scottish Government, Rural and Environment Research and Analysis Directorate.

References

  1. Allen SE (1989) Chemical analysis of ecological material, 2nd edn. Blackwell Scientific, OxfordGoogle Scholar
  2. Bååth E, Anderson TH (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem 35:955–963CrossRefGoogle Scholar
  3. Bardgett RD, Hobbs PJ, Frostegård Ǻ (1996) Changes in fungal:bacterial biomass ratios following reductions in the intensity of management on an upland grassland. Biol Fertil Soils 22:261–264CrossRefGoogle Scholar
  4. Bardgett RD, Yeates GW, Anderson JM (2005) Patterns and determinants of soil biological diversity. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils. Cambridge University Press, Cambridge, pp 100–118CrossRefGoogle Scholar
  5. Bezemer TM, Lawson CS, Hedlund K, Edwards AR, Brook AJ, Igual JM, Mortimer SR, van der Putten WH (2006) Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands. J Ecol 94:893–904CrossRefGoogle Scholar
  6. Bligh EG, Dyer WJ (1958) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917Google Scholar
  7. Casamayor EO, Massana R, Benlloch S, Øvreås L, Díez B, Goddard VJ, Gasol JM, Joint I, Rodríguez-Valera F, Perdrós-Alió C (2002) Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ Microbiol 4:338–348CrossRefPubMedGoogle Scholar
  8. Certini G, Campbell CD, Edwards AC (2004) Rock fragments in soil support a different microbial community from the fine earth. Soil Biol Biochem 36:1119–1128CrossRefGoogle Scholar
  9. Chen M-M, Zhu Y-G, Su Y-H, Chen B-D, Fu B-J, Marschner P (2007) Effects of soil moisture and plant interactions on the soil microbial community structure. Eur J Soil Biol 43:31–38CrossRefGoogle Scholar
  10. Frostegård Å, Tunlid A, Bååth E (1993) Phospholipid fatty acid composition, biomass and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59:3605–3617PubMedGoogle Scholar
  11. Frouz J, Prach K, Pizl V, Hanel L, Stary J, Tajovsky K, Materna J, Balik V, Kalcik J, Rehounkova K (2008) Interactions between soil development, vegetation and soil fauna during spontaneous succession in post mining sites. Eur J Soil Biol 44:109–121CrossRefGoogle Scholar
  12. Gardes M, Bruns TB (1993) ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhiza and rusts. Mol Ecol 2:113–118CrossRefPubMedGoogle Scholar
  13. Gardner WH (1965) Water content. In: Black C (ed) Methods of soil analysis. Part 1. Physical and mineralogical properties, including statistics of measurement and sampling. American Society of Agronomy, Madison, pp 82–127Google Scholar
  14. Goodwin J (1992) The role of mycorrhizal fungi in competitive interactions among native bunchgrasses and alien weeds—a review and synthesis. Northwest Sci 66:251–260Google Scholar
  15. Grayston SJ, Wang SQ, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378CrossRefGoogle Scholar
  16. Hackl E, Pfeffer M, Donat C, Bachmann G, Zechmeister-Boltenstern S (2005) Composition of the microbial communities in the mineral soil under different types of natural forest. Soil Biol Biochem 37:661–671CrossRefGoogle Scholar
  17. Haseman JF, Marshall CE (1945) The use of heavy minerals in studies of the origin and development of soils. University of Missouri College of Agriculture Experimental Station Research Bulletin No. 387Google Scholar
  18. Hauben L, Vauterin C, Swings J, Moore ERB (1997) Comparison of 16 S ribosomal DNA sequence of all Xanthomonas species. Int J Syst Bacteriol 47:328–335CrossRefPubMedGoogle Scholar
  19. van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310CrossRefPubMedGoogle Scholar
  20. Hester AJ, Miles J, Gimingham GH (1991a) Succession from heather moorland to birch woodland. I. Experimental alteration of specific environmental conditions in the field. J Ecol 79:303–315CrossRefGoogle Scholar
  21. Hester AJ, Miles J, Gimingham GH (1991b) Succession from heather moorland to birch woodland. II. Growth and competition between Vaccinium myrtillus, Deschampsia flexuosa and Agrostis capillaris. J Ecol 79:317–328CrossRefGoogle Scholar
  22. Högberg MN, Högbeg P, Myrold DD (2007) Is microbial community composition in boreal forest soils determined by pH, C to N ratio, the trees or all three? Oecologia 150:590–601CrossRefPubMedGoogle Scholar
  23. Janos DP (1980) Mycorrhizae influence tropical succession. Mycorrhizae 12:56–64Google Scholar
  24. Jurgens G, Lindstrom K, Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63:803–805PubMedGoogle Scholar
  25. Lavelle P, Bignell D, Lepage M, Wolters V, Roger P, Ineson P, Heal O, Dhillion S (1997) Soil function in a changing world: the role of invertebrate ecosystem engineers. Eur J Soil Biol 33:159–193Google Scholar
  26. Macdonald CA, Singh BK, Peck JA, van Schaik AP, Hunter LC, Horswell J, Campbell CD, Speir TW (2007) Long-term exposure to Zn-spiked sewage sludge alters soil community structure. Soil Biol Biochem 39:2576–2586CrossRefGoogle Scholar
  27. Maindonald J, Braun WJ (2009) Data Analysis and Graphics. R package version 0.98. Published at http://www.R-project.org.
  28. Marchesi JR, Sato T, Weightman AJ, Martin JC, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795–799PubMedGoogle Scholar
  29. McLean E (1982) Soil pH and lime requirement. In: Page A, Miller R, Keeney D (eds) Methods of soil analysis. Part 2. Chemical and microbiological properties. SSSA, Madison, pp 199–209Google Scholar
  30. Miles J (1985) The pedogenic effects of different species and vegetation types and the implications of succession. J Soil Sci 36:571–584CrossRefGoogle Scholar
  31. Miles J, Young WF (1980) The effects on heathland and moorland soils in Scotland and northern England following colonisation by birch. Bulletin Societé ď Ecoloie France 11:233–242Google Scholar
  32. Mitchell RJ, Marrs RH, Le Duc MG, Auld MHD (1997) A study of succession on lowland heaths in Dorset, southern England: changes in vegetation and soil chemical properties. J Appl Ecol 34:1426–1444CrossRefGoogle Scholar
  33. Mitchell RJ, Campbell CD, Chapman SJ, Cameron CM (2010) The engineering impact of a single tree species on the soil microbial community. J Ecol 98:50–61CrossRefGoogle Scholar
  34. Mitchell RJ, Campbell CD, Chapman SJ, Osler GHR, Vanbergen AJ, Ross LR, Cameron CM, Cole L (2007) The cascading effects of birch on heather moorland: a test for the top-down control of an ecosystem engineer. J Ecol 95:540–554CrossRefGoogle Scholar
  35. Orwin KH, Wardle DA, Greenfield LG (2006) Ecological consequences of carbon substrate identity and diversity in a laboratory study. Ecololgy 87:580–593CrossRefGoogle Scholar
  36. Pastor J, Cohen Y (1997) Herbivores, the functional diversity of plant species, and the cycling of nutrients in ecosystems. Theor Popul Biol 51:165–179CrossRefPubMedGoogle Scholar
  37. Pastor J, Cohen Y, Hobbs NT (2006) The roles of large herbivores in ecosystem nutrient cycles. In: Danell K, Bergstrom R, Duncan P, Pastor J (eds) Large herbivore ecology, ecosystem dynamics and conservation. Cambridge University Press, CambridgeGoogle Scholar
  38. Pella E, Colombo B (1973) Study of carbon, hydrogen and nitrogen by combustion gas chromatography. Mikrochim Acta 5:697–719Google Scholar
  39. Pennanen T, Fritze H, Vanhala P, Kiikkilå O, Neuvonen S, Bååth E (1998) Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain. Appl Environ Microbiol 64:2173–2180PubMedGoogle Scholar
  40. R Development Core Team (2006) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria, Published at http://www.R-project.org.
  41. Read DJ (1991) Mycorrhizas in ecosystems. Experientia 47:376–391CrossRefGoogle Scholar
  42. Reynolds HL, Packer A, Bever JD, Clay K (2003) Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84:2281–2291CrossRefGoogle Scholar
  43. Rinnan R, Michelsen A, Bååth E, Jonasson S (2007) Fifteen years of climate change manipulations alter soil microbial communities in a subarctic heath ecosystem. Glob Chang Biol 13:28–39CrossRefGoogle Scholar
  44. SAS (2005) SAS Software Version 9.1. SAS, CaryGoogle Scholar
  45. Schaffers AP, Raemakers IP, Sỳkora KV, ter Braak CJF (2008) Arthropod assemblages are best predicted by plant species composition. Ecology 89:782–794CrossRefPubMedGoogle Scholar
  46. Simpson GL (2005) Cocorresp: co-correspondence analysis ordination methods for community ecology. R foundation for statistical computing, Vienna, Austria, published at http://www.R-project.org.
  47. Singh BK, Nazaries L, Munro S, Anderson IC, Campbell CD (2006) Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community. Appl Environ Microbiol 72:7278–7285CrossRefPubMedGoogle Scholar
  48. Smith BFL, Bain DC (1982) A sodium-hydroxide fusion method for the determination of total phosphate in soils. Commun Soil Sci Plant Anal 13:185–190CrossRefGoogle Scholar
  49. Smith RS, Shield RS, Bardgettt RD, Millward D, Corkhill P, Rolph G, Hobbs PJ, Peacock S (2003) Diversification management of meadow grassland: plant species diversity and functional traits associated with change in meadow vegetation and soil microbial communities. J Appl Ecol 40:51–64CrossRefGoogle Scholar
  50. Sørensen LI, Mikola J, Kytöviita M-M, Olofsson J (2009) Trampling and spatial heterogeneity explain decomposer abundances in a sub-arctic grassland subjected to simulated reindeer grazing. Ecosystems 12:830–842CrossRefGoogle Scholar
  51. Stephan A, Meyer AH, Schmide B (2000) Plant diversity affects culturable soil bacteria in experimental grassland communities. J Ecol 88:988–998CrossRefGoogle Scholar
  52. Tarlera S, Jangid K, Ivester AH, Whitman WB, Williams MA (2008) Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiol Ecol 64:129–140CrossRefPubMedGoogle Scholar
  53. Ter Braak CJF, Smilauer P (2002) CANOCO reference manual and cano draw for windows user’s guide: software for canonical community ordination version 4.5. Microcomputer Power, IthacaGoogle Scholar
  54. Ter Braak CJF, Schaffers AP (2004) Co-correspondence analysis: a new ordination method to relate two community compositions. Ecology 85:834–846CrossRefGoogle Scholar
  55. Thomas G (1982) Exchangeable cations. In: Page A, Miller R, Keeney D (eds) Methods of soil analysis. Part 2. Chemical and microbiological properties. SSSA, Madison, pp 159–165Google Scholar
  56. Van der Putten WH, Van Dijk C, Peters BAM (1993) Plant-specific soil-borne diseases contribute to succession in foredune vegetation. Nature 362:53–56CrossRefGoogle Scholar
  57. Wardle DA (2005) How plant communities influence decomposer communities. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils. Cambridge University Press, Cambridge, pp 119–138CrossRefGoogle Scholar
  58. Wardle DA, Bonner KI, Barker GM, Yeates GW, Nicholson KS, Bardgett RD, Watson RN, Ghani A (1999) Plant removals in perennial grassland: vegetation dynamics, decomposers, soil biodiversity and ecosystem properties. Ecol Monogr 69:535–568CrossRefGoogle Scholar
  59. Wardle DA, Barker GM, Yeates GW, Bonner KI, Ghani A (2001) Introduced browsing mammals in natural new Zealand forests: aboveground and below ground consequences. Ecol Monogr 71:587–614CrossRefGoogle Scholar
  60. Webb NR (1998) The traditional management of European heathlands. J Appl Ecol 35:987–990CrossRefGoogle Scholar
  61. White TJ, Bruns TD, Lee S, Taylor J (1990) Analysis of phylogenetic relationship by amplification and direct sequencing of ribosomal RNA genes. In: Innis MA, Gelford DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, New York, pp 315–322Google Scholar
  62. Williamson WM, Wardle DA, Yeates GW (2005) Changes in soil microbial and nematode communities during ecosystem decline across a long-term chronosequence. Soil Biol Biochem 37:1289–1301CrossRefGoogle Scholar
  63. Wohlrab G, Tuveson RW, Olmsted CE (1963) Fungal populations from early stages of succession in Indiana dune sand. Ecology 44:734–740CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Ruth J. Mitchell
    • 1
    • 4
  • Alison J. Hester
    • 1
  • Colin D. Campbell
    • 1
    • 3
  • Stephen J. Chapman
    • 1
  • Clare M. Cameron
    • 1
  • Richard L. Hewison
    • 1
  • Jackie M. Potts
    • 2
  1. 1.Macaulay Land Use Research InstituteAberdeenUK
  2. 2.Biomathematics & Statistics ScotlandThe Macaulay InstituteAberdeenUK
  3. 3.Department Soil and EnvironmentSwedish University of Agricultural SciencesUppsalaSweden
  4. 4.Natural Research Projects, Brathens Business ParkAberdeenshireUK

Personalised recommendations