Plant and Soil

, Volume 283, Issue 1–2, pp 1–10 | Cite as

Functional Diversity of Culturable Bacterial Communities in the Rhizosphere in Relation to Fine-root and Soil Parameters in Alder Stands on Forest, Abandoned Agricultural, and Oil-shale Mining Areas

  • K. Lõhmus
  • M. Truu
  • J. Truu
  • I. Ostonen
  • E. Kaar
  • A. Vares
  • V. Uri
  • S. Alama
  • A. Kanal
Rhizosphere - Perspectives and Challenges - A Tribute to Lorenz Hiltner


Grey alder (Alnus incana) and black alder (Alnus glutinosa) stands on forest land, abandoned agricultural, and reclaimed oil-shale mining areas were investigated with the aim of analysing the functional diversity and activity of microbial communities in the soil–root interface and in the bulk soil in relation to fine-root parameters, alder species, and soil type. Biolog Ecoplates were used to determine community-level physiological profiles (CLPP) of culturable bacteria in soil–root interface and bulk soil samples. CLPP were summarized as AWCD (average well color development, OD 48 h−1) and by Shannon diversity index, which varied between 4.3 and 4.6 for soil–root interface. The soil–root interface/bulk soil ratio of AWCD was estimated. Substrate-induced respiration (SIR) and basal respiration (BAS) of bulk soil samples were measured and metabolic quotient (Q = BAS/SIR) was calculated. SIR and Q varied from 0.24 to 2.89 mg C g−1 and from 0.12 to 0.51, respectively. Short-root morphological studies were carried out by WinRHIZOTM Pro 2003b; mean specific root area (SRA) varied for grey alder and black alder from 69 to 103 and from 54 to 155 m2 kg−1, respectively. The greatest differences between AWCD values of culturable bacterial communities in soil–root interface and bulk soil were found for the young alder stands on oil-shale mining spoil and on abandoned agricultural land. Soil–root interface/bulk soil AWCD ratio, ratio for Shannon diversity indices, and SRA were positively correlated. Foliar assimilation efficiency (FOE) was negatively correlated with soil–root interface/bulk soil AWCD ratio. The impact of soil and alder species on short-root morphology was significant; short-root tip volume and mass were greater for black alder than grey alder. For the investigated microbiological characteristics, no alder-species-related differences were revealed.


Alnus glutinosa Alnus incana Biolog Ecoplates fine root morphology soil–root interface substrate-induced and basal respiration 


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  1. Anderson, J P E, Domsch, K H 1978A physiological method to the quantitative measurement of microbial biomass in soilsSoil Biol. Biochem.10215221CrossRefGoogle Scholar
  2. Bååth, E, Anderson, T H 2003Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA based methodsSoil Biol. Biochem.35955963CrossRefGoogle Scholar
  3. Butler, J L, Williams, M A, Bottomley, P J, Myrold, D D 2003Microbial community dynamics associated with rhizosphere carbon flowAppl. Environ. Microbiol.6967936800PubMedCrossRefGoogle Scholar
  4. Cheng, W, Zhang, Q, Coleman, D C, Carroll, C R, Hoffmann, C A 1996Is available carbon limiting microbial respiration in the rhizosphere?Soil Biol. Biochem.2812831288CrossRefGoogle Scholar
  5. Comas, L H, Bouma, T J, Eissenstat, D M 2002Linking root traits to potential growth rate in six temperate tree speciesOecologia1323443CrossRefGoogle Scholar
  6. Dawson, J O, Funk, D T 1981Seasonal change in foliar nitrogen concentration of Alnus glutinosa For. Sci.27239243Google Scholar
  7. Dilly, O, Bach, H-J, Buscot, F, Eschenbach, W, Kutsch, L, Middelhoff, U, Pritsch, K, Munch, J C 2000Characteristics and energetic strategies of the rhizosphere in ecosystems of the Bornhöved Lake districtAppl. Soil Ecol.15201210CrossRefGoogle Scholar
  8. Ekblad, A, Boström, B, Holm, A, Comstedt, D 2004Forest soil respiration rate and δ13C is regulated by recent above-ground weather conditionsOecologia143136142PubMedCrossRefGoogle Scholar
  9. Evans, J 1984Silviculture of broadleaved woodlandFor. Comm. Great Britain Bull.62187191Google Scholar
  10. FAO-UNESCO1994Soil Map of the World. Revised Legend with CorrectionsISRICWageningenGoogle Scholar
  11. Giardina, C P, Huffman, S, Binkley, D, Caldwell, B A 1995Alders increase soil phosphorus availability in a Douglas-fir plantationCan. J. For. Res.2516521657Google Scholar
  12. Girvan, M S, Bullimore, J, Pretty, J N, Osborn, A M, Ball, A S 2003Soil type is the primary determinanat of the composition of the total and active bacterial communities in arable soilsAppl. Environ. Microbiol.6918001809PubMedCrossRefGoogle Scholar
  13. Gobran, G, Clegg, S 1996A conceptual model for nutrient availability in the mineral soil–root systemCan. J. Soil Sci.76125131Google Scholar
  14. Gonzalez, J M P, Manero, F J G, Probanza, A, Acero, N, Decastro, F B 1995Effect of alder (Alnus glutinosa L. Gaertn.) roots on distribution of proteolytic, ammonifying, and nitrifying bacteria in soilGeomicrobiol. J.13129138CrossRefGoogle Scholar
  15. Grayston, S G, Campbell, C D 1996Functional biodiversity of microbial communities in the rhizospheres of hybrid larch (Larix eurolepis) and Sitka spruce (Picea sitchensis)Tree Physiol.1610311038PubMedGoogle Scholar
  16. Insam, H, Haselwandter, K 1989Metabolic quotient of the soil microflora in relation to plant successionOecologia79174178CrossRefGoogle Scholar
  17. Insam, H 1990Are the soil microbial biomass and basal respiration governed by the climatic regime?Soil Biol. Biochem.22525532CrossRefGoogle Scholar
  18. Kirk, J L, Beaudette, L A, Hart, M, Moutoglis, P, Khironomos, J N, Lee, H, Trevors, J T 2004Methods of studying soil microbial diversityJ. Microbiol. Methods58169188PubMedCrossRefGoogle Scholar
  19. Lõhmus, K, Mander, Ü, Tullus, H, Keedus, K 1996Productivity, Buffering Capacity and Resources of Grey Alder Forests in Estonia Vol. 57Swed. Univ. Agric. Sci., Dep. Short Rotation ForestryUppsala95105Google Scholar
  20. Lõhmus, K, Kuusemets, V, Ivask, M, Teiter, S, Augustin, J, Mander, Ü 2002Budgets of nitrogen fluxes in riparian grey alder forestsArch. Hydrobiol. Suppl.141321332Google Scholar
  21. Marschner, P, Yang, C H, Lieberei, R, Crowley, D E 2001Soil and plant specific effects on bacterial community composition in the rhizosphereSoil Biol. Biochem.3314371445CrossRefGoogle Scholar
  22. Marschner, P, Crowley, D, Yang, C H 2004Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil typePlant Soil261199208CrossRefGoogle Scholar
  23. Ostonen, I, Lõhmus, K, Lasn, R 1999The role of soil conditions in fine root ecomorphology in Norway spruce (Picea abies (L.) Karst.)Plant Soil208283292CrossRefGoogle Scholar
  24. Ostonen, I, Lõhmus, K 2003Proportion of fungal mantle, cortex and stele of ectomycorrhizas in Picea abies (L.) Karst. In different soils and site conditionsPlant Soil257435442CrossRefGoogle Scholar
  25. Pregitzer, K S, DeForest, J L, Burton, A J, Allen, M F, Ruess, R W, Hendrick, R L 2002Fine root architecture of nine North American treesEcol. Monogr.7293309Google Scholar
  26. Preston-Mafham, J, Boddy, L, Randerson, P F 2002Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles – a critiqueFEMS Microbiol. Ecol.42114Google Scholar
  27. Priha, O, Grayston, S J, Pennanen, T, Smolander, A 1999Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soilFEMS Microbiol. Ecol.30187199PubMedCrossRefGoogle Scholar
  28. Rozycki, H, Strzelczyk, E, Li, C Y 1998Preliminary studies on bacteria of soil and of the root zone of black (Alnus glutinosa (L.) Gaertn.) and grey (Alnus incana (L.) Moench.) alder seedlingsActa Microbiol. Pol.4791103Google Scholar
  29. Ruzicka, J, Hansen, E H 1981Flow Injection AnalysisJohn Wiley and Sons, IncNew York, USAGoogle Scholar
  30. Schinner, F, Öhlinger, R, Kandeler, E, Margesin, R 1996Methods in Soil BiologySpringer-VerlagBerlin426Google Scholar
  31. Seghers, D, Siciliano, S D, Tot, E M, Verstraete, W 2005Combined effect of fertilizer and herbicide applications an the abundance, community structure and performance of the soil methanothrophic communitySoil Biol. Biochem.37187193CrossRefGoogle Scholar
  32. Selmants, P C, Hart, S C, Boyle, S I, Stark, J M 2005Red alder (Alnus rubra) alters community-level soil microbial function in conifer forests of the Pacific Northwest, USASoil Biol. Biochem.3718601868CrossRefGoogle Scholar
  33. Singh, B K, Millard, P, Whiteley, A S, Murrell, J C 2004Unravelling rhizosphere – microbial interactions: opportunities and limitationsTrends Microbiol.12386393PubMedCrossRefGoogle Scholar
  34. Šlapokas, T, Granhall, U 1991Decomposition of litter in fertilized short rotation forests on a low-humified peat bogFor. Ecol. Manag.41143165CrossRefGoogle Scholar
  35. Smalla, K, Wachtendorf, U, Heuer, H, Liu, W, Forney, L 1998Analysis of Biolog GN substrate utilization patterns by microbial communitiesAppl. Env. Microbiol.6412201225Google Scholar
  36. Söderberg, K H, Probanza, A, Jumpponen, A, Bååth, E 2004The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil- and cfu-PLFA techniquesAppl. Soil Ecol.25135145CrossRefGoogle Scholar
  37. Stephan, A, Meyer, A H, Schmid, B 2000Plant diversity affects culturable soil bacteria in experimental grassland communitiesJ. Ecol.88988998CrossRefGoogle Scholar
  38. Treonis, A M, Ostle, N J, Stott, A W, Primrose, R, Grayston, S J, Ineson, P 2004Identification of groups of metabolically active rhizosphere microorganisms by stable isotope probing of PLFAsSoil Biol. Biochem.36533537CrossRefGoogle Scholar
  39. Truu J, Truu M, Lõhmus K, Ivask M, Kanal A 2001 Structure and activity of microbial communities in soil–root interface and bulk soil in coniferous and deciduous stands. In Roots: The Dynamic Interface Between Plants and the Earth. The 6th ISRR Symposium. Ed J. Abe, Nagoya. pp. 402–403 Japan, November 11–15Google Scholar
  40. Uri, V, Tullus, H, Lõhmus, K 2002Biomass production and nutrient accumulation in short-rotation grey alder (Alnus incana (L.) Moench) plantation on abandoned agricultural landForest. Ecol. Manag.161169179CrossRefGoogle Scholar
  41. Vares, A, Lõhmus, K, Truu, M, Truu, J, Tullus, H, Kanal, A 2004Productivity of black alder (Alnus glutinosa (L.) Gaertn.) plantations established on reclaimed oil shale mining spoil and mineral soils in relation to rhizosphere conditionsOil Shale214762Google Scholar
  42. White, C, Tardif, J C, Adkins, A, Staniforth, R 2005Functional diversity of microbial communities in the mixed boreal plain forest of central CanadaSoil Biol. Biochem.3713591372CrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • K. Lõhmus
    • 1
  • M. Truu
    • 3
  • J. Truu
    • 2
  • I. Ostonen
    • 1
  • E. Kaar
    • 4
  • A. Vares
    • 4
  • V. Uri
    • 4
  • S. Alama
    • 1
  • A. Kanal
    • 1
  1. 1.Institute of GeographyUniversity of TartuTartuEstonia
  2. 2.Institute of Molecular and Cell BiologyUniversity of TartuTartuEstonia
  3. 3.Department of Environmental ProtectionEstonian Agricultural UniversityTartuEstonia
  4. 4.Department of SilvicultureEstonian Agricultural UniversityTartuEstonia

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