Size fractionation and microbial community structure of soil aggregates


The microbial community structure in various microaggregates in a loamy sand soil was investigated. The microaggregates were separated into outer and inner aggregates using a series of soil washes. Further physical fractionation of inner aggregates was achieved by separation into coarse and fine sand as macroaggregate fractions, coarse and fine silt as microaggregate fractions, and clay. Research on microbial communities and soil microaggregates can aid in our understanding of soil microhabitats and microorganisms in soil structures, with applications that may contribute to increasing crop production and maintaining sustainable agriculture. In order to study the microbial community structure of aggregates, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was performed using 16S rRNA genes. The PCR-DGGE of the Bacteria Actinomycetes and Archaea showed divergent results between the different aggregate fractions. The results showed that the bacterial community structure was highly similar between bulk soil and clay; the inner aggregate community structure of Actinomycetes was closely related between coarse and fine sand and coarse silt, and the Archaea community structure of outer and inner aggregates was more similar than that of total bacteria or Actinomycetes.

Share and Cite:

J. Kim and D. E. Crowley, "Size fractionation and microbial community structure of soil aggregates," Journal of Agricultural Chemistry and Environment, Vol. 2 No. 4, 2013, pp. 75-80. doi: 10.4236/jacen.2013.24011.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Tisdall, J.M. and Oades, J.M. (1982) Organic matter and water-stable aggregates in soils. Journal of Soil Science, 33, 141-163.
[2] Tisdall, J.M. (1996) Formation of soil aggregates and accumulation of soil organic matter. In: Carter, M.R. and Stewart, B.A., Eds., Structure and Organic Matter Storage in Agricultural Soils, Boca Raton, FL Lewis.
[3] Ranjard, L. and Richaume, A. (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Research in Microbiology, 152, 707-716.
[4] Oades, J.M. and Waters, A.G. (1991) Aggregate hierarchy in soils. Australian Journal of Soil Research, 29, 815-828.
[5] Lynch, J.M. and Bragg, E. (1985) Microorganisms and soil aggregate stability. Advances in Soil Science, 2, 133-171.
[6] Mummey, D., Holben, W., Six, J. and Stahl, P. (2006) Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microbial Ecology, 51, 404-411.
[7] Mendes, I. and Bottomley, P. J. (1999) Distribution of a population of Rhizobium leguminosarum bv. trifolii among different size classes of soil aggregates. Applied and Environmental Microbiology, 64, 970-975.
[8] Hattori, T. and Hattori, R. (1976) The physical environment in soil microbiology an attempt to extend principles of microbiology to soil microorganisms. Critical Reviews in Microbiology, 4, 423-461.
[9] Kabir, M., Chotte, J.L., Rahman, M., Bally, R. and Jocteur, M.L. (1994) Distribution of soil fractions and location of soil bacteria in a vertisol under cultivation and perennial ryegrass. Plant Soil, 163, 243-255.
[10] Ranjard, L., Nazaret, S., Gourbiere, F., Thioulouse, J., Linet, P. and Richaume, A. (2000a) A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA finger-prints. FEMS Microbiology Ecology, 31, 107-115.
[11] Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbiere, F., Thioulouse, J. and Nazaret, S. (2000b) Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microbial Ecology, 39, 263-272.
[12] Schutter, M.E. and Dick, R.P. (2002) Microbial community profiles and activities among aggregates of winter fallow and cover-cropped soil. Soil Science Society of America Journal, 66, 142-153.
[13] Blackwood, C.B., Dell, C.J., Smucker, A.J.M. and Paul, E.A. (2006) Eubacterial communities in different soil macroaggregate environments and cropping systems. Soil Biology and Biochemistry, 38, 720-728.
[14] Monreal, C.M., Schulten, H.-R. and Kodama, H. (1997) Age, turnover and molecular diversity of soil organic matter in aggregates of a Gleysol. Canadian Journal of Soil Science, 77, 379-388.
[15] Kim, J.S, Dungan, R.S. and Crowley, D. (2008) Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil. Biology and Fertility of Soils, 44, 1003-1011.
[16] Muyzer, G, De Waal, E.D. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electro-phoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700.
[17] Kandeler, E., Tscherko, D., Bruce, K.D., Stemmer, M., Hobbs, P.J., Bardgett, R.D. and Amelung, W. (2000) Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biology and Fertility of Soils, 32, 390-400.
[18] Sessitsch, A., Weilharter, A., Gerzabek, M.H., Kirchmann, H. and Kandeler, E. (2001) Microbial population—In soil particle size fractions of a long-term fertilizer field experiment. Applied and Environmental Microbiology, 67, 4215-4224.
[19] Christensen, B.T. (1996) Carbon in primary and seconddary organomineral complexes. In: Carter, M.R. and Stewart, B.A., Eds., Structure and Organic Matter Storage in Agricultural Soils, Boca Raton, FL Lewis.
[20] Dalal, R.C. and Bridge, B.J. (1996) Aggregation and organic matter storage in subhumid and semiarid soils. In: Carter, M.R. and Stewart, B.A., Eds., Structure and Organic Matter Storage in Agricultural Soils, Boca Raton, FL Lewis.
[21] Heuer, H., Krsek, M., Baker, P., Smalla, K. and Wellington, E.M.H. (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Applied and Environmental Microbiology, 63, 3233-3241.
[22] Lane, D.J. (1991) 16S/23S rRNA sequencing. In: Stackebrandt, E. and Goodfellow, M. Eds., Nucleic Acid Techniques in Bacterial Systematics, Wiley, New York, 115-175.
[23] Raskin, L., Stromley, J.M., Rittmann, B.E. and Stahl, D.A. (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Applied and Environmental Microbiology, 60, 1232-1240.

Copyright © 2023 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.