Eubacterial communities in different soil macroaggregate environments and cropping systems Christopher B. Blackwood * , Curtis J. Dell 1 , Alvin J.M. Smucker, Eldor A. Paul 2 Center for Microbial Ecology and Department of Crop and Soil Sciences, Michigan State University, East Lansing, 48824, USA Received 23 April 2005; received in revised form 13 July 2005; accepted 20 July 2005 Available online 24 August 2005 Abstract Different positions within soil macroaggregates, and macroaggregates of different sizes, have different chemical and physical properties which could affect microbial growth and interactions among taxa. The hypothesis that these soil aggregate fractions contain different eubacterial communities was tested using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal gene. Communities were characterized from two field experiments, located at the Kellogg Biological Station (KBS), MI, USA and the Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA. Three soil management regimes at each site were sampled and management was found to significantly affect T-RFLP profiles. The soil aggregate erosion (SAE) method was used to isolate aggregate regions (external and internal regions). Differences between eubacterial T-RFLP profiles of aggregate exteriors and interiors were marginally significant at KBS (accounting for 12.5% of total profile variance), and not significant at OARDC. There were no significant differences among macroaggregate size classes at either site. These results are in general agreement with previous studies using molecular methods to examine microbial communities among different soil macroaggregate size fractions, although further study of communities within different aggregate regions is warranted. Analysis of individual macroaggregates revealed large inter-aggregate variability in community structure. Hence the tertiary components of soil structure, e.g. arrangement of aggregates in relation to shoot residue, roots, macropores, etc., may be more important than aggregate size or intra-aggregate regions in the determination of the types of microbial communities present in aggregates. Direct microscopic counts were also used to examine the bacterial population size in aggregate regions at KBS. The proportion of bacterial cells with biovolumes O0.18 mm 3 was higher in aggregate interiors than in exteriors, indicating potentially higher activity in that environment. This proportion was significantly related to percent C of the samples, while total bacterial cell counts were not. q 2005 Elsevier Ltd. All rights reserved. Keywords: Soil macroaggregates; Aggregate regions; Microbial community analysis; Terminal restriction fragment length polymorphism; Agricultural management; Soil structure 1. Introduction The most common model of the spatial structure of soil particles at millimeter and smaller scales is a hierarchical arrangement of soil aggregates (Edwards and Bremner, 1967; Tisdall and Oades, 1982; Christensen, 1996). The process of aggregation is viewed as dynamic, with microaggregates (!250 mm in diameter) being bound together by plant roots, fungi, organic polymers, and plant residues to form macroaggregates (O250 mm in diameter). As organic particles encrypted within macroaggregates decompose, some macroaggregates disintegrate forming new microaggregates (Beare et al., 1994b; Golchin et al., 1997). Larger macroaggregates generally contain more labile organic matter (Beare et al., 1994a; Elliott, 1986; Gupta and Germida, 1988; Six et al., 2000; Denef et al., 2001) with a more rapid turnover time (Buyanovsky et al., 1994; Monreal et al., 1997). The significance of soil aggregates in structuring microbial communities, however, continues to be debated. Another approach to studying aggregate structure is to divide aggregates into their internal and external regions. Soil Biology & Biochemistry 38 (2006) 720–728 www.elsevier.com/locate/soilbio 0038-0717/$ - see front matter q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.soilbio.2005.07.006 * Corresponding author. Present address: School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI 48109-1041, USA. Tel.: C1 734 763 8003; fax: C1 734 936 2195. E-mail address: cbwood@umich.edu (C.B. Blackwood). 1 Present address: USDA-ARS, Pasture Systems and Watershed Manage- ment Research Unit, University Park, PA 16802, USA. 2 Present address: Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523-1965, USA.