ARS | Publication request: Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil

Submitted to: Biology and Fertility of Soils
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2008
Publication Date: September 15, 2008
Citation: Kim, J., Dungan, R.S., 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.

Interpretive Summary: Soil aggregation is one of the most important factors associated with soil quality, and is one of the most important factors affecting the structure and function of microbial communities at small spatial scales. Given the interaction between aggregates and microbial community structure, there is currently great interest in understanding how linkages between the microbial community and function vary for different aggregates size classes. In this study, the microbial community structure of inner and outer layer fractions of microaggregates from a desert agricultural soil were examined using molecular methods. Molecular methods, such as polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and microarray analysis of ribonucleic acids (RNA) genes, are more sensitive than traditional culture-based techniques. Analysis of microbial community structures with PCR-DGGE, which detects differences in the predominant species revealed subtle shifts in community composition. However, analysis of the microbial community composition using genetic probes revealed that the overall broad taxonomic level structure was highly similar for both the inner and outer microaggregate fractions. The research conducted here suggests that in desert soils where microaggregates are the predominant organizational structure for spatial distribution of bacteria, there is high similarity in the taxonomic composition of bacterial communities associated with these fractions.

Technical Abstract: The microbial community structure of inner and outer layer fractions of microaggregates from a desert agricultural soil were examined using low and high resolution methods employing PCR-DGGE and microarray analysis of 16S rRNA genes. Analysis of microbial community structures with PCR-DGGE, which detects differences in the predominant species revealed subtle shifts in community composition. However, analysis of the microbial community composition using phylogenetic probes for phylum and division level taxons revealed that the overall broad taxonomic level structure was highly similar for both the inner and outer microaggregate fractions. Among the major taxonomic groups, alpha proteobacteria were predominant in both fractions, followed by Planctomycetes and Acidobacteria. The research conducted here suggests that in desert soils where microaggregates are the predominant organizational structure for spatial distribution of bacteria, there is high similarity in the taxonomic composition of bacterial communities associated with these fractions when characterized at the taxon levels of division and phylum.