Microbial diversity along a transect of agronomic zones

Abstract

The diversity of microbial communities constitutes a critical component of good soil-management practices. To characterize the effects of different management practices, molecular indicators such as phospholipid fatty acid (PLFA), denaturing gradient gel electrophoresis (DGGE) and composition of ammonia-oxidizing bacteria were used to analyze bacterial community structure and diversity from four eastern Washington State soils. Samples from four sites were collected representing a transect of high-precipitation to low-precipitation areas that covered different agronomic zones with different management and cropping practices. Biomass amounts estimated from extractable PLFA were significantly higher in the no-till (NT) soil than in the conventional-till (CT) soil. Similarities among the different 16S rDNA DGGE band profiles were analyzed quantitatively using correspondence analysis and this confirmed that the CT soil was the most dissimilar soil. DGGE analysis of 16S rDNA ammonia-oxidizing bacteria from the four soils revealed two identical bands, indicating little effect of agronomic practices and precipitation on these species. A second set of primers, specific for amoA (ammonia monooxygenase) genes, was used to examine ammonia oxidizers in the samples. Six banding patterns (clusters) from amplified rDNA restriction analysis of 16S rDNA fragments were observed after restriction analysis with HinfI. Sequencing of these clones revealed the presence of only Nitrosospira-like sequences. Analysis of the sequences showed that ammonia oxidizers from the NT soil were more diverse compared to those from the CT and conservation reserve program soils. Our data showed that management and agronomic practices had more impact on bacterial community structure than annual precipitation.