Assessing Agricultural Soil Health and Sustainability of Different Management Practices Using Profiles of Bacterial Communities

Assessing Agricultural Soil Health and Sustainability of Different Management Practices Using Profiles of Bacterial Communities

Summary

We sampled soils from farms managed under different agricultural practices such as organic, intensive, and reduced inputs. Our objective was to assess soil health and sustainability of agroecosystems by measuring bacterial community diversity by creating DNA reannealing curve plots for our soil samples. However, sufficient DNA could not be extracted for the work. We decided to use a polymerase chain reaction (PCR) based method to create denatured gradient gel electrophoresis (DGGE) profiles to compare bacterial diversity in soil maintained under different agricultural practices. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) methods were first used in the medical field into soil science to study microbial communities (Muyzer et. al. 1993). The PCR-DGGE was initially used in rather simple systems but has been extended more complex systems, including terrestrial ecosystem,s to study microbial diversity (Duineveld et al., 1998; Heuer et. al., 1997; Jensen et al., 1998; Nakatsu et. al., 2000).

Objectives/Performance Targets

1 - Compare soil health by relating bacterial community diversity observed in soils under different agricultural management practices.

2 - Promote farmer/grower/scientific knowledge about sustainability and agriculture practices.

Accomplishments/Milestones

DNA extraction and purification was carried out using the Megaprep Ultra Soil DNA Kit (MoBio Laoratories, CA). For each sample, we used 10 g soil instead of smaller quantities typically used for PCR-based methods. The reason for this is to capture the wide variety of bacterial species that may not be possible using smaller soil sample sizes.
Planned activities for the soil samples include a PCR using a set of universal bacterial primers (PRBA 338 and PRUN518R). These primers amplify the 338 to 518 region of the 16s rDNA gene of bacteria. DGGE profiles will be created using the PCR products obtained from the amplified DNA using template DNA from the soil samples.

Impacts and Contributions/Outcomes

This project will provide information about the impact of agricultural practices on soil health. The quantitative method of separating agricultural practices, based on bacterial community diversity, is a biological approach to assess overall soil health. It is hoped that the result of this study will clearly identify the soil management practices that have the greatest impact on bacterial diversity in soil.

Reference

Duineveld, B.M., A.S. Rosado, J.D. van Elsas, and J.A. van Veen. 1998. Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl. Environ. Microbiol. 64:4950–4957

Heuer, H., M. Krsek, P. Baker, K. Smalla, and E.M.H. Wellington. 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:3233–3241

Muyzer, G., E.C. de Waal, and A.G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695–700.

Nakatsu, C. H., V. Torsvik, and L. Øvrea°s. 2000. Soil Community Analysis Using DGGE of 16s rDNA Polymerase Chain Reaction Products. Soil Sci. Soc. Am. J. 64:1382–1388