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

View the project final report

• 2005 annual report
• 2006 annual report

Commodities

• Agronomic: corn, potatoes, grass (misc. perennial), hay

Practices

• Animal Production: feed/forage, manure management
• Crop Production: conservation tillage
• Education and Training: extension
• Natural Resources/Environment: biodiversity, indicators
• Production Systems: agroecosystems
• Soil Management: general soil management
• Sustainable Communities: sustainability measures

The objective of this study was to compare sustainable agricultural management practices using bacterial diversity as the measure of soil health. The original plan was to create a melting and re-association profile for the bacterial community from each soil type maintained under different agronomic management practices. This procedure was developed by Torsvik (1990) and requires a large amount of DNA (i.e. a total amount of 600 µg DNA in a 1.5 ml sample) to create the profiles. However the amount of DNA obtained from a 200 g soil sample by a fractionated centrifugation method yielded a much lower amount of DNA than is required for this specific analysis. Multiple combined DNA extractions also yielded insufficient amounts of DNA to follow the Torsvik procedure. After attempts to maximize the yields became unsuccessful, we used a polymerase chain reaction (PCR) based method to create Denatured Gradient Gel Electrophoresis (DGGE) profiles to compare bacterial diversity in soils maintained under different management practices. PCR-DGGE methods have been adapted from the medical field into soil science to study microbial community analysis (Muyzer et. al. 1993). Initially after being used for simpler ecosystems, PCR-DGGE has been applied to characterize the microbial diversity in more complex terrestrial ecosystems (Duineveld et al., 1998; Heuer et. al., 1997; Jensen et al., 1998; Nakatsu et. al., 2000).

The results of this study indicated that management practices greatly influence bacterial diversity in a particular ecosystem. Among the different soils, no-till soil had the most diverse dominant population of bacteria as evident from the highest number of distinct bands observed in the DGGE profiles. Other management practices such as organic farming and crop rotation resulted in less bacterial diversity. Since, no-till soil had the most number of distinct DGGE bands compared to any other soil, we conclude that tillage and especially excessive tillage, is a principal factor in reducing bacterial diversity. By extension, we also conclude that no-till soil has the widest diversity of soil biochemical functions compared to soils managed by other means. Organic farming practices that maintain long rotations with crops that would not require tillage, such as a legume hay crop, would also be predicted to have greater bacterial and functional diversity than crop rotations that require tillage every season.

Introduction:

Soil health can be characterized by the ability of a particular soil to perform a range of biochemical processes required for that system to sustain long-term agricultural productivity with minimal environmental impact (Arias et. al., 2005). Several studies have reported that soil microbial diversity is a key component in maintaining the long-term sustainability of agroecosystems (Garbeva et. al., 2004; Janvier et. al., 2007). Bacteria constitute a major component of the soil microbial pool that performs a host of soil biogeochemical functions and it is well known that bacterial diversity influences overall ecosystem function and health.

Soil health has been measured in various ways including the use of indices such as plant productivity, soil nutrient concentrations, soil organic carbon content, and the concentration of various chemical and biochemical components such as pesticides and microbial growth factors. Increasingly soil is being viewed as a living entity containing a mixture of inorganic and organic materials that are constantly being influenced and altered by soil animals, fungi and bacteria. Consequently, emphasis is being applied to the use of biological indicators such as enzyme activity, microbial biomass, and microbial respiration rate to determine soil health. Therefore it is appropriate to assess soil health using a biological component such as bacteria or, more precisely, bacterial diversity in a particular ecosystem.

The objective of this project was to assess soil health and sustainability of agro-ecosystems using bacterial diversity as an indicator.