Microbes, Roots and Nitrogen Cycling

Louise Jackson

A sustainable agricultural system provides for human needs over an indefinite period of time without degradation of soil and water resources. To achieve this goal, nutrients must be recycled and retained within the agricultural ecosystem, with greatest nutrient availability at the time of peak demand by plants. Increased use of renewable resources, e.g., composts, manure, and cover crops, will ensure that agriculture relies on sources of nutrients that are predictably available over the long-term.

Microbes are the major agents of nutrient transfer and release in soil. Microbes are especially important for supplying nutrients to crop plants in agricultural systems with high inputs of organic matter. Although the basic processes of the nitrogen (N) cycle are well defined, we have much to learn about the role of microbes in soil N transformations. For example, little is known about how specific microbial groups or communities of microbes control these transformations. Only recently have techniques been developed to assay soils for differences in microbial functional groups and community structure. Another issue is assaying complex and rapid N transformations in soil. While it is well-recognized that higher microbial biomass in soil increases the activity of soil N transformations, microbiologists are still grappling with how to measure in situ rates of processes of mineralization, nitrification, and denitrification. Moreover, a better understanding is needed of how different types of organic matter affect microbial activity and these N transformation processes.

In my research group, we have addressed the following questions about soil microbial ecology with an emphasis on improving N cycling in intensive vegetable production systems in California. Most of our research has been conducted on-farm with grower-cooperators in the Salinas Valley.

How do microbial communities differ among different cropping systems? Analysis of microorganisms in soil offers a complicated problem for analysis. Bacteria and fungi may exist attached to surfaces, embedded in biofilms around soil particles, or inside the tissues of a host. Direct counting methods thus are problematic for accurately quantifying organisms. Moreover, most soil microorganisms are not yet culturable or identifiable in the laboratory. Total microbial biomass is often measured as the release of carbon (C) or N upon chloroform fumigation, but this gives no information about the microbial constituents. Recent methods in soil microbiology rely on the extraction of unusual molecules that mark the presence of different groups of microbes in situ. For example, phospholipid fatty acid (PLFA) analysis is a method that uses cell membrane lipids, which are readily degraded as soon as microbes die, as biomarkers for specific groups of organisms. This technique has proven useful in differentiating microbial communities from organic and conventional farming systems, and among sites with different land use histories (i.e., intensively-farmed, dry-farmed, and grassland ecosystems).

Can we identify specific microbes that are beneficial in soil N cycling? At present, current methods in soil microbial ecology are not able to identify the species of microorganisms in a community that control rates of specific N transformations. Thus, a major focus in microbial ecology has been to examine factors important for increasing total microbial biomass and activity in soil.

Why is high microbial biomass considered advantageous for efficient N cycling? Microbes carry out the processes of N cycling, and higher microbial biomass is related to higher rates of N release and higher N availability. Ammonium (NH4+) and nitrate (NO3-) are the main forms of N taken up by crop plants. Ammonium is produced by microbial mineralization of soil organic matter. It is also a common component or product of most inorganic fertilizers. Nitrifiers utilize NH4+ as an energy source, and produce nitrite (NO2-) or NO3-. If microbes release NH4+ and NO3- at rapid rates, and plants also take up these ions at rapid rates, then concentrations of NH4+ and NO3- in the soil can be moderate or low. This is actually a desirable situation because N availability to plants is high, but the potential for loss of these ions via volatilization, leaching, and denitrification is limited.

What factors affect microbial biomass? Most microbes rely on C as an energy source, but C is limiting in many agricultural soils. Several long-term, farming-system experiments throughout the USA have shown that increasing inputs of organic matter increases microbial biomass. Some evidence suggests that combining inputs of readily decomposable organic material (e.g., cover crops) with more resistant materials (e.g., compost) may be useful in steadily increasing microbial biomass through time. On a shorter-term scale, our research shows that events such as tillage, irrigation and incorporation of plant residues often cause immediate net N mineralization and production of NO3-. In the absence of plant roots and plant N uptake, this can lead to net N losses via leaching and nitrous oxide production, which are detrimental to water and atmospheric quality.

Our knowledge of soil microbial ecology is increasing, and recent research has suggested important avenues for improved efficiency of N cycling. As we strive for more sustainable agroecosystems, more attention will be paid to the intricate relationships between soil microbes and plant roots, and associated nutrient turnover and availability.

Louise Jackson
College of Agricultural and Environmental Sciences
Department of Vegetable Crops
221 Asmundson Hall
University of California
One Shields Avenue
Davis, CA 95616-8746
Tel: (530) 754-9116

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