Long-term organic amendments to soil

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Microbial diversity in soil

The microbial diversity in soil is usually high and the maintenance of it may be important for sustainable ecosystem management. The reason for this is that a low microbial diversity in e.g. an arable soil might increase the vulnerability of the soil to attacks from pathogens on different crops. There is also a risk that the soil might become poorer in nutrients due to lack of key-role microbes involved in the nutrient cycling. However, even if soil in general is considered to have a high microbial diversity the abundance and composition of microbial communities between different soils can vary.

Effects of organic carbon amendments to soil

Arable soil often has a history of long-term amendments of different types of organic carbon compounds e.g. different crops have been grown in the soil for generations and/or different fertilizers have been applied. One could argue that this might have an effect on the structure and abundance of the microbial community in the soil. The addition of organic carbon compounds results in different types of concentrations of labile carbon fractions in the soil, which may lead to a specialization of different microbes depending on the nature of the labile carbon fractions. Due to this, a separation in the structure and abundance of the microbial community in the soils undergoing different treatments might be shown. Depending on which type of organic compounds are available in the soil, one group of microbes found in high abundance in one soil might represent a much smaller part of the total community composition in another soil. One explanation to this may be that the soils have for a long time been continuously affected with different organic amendments, influencing the amount of easily available carbon and thus also affecting the abundance and composition of the microbial community in the soil.

Examples of methods

To be able to answer questions of this kind, the microbial community structure and abundance have to be studied and there are many ways to study and evaluate possible effects of long-term organic amendments to soil. Today it is common to use molecular techniques. Two methods that might be used to study possible differences in overall microbial community structure composition between different soils are terminal restriction fragment length polymorphism (T-RFLP) and denaturating gradient gel electrophoresis (DGGE). Since these methods are PCR-based they may also be used to study possible differences between specific groups within e.g. bacterial community structure composition. It might be possible to study possible differences in the community structure of e.g. actinobacteria, denitrifying bacteria or nitrogen-fixing bacteria.

To address questions regarding the abundance of different microbial groups in soils one approach is to use Q-PCR. With this method it is possible to quantify either the amount of a specific group of bacteria of interest or a gene represented in many different bacteria but involved in a specific process of interest.

However, the methods available today are many (see[1]).

See also

  • Microbial diversity
  • Enwall, K., Philippot, L., Hallin, S. 2005. Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl. Env. Microbiol. 71:8335-8343 [2]
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