Measuring groups of microorganisms in soil

Some soil biological tests are relatively new. Information on interpretation and how to improve the values in soils is still in development.

DNA analyses can be used to identify changes that occur in fungal and bacterial communities because of different soil management practices. Research is comparing molecular data against the more traditional physical, chemical and biological measurements of soil health.

DNA technology can be used to:

• Estimate the effect of soil- and crop-management practices on soil microbiological diversity
• Study the population dynamics of beneficial or plant pathogenic fungi and bacteria

High-throughput sequencing technology compares DNA sequences of marker genes that are unique to all bacteria (16S rRNA) or fungi (ITS rRNA) in a process known as metabarcoding. Using this molecular technique, the numbers of taxonomically distinct individuals can be compared across different treatments.

The apparent microbial diversity measured using any nucleic acid analysis procedure is highly dependent on the method used to extract DNA from soil. Standardisation of methods is important when comparing samples collected from different locations and at different times.

Although this approach shows much promise in terms of improving the understanding of soil biology, it does not yet provide information that can form the basis of soil management decisions.

It does however provide an approach to assessing the presence of specific plant pathogens.

Another way of assessing soil biology is to carry out a detailed census of all the major groups of microorganisms in a soil sample using a combination of extraction techniques, staining and microscopy.

Key groups of organisms – bacteria, fungi, protists and nematodes – clearly play important roles in the functioning of soil, but there is a lack of understanding of all the factors that control the complex biological communities found in soil at different spatial and temporal scales.

Without this information, the significance of changes in absolute numbers of key functional groups or ratios of numbers (e.g. bacteria:fungi) is unclear.

The main factor to influence the ratio of bacteria to fungi is soil pH.

Read a case study on estimating the effect of long-term organic material additions on soil microbial diversity

Find out how to count earthworms as indicators of soil health

Read about how to measure soil respiration as an indicator of biological activity

Find out more about the functions of soil biology