The effect of organic material additions on soil microbial diversity

DNA methods were used to assess soil microbial diversity at a long-term experimental site where a range of organic amendments had been applied.

Back to: Measuring groups of microorganisms in soil

Back to: Soil assessments

Back to: GREATsoils

Molecular indicators of soil microbial diversity 

Research carried out as part of the AHDB-BBRO Soil Biology and Soil Health Partnership used molecular techniques to investigate the impact of repeatedly adding different organic materials to soil in a predominantly arable rotation (cereals and potatoes).

Long-term experimentation at Harper Adams University

Soil samples were collected from a long-term trial at Harper Adams University in October 2017, where different organic materials had been added to soil.

Organic material treatments at the long-term trial at Harper Adams University, Shropshire

Sandy loam (12% clay), arable rotation
TreatmentsApplications up to autumn 2017

Cattle FYM 

23 years 

Cattle slurry 

23 years 

Green compost 

13 years 

Green/food compost 

7 years 

Food-based digestate 

9 years 

Routine measurements of topsoil chemical, physical and biological properties were undertaken as part of an integrated soil health assessment.

DNA analysis

Soil samples were also taken for total DNA analysis. The DNA was extracted and purified using three different methods and then analysed using high-throughput sequencing technology. This 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, most soil organisms can be identified at higher taxonomic levels (e.g. phylum, class or order), although fewer can yet be accurately assigned at the levels of family, genus or species. The numbers of taxonomically distinct individuals can be compared across the different treatments, and bioinformatics software can be used to measure biological diversity in each sample.


Between 100,000 and 200,000 DNA sequences were obtained for both bacterial and fungal groups from each soil sample from the Harper Adams trial. Irrespective of the method used to extract the DNA, similar types of bacteria and fungi were recognised within the soil communities.

The extraction method did, however, influence estimates of the relative abundances of these types of bacteria and fungi. Standardisation of methods will therefore be important when comparing samples collected from different locations and at different times.

When results from plots with and without organic amendments were compared, no significant effects of any of the amendments on bacterial or fungal types or abundances were found.

Future work

Sampling will be repeated at this and other long-term trial sites. Standardised DNA analyses will be used to identify specific changes that occur in fungal and bacterial communities because of different soil-management practices. Molecular data will be compared against the more traditional physical, chemical and biological measurements of soil health also being collected by the Soil Biology and Soil Health Partnership.

Further information