High-throughput sequencing to measure changes in soil biology in response to long-term management practices (PhD)


Biological communities influence soil health and crop growth. For example, they help recycle nutrients, suppress plant pathogenic organisms and form symbiotic associations with plants.

This study aimed to improve understanding of soil biology and how it responds to common agricultural practices, such as organic and pH amendments, cultivations, crop rotations and cover cropping.

It also aimed to guide management decisions to sustain productive soils for crop production (grassland, arable and horticultural crops).

The work included analyses of soil samples from six long-term soil management experimental sites within the AHDB/BBRO Soil Biology and Soil Health Partnership (linked to project 5 of the partnership):

  • Organic soil amendments (ADAS Terrington, ADAS Gleadthorpe and Harper Adams University)
  • Drainage treatments (ADAS Boxworth)
  • Tillage approaches (GWCT Loddington)
  • pH levels and fertiliser applications (SRUC Craibstone)

Metabarcoding procedures (following PCR amplification of 16S and ITS rRNA gene markers) were used to help determine bacterial and fungal community diversity.

Open-source software (bioinformatics pipeline QIIME2) was used to assess the main changes in the soil microbiome arising from differences in soil management practices.

The results showed a significant effect of pH on fungal and bacterial communities.

Much smaller effects of fertiliser, cropping sequence, sampling season, organic amendments, soil compaction, drainage and tillage were also determined.

The most striking observation was that soil management had less impact on soil microbial diversity than the location or season.

Therefore, the main conclusion was that natural variation in soil biology (between soil types at different locations or between seasons at the same locations) was much greater than the variation attributed to soil management.

Because of the influence of location and season, close monitoring of sites over multiple seasons will be required to identify the most appropriate soil management practices.

Cereals & Oilseeds
Project code:
01 September 2018 - 31 December 2021
AHDB sector cost:
Total project value:
Project leader:
FERA and the University of Lincoln


SR57 final project report

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