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


Cereals & Oilseeds
Project code:
01 September 2018 - 01 September 2021
AHDB sector cost:
Total project value:
Project leader:
FERA and the University of Lincoln (Scientific partners: AHDB-BBRO Soil Biology and Soil Health Research Partnership (NIAB, SRUC, ADAS, GWCT, ORC, Natural England). Industry partners: AHDB-BBRO Soil Biology and Soil Health Research Partnership (LEAF, Innovation for Agriculture, The Wye & Usk Foundation, Frontier, NRM, BASF))

About this project

The challenge

Biological communities in soil affect nutrient cycling, suppress plant pathogenic organisms and, therefore, contribute to the overall soil health status.

Community population dynamics can change in response to the crop rotation cycle and management practices, such as organic amendment, tillage and liming.

Understanding soil biological communities can be challenging, but high-throughput sequencing technology is revolutionising the way in which the functions and diversities of soil communities are investigated through analysis of directly or indirectly extracted DNA.  

The project

This PhD studentship compliments a five-year soil biology and soil health research partnership, funded by AHDB and BBRO, designed to help people maintain and improve the productivity of UK agricultural and horticultural systems through a better understanding of soil biology and soil health. 

In this project, meta-barcoding and meta-transcriptomics analyses on DNA purified from soil will be used to investigate the effects of crop rotation and management practices (organic amendment, tillage and liming) on the diversity and function of biological communities. The hypothesis to be investigated is that biological communities and their functions in soil change according to long-term cropping and soil management practices. 

Soils with known disease and management histories, from field demonstration plots and experiments already planned at various long-term soil management sites within the research partnership, will be sampled and DNA will be extracted and purified using validated methods. Soil biodiversity will be analysed using meta-barcoding procedures, following PCR amplification of various markers, to assess bacterial, fungal and nematode communities at family and genus levels. Meta-transcriptomics will be used, where appropriate – for example, for functional analyses of genes involved in nitrogen, carbon, phosphorus and sulphur cycling or in active suppression of plant pathogens. Bioinformatics analysis of the data will be used to assess the main changes in soil microbiome arising from differences in soil management.

The benefits

High-throughput sequencing technology will allow for molecular markers to be exploited to monitor changes in soil biodiversity, microbial effects on nutrient availability, microbial symbionts, plant pathogens and nematode assemblages. Key markers will be recommended for use in routine assessment of soil health status.