Why crop rotation works
Crop rotation has been used since Roman times to improve plant nutrition and to control the spread of disease. A new study to be published in Nature’s ‘The ISME Journal’ reveals the profound effect it has on enriching soil with bacteria, fungi and protozoa.
“Changing the crop species massively changes the content of microbes in the soil, which in turn helps the plant to acquire nutrients, regulate growth and protect itself against pests and diseases, boosting yield,” said Professor Philip Poole from the John Innes Centre.
Soil was collected from a field near Norwich and planted with wheat, oats and peas. Next generation sequencing was performed at The Genome Analysis Centre to identify changes in abundance and composition of the soil communities. After growing wheat, the soil remained largely unchanged and the microbes in it were mostly bacteria. However, growing oat and peas in the same sample caused a huge shift towards protozoa and nematode worms. Soil grown with peas was highly enriched for fungi.
All organisms on our planet can be divided between prokaryotes (which include bacteria) and eukaryotes (which include humans, plants and animals as well as fungi). After only four weeks of growth, the soil surrounding wheat contained about 3% eukaryotes. This went up to 12-15% for oat and pea. The change of balance is likely to be even more marked in the field where crops are grown for months rather than weeks.
Analysis has previously relied on amplifying DNA samples. This limits scientists to analysing one taxonomic group at a time such as bacteria. It also means that everything present in that group is analysed rather than what is playing an active role. Every gram of soil contains over 50,000 species of bacteria so the task is enormous.
There are relatively fewer actively expressed genes, or RNA. It is now possible to sequence RNA across kingdoms so a full snapshot can be taken of the active bacteria, fungi, protozoa and other microbes in the soil. Sequencing was carried out in collaboration between The Genome Analysis Centre and the University of East Anglia.
“Analysis of complex environmental samples poses a significant challenge due to the variety and differential abundance of the organisms present in the community,” said David Swarbreck, Group Leader at The Genome Analysis Centre. “High throughput sequencing has enabled us to explore the rhizosphere community using an approach that is not dependent on the type of target organism or biases associated to PCR primers and with sufficient depth to examine the active community for bacteria, archaea (single celled organisms) and soil eukaryotes such as fungi and nematodes.”