Why crop rotation works

Small changes in a plant genotype can have complex and unexpected effects on soil microbes surrounding the roots.

Crop rotation has been used since Roman times to improve plant nutrition and to control the spread of disease. A new study reveals the profound effect it has on enriching soil with bacteria, fungi and protozoa. In the study, soil was collected from a field planted with wheat, oats and peas. After growing wheat, the samples remained largely unchanged and the microbes present were mostly bacteria. However, growing oats and peas in the same soil caused a huge shift towards protozoa and nematode worms. Soil grown with peas was highly enriched for fungi. The researchers also grew an oat variety unable to produce normal levels of avenacin, a compound that protects roots from fungal pathogens. They expected the soil to contain higher levels of fungi as a result, but instead found it contained a greater diversity of other eukaryotes such as protozoa. The findings of the study could be used to develop plant varieties that encourage beneficial microbes in the soil. John Innes Centre scientists are already investigating the possibility of engineering cereal crops able to associate with the nitrogen-fixing bacteria normally associated with peas.

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. The ISME Journal , 18 July 2013, doi:10.1038/ismej.2013.119
Plant–microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.