Investigating the impact of soil tillage and crop rotation on the bacterial microbiome associated with winter oilseed rape under Irish agronomic conditions

Abstract

Modern agriculture is challenged with sustaining a high quality food flow to an increasing global population. Therefore, the agriculture intensification is largely achieved through the use of farm equipment, intensive soil tillage, fertilizers, pesticides and other manufactured inputs. As a result, the farming industry is facing a significant profitability problem due to continuing high input costs, and consequently research into low input, more efficient and eco-friendly crop production systems are required. One way to assist in achieving these goals is to integrate beneficial plant microbiomes i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance into agricultural production. However, this plant microbiome is influenced by the agricultural management practices such as soil tillage and crop rotation which have major effect on structure, composition and function of soil, rhizosphere and endophytic bacterial microbiota. Oilseed rape (Brassica napus L.) is an important break crop in cereal crop rotation and can significantly reduce the rate of fungal disease incidence and as a result, improves the yield of subsequent cereal crops. Additionally, oilseed rape is the world’s third largest source of vegetable oil used in human nutrition and as a source of oil for biodiesel production. Therefore, the promotion of agricultural practices that maintain the natural diversity of the oilseed rape microbiome is receiving attention as an important element for a sustainable agricultural system that ensures crop productivity and quality, while reducing inputs. The plant microbiome can be considered as an extension of the host genome or even as the plant’s second genome. Therefore, even small changes in the host due to agronomic factors may influence the plant microbiome, and these changes may even feedback to modulate the behaviour of the host. The main objective of the current work was to explore the impact of soil tillage (plough based conventional tillage vs conservation strip tillage) in field-grown winter oilseed rape bacterial microbiome over the plant growth stages. We also focussed on the microbiome niche differentiation between the different plant environments (rhizosphere, root and shoot) due to influence of soil tillage. In this study a high-resolution methodology based on illumina sequencing of the bacterial 16S rRNA marker gene was adopted to characterize and compare soil and plant associated bacterial communities. Our results show that oilseed rape is preferentially colonized by Proteobacteria, Actinobacteria, Bacteroidetes and Chloroflexi, and each bacterial phylum is represented by a dominating class or family of bacteria. In general, soil tillage was found to have a profound effect on the bacterial community structure in the endosphere of oilseed rape (especially root and shoot), without perceptible effects on the rhizospheric bacterial communities. Moreover, oilseed rape plant selected a subset of microbes at different stages of development, presumably for specific functions. Furthermore, within the bacterial community structures, we observed strong clustering according to plant compartment whereby each compartment rendered microbiota significantly dissimilar from each other where soil tillage fine-tunes their composition. We also studied the impact of oilseed rape-wheat crop rotation, in combination with the soil tillage, to explore its influence on anti-microbial compound 2,4-diacetylpholroglucinol (2,4-DAPG) producing Pseudomonas spp. abundance, in rhizosphere and root of oilseed rape and wheat crops over the plant growth stages, by using the quantitative PCR technique. Overall, this study showed that crop rotation in combination with conservation strip tillage increase the population of the 2,4-DAPG+ Pseudomonas spp. in rhizosphere and root of oilseed rape and wheat crops. Overall, this practical study has broaden an understanding of how oilseed rape and its microbiome responded to different agriculture management practices, and provided new insights into the complex relationship between oilseed rape and its associated microbes.