Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline

Abstract

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality.

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

“…The consensus intergenic spacer of this OTU had 100% identity to Olpidium brassicae (Figure 4 and Supplementary Figures S12 and S7c -annotated as 'O'). O. brassicae is a fungal pathogen abundant in Brassica rhizospheres (Hartwright et al, 2010) that reduces production of pods and seeds (Hilton et al, 2013). The organism in our samples is likely to be O. brassicae, or a close relative, although ultimately this would require confirmation by culturing or more extensive sequencing.…”

The Role of Soil Microbes in Promoting Plant Growth

“…Interestingly, even though monoculture shows a decline in crop yield, Hilton et al still detected an increase in the abundance of two fungi pathogens, Olpidium brassicae and Pyrenochaeta lycopersici, which possibly arising a soil suppressiveness effect. In forestry, mixed forest not only has obvious economic and social benefits, but also has hidden ecological benefits (Hilton et al, 2013). Although supply sufficient fertilizer and the same cultivation measure, crop yield is still annual decline with long-term monoculture caused by the accumulation of harmful substance in rhizosphere (Lampurlané s et al, 2016).…”

Characterization of para -Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing

“…For terminal restriction fragment length polymorphism (TRFLP) analysis, bacterial 16S rRNA genes were amplified by PCR using primers 63F (33) and 1087R (34), and MspI and HhaI were used for restriction diges-tion. Capillary electrophoresis and analysis of TRFLP data were performed as described by Hilton et al (35).…”

“…Plasmid extraction and purification were carried out using a Qiagen HiSpeed plasmid midipurification kit (Qiagen, Crawley, United Kingdom) according to the manufacturer's instructions. Quantitative PCR (qPCR) was carried out using the primers designed for pnpA and mar (see Table S1 in the supplemental material) and the following cycling conditions: 95°C for 10 min, followed by 40 cycles of 95°C for 15 s, 60°C for 1 min, and 95°C for 15 s. The components of the reaction mixture were those described by Hilton et al (35). The products were sequenced to confirm the presence of the pnpA and mar sequences.…”