Crop Diseases and Mycotoxin Accumulation in Temperate Agroforestry Systems

Background: Temperate agroforestry is regarded as a sustainable alternative to monoculture agriculture due to enhanced provisioning of ecosystem services. Plant health and food safety are crucial requirements for sustainable agriculture; however, studies of fungal diseases and mycotoxin contamination of crops grown under temperate agroforestry are lacking. This study therefore aimed to compare fungal colonization and mycotoxin contamination of crops grown in temperate agroforestry against conventional monoculture. Methods: The biomass of plant pathogenic fungi in oilseed rape plants and barley and wheat grain harvested in 2016 to 2018 at four paired agroforestry and monoculture sites was quantified using species-specific real-time PCR. Mycotoxin content of barley and wheat grain was determined by HPLC-MS/MS. Results: The colonization of oilseed rape plants with the vascular pathogen Verticillium longisporum and wheat grain with the head blight pathogen Fusarium tricinctum was lower in agroforestry than in conventional monoculture. Mycotoxin content of barley and wheat grain did not differ between agroforestry and monoculture systems and did not exceed the legal limits of the EU. Remarkably, fumonisin B1 was detected in wheat grains at two sites in two years, yet the low levels found do not raise food safety concerns. No differences were found between the two production systems with regard to infection of wheat and barley grain with five Fusarium species (F. avenaceum, F. culmorum, F. graminearum, F. poae, and F. proliferatum) and oilseed rape with fungal pathogens Leptosphaeria biglobosa, Leptosphaeria maculans, and Sclerotinia sclerotiorum. Conclusions: Temperate agroforestry does not negatively affect the infection of wheat, barley and oilseed rape with major fungal pathogens though it may suppress the infection of oilseed rape with V. longisporum and wheat grain with F. tricinctum. Furthermore, temperate agroforestry does not increase mycotoxin contamination of barley and wheat. Therefore, temperate agroforestry does not negatively affect food safety

Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer

As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology