ARI Biennial Review for 2018-2019

ENVIRONMENTAL BIOTECHNOLOGY AND MICROBIOLOGY Characterisation of PrP genotypes in sheep and goats Scrapie is a fatal, neurodegenerative disease of sheep and goats that belongs to the family of transmissible spongiform encephalopathies. Sheep susceptibility to scrapie is associated with polymorphisms in the ovine prion protein ( PrP ) gene at codons 136, 154 and 171. Genomic DNA was isolated and purified from peripheral blood leucocytes using standard procedures. The identification of the allelic variants present in the DNA samples was performed in a simple multiplex PCR reaction and melting curve analysis of the PrP gene. Genetic analysis of blood samples of the Chios sheep (755 samples) continued in 2018/19, in order to identify and select genotypes resistant to the scrapie disease. Presently at the ARI, the Chios sheep nucleus unit counts over 350 breeding animals, exclusively of the scrapie resistant genotype ARR/ARR. In addition, the molecular fingerprinting for goats is in progress. In 2018/19, 789 blood samples were tested for scrapie disease genotypes. The data were submitted to the laboratory molecular databank for further analysis. Also, based on scrapie genotyping, a nucleus unit with all the different goat genotypes has been established at the Research Farm of the Animal Production Section. ( I.M. Ioannides, G. Hadjipavlou ). Depuration of citrus fruit industry fungicides The application of the fungicide thiabendazole (TBZ) in fruit packaging plants (FPP) results in the production of effluents that are often disposed in adjacent field sites. These require remediation to prevent further environmental dispersal of TBZ. We assessed the bioaugmentation potential of a newly isolated TBZ-degrading bacterial consortium in a naturally contaminated soil (NCS) exhibiting a natural gradient of TBZ levels (12000, 400, 250 and 12 mg kg −1 ). The effect of aging on bioaugmentation efficacy was comparatively tested in a soil with similar physicochemical properties and soil microbiota, which was artificially contaminated with the same TBZ levels (ACS). The impact of bioaugmentation and TBZ on the bacterial diversity in the NCS was explored via amplicon sequencing. Bioaugmentation effectively removed TBZ from both soils at levels up to 400 mg kg −1 but failed at the highest contamination level (12000 mg kg −1 ). Dissipation of TBZ in bioaugmented samples showed a concentration-dependent pattern, while aging of TBZ had a slight effect on bioaugmentation efficiency. Bioaugmentation had no impact on the soil bacterial diversity, in contrast to TBZ contamination. Soils from the hotspots of TBZ contamination (12000 mg kg −1 ) showed a drastically lower α-diversity driven by the dominance of β- and γ-proteobacteria at the expense of all other bacterial phyla, especially Actinobacteria. Overall, bioaugmentation with specialised microbial inocula could be an effective solution for the recovery of disposal sites contaminated with persistent chemicals like TBZ. (M. Omirou, I.M. Ioannides) The effects of different soil nutrient management schemes in nitrogen cycling It is imperative for sustainable agriculture to explore practices and inputs creating low N 2 O emission capacity without reducing the productivity of the agricultural system. To evaluate different nutrient management schemes, a microcosm study was conducted to assess the direct N 2 O emission from soil. Four different treatments were used to provide a preliminary assessment of N 2 O emissions, as well as the concentrations of nitrates (NO 3 − ) and ammonium (NH 4 + ) produced in soil: compost (derived from green plant residues), chickpea residues (green manure) in two different N concentrations (2.6% and 5.5%, respectively) and ammonium nitrate (fertiliser). The soil was thoroughly mixed with the organic amendments and ammonium nitrate, and incubated for 31 days. The emissions of N 2 O were higher in green manure with high-N content, as a source of nitrogen in the soil, and were similar to the emissions measured from the chemically fertilised soil. In particular, chickpea residues, with high-N content, exhibited cumulative N 2 O emissions, equal to 266.17 μg N/m 2 , whereas in 67 AGROBIOTECHNOLOGY