Skip to main content
Doctoral thesis, 2011

Tracking the fate of biocontrol microorganisms in the environment using intrinsic SCAR markers

Holmberg Anna-Ida Johnsson


Biocontrol microorganisms can be used as an alternative to conventional chemical pesticides to control plant diseases. This thesis investigated the fate and behaviour of three microbial model control agents with effect against fungal pathogens in cropping systems, and the spread of one of the model strains in bioaerosols. The bacterium Pseudomonas brassicacearum MA250 was monitored in winter wheat systems, in a climate chamber trial and in field conditions. The contribution of strain MA250 to the total microbial load in bioaerosols was also investigated. Two filamentous fungi, Hypocrea parapilulifera IMI206039 and Trichoderma atroviride IMI206040, were investigated on a golf green and in microcosms with soil sampled from the green and with agricultural soil. To track and enumerate the applied strains, intrinsic strain-specific sequence-characterised amplified region (SCAR) markers were utilised in quantitative real-time PCR. Supplementary methods, such as cultivation-based methods and analysis of the Gram-negative bacterial cell constituent endotoxin, were also included. In both winter wheat studies, MA250 colonised the roots of healthy seedlings. Withered seedlings that had died due to snow mould infection were not colonised, indicating the importance of a healthy seedling for proliferation of MA250. In the microcosm studies, with the two fungal biocontrol strains, populations of introduced cells behaved differently depending on the soil. On the golf green, the two fungal biocontrol strains were detected only sporadically, but nevertheless maintained their control effect. In the bioaerosol study, the SCAR marker consistently enabled detection of strain MA250, whereas other methods tested did not. The results showed that MA250 significantly contributed to the total microbial load in aerosols after 60 minutes of coating, when MA250 was added to the system. However, after 240 minutes of coating this significant increase was not seen and MA250 could only be detected against the background with use of the SCAR marker. In conclusion, the use of strain-specific SCAR markers proved a reliable method in quantifying added populations in soils, plants and aerosols. This type of information is valuable for optimising the use of the biocontrol microorganisms and to determine the risks associated with application of the strains.


biological control agents; pseudomonas fluorescens; genetic markers; winter wheat; trichoderma; pathogenic fungi; biological control; pcr

Published in

Acta Universitatis Agriculturae Sueciae
2011, number: 2011:30
ISBN: 978-91-576-7565-1
Publisher: Department of Microbiology, Swedish University of Agricultural Sciences

Authors' information

Johnsson, Anna-Ida
Swedish University of Agricultural Sciences, Department of Microbiology

UKÄ Subject classification


URI (permanent link to this page)