Occurrence of Phytophthora species in soils, and functional analysis of soil microbiomes on Biolog EcoPlates : a study on commercial soils, and forest and urban soils

Abstract: Tree pathogenic Phytophthora species have been identified as a threat to health and stability of forests und urban trees. In Sweden most Phytophthora species are non-native and potentially invasive, and thus it is important to control their spread. To identify the presence of Phytophthora species in soil from symptomatic forest stands, urban trees and commercial soils, laboratory analyses using a polymerase chain reaction (PCR) with the internal transcript spacers (ITS) pair ITS1oo/ITS4 were conducted. The results revealed that Phytophthora cambivora was present across all habitats and in commercial soils. Furthermore, P. plurivora was detected in one soil sample from an urban area. Indications of other Phytophthora species were found as well but could not be confirmed on species level. The results suggest that Phytophthora are widely present in southern Sweden and provide new evidence that commercial soil can be an important pathway spreading these pathogens. Biolog EcoPlate (Biolog, Inc., Hayward, CA, USA) is a tool recently developed for characterization of functional aspects (enzymatic capacity) in soil microbial communities and were used to study a subset of soil samples. Four soil samples from forests and one from an urban area were used. Clear patterns to categorize the soil microbial activity in different habitats were not detected, which is likely to be due to the low number of biological replicates. The test illustrates the apparent heterogeneity of soil as a substrate and underlines the importance of adequate number of replicates across habitats and the need to take care of standardized sampling and implementation of the method.