Around 20 pieces of each section of root were examined for each of the five plants from each ecotype– soil combination (i.e. approximately 60 root pieces per plant). DNA was extracted from approximately 0.5 g freeze-dried and ground root material (one root system for each ecotype–soil combination) as described by Ward et al. (2005). Polymyxa-specific rDNA primers Pxfwd1 (5′-CTG CGG AAG GAT CAT TAG CGT T-3′) and Pxrev7 (5′-GAG GCA TGC TTC CGA GGG CTC T-3′) were used in PCR (Ward & Adams, 1998). Plasmodiophora-specific PCR was performed as

in Cao et al. (2007) using primers TC1F/TC1R. For sequencing PF-562271 order studies, the Polymyxa-specific forward primer Pxfwd1 and the generic fungal ITS4 reverse primer (5′-TCC TCC GCT TAT TGA TAT GC-3′) (White et al., 1990) were used to amplify rDNA. CX-5461 concentration Each reaction mix (50 μL) contained 0.2 μM primers, 1 U Taq DNA polymerase (MBI), 0.2 mM dNTPs (Sigma), 1 × PCR buffer NH4 (MBI) and 0.02 mg μL−1 bovine serum albumin. Cycling conditions were 2 min at

95 °C, and then 30 cycles of 94 °C for 30 s, 50 °C for 1 min and 72 °C for 2 min, followed by 72 °C for 10 min. Products were analysed in 1% agarose gels. PCR products were cloned into the pGEM®-T Easy vector (Promega Corporation, Madison, WI). Plasmid DNA was prepared using the QIAprep spin miniprep kit (Qiagen, Crawley, UK) and sequenced using the ABI PRISM™ Big-Dye version 1.1 kit using M13 sequencing primers and run at the Geneservice sequencing facility (http://www.geneservice.co.uk). ITS rDNA sequences were aligned by clustalx and manually adjusted. Phylogenetic analysis was performed using the neighbour-joining method (maximum composite likelihood distances) in mega4 (Tamura et al., 2007) with 10 000 bootstrap replications. Examination by microscopy showed the presence of Polymyxa-like spores in numerous root hairs (but not the main root) of all five Arabidopsis ecotype Ler-0 plants grown in the Woburn soil (Fig. 1). Two of the Col-0 plants grown in the Woburn soil contained structures that resembled Polymyxa zoosporangia (Fig.

2). Three of these structures were seen in total and they were all located in the main root system rather Methocarbamol than the root hairs. No spore clusters were observed. In the root sections examined from Arabidopsis plants grown in the Wiltshire soil, no clusters of Polymyxa-like resting spores or zoosporangia were identified. PCR with the Polymyxa-specific primers Pxfwd1/Pxrev7 demonstrated the presence of Polymyxa spp. in the roots of all four combinations of Arabidopsis ecotypes and soils (Fig. 3). Using a Plasmodiophora-specific PCR assay, we also demonstrated that Plasmodiophora was not present in these samples (Fig. 3). A total of 28 clones were sequenced following the amplification of rDNA products from Arabidopsis roots using primers Pxfwd1/ITS4.