Binarisation of the images was undertaken using a modified auto-threshold (where the overflow value was set as 48%), since the default settings did not satisfactorily separate the soil solids from the pore space. No binary filters were applied to these images since no improvement to the previously acquired images were observed. From processed

binary images measurements of the overall image porosity, the individual pore size (area) and the distribution of pores (nearest neighbour statistics) were determined and expressed as an average of the 6 slices. All analyses were conducted using GenStat Release 13.1 (Lawes Agricultural Trust). Analysis of variance (ANOVA) was performed on data using soil dilution (10−1 and 10−6), planting regime (defined as either bare soil, planted non-mycorrhizal or planted mycorrhizal) PLX4032 nmr selleck chemical and harvest time (month) as factors. Data for pore size and nearest neighbour distance were analysed by

repeated measures ANOVA. Data were transformed where appropriate. TRF richness was determined from the number of peaks. Principal Components Analysis (PCA) was carried out on T-RFLP data that had been transformed into relative abundance data. Here, the peak height for each individual TRF was divided by the cumulative value for each sample. The covariance matrix was used on these normalised data as recommended by Culman et al. (2008) with principal component (PC) scores analysed by ANOVA. General Amoxicillin linear regressions were performed on biological measurements to determine which factors contributed to the soil physical parameters. In GenStat ‘all possible models’ were fitted and evaluated using Akaike and adjusted R2 values. This enabled more than one explanatory model to be selected if

appropriate. In the planted macrocosms, root biomass significantly increased each month (month as a single factor in ANOVA, F3,37 = 70.50, P < 0.001) whilst shoot growth only increased up to the third month and thereafter remained constant apart from a slight decrease in month seven (month as a single factor, F3,37 = 27.07, P < 0.001, Fig. 1). Root to shoot ratio remained constant in months 1 and 3 (mean ratios 0.4 and 0.3 respectively) but increased in months 5 and 7 (1.98 and 2.58 respectively; month as a single factor, F3,37 = 51.49, P < 0.001, LSD = 0.45) reflecting the difference in root and shoot biomass at these harvest points. Arbuscular mycorrhizal colonisation significantly reduced both root (AM colonisation as a single factor, F1,37 = 12.51, P = 0.001) and shoot (F1,37 = 13.93, P < 0.001) biomass but did not affect root/shoot ratio. Whole plant dry weight was 7.34 g in the absence of AMF and 5.00 g in the presence of inoculum (F1,37 = 14.