Figure 1.
In silico comparison of the primer sets nu-SSU-0817/nu-SSU-1196, FR1/FF390, nssu1088R-SR2 and nssu897R-nu-SSU-1196 for their fungal-specificity.
For each primer set, k mismatches (0 to 3) were allowed in the in silico analysis to test the specificity of the original primer set (k = 0) and its potential sequence improvement (k = 1 to 3). For each graph, each bar represents the hit frequency (%) of the primer set for the selected phylum with: k = 0: black, k = 1: dark grey, k = 2: white, k = 3: light grey. The number of sequences available for a phylum is indicated in brackets. Detailed hit frequencies are provided in Table S1.
Table 1.
Physico-chemical characteristics of the soil samples used for in vitro validation of the FR1/FF390 primer set.
Figure 2.
Threshold cycle against DNA quantity in the PCR mix for five soil DNA extracts with serial dilution.
DNA quantities are represented in logarithmic scale and correspond to a serial dilution series (10 ng, 5 ng, 2.5 ng, 1 ng, and 0.5 ng). The linear regressions were highly significant (r2>0.99) for each soil type. The equations of the regression line were for each soil sample: 858: y = −3.61x+29.86; 1012: y = −3.24x+31.06; 1051: −3.60x+31.84; 1101: y = −4.47x+29.55; 1143: y = −4.37x+30.94.
Figure 3.
Variation coefficient of 18S rRNA gene copy number with DNA quantity in the PCR mix for five soil DNA extracts with serial dilution.
The box limits represent the first and third quartiles of the variation coefficient (CV), the bold line represents the median and the error bars represent the standard deviation. Empty circles correspond to the minimum and maximum of the CV. The CV for each soil was determined from 3 independent measurements.
Figure 4.
Distribution of clones obtained by the cloning-sequencing approach in the different fungal phyla.
Symbols indicate the soil of origin of the clone: ♣: 858, ♦: 1012, ♥: 1051, ♠: 1101, •: 1143. *: Non fungal reference sequences. Genbank accession numbers of clones and their respective affiliation are provided in Table S2. Accession numbers of the non fungal reference sequences are provided in Table S3.
Table 2.
Physico-chemical characteristics and land-use of the soil samples used for ecological validation of the FR1/FF390 primer set combined with a real-time Q-PCR approach.
Figure 5.
Variations of 18S rRNA gene copy number with land use type for 24 soil samples.
Each dot represents the average 18S rRNA gene copy number for one soil sample. Cross and horizontal bars represent the mean and median 18S rRNA gene copy number for the land use type, respectively. Superscript letters indicate significant differences in copy numbers between land use (P<0.05).
Table 3.
Pearson's correlation coefficients of 18S copy number and physico-chemical parameters.