Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

Table 1 Quality metrics of pyrosequencing analysis

A. Total number of reads and read length before and after quality checking and trimming
Total # of raw reads before QC	341,915
Average read length before QC	405 ± 96
Total # of assigned reads after QC	204,723
Average read length after QC	207 ± 4
B. Assigned reads	Rhizosphere soil	Root	Stem	Leaf
Average # of reads	5058 ± 615	5311 ± 643	2761 ± 1174	3034 ± 960
Singletons (%)	26.09 ± 0.01a	5.01 ± 0.55b	2.60 ± 0.35b	2.21 ± 0.65b
Normalization to 2000 reads per sample
C. Non-target rRNA (%)	Rhizosphere soil	Root	Stem	Leaf
Chloroplast/plastid	0	0.01 ± 0.01	0.44 ± 0.17	0.03 ± 0.02
Mitochondria	0	0	0	0
Archaea	0.03 ± 0.01	0	0	0
D. Unclassified reads	Rhizosphere soil	Root	Stem	Leaf
Reads (%)	34.07 ± 1.10a	4.74 ± 0.32b	19.05 ± 4.32b	3.59 ± 1.03b

A: Quality metrics before and after quality control (QC), the average read length was calculated based on 52 samples across all plant compartments. B: Average number of assigned reads (± standard deviation) per plant compartment and percentages of singleton reads (± standard deviation). Numbers of singletons were statistically compared using one-way ANOVA and Tukey’s Honest significant differences post hoc tests. Statistical differences at the 95% confidence interval are indicated with lowercase letters. C: Comparison of the number of non-target 16S rRNA sequences (%) co-amplified during PCR amplification. and D: Reads that could not be unambiguously classified at the phylum level (“unclassified”) (%). Each plant compartment is evaluated separately and data represent 15 biologically independent replicates (± standard deviation) for the rhizosphere soil and root endosphere samples and 11 biologically independent replicates (± standard deviation) for the stem and leaf endosphere samples

ISSN: 2049-2618