Article Figures & Data
Figures
- FIG 1
Neighbor-joining topology showing sequence relationships for selected Frankia strains and uncultured endophytes in root nodules to demonstrate Frankia cluster assignments. Numbers above the branches represent the bootstrap values from maximum likelihood (1,000 replicates)/neighbor-joining (10,000 replicates) bootstrap analyses for clades with >50% bootstrap support. Support values less than 50% are indicated by a dash. These two phylogenetic criteria resolved generally similar topologies. The bar chart shows the percentage of nodules assigned to known Frankia strains per host plant (green, S. argentea; blue, A. glutinosa; orange, A. cordata; yellow, C. equisetifolia).
- FIG 2
Sybr green-based qPCR quantification of specific Frankia clusters in soils vegetated with host trees (Alnus glutinosa, Alnus cordata, Alnus viridis, Casuarina equisetifolia, Shepherdia argentea, and Hippophaë rhamnoides) or nonhost trees (Betula pendula). A control was kept nonvegetated. Quantification used nifH gene fragments as a target for the detection of clusters 1 and 3 (top) or 23S rRNA gene fragments generated with primer combinations for the detection of the genus Frankia (i.e., all clusters) (center) or with primer combinations specific for clusters 1a/d, 1b, 1c, 1e, 2, 3, and 4 (with results presented as the sum of the individual clusters and subgroups detected). Only frankiae of clusters 1b, 1e, and 3 were detected in these soils; the remaining clusters and subgroups remained undetected.
- FIG 3
(Top) Numbers of reads representing Frankia-specific nifH gene fragments obtained by Illumina sequencing of DNA extracts from soils vegetated with host trees (Alnus glutinosa, Alnus cordata, Alnus viridis, Casuarina equisetifolia, Shepherdia argentea, and Hippophaë rhamnoides) or nonhost trees (Betula pendula). A control was kept nonvegetated. (Bottom) Quantification of the major specific reads that were present in the majority of samples. These reads combined generally represented >90% of all reads obtained (except for A. cordata [78.1%]) and S. argentea [(85.4%]). The results revealed that most reads represented Frankia populations of cluster 3, and only a few represented those of cluster 1e, while reads representing other clusters were either absent or present in numbers below 1%.
Tables
- TABLE 1
Similarity of Frankia-specific nifH reads from soil microcosms to sequences of uncultured frankiae in root nodules of different plant species grown in these soils and to sequences of closest Frankia isolates or clones
Frankia-specific nifH read from soil microcosm Similarity (%) to sequences in the following species (sample): % similarity to closest Frankia sequence (sequence designation) Cluster assignment Shepherdia argentea Casuarina equisetifolia (T1P2-1) Alnus glutinosa Alnus cordata T2P1-7 T1P2-2 T1P1-2 T1P1-10 T1P1-24 T1P3-26 T1P3-1 T1P1-11 T1P1-8 T1P1-1 RPMa 5797 97.7 98.1 (Cc1.17) 3 34873 95.8 96.7 (BMG5.15) 3 101236 100 96.7 (EUN1f) 3 147378 94.9 95.8 (G2) 3 170193 95.8 95.8 95.8 95.8 96.8 (D11) 3 10509 95.3 95.3 95.3 95.3 94.9 (EUN1f) 3 148038 100 100 100 96.4 (CFN10) 1e RPFb 139714 100 100 (EAN1pec) 3 137910 97.2 96.3 (Chl7) 3 203721 98.6 99.1 (Cc1.17) 3 115049 95.3 96.3 (G2) 3 115039 96.7 96.7 97.2 (Cc1.17) 3 114592 96.7 94.9 97.2 (Cc1.17) 3 106934 95.8 95.8 95.8 95.8 (EAN1pec) 3 221741 97.7 97.7% (G2) 3 78840 96.7 96.7 96.7 96.8 (D11) 3 75193 97.7 97.2 (Cc1.17) 3 57086 96.7 100 (EUN1f) 3 43921 96.3 96.3 (BMG5.12) 3 39637 99.1 99.1 (BMG5.12) 3 16382 95.8 95.8 95.8 95.8 95.8 96.7 (EUN1f) 3 69195 97.2 100 (ArI3) 1a 192360 96.3 96.3 96.3 96.3 (Ai7a) 1b 255602 100 100% (Japan-nodA1) 1e
