Table 1. Experimental design and numbers of replicates per DNA sample across experimental setups.
Experimental setup comparing bacterial community composition under natural growth conditions (‘soil type and environment’ experiments), prolonged residence time of plants in soil (‘time-course’ experiment) and on three different plant species (‘diversification’ experiment). The first two columns characterize the tested compartment, host plant and plant genotype. The numbers indicate the number of sequenced DNA samples. ‘Soil type and environment’ experiment: Plants were grown in Cologne soil (CS) or French soil (FS) under controlled environmental conditions (C) or in their native habitat in France (N). ‘Time course’ experiment: A. alpina plants were grown under controlled environmental conditions in Cologne soil for 6, 12 and 28 weeks. ‘Diversification’ experiment: A. alpina, C. hirsuta and A. thaliana were grown under controlled environmental conditions in Cologne soil for 6 weeks. Indicated are the number of independent biological replicates (rep1-rep3), the soil type used for growing plants (see also Supplementary Tables S3-S4), the harvest date of the soil, the environmental conditions used for plant growth and the employed sequencing technology. n.d.: not determined. * Represents the same DNA samples that were processed with both 454 and Illumina sequencing technologies. w: weeks.
| Soil type and environment | Time course | Diversification | 454 vs. Illumina | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compartment | Host plant | CS-C | FS-C | FS-N | 6 weeks | 12 weeks | 28 weeks | |||||||
| rep1 | rep2 | rep1 | rep2 | rep1 | rep2 | rep1 | rep2* | rep3 | rep2* | |||||
| Soil | - | 4 | 4 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| Rhizosphere | A. alpina (Paj) | 4 | 5 | - | 3 | 3 | 4 | 4 | 4 | 4 | - | - | - | - |
| A. alpina (pep1) | - | - | - | 3 | 3 | 4 | 4 | 4 | 4 | - | - | - | - | |
| A. alpina (Gal5) | - | 5 | - | - | - | - | - | - | - | - | - | - | - | |
| A. alpina (Gal60) | - | 5 | 5 | - | - | - | - | - | - | - | - | - | - | |
| Root | A. thaliana (Col-0) | - | - | - | - | - | - | - | - | - | 3 | 3 | 3 | 3 |
| C. hirsuta (Ox) | - | - | - | - | - | - | - | - | - | 3 | 3 | 3 | 2 | |
| A. alpina (Paj) | 4 | 5 | - | 3 | 3 | 4 | 4 | 4 | 4 | 3 | 3 | 3 | 3 | |
| A. alpina (pep1) | - | - | - | 3 | 3 | 4 | 4 | 4 | 4 | - | - | - | - | |
| A. alpina (Gal5) | - | 5 | - | - | - | - | - | - | - | - | - | - | - | |
| A. alpina (Gal60) | - | 5 | 5 | - | - | - | - | - | - | - | - | - | - | |
| Soil type | Cologne | France | Cologne | Cologne | Cologne | |||||||||
| Residence time | 12w | 12w | n.d. | 6w | 6w | 12w | 12w | 28w | 28w | 6w | 6w | 6w | 6w | |
| Harvest date soil | Spring-13 | Fall-12 | Spring-13 | Fall-13 | Spring-13 | Fall-13 | Spring-13 | Fall-13 | Fall-10 | Spring-13 | Fall-13 | Spring-13 | ||
| Environmnent | Controlled | Native | Controlled | Controlled | Controlled | |||||||||
| Seq. technology | Illumina | Illumina | 454 | Illumina | ||||||||||