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. 2016 Aug 2;11(1):43–55. doi: 10.1038/ismej.2016.109

Table 2. Determining drivers of bacterial community assembly using CAP.

  Constrained factor Bray–Curtis
Weighted Unifrac
Unweighted Unifrac
    % P-value CI % P-value CI % P-value CI
Soil type+environment Compartmenta 31 *** 21, 48 33 *** 20, 52 36 *** 23, 64
  Environmenta 11 *** 8, 16 8.2 *** 5, 13 9.8 *** 7, 14
  Compartmentb 25 *** 15, 47 24 *** 13, 46 37 *** 19, 78
  Genotypeb 9.1 *** 7.3, 11 12 *** 8.5, 16 4.8 * 4.2, 5.5
  Compartmentc 31 *** 20, 50 39 *** 22, 67 33 *** 21, 53
  Soil typec 15 *** 9, 26 11 *** 6, 20 15 *** 10, 25
Time course Compartment 19 *** 14, 27 25 *** 17, 39 18 *** 14, 26
  Time point 9.9 *** 7.8, 13 12 *** 8.5, 18 6.6 *** 5.7, 7.8
  Soil batch 6.6 *** 4.9, 9.1 5.3 *** 3.6, 8 8.4 *** 6.6, 11
  Flowering stage 1.5 NS 1.2, 1.9 1.3 NS 1.0, 1.9 1.8 * 1.3, 2.5
  Mutant background 0.6 NS 0.4, 0.8 0.8 NS 0.5, 1.2 0.7 NS 0.5, 1.1
Diversification Compartment 21 *** 12, 37 26 *** 12, 51 18 *** 12, 31
  Soil batch 19 *** 14, 28 20 *** 12, 32 18 *** 14, 24
  Plant species 10 *** 8, 14 10 *** 7, 15 7.3 *** 6, 9

Abbreviations: CAP, constrained analysis of principal coordinates; CI, confidence interval; NS, non-significant; PERMANOVA, permutation-based analysis of variance.

Variation (in %) between samples in the ‘soil type and environment', ‘time course' and ‘diversification' experiments based on Bray–Curtis, weighted and unweighted UniFrac distances, constraining for the indicated factors. P-value based on PERMANOVA (999 permutations). *P<0.05, **P<0.01, ***P<0.001. Samples were analyzed separately according to the three different experimental setups as stated in Table 1. In addition, the ‘soil type and environment' samples were separated as follows:

a

Gal60 grown at the natural site and the greenhouse.

b

Gal60, Gal5 and Paj grown in French soil in the greenhouse.

c

Paj grown in the French and Cologne soil in the greenhouse.