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Table 2 Permutational multivariate ANOVA results with Bray–Curtis distance matrices implemented to partition sources of variation in this study (niche, genotype, interaction between niche and genotype (N × G)) for both archaeal/bacterial and fungal communities. Leaves, stems, roots, and soil communities were analyzed separately; therefore, habitat effects refer to finer-scale niches within these respective broad habitat categories. Statistical significance (P(perm)) was computed based on sequential sums of squares from 9999 permutations

From: The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

Community

Habitat

Source of variation

SS

MS

R 2

Pseudo-F

P(perm)

Bacteria

Leaves

Niche

78,980

8775.6

0.29

5.0

0.0001

Genotype

26,849

26,849

0.10

15.2

0.0001

N × G

37,557

4173

0.14

2.4

0.0001

Residuals

125,080

1761.7

0.46

  

Total

272,940

 

1.00

  

Fungi

Leaves

Niche

48,697

6087.1

0.21

5.6

0.0001

Genotype

72,650

72,650

0.32

66.9

0.0001

N × G

29,836

3729.5

0.13

3.4

0.0001

Residuals

73,840

1085.9

0.32

  

Total

229,760

 

1.00

  

Bacteria

Stem

Niche

58,966

7370.8

0.31

5.4

0.0001

Genotype

19,362

19,362

0.10

14.3

0.0001

N × G

20,049

2506.2

0.10

1.8

0.0001

Residuals

92,356

1358.2

0.48

  

Total

191,000

 

1.00

  

Fungi

Stem

Niche

90,054

11,257

0.36

7.0

0.0001

Genotype

22,613

22,613

0.09

14.0

0.0001

N × G

21,776

2722

0.09

1.7

0.0001

Residuals

114,460

1612.1

0.46

  

Total

249,640

 

1.00

  

Bacteria

Roots

Niche

81,253

13,542

0.39

6.9

0.0001

Genotype

6752.2

6752.2

0.03

3.4

0.0001

N × G

13,966

2327.6

0.07

1.2

0.0213

Residuals

106,410

1970.6

0.51

  

Total

210,180

 

1.00

  

Fungi

Roots

Niche

53,637

8939.5

0.20

2.8

0.0001

Genotype

9286

9286

0.04

2.9

0.0001

N × G

23,063

3843.8

0.09

1.2

0.0183

Residuals

177,350

3167

0.67

  

Total

263,340

 

1.00

  

Bacteria

Soil

Niche

41,055

13,685

0.51

18.9

0.0001

Genotype

8807.4

8807.4

0.11

12.2

0.0001

N × G

7020.7

2340.2

0.09

3.2

0.0001

Residuals

23,182

724.5

0.29

  

Total

80,066

 

1.00

  

Fungi

Soil

Niche

28,882

9627.3

0.31

5.9

0.0001

Genotype

8470.1

8470.1

0.09

5.2

0.0001

N × G

8920.8

2973.6

0.10

1.8

0.0001

Residuals

45,882

1638.6

0.50

  

Total

92,296

 

1.00