Thalli before sampling. All lichen thalli were checked for infection with lichenicolous fungi and other contaminants




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Fig. S1: Lobaria pulmonaria thalli before sampling. All lichen thalli were checked for infection with lichenicolous fungi and other contaminants.



Fig. S2: Rarefaction analysis indicating species richness that can be expected in the Lobaria metagenome. The data was compared to Greengenes using standard MG-RAST terms for RNA databases.


Fig. S3: Colloidal Coomassie-stained 1D SDS-PAGE of three technical replicates T1 – T3 of proteins extracted from L. pulmonaria. The cutting of the lanes into 20 individual gel pieces is indicated by the lines.

Fig. S4. Functional assignments processed with MEGAN (v4.70.4) and SEED Subsystems analysis. SEED functions were arranged in a decreasing sequence based on the total contig count assigned to certain functions. The most prominent assignments are connected to functions involved in primary metabolism, but also to virulence-related genes, biosynthesis and transport of vitamins, cofactors, prosthetic groups and pigments as well as genes involved in stress response.


Table S1. Brief sample description and corresponding MG-RAST metagenome IDs for all datasets used in the PCoA.

Table S2. Comparison of the numbers of contigs assigned to selected functions of the lichen microbiome (described in the Results section), between Lobaria pulmonaria metagenome and Dictyochloropsis reticulata transcriptome (Transcriptome assembly downloaded from http://genome.jgi.doe.gov/Lobpulcupartners/Lobpulcupartners.info.html)



SEED function

Lobaria pulmonaria

contigs assigned (total=69,823)



Dictyochloropsis reticulata contigs assigned (total=28,072)

Number

Percentage

Number

Percentage

Ton and Tol transport systems

2,793

4.00

8

0.03

TonB-dependent receptor

2,094

3.00

0

0.00

Phosphate metabolism

885

1.27

11

0.04

Multidrug resistance efflux pumps

1,152

1.65

1

0.00

Type III, Type IV, Type VI, ESAT secretion systems

955

1.37

0

0.00

Secondary Metabolism

548

0.78

53

0.19

Stress Response

2,769

3.97

155

0.55

Oxidative stress

1,238

1.77

63

0.22

Cofactors, Vitamins, Prosthetic Groups, Pigments

3,799

5.44

258

0.92

Tetrapyrroles

1,203

1.72

107

0.38

Coenzyme B12 biosynthesis

365

0.52

3

0.01

Thiamin biosynthesis

312

0.45

11

0.04

Biotin biosynthesis

174

0.25

5

0.02

Auxin biosynthesis

156

0.22

15

0.05

Chitin and N-acetylglucosamine utilization

341

0.49

5

0.02

Protein degradation

1,000

1.43

111

0.40

Table S3. Comparison of the numbers of contigs assigned to top-level SEED functions (as depicted in Fig. S4) between Lobaria pulmonaria metagenome and Dictyochloropsis reticulata transcriptome (Transcriptome assembly downloaded from http://genome.jgi.doe.gov/Lobpulcupartners/Lobpulcupartners.info.html)

Top-level SEED functions

Lobaria pulmonaria

contigs assigned (total=69,823)



Dictyochloropsis reticulata contigs assigned

(total=28,072)



Number

Percentage

Number

Percentage

Carbohydrates

11,462

16.42

329

1.17

Virulence

8,861

12.69

70

0.25

Amino Acids and Derivatives

6,440

9.22

264

0.94

Protein Metabolism

5,481

7.85

527

1.88

DNA Metabolism

4,446

6.37

68

0.24

Cell Wall and Capsule

4,325

6.19

44

0.16

Cofactors, Vitamins, Prosthetic Groups, Pigments

3,799

5.44

258

0.92

Respiration

3,299

4.72

70

0.25

RNA Metabolism

3,248

4.65

121

0.43

Stress Response

2,769

3.97

155

0.55

Nucleosides and Nucleotides

2,761

3.95

92

0.33

Fatty Acids, Lipids, and Isoprenoids

2,721

3.90

111

0.40

Clustering-based subsystems

2,328

3.33

112

0.40

Motility and Chemotaxis

1,880

2.69

15

0.05

Metabolism of Aromatic Compounds

1,734

2.48

48

0.17

Regulation and Cell signaling

1,673

2.40

21

0.07

Cell Division and Cell Cycle

1,669

2.39

36

0.13

Membrane Transport

1,361

1.95

27

0.10

Nitrogen Metabolism

1,060

1.52

30

0.11

Phosphorus Metabolism

1,011

1.45

11

0.04

Sulfur Metabolism

836

1.20

17

0.06

Miscellaneous

767

1.10

23

0.08

Secondary Metabolism

548

0.78

53

0.19

Phages, Prophages, Transposable elements

275

0.39

7

0.02

Photosynthesis

139

0.20

27

0.10

Potassium metabolism

103

0.15

5

0.02

Dormancy and Sporulation

13

0.02

1

0.00





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