Additional file 1 of A glimpse of the paleome in endolithic microbial communities
Creators: name: Wegner, Carl-Eric
name: Stahl, Raphaela
name: Velsko, Irina
name: Hübner, Alex
name: Fagernäs, Zandra
name: Warinner, Christina
name: Lehmann, Robert
name: Ritschel, Thomas
name: Totsche, Kai U.
name: Küsel, Kirsten
Publisher: name: figshare
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Geology
subject: FOS: Earth and related environmental sciences

description: Additional file 1: Supplementary figures: Fig. S1. Pore size distribution of limestone samples with connected pore space (throats &gt;26 µm). LOD = limit of detection. Fig. S2. Pore space characteristics of sample H22-30 determined by µCT analysis. a) Moldic pores (up to large mesopores) dominate over fine fractures in the oolithic packstone. Scale: 0.5 mm. Plug diameter 13 mm. b) Vertical section shows porosity &gt;26 µm. The dashed line marks the position of c. c) Horizontal section shows a moldic pore in a gastropod fossil. d) Reconstructed pore space. Colors mark parts of the pore system connected by throats &gt;26 µm. Fig. S3. Pore space characteristics of sample KS36-H32 determined by µCT analysis. a) The packstone shows minimal alteration (Fe-mineral-stained spots, not visible). Scale: 0.5 mm. Plug diameter 13 mm. b) In the vertical section, connected pores up to ~26 µm (resolution limit) are assumed. The dashed line marks the position of c. c) Horizontal section showing the tight matrix that exhibits no pores connected by throats &gt;26 µm. Fig. S4. Pore space characteristics of sample CM1-H32 determined by µCT analysis. a) The wackestone lacks alteration. Scale: 0.5 mm. Plug diameter 13 mm. b) In the vertical section, connected pores up to ~26 µm (resolution limit) are assumed. The dashed line marks the position of c. c) Horizontal section showing the tight matrix that exhibits no pores connected by throats &gt;26 µm. Fig. S5. Pore space characteristics of sample INF-MB2 determined by µCT analysis. a) The calcareous mudstone lacks alteration. Scale: 0.5 mm. Plug diameter 13 mm. b) In the vertical section, connected pores up to ~26 µm (resolution limit) are assumed. The dashed line marks the position of c. c) Horizontal section showing the tight matrix that exhibits no pores connected by throats &gt;26 µm. Fig. S6. Pore space characteristics of sample INF-MB3 determined by µCT analysis. a) The packstone/grainstone sample lacks alteration. Scale: 0.5 mm. Plug diameter 13 mm. b) Vertical section shows minor porosity &gt;26 µm. The dashed line marks the position of c. c) Reconstructed pore space. Colors mark parts of the pore system connected by throats &gt;26 µm. Fig. S7. Number of bp and sequences before and after sequence trimming visualized as a combined box plot and violin plot. Statistical significance was tested using Wilcoxon signed-rank test. Fig. S8. Estimated coverage of metagenome data sets based on k-mer based redundancy using nonpareil [56, 111]. The dashed red line indicates 95% coverage. Fig. S9. Assembly statistics for megahit (v1.2.9) [58] and metaspades (v3.13.0) [60] assemblies. Fig. S10. DNA fragment size distribution. Fragment sizes were deduced from 100k sampled read pairs mapped onto assembled contigs (&gt; 1 kbp). Fig. S11. DNA damage pattern analysis of Cand. Rokubacteria contigs. Contigs were subsampled based on the taxonomic affiliation, which was determined with kaiju 5. Quality-controlled sequence reads were mapped onto assembled contigs (&gt; 1 kbp). The damage pattern analysis was carried out with mapdamage (v2.2.1) 6. The plots show the substitution frequency (5pCtoT [5' cytosine to thymine substitutions], 3pGtoA [3' guanine to adenine substitutions]) versus the relative position (from the 5p and 3p end). n = number of contigs &gt; 1kbp considered for the analysis, cov = mean coverage of the contigs.