Additional file 2 of Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China
Creators: name: Liang, Jie-Liang
name: Feng, Shi-wei
name: Jia, Pu
name: Lu, Jing-li
name: Yi, Xinzhu
name: Gao, Shao-ming
name: Wu, Zhuo-hui
name: Liao, Bin
name: Shu, Wen-sheng
name: Li, Jin-tian
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Supplementary Material 2: Supplementary Figure S1. Length distributions of NCLDV polB sequences recovered from this study (a) and from Tara Oceans (b). The pie charts shown in the insets denote the percentages of polB sequences ≥ 1 kb and &lt; 1 kb. The polB sequences from Tara Oceans were obtained from Endo et al. [1]. Supplementary Figure S2. Sample-size dependence of the observed NCLDV phylotypes in this study. Sample-based rarefaction curves showing accumulated richness of NCLDV polB genes detected in individual habitat types. Supplementary Figure S3. Relationships between environmental ranges of individual NCLDV phylotypes and the numbers of sampling sites where they occurred (a) or the total abundances of individual phylotypes in all sampling sites (b). Each dot in each panel denotes a NCLDV phylotype. The color intensity of a given dot represents the number of habitat types where that NCLDV phylotype could be recovered. The solid red lines represent the linear regression models with statistically significant Pearson coefficients (P &lt; 0.001). The total abundance of each phylotype and environmental range in (b) are normalized by logarithm. Supplementary Figure S4. Correlations between average abundances of the NCLDV phylotypes belonging to individual families and the numbers of sampling sites where the corresponding phylotypes could be detected. Each dot in each panel denotes a NCLDV phylotype. The color intensity of a given dot represents the number of habitats where that NCLDV phylotype could be recovered. The solid red lines represent the linear regression with statistically significant Pearson coefficients (P &lt; 0.01). The phylotypes affiliated with Phycodnaviridae and Prasinoviridae were excluded for analysis due to the limited number of sampling sites (n &lt; 3) where these phylotypes could be detected. Supplementary Figure S5. Variable clustering for assessment of the environmental variable redundancy. Environmental variables with Spearman r2 &gt; 0.7 are excluded from subsequent analyses. LAT, latitude; ALT, altitude; MAP, mean annual 66 precipitation; EC, electrical conductivity; EX-Ca, exchangeable calcium; CEC, cation exchange capacity; TC, total carbon; TN, total N; TP, total P; TK, total K. Supplementary Figure S6. Relationships between selected environmental factors and NCLDV phylotype richness in individual habitat types. Colors of dots in each panel represent habitat types. Each dot represents one soil sample. The solid blue lines represent the linear regression with statistically significant Pearson coefficients. The solid red curves represent the polynomial fit determined on the basis of the corrected Akaike Information Criterion (AIC). Abbreviations are as those in Supplementary Figure S4. Supplementary Figure S7. Relative similarity of all samples in NCLDV community composition. (a) Non-metric multidimensional scaling (NMDS) ordination biplot showing the relative similarity of all samples. Samples are grouped and color-coded by habitat types. All groups are significantly different from each other as analyzed using Adonis (P = 0.001). (b) Results of multilevel pairwise comparison between habitat types. It was performed by pairwise.adonis from the package “pairwiseAdonis”. Supplementary Figure S8. The distance–decay relationships for soil NCLDV communities in individual habitat types. Pairwise NCLDV community dissimilarity (Bray–Curtis) significantly increases with pairwise geographic distance in the five habitat types: farmland (a), forest (b), grassland (c), Gobi desert (d) and mine wasteland (e). Supplementary Figure S9. The co-occurrence networks of NCLDVs–eukaryotes in different habitat types. Those NCLDV phylotypes and eukaryotic amplicon sequence variants (ASVs) that were present in ≥ 10% of all soil samples for each habitat type were included in our co-occurrence network analysis. Triangles represent eukaryotic ASVs and circles represent NCLDV phylotypes. The sizes of triangles and circles are proportional to the number of connections. Significant Spearman correlation coefficients (ρ ≥ 0.60, P &lt; 0.05) for NCLDVs-eukaryotes pairs are drawn as edges. Supplementary Figure S10. The co-occurrence networks of the 14 ubiquitous NCLDVs across four or five habitat types and eukaryotic ASVs. Triangles represent eukaryotic ASVs and circles represent NCLDV phylotypes. Significant Spearman correlation coefficients (ρ ≥ 0.60, P &lt; 0.05) for NCLDV-eukaryote pairs are drawn as edges. Supplementary Figure S11. The maximum-likelihood phylogenetic tree of giant virus metagenome-assembled genomes (GVMAGs) reconstructed in this study and available in public databases [2]. The tree was built from a concatenated protein alignment of seven marker genes (SFII, RNAPL, PolB, TFIIB, TopoII, A32 and VLTF3) using the model of LG + I + F + G4 and rooted at Poxviridae [2]. Tree branches are colored according to the order-level taxonomic assignment. The GVMAGs recovered from this study are labeled in red background. The outer strip is colored according to the family level taxonomic assignment. SFII, DEAD/SNF2-like helicase; RNAPL, DNA directed RNA polymerase alpha subunit; PolB, DNA polymerase family B; TFIIB, transcription initiation factor IIB; TopoII, DNA topoisomerase II; A32, Packaging ATPase; VLTF3, Poxvirus late transcription factor VLTF3. Supplementary Figure S12. The pH-relevant distribution profiles of the numbers of phylotypes belonging to individual NCLDV families. The color intensity of a given grid is proportionate to the number of NCLDV phylotypes belonging to a specific family that can be observed in a given pH range. Given that some phylotypes can occur in a wide range of soil pH, the sum of the numbers shown in the figure is greater than the total number of the NCLDV phylotypes identified in this study. Supplementary Figure S13. Relationships between and the number of NCLDV polB genes detected in individual samples and sequencing depth. Each dot in each panel represents one soil sample. The solid red lines represent the linear regression with statistically significant Pearson coefficients.