Cyanophage lysis of the cyanobacterium Nodularia spumigena affects the variability and fitness of the host-associated microbiome
Creators: name: Šulčius, Sigitas
name: Alzbutas, Gediminas
name: Lukashevich, Valiantsin
Publisher: name: Zenodo
Year: 2025
Subjects: Cyanophage
Aquatic virus ecology
Baltic Sea
Nodularia spumigena
Microbiome
microbial ecology
harmful algal blooms

description: Supplemental Files

Figure S1. Design of the cyanophage amendment experiment and schematic representation of the analyses conducted.

Figure S2. Blast results of putative plasmids (bin.6_contog_507, bin.6_contog_750, bin.6_contog_985) identified in the genome of Nodularia spumigena.

Figure S3. Elements of CRISPR-Cas systems identified in the genome of Nodularia spumigena.

Figure S4. Representation of the highly compact region of cyanophage genes in the genome of Nodularia spumigena strain KAC68.

Figure S5. Amino acid sequence-based phylogenetic tree reconstruction of large terminase (TerL) subunit. Blue labels indicate bacteriophages infecting various heterotrophic bacteria hosts, while green labels indicate bacteriophages infecting cyanobacteria. Cluster of cyanophages infecting Nodularia spumigena is coloured in yellow. DNA packaging mechanisms is indicated for some bacteriophages.

Figure S6. Adsorption curve of the cyanophage Ravarandavirus kac68v161 to Nodularia spumigena strain KAC68 cells (a) and changes in the proportion of adsorbed cyanophages during first 6 hours post inoculation (b).

Figure S7. Gene enrichments in heterotrophic bacteria comprising the microbiome of Nodularia spumigena strain KAC68. Only terms with adjusted p - values calculated using the Benjamini-Hochberg procedure (p_fdr_bh) < 0.01 are shown. Commonly purified terms detected as purified in more than 70% of non-N. spumigena bins are not shown (e.g., GO terms related to photosynthesis). The terms' names are arranged based on the matching GO ID. The bins on the x-axis are arranged from left to right based on the decreasing number of significant differences. Red color denotes enrichment of a term, while cyan color denotes purification of a term. The dot size denotes the p - value.

Figure S8. Representation of horizontal gene transfer (HGT) between bacteria. A) searched against NCBI database (accessed April 2024); B) search only between bacteria within N. spumigena microbiome.

Figure S9. The ANOVA results indicating effect of cyanophage infection on the variance of N. spumigena abundance between different MOI treatments (A), and changes in p values derived from multiple post hoc Tukey’s test comparison representing significant differences in timing of N. spumigena cell lysis between different treatment pairs (B). Signif.:  0.001<***,  0.01<**, 0.05<*.

Table S1. Functional annotation of N. spumigena genome.

Table S2. Putative anti-phage defense systems identified in N. spumigena KAC68 genome using DefenseFinder and TAfinder tools.

Table S3. Putative CRISPR-Cas arrays identified in N. spumigena KAC68 genome using CRISPRCasTyper tool.

Table S4. Assembly statistics, classification and general features of genomes recovered from N. spumigena culture.

Table S5. List of prophage-like regions (>30Kb) in N. spumigena-associated bacteria genomes identified with PHASTEST prophage finder tool.

Table S6. Predicted ORFs from the genome of Nodularia phage vB_NspS-kac68v162 (NACBI Accession No. MK605246) with identified putative homologues and functions in other organisms.

Table S7. Gene enrichments in Nodularia spumigena microbiome.

Table S8. Genes encoding reactions associated with riboflavin biosynthesis and metabolism identified in the genomes of heterotrophic bacteria comprising N. spumigena microbiome.

Table S9. Putative horizontally transferred genes between bacteria of N. spumigena microbiome and bacterial genomes availible in the NCBI database (accessed April 2024).

Table S10. Putative horizontally transferred genes within N. spumigena microbiome.

Table S11. Results of PERMANOVA and db-RDA analyses comparing N. spumigena-associated bacterial consortium composition between control and different inital MOI treatments.