Supplementary Material 1: Supplementary Table S1. Detailed information of the sampling sites of this study and their corresponding environmental factors. Supplementary Table S2. Information on metagenomics data used in this study. Supplementary Table S3. PolB sequences used to benchmark our phylogenetic mapping approach (as per Kazlauskas et al. [31]). Supplementary Table S4. Selected detailed information on the soil NCLDV phylotypes identified in this study. Supplementary Table S5. Taxonomic affiliations of marine NCLDV phylotypes identified in a previous study (Endo et al. [17]). Supplementary Table S6. Detailed information of soil NCLDV-eukaryote pairs in the co-occurrence networks shown in Supplementary Figure S9. Supplementary Table S7. Detailed information on giant virus metagenome-assembled genomes recovered in this study. Supplementary Table S8. Functional annotation of giant virus metagenome-assembled genomes recovered in this study. Supplementary Table S9. Reported NCLDVs-eukaryotes relationships in the references.

Supplementary Material 1: Supplementary Table S1. Detailed information of the sampling sites of this study and their corresponding environmental factors. Supplementary Table S2. Information on metagenomics data used in this study. Supplementary Table S3. PolB sequences used to benchmark our phylogenetic mapping approach (as per Kazlauskas et al. [31]). Supplementary Table S4. Selected detailed information on the soil NCLDV phylotypes identified in this study. Supplementary Table S5. Taxonomic affiliations of marine NCLDV phylotypes identified in a previous study (Endo et al. [17]). Supplementary Table S6. Detailed information of soil NCLDV-eukaryote pairs in the co-occurrence networks shown in Supplementary Figure S9. Supplementary Table S7. Detailed information on giant virus metagenome-assembled genomes recovered in this study. Supplementary Table S8. Functional annotation of giant virus metagenome-assembled genomes recovered in this study. Supplementary Table S9. Reported NCLDVs-eukaryotes relationships in the references.

Additional file 2: Dataset 1. Information for 162 sequenced cyanobacteria strains from FACHB. Dataset 2. Genomic information for 647 high-quality phycospheric heterotrophic bacterial bins. Dataset 3. Information of 128 high-quality phycospheric heterotrophic bacterial bins that encode C-P lyase gene clusters and their NCBI accession numbers. Dataset 4. Information and environmental parameters of bloom water samples used in this study from Taihu Lake and Dianchi Lake. Dataset 5. Information regarding 22 phosphonate catabolizing phycospheric heterotrophic bacterial isolates and NCBI accession numbers of 16s rDNA and phnJ genes. Dataset 6. Reports of phosphonate and phosphate concentrations from previous published studies.

Additional file 2: Dataset 1. Information for 162 sequenced cyanobacteria strains from FACHB. Dataset 2. Genomic information for 647 high-quality phycospheric heterotrophic bacterial bins. Dataset 3. Information of 128 high-quality phycospheric heterotrophic bacterial bins that encode C-P lyase gene clusters and their NCBI accession numbers. Dataset 4. Information and environmental parameters of bloom water samples used in this study from Taihu Lake and Dianchi Lake. Dataset 5. Information regarding 22 phosphonate catabolizing phycospheric heterotrophic bacterial isolates and NCBI accession numbers of 16s rDNA and phnJ genes. Dataset 6. Reports of phosphonate and phosphate concentrations from previous published studies.

Additional file 1: Table S1 Biotic and abiotic data for the tailings samples from the Fankou Pb/Zn Mine located in Guangdong Province, P.R. China. Table S2 Detailed information of viral sequences identified in the tailings samples. Table S3 Normalized coverage and taxonomic affiliation of the viral OTUs (vOTUs) identified in the tailings samples. Table S4 16S rRNA gene OTU table and taxonomy of the prokaryotes in the tailings samples. Table S5 Virus-host linkages predicted by prophages and shared genomic matches with host genomes and by protospacer-spacer matches. Table S6 Detailed functional and taxonomic descriptions of viral genes predicted with viral sequences identified in the tailings samples. Indicator COGs in the surface and deeper mine tailings are shown in red and blue, respectively. Table S7 Normalized coverage and functional description of indicator COGs in the surface tailings (red) and deeper layers (blue). Table S8 Detailed information of predicted viral sequences encoding indicator COGs in the surface tailings (red), deeper layers (blue), and both communities (black). Table S9 Detailed functional description and sequence information of the seven viral genomes containing genes involved in assimilatory sulfate reduction (COG0175). Table S10 Homologs of assimilatory sulfate reduction genes (COG0175) and corresponding taxonomy recruited from eggNOG v5.0.0 database.

Additional file 1: Table S1 Biotic and abiotic data for the tailings samples from the Fankou Pb/Zn Mine located in Guangdong Province, P.R. China. Table S2 Detailed information of viral sequences identified in the tailings samples. Table S3 Normalized coverage and taxonomic affiliation of the viral OTUs (vOTUs) identified in the tailings samples. Table S4 16S rRNA gene OTU table and taxonomy of the prokaryotes in the tailings samples. Table S5 Virus-host linkages predicted by prophages and shared genomic matches with host genomes and by protospacer-spacer matches. Table S6 Detailed functional and taxonomic descriptions of viral genes predicted with viral sequences identified in the tailings samples. Indicator COGs in the surface and deeper mine tailings are shown in red and blue, respectively. Table S7 Normalized coverage and functional description of indicator COGs in the surface tailings (red) and deeper layers (blue). Table S8 Detailed information of predicted viral sequences encoding indicator COGs in the surface tailings (red), deeper layers (blue), and both communities (black). Table S9 Detailed functional description and sequence information of the seven viral genomes containing genes involved in assimilatory sulfate reduction (COG0175). Table S10 Homologs of assimilatory sulfate reduction genes (COG0175) and corresponding taxonomy recruited from eggNOG v5.0.0 database.