Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns

Abstract

Marine viral communities harbor an astounding diversity of phages infecting diverse marine bacteria. The double-stranded DNA phage family Autographiviridae is among the most abundant phage families in the ocean. However, the current understanding of marine Autographiviridae phages is predominantly derived from isolates infecting cyanobacteria, SAR11, and Roseobacter. To achieve a more comprehensive understanding of the diversity, ecological traits, and functional profiles of this phage family, we recovered 1253 complete marine Autographiviridae uncultivated viral genomes (UViGs). Comparative genomic analysis showed that marine-derived Autographiviridae phages display genome synteny and share a conserved core of seven genes. The core gene-based phylogenomic analysis classified them into 14 groups, 6 of which were previously undescribed. These groups varied in G + C content, genome size, and presence of specific genes. Metagenomic recruitment analysis demonstrated that Autographiviridae phages are globally distributed and enriched in the upper ocean layers of tropical and temperate zones. The differential distribution patterns among these groups mirror the ecological niches of their potential hosts, emphasizing the top-down control these phages exert on their host populations. Collectively, our study substantially expands knowledge regarding the diversity, potential hosts, functional capacity, and ecological distribution of Autographiviridae phages in the ocean, emphasizing their ecological implications in marine environments.

Fig. 1. Phylogenomic analyses of all known marine Autographiviridae phage isolates, as well as Autographiviridae UViGs identified in this study.

A A maximum-likelihood phylogenetic tree was constructed using concatenated sequences. Phylogenetic inference was performed using the maximum-likelihood method implemented in IQ-TREE. Marine Autographiviridae phages were clustered into 14 groups based on the phylogeny and genome content. Shading indicates the distinct groups. Reference isolates are shown with colored dashed lines. Gray circles on the nodes indicate bootstrap values of >80%. B Boxplots showing the genome size and G + C content of each Autographiviridae group along the x-axis.

Fig. 2. Distribution of key genes identified across genomic groups.

Each row represents an Autographiviridae group (with parenthetical numbers indicating total group members), while each column corresponds to a specific gene. Color intensity reflects the proportion of gene carriers within each group, with numerical values showing detection counts for each gene in each group. PAPS Reductase: 3’-phosphoadenosine-5’-phosphosulfate reductase.

Fig. 3. Comparison of marine Autographiviridae groups.

A Comparison of genetic maps of representative Autographiviridae phages that lack the DNA polymerase (DNAP) gene from AG-1.2, AG-1.3, AG-1.4, and AG-11. Predicted open reading frames are represented by arrows and colored based on their putative functions. The scale color bar indicates amino acid identities between homologous genes. B Comparison of genetic maps of representative Autographiviridae phages that possess two RNA polymerase (RNAP) genes from AG-14 and AG-10.1. All RNAP genes are indicated in red and the additional RNAP genes are indicated with red asterisks. C Unrooted maximum-likelihood phylogenetic tree of RNAP in Autographiviridae phages. The typical Autographiviridae RNAPs (located upstream of DNA replication genes) are colored according to groups, and the additional RNAP genes in AG-10.1 and AG-14 are indicated with arrows.

Fig. 4. The biogeographic distribution of marine Autographiviridae phages across the global ocean.

A Map of the number of Autographiviridae populations detected in each virome. The size of each dot represents the number of Autographiviridae populations detected in that virome. Right: area plot showing the relationship between the population size (x-axis) and latitude (y-axis). Boxplot showing the numbers of Autographiviridae populations (y-axis) in different climate zones. B Box plots of the number of Autographiviridae populations (y-axis) detected in viromes from different ecological zones. The significance of pairwise comparisons calculated using t-test was shown with the asterisk corresponding to the p-value (*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001). C Box plots showing the number of stations (y-axis) where each Autographiviridae group was detected. The significance of pairwise comparisons was calculated using t-test and is indicated by the different letters above the boxes (p < 0.05). SRF surface, DCM deep chlorophyll maximum; MES Mesopelagic, BATHY bathypelagic.

Fig. 5. The biogeographical distribution of marine Autographiviridae phages across global ocean viromes.

A Heatmap showing the relative abundance of each Autographiviridae phage in different marine viromic datasets. The relative abundance was normalized as reads per kilobase of genome per million mapped reads (RPKM). Environmental metadata associated with each station are shown above the heatmap using color bars. Box plots showing the relative abundance of Autographiviridae phages across different oceanic zones (B), biome types (C), and depth layers (D). The significance of pairwise comparisons calculated using the two-tailed Mann–Whitney U test is indicated with asterisks corresponding to the p-value (***p < 0.001, ****p < 0.0001).

Fig. 6. The dominance of Autographiviridae groups.

A Box plot showing the relative abundance of Autographiviridae groups in marine viromes. The relative abundance of each group at each virome was calculated by summing the RPKM values of all phages in each group. Autographiviridae groups were sorted according to their median RPKM value in marine viromes. The significance of pairwise comparisons was calculated using the two-tailed Mann–Whitney U test and is indicated by the different letters above the boxes (p < 0.05). B Map of the most abundant Autographiviridae groups detected in each virome. C Barchart showing the number of stations where each group displays the highest abundance. The number of stations with the highest abundance in different environments for each group is shown.