Genetic Diversity and Cooccurrence Patterns of Marine Cyanopodoviruses and Picocyanobacteria

Abstract

Picocyanobacteria Prochlorococcus and Synechococcus are abundant in the global oceans and subject to active viral infection. In this study, the genetic diversity of picocyanobacteria and the genetic diversity of cyanopodoviruses were synchronously investigated along water columns in the equatorial Indian Ocean and over a seasonal time course in the coastal Sanya Bay, South China Sea. Using the 16S-23S rRNA internal transcribed spacer (ITS)-based clone library and quantitative PCR (qPCR) analyses, the picocyanobacterial community composition and abundance were determined. Sanya Bay was dominated by clade II Synechococcus during all the seasons, and a typical population shift from high-light-adapted Prochlorococcus to low-light-adapted Prochlorococcus was found along the vertical profiles. Strikingly, the DNA polymerase gene sequences of cyanopodoviruses revealed a much greater genetic diversity than we expected. Nearly one-third of the phylogenetic groups were newly described here. No apparent seasonal pattern was observed for the Sanya Bay picocyanobacterial or cyanopodoviral communities. Different dominant cyanopodovirus lineages were identified for the coastal area, upper euphotic zone, and middle-to-lower euphotic zone of the open ocean. Diversity indices of both picocyanobacteria and cyanopodoviruses were highest in the middle euphotic zone and both were lower in the upper euphotic zone, reflecting a host-virus interaction. Cyanopodoviral communities differed significantly between the upper euphotic zone and the middle-to-lower euphotic zone, showing a vertical pattern similar to that of picocyanobacteria. However, in the surface waters of the open ocean, cyanopodoviruses exhibited no apparent biogeographic pattern, differing from picocyanobacteria. This study demonstrates correlated distribution patterns of picocyanobacteria and cyanopodoviruses, as well as the complex biogeography of cyanopodoviruses.IMPORTANCE Picocyanobacteria are highly diverse and abundant in the ocean and display remarkable global biogeography and a vertical distribution pattern. However, how the diversity and distribution of picocyanobacteria affect those of the viruses that infect them remains largely unknown. Here we synchronously analyzed the community structures of cyanopodoviruses and picocyanobacteria at spatial and temporal scales. Both spatial and temporal variations of cyanopodoviral communities can be linked to those of picocyanobacteria. The coastal area, upper euphotic zone, and middle-to-lower euphotic zone of the open ocean have distinct cyanopodoviral communities, showing horizontal and vertical variation patterns closely related to those of picocyanobacteria. These findings emphasize the driving force of host community in shaping the biogeographic structure of viruses. Our work provides important information for future assessments of the ecological roles of viruses and hosts for each other.

Keywords: DNA polymerase; community composition; cyanophages; cyanopodoviruses; picocyanobacteria.

FIG 1

Hydrographic features (A, B, E, F, I, and J) and abundances of Prochlorococcus (C, G, and K) and Synechococcus (D, H, and L) ecotypes at Indian Ocean stations I205 (A to D) and I211 (E to H) and Sanya Bay station W4 (I to L). Hydrographic parameters include concentrations of macronutrients and chlorophyll a, fluorescence intensity, water temperature, and water density (σ_T). The mixing layer depth is indicated by gray dashed lines. Abundances of 14 Prochlorococcus and Synechococcus ecotypes and total bacteria (16S rRNA gene copies) were measured, but only the detectable ecotypes are shown. Pink dashed lines (C, D, G, H, K, and L) indicate summed ecotype abundance. Note that, in panel L, the black line representing Synechococcus clade II overlaps the pink line representing total Synechococcus.

FIG 2

Clustering of the samples on the basis of compositions of ITS (A) and pol sequences (B). OTU was defined at a cutoff of 90% DNA sequence similarity for both ITS and pol. ANOSIM was used to test the significance of the grouping, which is indicated by light blue shading in the clustering dendrograms. Phylotype-based community composition of each sample is shown to the right of the dendrograms. Spearman correlation coefficient (Mantel test) that reflects the relationship between picocyanobacterial and cyanopodoviral communities is shown below the chart. “Other LL” Prochlorococcus does not represent a real clade but is comprised of other sequences that cannot be assigned to any known LL lineages.

FIG 3

Maximum likelihood phylogenetic trees based on the viral DNA polymerase protein sequence of cyanopodoviruses. Trees for the MPP-A cluster (A) and the MPP-B cluster (B) were built independently. Environmental sequences obtained in this study are labeled in the format “representative sequence identifier (ID) OTU (no. of sequences assigned to the OTU).” Bootstrap values for 100 sampling replicates are listed only for those higher than 50%. Reference sequence shown in green is from phage isolates infecting Prochlorococcus, those in blue are from phage isolates infecting Synechococcus, and those in black are from environmental clones or from the Global Ocean Sampling metagenomes. Percentages of sequences assigned to each of the genotypes are listed to the right. Genotype labels are according to the numbering by Dekel-Bird and colleagues (30). Genotypes labeled in red indicate those defined in this study, and red star symbols indicate those newly detected here.

FIG 3

Maximum likelihood phylogenetic trees based on the viral DNA polymerase protein sequence of cyanopodoviruses. Trees for the MPP-A cluster (A) and the MPP-B cluster (B) were built independently. Environmental sequences obtained in this study are labeled in the format “representative sequence identifier (ID) OTU (no. of sequences assigned to the OTU).” Bootstrap values for 100 sampling replicates are listed only for those higher than 50%. Reference sequence shown in green is from phage isolates infecting Prochlorococcus, those in blue are from phage isolates infecting Synechococcus, and those in black are from environmental clones or from the Global Ocean Sampling metagenomes. Percentages of sequences assigned to each of the genotypes are listed to the right. Genotype labels are according to the numbering by Dekel-Bird and colleagues (30). Genotypes labeled in red indicate those defined in this study, and red star symbols indicate those newly detected here.

FIG 4

Alpha diversity and beta diversity of ITS and pol clone libraries. Previously published ITS and pol clone libraries from the Chesapeake Bay surface water samples (CB0205-858, CB0205-804, CB0205-707, CB0705-858, CB0705-804, and CB0705-707) (41, 54) and the Atlantic and Pacific surface ocean samples (UTK202, UTK211, UTK220, UTK229, UTK240, UTK250, UTK255, and UTK262) (40, 52) were compared to those derived here. (A) Locations of the samples are shown. The map was created using Ocean Data View, version 4. Alpha diversity Chao indices (B) and Shannon indices (C). Pearson correlation analysis results that indicate the relationship between diversity levels of picocyanobacteria and cyanopodoviruses are listed under the bar charts. Nonmetric multidimensional scaling (nMDS) plot based on compositions of ITS (D) and pol (E) OTUs. The inset plot in panel D covers all the 32 samples, and the outside plot shows the detailed relationship of a portion of 29 samples (dashed box in the inset plot). ANOSIM was used to test the significance of grouping, and the Mantel test (Spearman correlation) was used to assess the correlation between picocyanobacterial and cyanopodoviral communities. Coefficients (global R and ρ) and P values are shown.