The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea

Abstract

Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.

Keywords: South China Sea; T4-like cyanophage; community assembly; g20.

Fig 1

Location of the study area in the nSCS (A). Nonmetric multidimensional scaling (NMDS) of the T4-like cyanophage community based on all g20 operational taxonomic units (OTUs) (B). Different oceanic water masses are marked in grey (CWM), red (sOWM), and blue (ssOWM), respectively.

Fig 2

Heatmap of the g20 OTUs that occurred in all the samples. The most related phage isolates are illustrated based on the most similar isolated cyanophage found using BlastN in the NCBI non-redundant database (E value < 10⁻⁵). The host range of the most related isolate is indicated as either high-light adapted Prochlorococcus (green), low-light adapted Prochlorococcus (blue), or Synechococcus (orange). The circles represent cross-infection observed within this group of hosts, whereas a dash indicates that no cross-infection has been observed.

Fig 3

Maximum-likelihood phylogenetic analysis based on amino acid sequences of g20 OTUs. Black dots show internal nodes with >90% bootstrap support. Different clusters are marked in yellow (Cluster I), blue (Cluster II), brown (Cluster III), green (Cluster IV), red (Cluster V), and black (Unassigned).

Fig 4

Comparison of the relative distribution of each g20 cyanophage cluster obtained from each sample and water mass in the nSCS.

Fig 5

Distance-decay pattern of surface g20 cyanophage (A), T4-like cyanophage (B), and T4-like heterotrophic bacteriophage (C) communities. Spearman’s correlation and significance (P) values are indicated. Canonical correspondence analysis (CCA) was conducted to show abiotic and abundance variables in shaping the assembly of the g20 cyanophage community (D). HB^a, Heterotrophic bacterial abundance; Pro^a, Prochlorococcus abundance; Syn^a, Synechococcus abundance. Samples of different oceanic water masses are marked with grey (CWM), red (sOWM), and blue (ssOWM) spots.

Fig 6

Variation in the g20 cyanophage community explained by temperature and salinity (E), the cyanobacterial community (B), and spatial variables (S). (A) Variation partitioning analysis of the g20 cyanophage community composition between cyanobacterial community composition, temperature and salinity, and spatial variables. The out circles represent 100% of the variation. Values < 0 not shown. (B) Mantel and partial Mantel tests to identify the correlations between the g20 cyanophage community structure and cyanobacteria community composition, temperature, salinity, and spatial variables using Pearson's coefficient. “|” indicates partial mantel test. **P < 0.01.

Fig 7

Relative importance of ecological processes in shaping the g20 cyanophage, T4-like Exo T-evens, and T4-like heterotrophic bacteriophage communities.