Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages

Abstract

SAR11 bacteria dominate ocean surface bacterioplankton communities, and play an important role in marine carbon and nutrient cycling. The biology and ecology of SAR11 are impacted by SAR11 phages (pelagiphages) that are highly diverse and abundant in the ocean. Among the currently known pelagiphages, HTVC010P represents an extremely abundant but under-studied phage group in the ocean. In this study, we have isolated seven new HTVC010P-type pelagiphages, and recovered 77 nearly full-length HTVC010P-type metagenomic viral genomes from marine metagenomes. Comparative genomic and phylogenomic analyses showed that HTVC010P-type pelagiphages display genome synteny and can be clustered into two major subgroups, with subgroup I consisting of strictly lytic phages and subgroup II mostly consisting of phages with potential lysogenic life cycles. All but one member of the subgroup II contain an integrase gene. Site-specific integration of subgroup II HTVC010P-type pelagiphage was either verified experimentally or identified by in silico genomic sequence analyses, which revealed that various SAR11 tRNA genes can serve as the integration sites of HTVC010P-type pelagiphages. Moreover, HTVC010P-type pelagiphage integration was confirmed by the detection of several Global Ocean Survey (GOS) fragments that contain hybrid phage-host integration sites. Metagenomic recruitment analysis revealed that these HTVC010P-type phages were globally distributed and most lytic subgroup I members exhibited higher relative abundance. Altogether, this study significantly expands our knowledge about the genetic diversity, life strategies and ecology of HTVC010P-type pelagiphages.

Keywords: SAR11; distribution patterns; genomic diversity; life strategies; metagenomic viral genomes; pelagiphages.

Fig. 1.

Genomic map of nine HTVC010P-type pelagiphage isolates. Open reading frames (ORFs) are represented by arrows and the left or right depending on the transcription orientation. The number in the arrow indicates the number of ORFs. ORFs annotated with known functions are marked with different colors according to their functions. The asterisk represents the coregene. The red asterisk represents the core genes used for phylogenomic analysis. Shadows indicate similarities between homologous genes.

Fig. 2.

Maximum-likelihood phylogenomic trees of HTVC010P-type pelagiphages and metagenomic viral genomes (MVGs) showing the two subgroups (I and II) defined in this study. The HTVC010P-type pelagiphage isolates and prophage PNP1 are shown in red. Genomes that contain an integrase gene are indicated by red triangles. The predicted bacterial attachment (attB) sites are shown. Bar represents 0.10 substitutions per site.

Fig. 3.

(a) Alignment of DNA sequences around HTVC028P and HTCC1062 integration sites. The HTCC1062 genomic sequences and HTVC028P sequences are shown in red and blue, respectively. The identical core sequences are indicated with light gray boxes. The tRNA genes found in the integration sites are boxed. (b) Gene map of HTVC028P and HTCC1062 integration sites. Host and phage genes are shown in pink and blue, respectively. The positions of PCR primers are indicated by red arrows.

Fig. 4.

Gene map and the putative attP site of representative HTVC010-type MVGs. The genes are coloured according to the degree of amino acid sequence identity to the genes in HTVC028P. The red asterisks indicate the integrase genes. Core sequences that are identical to SAR11 tRNA genes are shaded.

Fig. 5.

SAR11-pelagiphage hybrid sequences identified from the GOS database. Host and phage genes are shown in pink and blue, respectively.

Fig. 6.

Heatmap displaying the relative abundance of each HTVC010P-type pelagiphage genome in different marine viromic datasets. Normalized relative abundance is depicted as total recruited nucleotides (kb) per kb of genome per gigabase of metagenome (KPKG). Pelagiphages located at the same branch with HTVC010P and HTVC034P are boxed in the phylogenomic tree. DCM, Deep chlorophyll maximum; MESO, mesopelagic; SRF, surface; MIX, bottom of mixed layer; NA, not available.