Pelagiphages in the Podoviridiae family integrate into host genomes

Abstract

17The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface 18 bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. 19SAR11 phages, known as pelagiphages, are among the most abundant phages in the 20 ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here 21 we report 11 new pelagiphages in the Podoviridae family. Comparative genomic analysis 22 revealed that they are all closely related to previously reported pelagiphages HTVC011P 23 and HTVC019P, in the HTVC019Pvirus genus. HTVC019Pvirus pelagiphages share a 24 core genome of 15 genes, with a pan-genome of 234 genes. Phylogenomic analysis 25 clustered these pelagiphages into three subgroups. Integrases were identified in all but 26 one pelagiphage genomes. Evidence of site-specific integration was obtained by 27 high-throughput sequencing and sequencing PCR amplicons containing predicted 28 integration sites, demonstrating the capacity of these pelagiphages to propagate by both 29 lytic and lysogenic infection. HTVC019P, HTVC021P, HTVC022P, HTVC201P and 30 HTVC121P integrate into tRNA-Cys genes. HTVC011P, HTVC025P, HTVC105P, 31 HTVC109P, HTVC119P and HTVC200P target tRNA-Leu genes, while HTVC120P 32 integrates into the tRNA-Arg. Evidence of pelagiphage integration was also retrieved 33 from Global Ocean Survey (GOS) database, suggesting the occurrence of pelagiphage 34 integration in situ. The capacity of HTVC019Pvirus pelagiphages to integrate into host 35 genomes suggests they could impact SAR11 populations by a variety of mechanisms, 36 including mortality, genetic transduction, and prophage-induced viral immunity. 37HTVC019Pvirus pelagiphages are a rare example of a lysogenic phage that can be 38 implicated in ecological processes on broad scales, and thus have potential to become a 39 3 useful model for investigating strategies of host infection and phage-dependent horizontal 40 gene transfer. 41 42 IMPORTANCE 43 Pelagiphages are ecologically important because of their extraordinarily high census 44 numbers, which makes them potentially significant agents in the viral shunt, a concept 45 that links viral predation to the recycling of dissolved organic matter released from lysing 46 plankton cells. Lysogenic Pelagiphages, such as the HTVC019Pvirus pelagiphages we 47 investigate here, are also important because of their potential to contribute to the 48 hypothesized processes such as the "Piggy-Back-the-Winner" and 49 "King-of-the-Mountain". The former explains nonlinearities in virus to host ratios by 50 postulating increased lysogenization of successful host cells, while the latter postulates 51 host-density dependent propagation of defensive alleles. Here we report multiple 52 Pelagiphage isolates, and provided detailed evidence of their integration into SAR11 53 genomes. The development of this ecologically significant experimental system for 54 studying phage-dependent processes is progress towards the validation of broad 55 hypotheses about phage ecology with spe...

Culturing novel and abundant pelagiphages in the ocean

“…1A). It is noteworthy that among 15 previously isolated pelagiphages (Zhao et al ., 2013; Zhao et al ., 2019), 14 are podoviruses, and only one is myovirus.…”

“…The filtrates were stored in the dark at 4°C until used for phage isolation. The isolation procedures for pelagiphages have been described in detail previously (Zhao et al ., 2013; Zhao et al ., 2019). Briefly, 0.1 μm filtered samples were inoculated with SAR11 cultures.…”

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

“…Single amplified genomes (SAGs) assembled from deep ocean samples support the notion that temperate pelagiphages are present throughout the oceans as phage proteins have been detected within genomes of a deep‐sea subclade (Ic) of SAR11 bacteria (Thrash et al ., 2014; Mizuno et al ., 2016). Among isolated pelagiphages, 14 are presumed to be temperate, one myovirus (Eggleston and Hewson, 2016) and 13 podoviruses (Zhao et al ., 2019; Morris et al ., 2020). Cross‐infection experiments using a panel of podoviruses challenging three SAR11 hosts showed these phages integrate into host tRNA genes and suggested narrow host ranges (Zhao et al ., 2019).…”

“…Among isolated pelagiphages, 14 are presumed to be temperate, one myovirus (Eggleston and Hewson, 2016) and 13 podoviruses (Zhao et al ., 2019; Morris et al ., 2020). Cross‐infection experiments using a panel of podoviruses challenging three SAR11 hosts showed these phages integrate into host tRNA genes and suggested narrow host ranges (Zhao et al ., 2019). Pelagiphage PNP1 also exhibited high incidence of SPI in culture.…”

“…All these lineages were overrepresented among the genomes predicted to be lysogenized relative to their abundance within the queried dataset (Supporting Information Datasets S1 and S3). Interestingly, none of the genomes belonging to the Pelagibacterales order of Alphaproteobacteria were predicted to be lysogenized (Supporting Information Dataset S3) despite several pelagiphage isolates in culture that are presumed to be temperate (Eggleston and Hewson, 2016; Zhao et al ., 2019; Morris et al ., 2020). Low incidence of lysogeny among Pelagibacterales may, in part, be due to their small, streamlined genomes (Giovannoni, 2017) a trend also seen among Prochlorococcus , a genus of Cyanobacteria believed to have a low incidence of lysogeny (Biller et al ., 2014).…”