Unveiling Infection Strategies across Diverse Marine Phage–Host Systems

Bacterial viruses (phages) are amongst the smallest, most powerful biological entities on Earth. Through infection, phages impact host metabolism, bacterial mortality, and evolution. In the oceans, 20–40% of surface microbes are infected, with 1023 new infections each second. Yet, infections remain virtually uncharacterized, as the available phage isolates underrepresent the diversity of marine phage–host interactions. Additionally, while sequencing efforts reveal “who is there?”, a gap between sequence and function prevents answering “what are they doing?” and “how?”. We have developed new Bacteroidetes and Proteobacteria marine phage–host model systems with which to connect genomes, infection strategies, and functions using both traditional and genome-wide “-omics” experiments. We ask: How do infections by genomically divergent phages compare? Are there links between phage–host genomes and infection strategies? Our findings are as follows. In Bacteroidetes, a phage infecting two nearly identical strains (host38 and host18) under identical conditions is more fit and efficient on host38. By contrast, on host18, it is less fit and, except for phage transcription, it fails at efficiently mastering all stages of the infection: from adsorption through to cell lysis. In Proteobacteria, genomically unrelated podovirus and siphovirus phages infecting the same strain reprogram host metabolisms very differently. Namely, siphovirus-infected cells hardly differ from uninfected and mainly repress energy-consuming processes such as motility and translation. By contrast, podovirus-infected cells greatly differ from uninfected cells in transcription and in uniquely shifting central carbon and energy metabolism. Additionally, the siphovirus is more complementary to the host than the podovirus in %GC, amino acids, and codon usage. We found that phage–host genome complementarity may drive the resource demand and fitness of a phage: the phage most complementary to its host easily accesses intracellular resources, infects with little reprogramming, and accomplishes the largest fitness, which has not previously been shown. Together, this work helps to uncover infection efficiency strategies, and connect genomes with metabolisms in marine phage–host systems.

Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage

ABSTRACT Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but “unculturable” bacteria. IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.

Novel pelagiphages prevail in the ocean

Viruses play a key role in biogeochemical cycling and host mortality, metabolism, physiology and evolution in the ocean. Viruses that infect the globally abundant marine SAR11 bacteria (pelagiphages) were reported to be an important component of the marine viral community. In this study, ten pelagiphages that infect three different Pelagibacter strains were isolated from various geographical locations and were genomically characterized. All ten pelagiphages are novel, representing four new lineages of the Podoviridae family. Although they share limited homology with cultured phage isolates, they are all closely related to some environmental viral fragments. Two HTVC023P-type pelagiphages are shown to be related to the abundant VC_6 and VC_8 viral populations of the Global Oceans Viromes (GOV) datasets. Interestingly, HTVC103P-type pelagiphages contain a structural module similar to that in SAR116 phage HMO-2011. Three HTVC111P-type pelagiphages and HTVC106P are also novel and related to GOV VC_41 and VC_67 viral populations, respectively. Remarkably, these pelagiphage represented phage groups are all globally distributed and predominant. Half of the top ten most abundant known marine phage groups are represented by pelagiphages. The HTVC023P-type group is the most abundant known viral group, exceeding the abundance of HTVC010P-type and HMO-2011-type groups. Furthermore, the HTVC023P-type group is also abundant throughout the water column. Altogether, this study has greatly broadened our understanding of pelagiphages regarding their genetic diversity, phage-host interactions and the distribution pattern. Availability of these newly isolated pelagiphages and their genome sequences will allow us to further explore their phage-host interactions and ecological strategies.

Complete Genome Sequence of Sinorhizobium Phage ΦM6, the First Terrestrial Phage of a Marine Phage Group

Sinorhizobium phage ΦM6 infects the nitrogen-fixing rhizobial bacterium Sinorhizobium meliloti. ΦM6 most closely resembles marine phages, such as Puniceispirillum phage HMO-2011, rather than previously sequenced rhizobial phages.

Development ofphoHas a Novel Signature Gene for Assessing Marine Phage Diversity

ABSTRACTPhages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified,phoHwas the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phagephoHsequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of thephoHgene were used to determine the diversity of phagephoHsequences throughout a depth profile in the Sargasso Sea and at six locations worldwide.phoHwas present at all sites examined, and a high diversity ofphoHsequences was recovered. MostphoHsequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinctphoHcomposition, although mostphoHclusters were recovered from multiple sites. Overall,phoHis an effective signature gene for examining phage diversity in the marine environment.