A newly isolated roseophage represents a distinct member of Siphoviridae family
Members of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts’ population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade.
vB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12T, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis.
The double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the ‘cohesive ends’ DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean.
Information about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.
KeywordsDinoroseobacter Roseophage Siphoviridae Genome sequence
Large terminase subunit
Global Ocean Sampling
Gene transfer agent
National Center for Biotechnology Information
Open reading frames
Polymerase chain reaction
Plaque forming unit
Pacific Ocean Virome
Sodium chloridemagnesium sulfate
Transmission electron microscopy
Bacteriophages or ‘phages’ are abundant and play important roles in shaping microbial population structures, mediating genetic exchange, and modulating biogeochemical cycling in the ocean [1, 2]. With rapid technological advances in DNA sequencing, culture-independent viral metagenomic studies have revealed that marine viruses carry extremely high, but largely uncharacterized genetic diversity [3, 4]. The large amount of unknown sequences is in great part due to the paucity of viral reference genome in the database. As an irreplaceable technique, the isolation and genomic analysis of new viruses could significantly contribute to the interpretation of overwhelming unknown sequences in the viromes [5, 6]. In addition, novel characterized phages can also provide valuable information on the biological features of viruses (such as morphology, infectious cycle, and host specificity) and extend our understanding of genome evolution, phage–host interactions, and phage ecology.
The Roseobacter lineage represents a major clade of marine heterotrophic bacteria, with versatile metabolic features, high genomic plasticity, and important biogeochemical roles [7, 8, 9]. The bacteria in this clade are globally distributed throughout the surface oceans, and have emerged as an important model organism for the study of marine microbial ecology . Interestingly, many Roseobacter genomes contain intact prophages and nearly all harbor a conserved gene transfer agent (GTA) operon [10, 11], suggesting that they interact closely with phages. However, only a handful of roseophages have been isolated and characterized. Recently, Zhan et al. provided an up-to-date overview of the roseophages isolated from different lineages of Roseobacter, demonstrating the phylogenetic diversity of the roseophages and their multiple mutual effects on Roseobacter . Therefore, the roseophage–Roseobacter could offer an ideal system to gain new insights into the diversity and evolution of phages and the relationships between phages and their bacterial hosts.
Dinoroseobacter shibae DFL12T is one of the most prominent and well-studied members of the Roseobacter clade . It has interesting and important metabolic traits, such as the ability to grow anaerobically and the adaption to dark-light cycles which allows the additional energy generation from light under heterotrophic and starvation conditions . So far, four phages that infect D. shibae DFL12T have been reported, three of which have a highly conserved genomic organization and belong to the N4-like genus of the family Podoviridae [15, 16, 17]. Only one D. shibae siphophage, which was isolated from an oligotrophic environment, has been sequenced and showed little similarity to known phages .
In this study, we report the isolation and characterization of another novel siphophage, vB_DshS-R4C, infecting D. shibae DFL12T. Microbiological and genomic analyses provide an overview of its features and its evolutionary relationships with other previously characterized phages. We demonstrate that R4C is a distinct member of the family Siphoviridae.
Phage isolation and purification
The host strain D. shibae DFL12T was incubated in rich organic (RO) medium (1 M yeast extract, 1 M peptone, 1 M sodium acetate, artificial seawater, pH 7.5) at 37 °C with shaking at 180 rpm/min. The samples for virus isolation were collected from the coastal seawater of Xiamen, China, and filtered through a 0.2 μm membrane. To improve the chance of successful phage isolation, the viruses in the seawater were concentrated with tangential flow filtration through a 30-kDa cartridge (Millipore, CA, USA) and then mixed with D. shibae DFL12T using double-layer agar method . After overnight incubation at 37 °C, individual clear lytic plaques were picked, suspended in 1 mL of SM buffer (50 mM Tris-HCl [pH 7.5], 0.1 M NaCl, 8 mM MgSO4), and purified by replating at least five times to obtain a pure phage culture. The purified plaques were then eluted with SM buffer and stored at 4 °C for further usage.
The lytic host range of the phage was determined by spotting dilutions onto lawns of 19 bacterial test strains, mainly from the genera Roseobacter, Erythrobacter, Citromicrobium, Roseomonas, and Silicibacter, as shown in Additional file 1: Table S1 . The bacterial cultures (1 mL) in the exponential growth phase were added to 3 mL of molten RO agar medium (0.5% w/v agar). The mixture was then poured onto a solid agar plate (1.5% w/v agar), which was placed at room temperature (approximately 25 °C) to solidify. Diluted phage lysate (10 μL) was spotted onto the surface of each plate, incubated overnight at 37 °C, and then checked for the presence of lytic plaques.
To investigate the presence of lipid in R4C, the phages were incubated with 0.2, 2%, or 20% (v/v) chloroform with vibration for 1 min and then kept at room temperature for 30 min. The titers of the phage were then determined by dropping it onto D. shibae DFL12T plate to examine its sensitivity to chloroform.
One-step growth curve
One-step growth curve was constructed to analyze the life cycle of R4C . Briefly, the phage was added to 1 mL of log-phase D. shibae DFL12T at a multiplicity of infection of 0.01, and then incubated for 25 min at room temperature in the dark. The unabsorbed phage particles were removed by centrifugation at 10,000×g for 5 min. After resuspended in 50 mL of RO medium, the suspension was incubated at 37 °C with continuous shaking. Samples were collected every 30 min and viral abundance was quantified with a double-agar plaque assay.
Preparation of high-titer phage suspensions
High-titer phage suspensions for morphological observation and DNA extraction were prepared with cesium chloride (CsCl) gradient ultracentrifugation. Briefly, the phage was propagated in strain DFL12T and collected after complete bacterial lysis. The culture was centrifuged at 10,000×g for 10 min and filtered through a 0.2 μm membrane. The phage suspension was precipitated with 1 M NaCl and polyethylene glycol (PEG) 8000 (10% w/v) overnight at 4 °C. The phage particles from the PEG pellet were purified with CsCl (1.5 g/mL in SM buffer) gradient centrifugation (200,000×g, 4 °C, 24 h). The phage bands were collected and dialyzed against SM buffer at 4 °C.
Transmission electron microscopy (TEM)
The phage morphology was investigated with TEM. In brief, 10 μL of high-titer phage concentrate was placed on formvar, carbon-coated copper electron microscopy grids (200 mesh) and allowed to adsorb for 20 min. The phage particles were negatively stained with 1% (w/v) phosphotungstic acid for 1 min. Excess stain was removed with filter paper and the grids were air dried before examination with a JEM-2100 electron microscope (accelerating voltage of 120 kV).
For DNA extraction, the high-titer phage concentrate was treated with DNase I and RNase A at room temperature for 1 h to reduce host DNA contamination and then the DNase was inactivated at 65 °C for 15 min. The phage was lysed with proteinase K (50 μM), EDTA (20 mM), and sodium dodecyl sulfate (0.5% w/v) at 55 °C for 3 h. The phage DNA was extracted with the phenol/chloroform/isoamyl alcohol method and precipitated with ethanol. After quality and quantity checks with NanoDrop 2000 spectrophotometer and agarose gel electrophoresis, the genomic DNA was stored at − 80 °C until sequencing.
Genome sequencing and analysis
The genomic DNA was sequenced on the Illumina HiSeq 2500 platform with pair-end (PE) read sizes of 100 bp. The raw reads were quality checked with FastQC and trimmed with FASTX-Toolkit. On average, Illumina PE reads 1 and reads 2 had > 90% and > 75% of bases with a quality score of at least 30 (Q30), respectively. The sequences were assembled with the Velvet software (v1.2.03) . The phage termini and DNA-packing strategy were predicted with PhageTerm , with a mapping coverage setting of 20,000. The GeneMarkS online server and RAST (http://rast.nmpdr.org/) were used to identify putative open reading frames (ORFs), and the results were merged and checked manually. Gene annotation was performed with the algorithms of a BLAST search (National Center for Biotechnology Information, NCBI) against the nonredundant (nr) nucleotide database, with e-values of < 10− 5. The presence of tRNAs was examined with tRNAscan-SE. Comparison of genomes between R4C and other related phages were performed using BLAST. The complete genome sequence was submitted to the GenBank database under accession number MK882925.
In this study, the major capsid protein, large terminase subunit (TerL), and GTA-like sequences of R4C were used to construct phylogenetic trees to analyze its evolutionary relationships. Homologues were identified with BLASTP against the NCBI nr database using the acid-amino sequences as queries. Multiple sequence alignments were constructed with ClustalW, with the default parameters. Phylogenetic trees were constructed with the maximum likelihood method, with 1000 bootstrap replicates, in the MEGA 6.0 software (http://www.megasoftware.net/). The accession numbers of the viruses used in the alignments and phylogenetic analyses are listed on the trees.
Recruitment of metagenomic data
To analyze the distribution of the R4C genome in different environments, homologues of the R4C ORFs were recruited from the Global Ocean Sampling (GOS) metagenomes and Pacific Ocean Virome (POV). The reads was recruited with tBLASTn using a threshold e-value of 10− 5, a bit score of > 40, and a minimum amino-acid length of 30, as previously described .
Results and discussion
Biological characterization of R4C
A TEM analysis revealed that R4C has an isometric and icosahedral head, with an estimated diameter of 55 ± 2 nm. The phage has a long noncontractile tail, measuring 82 ± 3 nm (Fig. 1b). According to its morphological characteristics and the guidelines of the International Committee on the Taxonomy of Viruses, phage R4C belongs to the family Siphoviridae in the order Caudovirales (tailed phages). Until now, over 96% of the phages reported in the scientific literature belong to the order Caudovirales, and the siphoviruses comprise approximately 61% of the tailed phages . However, only 33% of the known roseophages belong to Siphoviridae, and the rest to the families Podoviridae and Microviridae .
The host range of this newly isolated phage was assayed with the spot test. Among all the 19 strains tested, phage R4C can only infect D. shibae DFL12 (Additional file 1: Table S1), but other yet-to-be discovered hosts cannot be ruled out here. This result is consistent with the previous finding that roseophages seem to have narrow host ranges . The suspensions of R4C treated with three different concentrations of chloroform showed obvious lytic plaques, indicating the absence of lipids outside the capsid, which is commonly observed in phages of the order Caudovirales .
Bioinformatic analysis of the genomic sequence
General genomic features
Genome assembly based on 3,048,949 PE reads yielded a single contig with an average coverage of 19,731×. The genome of R4C is a double-stranded DNA (dsDNA) molecule consisting of 36,291 bp, with a high G + C content of 66.75%, which is very similar to the average G + C content (66.02%) of its host. The average genome size of the phages within the family Siphoviridae is estimated to be 53.70 kb . Therefore, R4C has a relatively small genome within this family, reflecting the more retrenching virion structure. The properties of the genome, such as the positions, directions, and putative functions of each gene, are summarized in Additional file 1: Table S2. In total, 49 putative ORFs were predicted in the R4C genome, with 48 ORFs on the positive strand and one ORF on the negative strand. A total of 35,145 nucleotides (96.59% of the genome) are involved in coding putative proteins. The average gene length is 715 bp, with a range of 111 to 4344 nucleotides. Only 22 predicted ORFs (44.90%) were predicted to be functional, whereas 27 were assigned to hypothetical proteins. No tRNA sequences were detected in the R4C genome with the tRNAscan-SE program, indicating that the phage is completely reliant on the host tRNA for its protein synthesis. Genome annotation with BLASTP identified different functional clusters, including those involved in DNA packaging, virion morphogenesis, DNA manipulation, and regulation.
Phage DNA-packaging mechanism
A termini analysis that can detect the DNA-packaging mechanisms of dsDNA phages was implemented using the PhageTerm software. Toward the end of the infection cycle, dsDNA phages generally form concatemeric DNA, which is cleaved by terminase and then encapsulated in a preformed empty prohead. Although there are several different phage DNA-packaging mechanisms, two modes are well characterized: the cohesive ends (cos) and headful (pac) packaging types. For phages with DNA cohesive ends, such as the λ-like phages, terminase recognizes the cos site and introduces a staggered cut, generating a unit-length encapsidated genome. By comparison, in the headful packaging phages (such as the T4, P22, or P1 phages), packaging starts by cleavage at a pac site and ends when the procapsid reaches its capacity. These phages encapsidate more than one unit-length of the phage genome (typically 102–110%), producing a virion DNA with a terminally redundant sequence. Analysis of the phage R4C genome identified a 14-bp 5′ protruding cohesive end region, upstream from the terminase small subunit gene, suggesting that the R4C genome utilizes the cohesive ends packaging strategy of the λ-like phages. The large terminase subunit gene is often conserved amongst the tailed bacteriophages that use either the cos- or pac-type packaging mechanisms. A phylogenetic analysis of R4C TerL, together with those of phages with known packaging mechanisms, also clustered R4C into the clade of phages that utilize λ-like DNA packaging (see below).
Comparative genomic analysis
Recruitment of metagenomic data
Characteristics of R4C ORF homologous reads recruited from different metagenomes
Proportion of ORF homologue (%)
ORF coverage (%)
ORF aa identity (%)
In this study, a novel representative of the roseophages was characterized in terms of its microbiological characteristics, genomic organization, phylogenetic relationships, and geographic distribution. Phylogenetic and comparative genomic analyses showed that R4C is a new member of the family Siphoviridae. The integrase gene in R4C implies that the phage has a potential lysogenic cycle. Ecologically, a metagenomic analysis showed that the homologues of R4C are more prevalent in coastal areas than in the open ocean. Our comprehensive analysis of this new phage provides insights into the diversity of the tailed phages and the evolutionary relationships between the roseophages and roseobacters. The information provided should also be a useful reference for the identification of the bacterial hosts of phages retrieved from viral metagenomes.
We thank Zhenqin Chen and Dingxun Wu for their help with the microscopy. We greatly appreciated the suggestions from Yongle Xu during the experiments and the data analysis.
RZ and LC organized the study; LC, RZ, RM, HC, and YY performed the experiments and analyzed the data; LC, RZ, and NJ wrote the paper. All authors read and approved the final manuscript.
This work was supported by the China Ocean Mineral Resources R & D Association (DY135-E2–1-04), Qingdao National Laboratory for Marine Science and Technology (QNLM2016ORP0303), and the National Natural Science Foundation of China (31570172) to R.Z.; the National Natural Science Foundation of China (41706154) and Science and Technology Program of Guangzhou, China (201904020029) to L.C.; the PhD Fellowship of the State Key Laboratory of Marine Environmental Science at Xiamen University to R.M..
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
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