Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family.

Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.

Genome analysis of vB_SupP_AX, a novel N4-like phage infecting Sulfitobacter.

Sulfitobacter is a bacterium recognized for its production of AMP-independent sulfite oxidase, which is instrumental in the creation of sulfite biosensors. This capability underscores its ecological and economic relevance. In this study, we present a newly discovered phage, Sulfitobacter phage vB_SupP_AX, which was isolated from Maidao of Qingdao, China. The vB_SupP_AX genome is linear and double-stranded and measures 75,445 bp with a GC content of 49%. It encompasses four transfer RNA (tRNA) sequences and 79 open reading frames (ORFs), one of which is an auxiliary metabolic gene encoding thioredoxin. Consistent with other N4-like phages, vB_SupP_AX possesses three distinct RNA polymerases and is characterized by the presence of four tRNA molecules. Comparative genomic and phylogenetic analyses position vB_SupP_AX and three other viral genomes from the Integrated Microbial Genomes/Virus v4 database within the Rhodovirinae virus subfamily. The identification of vB_SupP_AX enhances our understanding of virus-host interactions within marine ecosystems.

Identification of hidden N4-like viruses and their interactions with hosts.

IMPORTANCE: The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m.

Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.

Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus.

Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.

The effects of Pandanus tectorius leaf extract on the resistance of White-leg shrimp Penaeus vannamei towards pathogenic Vibrio parahaemolyticus.

Pandanus tectorius leaf extract effect on the White-leg shrimp Penaeus vannamei tolerance against Vibrio parahaemolyticus were investigated in this study. Thirty shrimp post-larvae measured at approximately 1 cm were exposed for 24 h to 0.5, 1, 2, 3, 4, 5 and 6 g/L leaf extract and subsequently observed for survival and immune-related genes expression (Hsp70, ProPO, peroxinectin, penaeidin, crustin and transglutaminase), followed by determination of their tolerance and histological tissue profiles upon Vibrio challenge. Survival of shrimps treated with 6 g/L of leaf extract improved by up to 95% to controls. Hsp70, crustin, and prophenoloxidase mRNA levels were observed to be 8.5, 10.4, and 1.5-fold higher, respectively. Histopathological analysis of the hepatopancreas and the muscle tissues revealed major tissue degeneration in Vibrio-challenged shrimps but not in shrimps primed with P. tectorius leaf extract. Of all the dose examined, the best pathogen resistance results were obtained with a 24 h incubation of shrimp in 6 g/L P. tectorius methanolic leaf extract. The tolerance towards V. parahaemolyticus might be associated with the increased regulation of Hsp70, prophenoloxidase and crustin upon exposure to the extract, all immune-related proteins essential for pathogen elimination in Penaeid shrimp. The present study primarily demonstrated that P. tectorius leaf extract is a viable alternative for enhancing P. vannamei post-larvae resistance against V. parahaemolyticus, a major bacterial pathogen in aquaculture.

Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus.

Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.

Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family.

Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.

Correction: Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.

[This corrects the article DOI: 10.1007/s42995-022-00160-z.].

Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.

Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-022-00160-z.

Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.

Introduction: Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed. Methods: Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method. Results and Discussion: Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.

Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.

The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.

Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide.

The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.

Quality assessment of yellowtail (Seriola quinqueradiata) meat cultured in an offshore floating flexible facility.

Commercial aquaculture of yellowtail (Seriola quinqueradiata) is challenging, owing to deterioration of aquaculture environments. Offshore aquaculture may be a means of overcoming these problems. Here, we assessed the quality of flesh from offshore yellowtail (OY) bred for 1 year in an offshore floating flexible facility compared with coastal yellowtail (CY) cultured simultaneously in a coastal cage facility. The survival rate of the OY group was 94.46%, which was slightly lower than that of CY (98.18%). The feeding rate (feeding weight/fish weight) of CY was 0.4-0.5, whereas that of OY was only 0.3, possibly because poor weather conditions prevented feeding at the offshore facility. However, final fish weights did not differ significantly between both groups. In sensory tests, OY was inferior to CY in terms of oily taste. The lipid content in CY was significantly higher than that in OY. Hardness analysis revealed that OY muscles were harder than those of CY. There were no significant differences between OY and CY in overall sensory evaluations; thus, OY was judged as having equivalent value as a food product with CY. The redness of dark muscles was not significantly different on day 1 of refrigeration. However, the redness value of OY was significantly higher than that of CY on day 2. The inferior fattiness of OY relative to that of CY can be overcome by improving the feeding method. Therefore, offshore aquaculture with negligible environmental pollution may be effective for further development of aquaculture.

Distributions and relationships of virio- and picoplankton in the epi-, meso- and bathypelagic zones of the Amundsen Sea, West Antarctica during the austral summer.

Virioplankton and picoplankton are the most abundant marine biological entities on earth and mediate biogeochemical cycles in the Southern Ocean. However, understanding of their distribution and relationships with environmental factors is lacking. Here, we report on their distribution and relationships with environmental factors at 48 stations from 112.5° to 150°W and 67° to 75.5°S in the Amundsen Sea of West Antarctica. The epipelagic stations were grouped into four clusters based on the virio- and picoplankton composition and abundance. Clusters three and four, which were associated with the ice-edge blooms in the coastal and Amundsen Sea Polynya (ASP) areas, had high abundances of autotrophic picoeukaryotes; this resulted in subsequent high abundances of heterotrophic prokaryotes and viruses. Cluster two stations were in open oceanic areas, where the abundances of autotrophic and heterotrophic picoplankton were low. Cluster one stations were located between the areas of blooms and the oceanic areas, which had a low abundance of heterotrophic prokaryotes and picoeukaryotes and a high abundance of virioplankton. The abundance of viruses was significantly correlated with the abundances of autotrophic picoeukaryotes and Chl-a concentration in oceanic areas, although this reflected a time-lag with autotrophic picoeukaryote and heterotrophic prokaryotes abundances in ice-edge bloom areas. The upwelling of Circumpolar Deep Water (CDW) might have induced the high abundance of autotrophic picoeukaryotes in the epipelagic zone, and the sinking particulate organic carbon (POC) might have induced the high abundance of heterotrophic prokaryotes and virioplankton in the meso- and bathypelagic zones. This study shows that the summer distribution of virio- and picoplankton in the Amundsen Sea of West Antarctica was mainly controlled by upwelling of the CDW and the timing of ice-edge blooms.

Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae, Representing a Novel Viral Genus.

Vibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus. IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster.

Shewanella is a common bacterial genus in marine sediments and deep seas, with a variety of metabolic abilities, suggesting its important roles in the marine biogeochemical cycles. In this study, a novel lytic Shewanella phage, vB_SInP-X14, was isolated from the surface coastal waters of Qingdao, China. The vB_SInP-X14 contains a linear, double-strand 36,396-bp with the G + C content of 44.1% and harbors 40 predicted open reading frames. Morphological, growth, and genomic analysis showed that it is the first isolated podovirus infecting Shewanella, with a short propagation time (40 min), which might be resulted from three lytic-related genes. Phylogenetic analysis suggested that vB_SInP-X14 could represent a novel viral genus, named Bocovirus, with four isolated but not classified phages. In addition, 14 uncultured viral genomes assembled from the marine metagenomes could provide additional support to establish this novel viral genus. This study reports the first podovirus infecting Shewanella, establishes a new interaction system for the study of virus-host interactions, and also provides new reference genomes for the marine viral metagenomic analysis.

Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus.

Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.

Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas.

Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.

Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.