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1.
Appl Environ Microbiol ; : e0036724, 2024 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-38953371

RESUMEN

Flavobacteriia are the dominant and active bacteria during algal blooms and play an important role in polysaccharide degradation. However, little is known about phages infecting Flavobacteriia, especially during green tide. In this study, a novel virus, vB_TgeS_JQ, infecting Flavobacteriia was isolated from the surface water of the Golden Beach of Qingdao, China. Transmission electron microscopy demonstrated that vB_TgeS_JQ had the morphology of siphovirus. The experiments showed that it was stable from -20°C to 45°C and pH 5 to pH 8, with latent and burst periods both lasting for 20 min. Genomic analysis showed that the phage vB_TgeS_JQ contained a 40,712-bp dsDNA genome with a GC content of 30.70%, encoding 74 open-reading frames. Four putative auxiliary metabolic genes were identified, encoding electron transfer-flavoprotein dehydrogenase, calcineurin-like phosphoesterase, phosphoribosyl-ATP pyrophosphohydrolase, and TOPRIM nucleotidyl hydrolase. The abundance of phage vB_TgeS_JQ was higher during Ulva prolifera (U. prolifera) blooms compared with other marine environments. The phylogenetic and comparative genomic analyses revealed that vB_TgeS_JQ exhibited significant differences from all other phage isolates in the databases and therefore was classified as an undiscovered viral family, named Zblingviridae. In summary, this study expands the knowledge about the genomic, phylogenetic diversity and distribution of flavobacterial phages (flavophages), especially their roles during U. prolifera blooms. IMPORTANCE: The phage vB_TgeS_JQ was the first flavobacterial phage isolated during green tide, representing a new family in Caudoviricetes and named Zblingviridae. The abundance of phage vB_TgeS_JQ was higher during the Ulva prolifera blooms. This study provides insights into the genomic, phylogenetic diversity, and distribution of flavophages, especially their roles during U. prolifera blooms.

2.
Int Microbiol ; 2024 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-38190086

RESUMEN

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.

3.
Appl Environ Microbiol ; 89(4): e0189622, 2023 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-36975807

RESUMEN

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.


Asunto(s)
Bacteriófagos , Oceanospirillaceae , Filogenia , Clima Frío , Genómica , Genoma Viral
4.
Environ Res ; 237(Pt 1): 116743, 2023 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-37500038

RESUMEN

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

5.
Microb Ecol ; 83(1): 34-47, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33811505

RESUMEN

Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.


Asunto(s)
Alveolados , Rhizaria , Agua de Mar/microbiología , Estramenopilos , Alveolados/clasificación , Océano Pacífico , ARN Ribosómico 18S/genética , Rhizaria/clasificación , Estramenopilos/clasificación
6.
Curr Microbiol ; 79(7): 213, 2022 Jun 07.
Artículo en Inglés | MEDLINE | ID: mdl-35672590

RESUMEN

PHS21 against Pseudoalteromonas is isolated from Qingdao offshore seawater. The phage was characterized and identified by morphological examination, stability, whole genome sequencing, and bioinformatics analysis. Morphological analysis of PHS21 by transmission electron microscopy shows that belonged to the Siphoviridae family. PHS21 showed strong tolerance with a wide range of temperatures and pH. One-step growth assay indicates that the latent period is about 48 min and the burst size is approximately 218 PFU/cell (plaque forming unit/cell). Its complete genomic sequence is 35,802-bp long with 50 putative open reading frames. Phage PHS21 and PHS3 displayed a very close evolutionary relationship; however, having different DNA packaging proteins indicates that they may have already evolved distinct ways to package DNA in host cells. This study provides the detailed description and genomic characterization of a novel Pseudoalteromonas phage.


Asunto(s)
Bacteriófagos , Pseudoalteromonas , Siphoviridae , Bacteriófagos/genética , ADN Viral/química , ADN Viral/genética , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Pseudoalteromonas/genética , Análisis de Secuencia de ADN , Siphoviridae/genética
7.
BMC Genomics ; 22(1): 675, 2021 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-34544379

RESUMEN

BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown. RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans. CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.


Asunto(s)
Bacteriófagos , Siphoviridae , Bacteriófagos/genética , ADN Viral/genética , Genoma Viral , Genómica , Filogenia , Siphoviridae/genética
8.
Appl Environ Microbiol ; 87(22): e0116021, 2021 10 28.
Artículo en Inglés | MEDLINE | ID: mdl-34469192

RESUMEN

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.


Asunto(s)
Metagenómica , Agua de Mar , Viroma , Regiones Árticas , Océano Atlántico , Agua de Mar/virología , Temperatura
9.
Arch Virol ; 165(6): 1397-1407, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32307604

RESUMEN

A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.


Asunto(s)
Genoma Viral , Myoviridae/clasificación , Myoviridae/aislamiento & purificación , Agua de Mar/virología , Synechococcus/virología , Composición de Base , Secuencia de Bases , China , Especificidad del Huésped , Metagenómica , Myoviridae/ultraestructura , Sistemas de Lectura Abierta , Océano Pacífico , Filogenia , Microbiología del Agua , Secuenciación Completa del Genoma
10.
Curr Microbiol ; 77(2): 279-285, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31760453

RESUMEN

A novel Pseudoalteromonas atlantica phage C7 was isolated from the coastal surface water in the Yellow Sea of China using the agar overlay method. Transmission electron microscopy analysis reveals that it belongs to Siphoviridae with a head of 56 nm in diameter and a tail of 102 nm in length. Microbiological characterization suggests that the phage is stable at a range of temperatures (from - 20 to 65 °C) and the optimal pH range is 6-12. One-step growth curve shows a 45-min latent period and a 105-min rise period. Genomic analysis shows that C7 has a linear, double-stranded 42,261-bp DNA molecule with 40.6% GC content and 76 putative open reading frames (ORFs) with one tRNA. The ORFs are classified into six functional groups as follows: hypothetical protein, phage structure, phage packaging, DNA replication and regulation, transcription, and some additional functions. There are many obviously similarities between C7 and a previously published Pseudoalteromonas phage vB_PspS-H40/1 by genomic comparison. This study provides an important data for further research on the interaction between marine bacteriophages and their hosts.


Asunto(s)
Genoma Viral , Pseudoalteromonas/virología , Agua de Mar/virología , Siphoviridae/genética , Composición de Base , China , ADN Viral/aislamiento & purificación , Interacciones Microbiota-Huesped , Sistemas de Lectura Abierta , Agua de Mar/microbiología , Siphoviridae/aislamiento & purificación
11.
Curr Microbiol ; 77(9): 2385-2390, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32451684

RESUMEN

Cyanophages, which play a significant role in food web and global biochemical cycle, are one of the main causes of microbial death in aquatic environment. A novel cyanophage S-B68 was isolated from the surface water of the Bohai Sea, northern China. It can infect marine Synechococcus sp. (strain WH7803). The transmission electron microscopy results demonstrate that this cyanophage has an icosahedral head (51 nm in diameter) and a long tail (110 nm in length) and belongs to family Siphophages. The complete genome sequence of cyanophage S-B68 contains a linear, double-stranded 163,982 bp DNA molecule with a 51.7% G+C content. Except for four tRNAs, the genome contains 229 open reading frames (ORFs) which were grouped into six functional modules as follows: structure, hypothetical protein, DNA replication and expression, lysis, packaging, and some additional functions. It was found in one-step growth curve that the latent period of the S-B68 was about 49 h after infection with Synechococcus, and then it entered the rising period, and tended to stable after 61 h. Using the BLASTN tool in the NCBI database for genome comparison, there was no significant similarity between S-B68 and other known cyanophages. Present study adds a novel Siphoviridae genome to marine cyanophage dataset and provides useful basic information for its further research.


Asunto(s)
Bacteriófagos , Siphoviridae , Bacteriófagos/genética , Composición de Base , China , Genoma Viral , Sistemas de Lectura Abierta , Siphoviridae/genética
12.
Curr Microbiol ; 77(10): 2813-2820, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32588135

RESUMEN

Although Alteromonas is ubiquitous in the marine environment, very little is known about Alteromonas phages, with only ten, thus far, being isolated and reported on. In this study, a novel double-stranded DNA phage, Alteromonas phage P24, which infects Alteromonas macleodii, was isolated from the coastal waters off Qingdao. Alteromonas phage P24 has a siphoviral morphology, with an icosahedral head, 61 ± 1 nm in diameter, and a tail length of 105 ± 1 nm. Alteromonas phage P24 contains lipids. It has an optimal temperature and pH for growth of 20℃ and 5-7, respectively. A one-step growth curve shows a latent period of 55 min, a rise period of 65 min, and an average burst size of approximately 147 virions per cell. Alteromonas phage P24 has the genome of 46,945 bp with 43.80% GC content and 74 open reading frames (ORFs) without tRNA. The results of the phylogenetic tree, based on the mcp and terL genes, show that Alteromonas phage P24 is closely related to Aeromonas phage phiARM81ld. Meanwhile, phylogenetic analysis based on the whole genome of P24 indicates that it forms a unique viral sub-cluster within Siphoviridae. This study contributes to the understanding of the genomic characteristics and the virus-host interactions of Alteromonas phages.


Asunto(s)
Alteromonas , Bacteriófagos , Genoma Viral , Siphoviridae , Alteromonas/virología , Bacteriófagos/clasificación , Bacteriófagos/genética , ADN Viral/genética , Genoma Viral/genética , Sistemas de Lectura Abierta , Filogenia , Siphoviridae/clasificación , Siphoviridae/genética
13.
Virus Genes ; 55(6): 834-842, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31420829

RESUMEN

A novel Vibrio phage, P23, belonging to the family Siphoviridae was isolated from the surface water of the Yellow Sea, China. The complete genome of this phage was determined. A one-step growth curve showed that the latent period was approximately 30 min, the burst size was 24 PFU/cell, and the rise period was 20 min. The phage is host specific and is stable over a range of pH (5-10) and temperatures (4-65 °C). Transmission electron microscopy showed that phage P23 can be categorized into the Siphoviridae family, with an icosahedral head of 60 nm and a long noncontractile tail of 144 nm. The genome consisted of a linear, double-stranded 40.063 kb DNA molecule with 42.5% G+C content and 72 putative open reading frames (ORFs) without tRNA. The predicted ORFs were classified into six functional groups, including DNA replication, regulation and nucleotide metabolism, transcription, phage packaging, phage structure, lysis, and hypothetical proteins. The Vibrio phage P23 genome is a new marine Siphoviridae-family phage genome that provides basic information for further molecular research on interaction mechanisms between bacteriophages and their hosts.


Asunto(s)
Bacteriófagos/genética , Genoma Viral/genética , Filogenia , Secuenciación Completa del Genoma , Bacteriófagos/clasificación , Composición de Base/genética , China , Genómica , Anotación de Secuencia Molecular , Sistemas de Lectura Abierta/genética , Análisis de Secuencia de ADN , Siphoviridae/genética , Vibrio/genética , Vibrio/virología
14.
Curr Microbiol ; 76(10): 1225-1233, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31302725

RESUMEN

Two novel Vibrio phages, LP.1 and LP.2 that infected Vibrio maritimus R-40493, were isolated from surface seawater in Qingdao coastal area by the double-agar layer method. Morphological analysis by transmission electron microscope showed that the two phages displayed head-tail structures with icosahedral heads of 62.37 and 54.00 nm in diameter and long non-contractile tails of 119.00 and 105.20 nm in length, respectively, and can be grouped into the Siphoviridae family. Thermal and pH sensitivity tests exhibited that LP.1 was stable at temperature ranging from - 20 to 65 °C and at pH ranging from 5 to 12, and LP.2 showed vitality over a wider range of temperature (- 20-75 °C) and pH (3-12). Both LP.1 and LP.2 contained linear and double-stranded DNA genomes with a length of 46,791-bp and 37,128-bp, respectively. The genome of both phages can be classified into four functional groups, including DNA replication and regulation, phage packaging, phage structure, and additional function. The bioinformatic analysis demonstrated that the Vibrio phages LP.1 and LP.2 are novel phages. By conducting morphological, biochemical, and genomic analysis, our study provides useful information for further research on the interaction between Vibrio phages and their host.


Asunto(s)
Genoma Viral/genética , Agua de Mar/virología , Siphoviridae/genética , Vibrio/virología , China , ADN Viral/genética , Especificidad del Huésped , Filogenia , Análisis de Secuencia de ADN , Siphoviridae/clasificación , Siphoviridae/fisiología , Siphoviridae/ultraestructura , Proteínas Virales/genética , Proteínas Virales/metabolismo
15.
Curr Microbiol ; 76(6): 681-686, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30949805

RESUMEN

A novel cyanophage, S-B64, which can infect marine Synechococcus WH8102, was isolated from the coastal waters of the Yellow Sea using the liquid serial dilution method. Morphological study by transmission electron microscopy revealed that the cyanophage belongs to Podovirus. It's genome, which was completely sequenced, contains a 151,867 bp DNA molecule with a G+C content of 41.78% and 186 potential open reading frames. The functions of the genes include cyanophage structure, cyanophage packaging, DNA replication and regulation. After primary characterization, it was found that the latent period is about 3 h, and it lysed after 8 h, the burst size is about 23 virions per cell. This information will provide an important benchmark for further research on the interaction between cyanophages and their hosts.


Asunto(s)
Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación , Genoma Viral , Podoviridae/genética , Podoviridae/aislamiento & purificación , Agua de Mar/virología , Synechococcus/virología , Bacteriófagos/clasificación , Bacteriófagos/ultraestructura , Composición de Base , China , Genes Virales , Microscopía Electrónica de Transmisión , Podoviridae/clasificación , Podoviridae/ultraestructura , Análisis de Secuencia de ADN , Virión/ultraestructura
16.
Curr Microbiol ; 76(11): 1256-1263, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31372731

RESUMEN

A novel Alteromonas phage JH01, with the host strain identified to be Alteromonas marina SW-47(T), was isolated from the Qingdao coast during the summer of 2017. Transmission electron microscopy analysis showed that phage JH01 can be categorized into the Siphoviridae family, with an icosahedral head of 62 ± 5 nm and a long contractile tail of 254 ± 10 nm. The bioinformatic analysis shows that this phage consists of a linear, double-stranded 46,500 bp DNA molecule with a GC content of 44.39%, and 58 ORFs with no tRNA genes. The ORFs are classified into four groups, including phage packaging, phage structure, DNA replication and regulation, and hypothetical protein. The phylogenetic tree, constructed using neighbor-joining analysis, shows that phage JH01 has altitudinal homology with some Vibrio and Pseudoalteromonas phage B8b. Comparative analysis reveals the high similarity between phage JH01 and phage B8b. Additionally, our study of phage JH01 provides useful information for further research on the interaction between Alteromonas phages and their hosts.


Asunto(s)
Alteromonas/virología , Bacteriófagos/aislamiento & purificación , Genoma Viral , Agua de Mar/virología , Siphoviridae/aislamiento & purificación , Bacteriófagos/clasificación , Bacteriófagos/genética , Secuencia de Bases , China , ADN Viral , Filogenia , Siphoviridae/clasificación , Siphoviridae/genética
17.
Curr Microbiol ; 75(12): 1619-1625, 2018 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-30218176

RESUMEN

We used the double-agar layer method to isolate a novel Marinobacter marina bacteriophage, B23, from the surface water sample of the Bohai sea of China. There is some work to better understand the phage. The result of transmission electron microscopy revealed that B23 belongs to the family Siphoviridae with a head of 80 nm in diameter and a tail of 230 nm. Microbiological characterization evidenced that phage B23 is stable at the temperatures from - 25 to 60 °C, and showed vigorous vitality at pH between 4.0 and 12.0. One-step growth experiment showed that it had a longer latent period and higher lysis efficiency. Furthermore, the complete genome of B23 was sequenced and analyzed, which consists of a 35132 bp DNA with a G + C content of 59.8% and 50 putative open reading frames. The genome was divided into five parts, consisting of DNA replication and regulation, phage packaging, phage structure, host lysis and hypothetical protein.


Asunto(s)
Genoma Viral , Marinobacter/virología , Siphoviridae/genética , Concentración de Iones de Hidrógeno , Filogenia , Siphoviridae/crecimiento & desarrollo , Siphoviridae/aislamiento & purificación , Siphoviridae/ultraestructura , Temperatura , Secuenciación Completa del Genoma
18.
Curr Microbiol ; 74(2): 212-218, 2017 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-27942842

RESUMEN

The family Pseudoalteromonas is highly adaptable to dissimilar ecological habitats and plays an important ecological role in the marine environment. In this study, a new Pseudoalteromonas phage PH1 was isolated from the Yellow Sea. To better understand the bacteriophage, its biological properties, including morphology, host range, growth phenotype, thermal and pH stability, and nucleic acid composition, were investigated in detail. The result showed that the phage PH1 is a Podoviridae-phage with an icosahedral head (60 nm of diameter) and a short tail (26 nm in length). The phage PH1 genome consists of 42,685 bp length double-stranded DNA with a G+C content of 42.24% and is predicted to have 55 open reading frames (ORFs) with an average length of 740 bp nucleotides each. The phage PH1 genome adds a new Podoviridae-phage genome to marine bacteriophage dataset, which will provide useful basic information for further molecular research on interaction mechanisms between bacteriophages and their hosts.


Asunto(s)
Bacteriófagos/aislamiento & purificación , Genoma Viral , Podoviridae/aislamiento & purificación , Pseudoalteromonas/virología , Análisis de Secuencia de ADN , Bacteriófagos/clasificación , Bacteriófagos/genética , Bacteriófagos/ultraestructura , Composición de Base , ADN/química , ADN/genética , ADN Viral/química , ADN Viral/genética , Especificidad del Huésped , Concentración de Iones de Hidrógeno , Sistemas de Lectura Abierta , Podoviridae/clasificación , Podoviridae/genética , Podoviridae/ultraestructura , Agua de Mar/virología , Temperatura , Virión/ultraestructura
19.
Curr Microbiol ; 74(7): 821-826, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28424938

RESUMEN

A novel marine Alteromonas gracilis siphovirus, phage PB15, was isolated from the surface water of the Yellow Sea in August 2015. It has a head diameter of 58 ± 5 nm head and a contractile tail approximately 105 ± 10 nm in length, and overall, the morphology suggests that PB15 belongs to the family Siphoviridae. PB15 phage is stable at over the temperature range 0-60 °C. The best MOI of these phage was 0.1, and infectivity decreased above 60 °C. The results suggest that phage is stable at pH value ranging between 3.0 and 11.0. Chloroform test shows that PB15 is not a lipid-containing phage. A one-step growth curve with a strain of A. gracilis gave a latent period of 16 min and rise period of 24 min and burst size of 60 PFU/cell. Genomic analysis of PB15 reveals a genome size of 37,333 bp with 45.52% G+C content, and 61 ORFs. ORF sequences accounted for 30.36% of the genome sequence. There is no obvious similarity between PB15 and other known phages by genomic comparison using the BLASTN tool in the NCBI database.


Asunto(s)
Alteromonas/virología , Bacteriófagos/aislamiento & purificación , Genoma Viral , Agua de Mar/virología , Siphoviridae/aislamiento & purificación , Bacteriófagos/clasificación , Bacteriófagos/genética , Composición de Base , Secuencia de Bases , China , ADN Viral/genética , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , Análisis de Secuencia de ADN , Siphoviridae/clasificación , Siphoviridae/genética
20.
Curr Microbiol ; 74(7): 815-820, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28424939

RESUMEN

A novel Siphoviridae family Phage BS5, which infects Pseudoalteromonas atlantica, was isolated from the surface waters of the Yellow Sea. Morphological study by transmission electron microscopy revealed that the novel phage belongs to Siphoviridae. The complete genome sequence of PBS5 contained a linear, double-strand 39949-bp DNA molecule with a G + C content of 40.6% and 65 putative open reading frames. Twelve conserved domains were detected by BLASTP in NCBI, and of these the functions of 5 were known. The genome was grouped into four modules as follows: phage structure, phage packaging, DNA replication and regulation, and some additional functions.16 S rDNA sequence analysis was also applied to identify the host bacteria. After initial characterization of bacteriophage PBS5, it was found that the optimal pH was 7.0, the optimal temperature was 30 °C, and the burst size was about 95 virions per cell. This information will provide an important benchmark for further research on the interaction between bacteriophages and their hosts.


Asunto(s)
Bacteriófagos/aislamiento & purificación , Genoma Viral , Siphoviridae/aislamiento & purificación , Bacteriófagos/clasificación , Bacteriófagos/genética , Composición de Base , Sistemas de Lectura Abierta , Filogenia , Pseudoalteromonas/virología , Siphoviridae/clasificación , Siphoviridae/genética , Proteínas Virales/genética
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