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Zhi S, Wu W, Ding Y, Zhang Y, Pan L, Liu G, Li W. Development of rapid nucleic acid testing techniques for common respiratory infectious diseases in the Chinese population. Front Chem 2024; 12:1381738. [PMID: 38694405 PMCID: PMC11061412 DOI: 10.3389/fchem.2024.1381738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/01/2024] [Indexed: 05/04/2024] Open
Abstract
Background: Most respiratory viruses can cause serious lower respiratory diseases at any age. Therefore, timely and accurate identification of respiratory viruses has become even more important. This study focused on the development of rapid nucleic acid testing techniques for common respiratory infectious diseases in the Chinese population. Methods: Multiplex fluorescent quantitative polymerase chain reaction (PCR) assays were developed and validated for the detection of respiratory pathogens including the novel coronavirus (SARS-CoV-2), influenza A virus (FluA), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). Results: The assays demonstrated high specificity and sensitivity, allowing for the simultaneous detection of multiple pathogens in a single reaction. These techniques offer a rapid and reliable method for screening, diagnosis, and monitoring of respiratory pathogens. Conclusion: The implementation of these techniques might contribute to effective control and prevention measures, leading to improved patient care and public health outcomes in China. Further research and validation are needed to optimize and expand the application of these techniques to a wider range of respiratory pathogens and to enhance their utility in clinical and public health settings.
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Affiliation(s)
- Shenshen Zhi
- Department of Blood Transfusion, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyan Wu
- Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Yan Ding
- Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Yuanyuan Zhang
- Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Liyan Pan
- Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Guo Liu
- Zeal Dental, Chongqing, China
| | - Wei Li
- Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
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Wallace BA, Varona NS, Hesketh-Best PJ, Stiffler AK, Silveira CB. Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions. THE ISME JOURNAL 2024; 18:wrae132. [PMID: 39030686 PMCID: PMC11309003 DOI: 10.1093/ismejo/wrae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 07/18/2024] [Indexed: 07/21/2024]
Abstract
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.
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Affiliation(s)
- Bailey A Wallace
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Poppy J Hesketh-Best
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, United States
| | - Alexandra K Stiffler
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
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Chen Q, Lønborg C, Chen F, Zhang R, Cai R, Li Y, He C, Shi Q, Jiao N, Zheng Q. Bottom-up and top-down controls on Alteromonas macleodii lead to different dissolved organic matter compositions. ISME COMMUNICATIONS 2024; 4:ycae010. [PMID: 38469454 PMCID: PMC10926778 DOI: 10.1093/ismeco/ycae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/24/2023] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
The effects of both bottom-up (e.g. substrate) and top-down (e.g. viral lysis) controls on the molecular composition of dissolved organic matter have not been investigated. In this study, we investigated the dissolved organic matter composition of the model bacterium Alteromonas macleodii ATCC 27126 growing on different substrates (glucose, laminarin, extracts from a Synechococcus culture, oligotrophic seawater, and eutrophic seawater), and infected with a lytic phage. The ultra-high resolution mass spectrometry analysis showed that when growing on different substrates Alteromonas macleodii preferred to use reduced, saturated nitrogen-containing molecules (i.e. O4 formula species) and released or preserved oxidized, unsaturated sulfur-containing molecules (i.e. O7 formula species). However, when infected with the lytic phage, Alteromonas macleodii produced organic molecules with higher hydrogen saturation, and more nitrogen- or sulfur-containing molecules. Our results demonstrate that bottom-up (i.e. varying substrates) and top-down (i.e. viral lysis) controls leave different molecular fingerprints in the produced dissolved organic matter.
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Affiliation(s)
- Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, China
| | - Christian Lønborg
- Section for Marine Diversity and Experimental Ecology, Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, United States
| | - Rui Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, China
| | - Yunyun Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, China
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Zhang T, Zhou K, Wang Y, Xu J, Zheng Q, Luo T, Jiao N. Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen. Front Microbiol 2023; 14:1292150. [PMID: 38059125 PMCID: PMC10696648 DOI: 10.3389/fmicb.2023.1292150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.
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Affiliation(s)
- Ting Zhang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Kun Zhou
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Yanhui Wang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jinxin Xu
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zheng
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Tingwei Luo
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Nianzhi Jiao
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
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Li Y, Yun H, Chen R, Jiao N, Zheng Q, Yang Y, Zhang R. Characterization of a Vibriophage Infecting Pathogenic Vibrio harveyi. Int J Mol Sci 2023; 24:16202. [PMID: 38003392 PMCID: PMC10671443 DOI: 10.3390/ijms242216202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial diseases caused by Vibrio spp. are prevalent in aquaculture and can lead to high mortality rates among aquatic species and significant economic losses. With the increasing emergence of multidrug-resistant Vibrio strains, phage therapy is being explored as a potential alternative to antibiotics for biocontrol of infectious diseases. Here, a new lytic phage named vB_VhaS_R21Y (R21Y) was isolated against Vibrio harveyi BVH1 obtained from seawater from a scallop-farming area in Rongcheng, China. Its morphology, infection cycle, lytic profile, phage stability, and genetic features were characterized. Transmission electronic microscopy indicated that R21Y is siphovirus-like, comprising an icosahedral head (diameter 73.31 ± 2.09 nm) and long noncontractile tail (205.55 ± 0.75 nm). In a one-step growth experiment, R21Y had a 40-min latent period and a burst size of 35 phage particles per infected cell. R21Y was highly species-specific in the host range test and was relatively stable at pH 4-10 and 4-55 °C. Genomic analysis showed that R21Y is a double-stranded DNA virus with a genome size of 82,795 bp and GC content of 47.48%. Its high tolerance and lytic activity indicated that R21Y may be a candidate for phage therapy in controlling vibriosis in aquacultural systems.
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Affiliation(s)
- Yingying Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
| | - Huayi Yun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Ruo Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Yunlan Yang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
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Peng Y, Lu Z, Pan D, Shi LD, Zhao Z, Liu Q, Zhang C, Jia K, Li J, Hubert CRJ, Dong X. Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species. THE ISME JOURNAL 2023; 17:1774-1784. [PMID: 37573455 PMCID: PMC10504277 DOI: 10.1038/s41396-023-01491-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial and archaeal viruses. However, little is known about viral genetic features and evolutionary patterns in these environments. Here, we examined the evolutionary ecology of viruses across active and extinct seep stages in the area of Haima cold seeps in the South China Sea. A total of 338 viral operational taxonomic units are identified and linked to 36 bacterial and archaeal phyla. The dynamics of host-virus interactions are informed by diverse antiviral defense systems across 43 families found in 487 microbial genomes. Cold seep viruses are predicted to harbor diverse adaptive strategies to persist in this environment, including counter-defense systems, auxiliary metabolic genes, reverse transcriptases, and alternative genetic code assignments. Extremely low nucleotide diversity is observed in cold seep viral populations, being influenced by factors including microbial host, sediment depth, and cold seep stage. Most cold seep viral genes are under strong purifying selection with trajectories that differ depending on whether cold seeps are active or extinct. This work sheds light on the understanding of environmental adaptation mechanisms and evolutionary patterns of viruses in the sub-seafloor biosphere.
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Affiliation(s)
- Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Zijian Lu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Donald Pan
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhao Zhao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Qing Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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Chen Y, Li W, Shi K, Fang Z, Yang Y, Zhang R. Isolation and characterization of a novel phage belonging to a new genus against Vibrio parahaemolyticus. Virol J 2023; 20:81. [PMID: 37127579 PMCID: PMC10152775 DOI: 10.1186/s12985-023-02036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. METHODS A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. RESULTS R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. CONCLUSIONS In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.
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Affiliation(s)
- Yubing Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Wenqing Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Keming Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zheng Fang
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China.
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An Estuarine Cyanophage S-CREM1 Encodes Three Distinct Antitoxin Genes and a Large Number of Non-Coding RNA Genes. Viruses 2023; 15:v15020380. [PMID: 36851594 PMCID: PMC9964418 DOI: 10.3390/v15020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Cyanophages play important roles in regulating the population dynamics, community structure, metabolism, and evolution of cyanobacteria in aquatic ecosystems. Here, we report the genomic analysis of an estuarine cyanophage, S-CREM1, which represents a new genus of T4-like cyanomyovirus and exhibits new genetic characteristics. S-CREM1 is a lytic phage which infects estuarine Synechococcus sp. CB0101. In contrast to many cyanomyoviruses that usually have a broad host range, S-CREM1 only infected the original host strain. In addition to cyanophage-featured auxiliary metabolic genes (AMGs), S-CREM1 also contains unique AMGs, including three antitoxin genes, a MoxR family ATPase gene, and a pyrimidine dimer DNA glycosylase gene. The finding of three antitoxin genes in S-CREM1 implies a possible phage control of host cells during infection. One small RNA (sRNA) gene and three cis-regulatory RNA genes in the S-CREM1 genome suggest potential molecular regulations of host metabolism by the phage. In addition, S-CREM1 contains a large number of tRNA genes which may reflect a genomic adaption to the nutrient-rich environment. Our study suggests that we are still far from understanding the viral diversity in nature, and the complicated virus-host interactions remain to be discovered. The isolation and characterization of S-CREM1 further our understanding of the gene diversity of cyanophages and phage-host interactions in the estuarine environment.
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Zhang X, Liang Y, Zheng K, Wang Z, Dong Y, Liu Y, Ren L, Wang H, Han Y, McMinn A, Sung YY, Mok WJ, Wong LL, He J, Wang M. Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms. Front Microbiol 2023; 14:1161265. [PMID: 37213492 PMCID: PMC10196503 DOI: 10.3389/fmicb.2023.1161265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 05/23/2023] Open
Abstract
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.
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Affiliation(s)
- Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Antarctic Great Wall Ecology National Observation and Research Station, MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ying Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Jianfeng He
- Antarctic Great Wall Ecology National Observation and Research Station, MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
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10
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Zhang Z, Wu Z, Liu H, Yang M, Wang R, Zhao Y, Chen F. Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus. Front Microbiol 2023; 14:1164101. [PMID: 37138617 PMCID: PMC10149686 DOI: 10.3389/fmicb.2023.1164101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world's oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters.
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Affiliation(s)
- Zefeng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yanlin Zhao,
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
- Feng Chen,
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11
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Jia K, Peng Y, Chen X, Jian H, Jin M, Yi Z, Su M, Dong X, Yi M. A Novel Inovirus Reprograms Metabolism and Motility of Marine Alteromonas. Microbiol Spectr 2022; 10:e0338822. [PMID: 36301121 PMCID: PMC9769780 DOI: 10.1128/spectrum.03388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023] Open
Abstract
Members from the Inoviridae family with striking features are widespread, highly diverse, and ecologically pervasive across multiple hosts and environments. However, a small number of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ϕAFP1, was isolated from the South China Sea and represented a novel genus of Inoviridae. ϕAFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed ϕAFP1 could be regarded as genetic mosaics having homologous sequences with Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to ϕAFP1 infection revealed that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways, and degradation of multiple amino acid pathways at the plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that ϕAFP1 might hijack the energy of the host for the synthesis of phage proteins. ϕAFP1 exerted step-by-step control on host genes through the appropriate level of utilizing host resources. Our study provided novel information for a better understanding of filamentous phage characteristics and phage-host interactions. IMPORTANCE Alteromonas is widely distributed and plays a vital role in biogeochemical in marine environments. However, little information about Alteromonas phages is available. Here, we isolated and characterized the biological characteristics and genome sequence of a novel inovirus infecting Alteromonas abrolhosensis, designated ϕAFP1, representing a novel viral genus of Inoviridae. We then presented a comprehensive view of the ϕAFP1 phage-Alteromonas abrolhosensis interactions, elucidating reprogramed host metabolism and motility. Our study provided novel information for better comprehension of filamentous phage characteristics and phage-host interactions.
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Affiliation(s)
- Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xueji Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Min Jin
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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12
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Abstract
Alteromonas is an opportunistic marine bacterium that persists in the global ocean and has important ecological significance. However, current knowledge about the diversity and ecology of alterophages (phages that infect Alteromonas) is lacking. Here, three similar phages infecting Alteromonas macleodii ATCC 27126T were isolated and physiologically characterized. Transmission electron microscopy revealed Siphoviridae morphology, with an oblate icosahedral head and a long noncontractile tail. Notably, these members displayed a small burst size (15–19 plaque-forming units/cell) yet an extensively broad host spectrum when tested on 175 Alteromonas strains. Such unique infection kinetics are potentially associated with discrepancies in codon usage bias from the host tRNA inventory. Phylogenetic analysis indicated that the three phages are closely evolutionarily related; they clustered at the species level and represent a novel genus. Three auxiliary metabolic genes with roles in nucleotide metabolism and putative biofilm dispersal were found in these phage genomes, which revealed important biogeochemical significance of these alterophages in marine ecosystems. Our isolation and characterization of these novel phages expand the current understanding of alterophage diversity, evolution, and phage–host interactions. IMPORTANCE The marine bacterium Alteromonas is prevalent in the global ocean with crucial ecological significance; however, little is known about the diversity and evolution of its bacteriophages that profoundly affect the bacterial communities. Our study characterized a novel genus of three newly isolated Alteromonas phages that exhibited a distinct infection strategy of broad host spectrum and small burst size. This strategy is likely a consequence of the viral trade-off between virulence and lysis profiles during phage–host coevolution, and our work provides new insight into viral evolution and infection strategies.
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13
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Dong Y, Zheng K, Zou X, Liang Y, Liu Y, Li X, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster. Front Microbiol 2022; 13:853973. [PMID: 35432264 PMCID: PMC9011153 DOI: 10.3389/fmicb.2022.853973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
- *Correspondence: Yantao liang,
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Xiang Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
- Min Wang,
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14
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Zheng H, Liu B, Xu Y, Zhang Z, Man H, Liu J, Chen F. An Inducible Microbacterium Prophage vB_MoxS-R1 Represents a Novel Lineage of Siphovirus. Viruses 2022; 14:v14040731. [PMID: 35458461 PMCID: PMC9030533 DOI: 10.3390/v14040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a Microbacterium strain isolated from an estuarine Synechococcus culture. vB_MoxS-R1 has a high replication capability, with an estimated burst size of 2000 virions per cell. vB_MoxS-R1 represents a novel phage genus-based genomic analysis. Six transcriptional regulator (TR) genes were predicted in the vB_MoxS-R1 genome. Four of these TR genes are involved in stress responses, virulence and amino acid transportation in bacteria, suggesting that they may play roles in regulating the host cell metabolism in response to external environmental changes. A glycerophosphodiester phosphodiesterase gene related to phosphorus acquisition was also identified in the vB_MoxS-R1 genome. The presence of six TR genes and the phosphorus-acquisition gene suggests that prophage vB_MoxS-R1 has the potential to influence survival and adaptation of its host during lysogeny. Possession of four endonuclease genes in the prophage genome suggests that vB_MoxS-R1 is likely involved in DNA recombination or gene conversion and further influences host evolution.
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Affiliation(s)
- Hongrui Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361000, China
- Correspondence: (Y.X.); (J.L.)
| | - Zefeng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Hongcong Man
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China
- Correspondence: (Y.X.); (J.L.)
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA;
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15
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Ma R, Shao S, Wei S, Ye J, Yang Y, Jiao N, Zhang R. A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum. Viruses 2022; 14:v14030512. [PMID: 35336919 PMCID: PMC8953757 DOI: 10.3390/v14030512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/26/2022] [Accepted: 03/01/2022] [Indexed: 02/05/2023] Open
Abstract
This study isolated and characterized a new phage infecting the marine photoheterotrophic bacterium Citromicrobium bathyomarinum, which fills the gap in research on phages targeting this ecologically important species. The phage vB_CbaS-RXM (RXM) has a dsDNA genome with a length of 104,206 bp and G+C content of 61.64%. The taxonomic analysis found a close evolutionary relationship between RXM, Erythrobacter phage vB_EliS-L02, and Sphingobium phage Lacusarx, and we propose that RXM represents a new species of the Lacusarxvirus genus. A one-step growth curve revealed a burst size of 75 plaque-forming units (PFUs) per cell in a 3-hour infection cycle. The lysis profile of RXM showed an intraspecific lethal rate of 26.3% against 38 citromicrobial strains. RXM contains 15 auxiliary metabolic genes (AMGs) related to diverse cellular processes, such as putative metabolic innovation and hijacking of host nucleotide metabolism to enhance its biosynthetic capacity. An in-depth analysis showed that phage functional genes strongly rely on the host for translation, while the translation of unique phage genes with less host dependency may be complemented by phage tRNA. Overall, our study investigated the infection kinetics, genetic traits, taxonomy, and predicted roles of AMGs and tRNA genes of this new phage, which contributes to a better understanding of phage diversity and phage–bacterium interactions.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.M.); (S.W.); (Y.Y.); (N.J.)
| | - Shuai Shao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (S.S.); (J.Y.)
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.M.); (S.W.); (Y.Y.); (N.J.)
| | - Junlei Ye
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (S.S.); (J.Y.)
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.M.); (S.W.); (Y.Y.); (N.J.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.M.); (S.W.); (Y.Y.); (N.J.)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.M.); (S.W.); (Y.Y.); (N.J.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
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16
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Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021; 9:e0046321. [PMID: 34643440 PMCID: PMC8515928 DOI: 10.1128/spectrum.00463-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
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.
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17
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A New Enterobacter cloacae Bacteriophage EC151 Encodes the Deazaguanine DNA Modification Pathway and Represents a New Genus within the Siphoviridae Family. Viruses 2021; 13:v13071372. [PMID: 34372577 PMCID: PMC8310023 DOI: 10.3390/v13071372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.
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