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Li Y, Yu H, Xiong L, Zeng K, Wei Y, Li H, Ji X. Diversity and function of viral AMGs associated with DNA biosynthesis in the Napahai plateau wetland. Environ Technol 2023:1-15. [PMID: 38126212 DOI: 10.1080/09593330.2023.2296531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Viruses play an important role in microbial community structure and biodiversity by lysing host cells, and can also affect host metabolic pathways by expressing auxiliary metabolic genes (AMGs). As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai has high research value. However, studies on the genetic diversity of AMGs and viruses associated with DNA biosynthesis have not been reported. Based on metagenomics, with the phylogenetic tree, PCoA, and α diversity analysis, we found that three DNA biosynthesis-related viral AMGs (cobS, mazG, and purM) in the Napahai plateau wetland were rich in genetic diversity, uniqueness, and differences compared with other habitats and host sources. Through the KEGG metabolic pathway and metabolic flow analysis of Pseudomonas mandelii (SW-3) and phage (VSW-3), the AMGs (cobS, mazG, and purM) genes of the three related viruses involved in DNA biosynthesis were upregulated and their expression increased significantly. In general, we systematically described the genetic diversity of AMGs associated with DNA biosynthesis in plateau wetland ecosystems and clarified the contribution of viral AMGs in the Napahai plateau wetland to DNA biosynthesis, as well as the changes of metabolites and genes. It further expands the understanding of phage-host interactions, which is of great significance for further revealing the role of viral AMGs in the biological evolution and biogeochemical cycle of wetland ecosystems.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
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Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
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Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
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Li Y, Xiong L, Yu H, Xiang Y, Wei Y, Zhang Q, Ji X. Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland. Environ Sci Pollut Res Int 2023; 30:44430-44438. [PMID: 36692711 DOI: 10.1007/s11356-023-25408-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/15/2023] [Indexed: 01/25/2023]
Abstract
Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yingying Xiang
- Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M, Ravasi T, Webster NS. Viral ecogenomics across the Porifera. Microbiome 2020; 8:144. [PMID: 33008461 PMCID: PMC7532657 DOI: 10.1186/s40168-020-00919-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. RESULTS Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. CONCLUSIONS Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.
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Affiliation(s)
- Cecília Pascelli
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
- James Cook University, Townsville, Australia
| | - Patrick W Laffy
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Emmanuelle Botté
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Miguel Lurgi
- Biosciences Department, University of Swansea, Swansea, Wales
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- AIMS@JCU, Townsville, Queensland, Australia.
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia.
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia.
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Jiang T, Guo C, Wang M, Wang M, Zhang X, Liu Y, Liang Y, Jiang Y, He H, Shao H, McMinn A. Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses. Viruses 2020; 12:v12080800. [PMID: 32722486 PMCID: PMC7472177 DOI: 10.3390/v12080800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/01/2023] Open
Abstract
The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.
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Affiliation(s)
- Tong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Correspondence:
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
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