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Lin W, Li D, Pan L, Li M, Tong Y. Cyanobacteria-cyanophage interactions between freshwater and marine ecosystems based on large-scale cyanophage genomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175201. [PMID: 39102952 DOI: 10.1016/j.scitotenv.2024.175201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
The disparities in harmful algal blooms dynamics are largely attributed to variations in cyanobacteria populations within aquatic ecosystems. However, cyanobacteria-cyanophage interactions and their role in shaping cyanobacterial populations has been previously underappreciated. To address this knowledge gap, we isolated and sequenced 42 cyanophages from diverse water sources in China, with the majority (n = 35) originating from freshwater sources. We designated these sequences as the "Novel Cyanophage Genome sequence Collection" (NCGC). NCGC displayed notable genetic variations, with 95 % (40/42) of the sequences representing previously unidentified taxonomic ranks. By integrating NCGC with public data of cyanophages and cyanobacteria, we found evidence for more frequent historical cyanobacteria-cyanophage interactions in freshwater ecosystems. This was evidenced by a higher prevalence of prophage integrase-related genes in freshwater cyanophages (37.97 %) than marine cyanophages (7.42 %). In addition, freshwater cyanophages could infect a broader range of cyanobacteria orders (n = 4) than marine ones (n = 0). Correspondingly, freshwater cyanobacteria harbored more defense systems per million base pairs in their genomes, indicating more frequent phage infections. Evolutionary and cyanophage epidemiological studies suggest that interactions between cyanobacteria and cyanophages in freshwater and marine ecosystems are interconnected, and that brackish water can act as a transitional zone for freshwater and marine cyanophages. In conclusion, our research significantly expands the genetic information database of cyanophage, offering a wider selection of cyanophages to control harmful cyanobacterial blooms. Additionally, we represent a pioneering large-scale and comprehensive analysis of cyanobacteria and cyanophage sequencing data, and it provides theoretical guidance for the application of cyanophages in different environments.
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Affiliation(s)
- Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lingting Pan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China.
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Ren Y, Shi W, Chen J, Li J. Water quality drives the reconfiguration of riverine planktonic microbial food webs. ENVIRONMENTAL RESEARCH 2024; 249:118379. [PMID: 38331144 DOI: 10.1016/j.envres.2024.118379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
The food web is a cycle of matter and energy within river ecosystems. River environmental changes resulting from human activities are increasingly threatening the composition and diversity of global aquatic organisms and the multi-trophic networks. How multiple environmental factors influence food web patterns among multi-trophic microbial communities in rivers remains largely unknown. Using water quality evaluation and meta-omics techniques, we investigated the composition, structure and interaction characteristics, and drivers of food webs of microorganisms (archaea, bacteria, fungi, protists, metazoa, viridiplantae and viruses) at multiple trophic levels in different water quality environments (Classes II, III, and IV). First, water quality deterioration led to significant changes in the composition of the microbial community at multiple trophic levels, which were represented by the enrichment of Euryarchaeota in the archaeal community, the increase of r-strategists in the bacterial community, and the increase of the proportion of predators in the protist community. Second, deteriorating water quality resulted in a significant reduction in the dissimilarity of community structure (homogenization of community structure in Class III and IV waters). Of the symbiotic, parasitic, and predatory networks, the community networks in Class II water all showed the most stable symbiotic, parasitic, and predatory correlations (higher levels of modularity in the networks). In Class III and IV waters, nutrient inputs have led to increased reciprocal symbiosis and decreased competition between communities, which may have the risk of a positive feedback loop driving a system collapse. Finally, inputs of phosphorus and organic matter could be the main drivers of changes in the planktonic microbial food web in the Fen River. Overall, the results indicated the potential ecological risks of exogenous nutrient inputs, which were important for aquatic ecosystem conservation.
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Affiliation(s)
- Yanmin Ren
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Wei Shi
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China.
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Liu YQ, Chen Y, Li YY, Ding CY, Li BL, Han H, Chen ZJ. Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134085. [PMID: 38522197 DOI: 10.1016/j.jhazmat.2024.134085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/10/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.
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Affiliation(s)
- Yong-Qi Liu
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Yan Chen
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Yu-Ying Li
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Chuan-Yu Ding
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Bai-Lian Li
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Hui Han
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China.
| | - Zhao-Jin Chen
- International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China.
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Duan LY, Zhang Y, Li YY, Li XQ, Liu YQ, Li BL, Ding CY, Ren XM, Duan PF, Han H, Chen ZJ. Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116380. [PMID: 38677068 DOI: 10.1016/j.ecoenv.2024.116380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/30/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 μm, 550 μm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 μm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.
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Affiliation(s)
- Li-Yang Duan
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Yu Zhang
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Yu-Ying Li
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China.
| | - Xiao-Qi Li
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Yong-Qi Liu
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - B Larry Li
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Chuan-Yu Ding
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Xue-Min Ren
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Peng-Fei Duan
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Hui Han
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Zhao-Jin Chen
- Overseas Expertise Introduction Center for Discipline Innovation of Watershed Ecological Security in the Water Source Area of the Mid-line Project of South-to-North Water Diversion, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China.
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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Hu M, Xing B, Yang M, Han R, Pan H, Guo H, Liu Z, Huang T, Du K, Jiang S, Zhang Q, Lu W, Huang X, Zhou C, Li J, Song W, Deng Z, Xiao M. Characterization of a novel genus of jumbo phages and their application in wastewater treatment. iScience 2023; 26:106947. [PMID: 37324530 PMCID: PMC10265529 DOI: 10.1016/j.isci.2023.106947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 05/20/2023] [Indexed: 06/17/2023] Open
Abstract
Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due to their large genome (>200 kb) and unusual biology. To date, only six strains of jumbo phages infecting Klebsiella pneumoniae have been described. Here, we report the isolation and characterization of two jumbo phages from hospital wastewater representing the sixth genus: φKp5130 and φKp9438. Both phages showed lytic activity against broad range of clinical antibiotic-resistant K. pneumoniae strains and distinct physiology including long latent period, small burst size, and high resistance to thermal and pH stress. The treatment of sewage water with the phages cocktail resulted in dramatic decline in K. pneumoniae population. Overall, this study provides detailed molecular and genomics characterization of two novel jumbo phages, expands viral diversity, and provides novel candidate phages to facilitate environmental wastewater treatment.
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Affiliation(s)
- Ming Hu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Bo Xing
- BGI-Shenzhen, Shenzhen 518083, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghua Yang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI College, Zhengzhou University, Zhengzhou 450000, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Rui Han
- BGI-Beijing, Beijing 102601, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huazheng Pan
- Department of The Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Hui Guo
- Department of The Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Zhen Liu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Tao Huang
- Department of Kidney Transplantation, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Kang Du
- University of Science and Technology of China, Hefei 230026, China
| | | | - Qian Zhang
- Department of Prosthodontics, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Wenjing Lu
- Department of Dermatology, Qilu Hospital of Shandong University (Qingdao), Qingdao 266000, China
| | - Xun Huang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410011, China
| | - Congzhao Zhou
- University of Science and Technology of China, Hefei 230026, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Beijing, Beijing 102601, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
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Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages. Viruses 2023; 15:v15020442. [PMID: 36851656 PMCID: PMC9958718 DOI: 10.3390/v15020442] [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: 11/03/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Cyanobacterial expansion is harmful to the environment, the ecology of Lake Baikal and the economy of nearby regions and can be dangerous to people and animals. Since 2011, the process of colonisation of the lake with potentially toxic cyanobacteria belonging to the genus Tychonema has continued. An understanding of the mechanism of successful expansion of Tychonema requires scrutiny of biological and genomic features. Tychonema sp. BBK16 was isolated from the coastal zone of Lake Baikal. The morphology of BBK16 biofilm was studied with light, scanning electron and confocal microscopy. The biofilm is based on filaments of cyanobacteria, which are intertwined like felt; there are also dense fascicles of rope-like twisted filaments that impart heterogeneity to the surface of the biofilm. Genome sequencing, intergenomic comparisons and phylogenetic analyses indicated that Tychonema sp. BBK16 represent a new species related to planktic cyanobacterium Tychonema bourrellyi, isolated from Alpine lentic freshwater. Genome investigation revealed the genes possibly responsible for the mixotrophic lifestyle. The presence of CRISPR-Cas and restriction modification defence mechanisms allowed to suggest the existence of phages infecting Tychonema sp. BBK16. Analysis of CRISPR spacers and prophage-derived regions allowed to suggest related cyanophages. Genomic analysis supported the assumption that mobile elements and horizontal transfer participate in shaping the Tychonema sp. BBK16 genome. The findings of the current research suggest that the aptitude of Tychonema sp. BBK16 for biofilm formation and, possibly, its mixotrophic lifestyle provide adaptation advantages that lead to the successful expansion of this cyanobacterium in the Baikal's conditions of freshwater lake environments.
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Fine structure and assembly pattern of a minimal myophage Pam3. Proc Natl Acad Sci U S A 2023; 120:e2213727120. [PMID: 36656854 PMCID: PMC9942802 DOI: 10.1073/pnas.2213727120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
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Zhu J, Yang F, Du K, Wei ZL, Wu QF, Chen Y, Li WF, Li Q, Zhou CZ. Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer. ENVIRONMENTAL MICROBIOME 2023; 18:3. [PMID: 36639816 PMCID: PMC9837993 DOI: 10.1186/s40793-023-00461-5] [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: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. RESULTS Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. CONCLUSION In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.
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Affiliation(s)
- Jie Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zi-Lu Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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Structural Insights into the Chaperone-Assisted Assembly of a Simplified Tail Fiber of the Myocyanophage Pam3. Viruses 2022; 14:v14102260. [PMID: 36298815 PMCID: PMC9608196 DOI: 10.3390/v14102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail fibers usually requires a chaperone encoded by the phage genome. Despite extensive studies on phage structures, the molecular mechanism of phage tail fiber assembly remains largely unknown. Here, using a minimal myocyanophage, termed Pam3, isolated from Lake Chaohu, we demonstrate that the chaperone gp25 forms a stable complex with the tail fiber gp24 at a stoichiometry of 3:3. The 3.1-Å cryo-electron microscopy structure of this complex revealed an elongated structure with the gp25 trimer embracing the distal moieties of gp24 trimer at the center. Each gp24 subunit consists of three domains: the N-terminal α-helical domain required for docking to the baseplate, the tumor necrosis factor (TNF)-like and glycine-rich domains responsible for recognizing the host receptor. Each gp25 subunit consists of two domains: a non-conserved N-terminal β-sandwich domain that binds to the TNF-like and glycine-rich domains of the fiber, and a C-terminal α-helical domain that mediates trimerization/assembly of the fiber. Structural analysis enabled us to propose the assembly mechanism of phage tail fibers, in which the chaperone first protects the intertwined and repetitive distal moiety of each fiber subunit, further ensures the proper folding of these highly plastic structural elements, and eventually enables the formation of the trimeric fiber. These findings provide the structural basis for the design and engineering of phage fibers for biotechnological applications.
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