1
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Su Y, Yu H, Gao C, Sun S, Liang Y, Liu G, Zhang X, Dong Y, Liu X, Chen G, Shao H, McMinn A, Wang M. Effects of vegetation cover and aquaculture pollution on viral assemblages in mangroves sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135147. [PMID: 39029189 DOI: 10.1016/j.jhazmat.2024.135147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/07/2024] [Accepted: 07/06/2024] [Indexed: 07/21/2024]
Abstract
Mangrove forests, a critical coastal ecosystem, face numerous anthropogenic threats, particularly from aquaculture activities. Despite the acknowledged significance of viruses in local and global biogeochemical cycles, there is limited knowledge regarding the community structure, genomic diversity, and ecological roles of viruses in mangrove forests ecosystems, especially regarding their responses to aquaculture. In this study, we identified 17,755 viral operational taxonomic units (vOTUs) from nine sediments viromes across three distinct ecological regions of the mangrove forests ecosystem: mangrove, bare flat, and aquaculture regions. Viral assemblages varied among three regions, and the pathogenic viruses associated with marine animals, such as the white spot syndrome virus (WSSV) from Nimaviridae, were identified in this study. The relative abundance of Nimaviridae in the bare flat region was higher than in other regions. Furthermore, viruses in distinct mangrove forests sediments regions have adapted to their environments by adopting distinct survival strategies and encoding various auxiliary metabolic genes involved in carbon metabolism and antibiotic resistance. These adaptations may have profound impacts on biogeochemical cycles. This study provides the first insights into the effects of vegetation cover and aquaculture on the community structure and ecological roles of viruses in mangrove forests sediments. These findings are crucial for understanding the risks posed by anthropogenic threats to mangrove forests ecosystems and informing effective management strategies.
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Affiliation(s)
- Yue Su
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Chen Gao
- Haide College, Ocean University of China, Qingdao, China
| | - Shujuan Sun
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China.
| | - Gang Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xiaoshou Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, 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, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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2
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Kutralam-Muniasamy G, Shruti VC, Pérez-Guevara F. Plastisphere-hosted viruses: A review of interactions, behavior, and effects. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134533. [PMID: 38749241 DOI: 10.1016/j.jhazmat.2024.134533] [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: 03/06/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.
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Affiliation(s)
- Gurusamy Kutralam-Muniasamy
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Ciudad de México, México.
| | - V C Shruti
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Ciudad de México, México
| | - Fermín Pérez-Guevara
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Ciudad de México, México; Nanoscience & Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Ciudad de México, México
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3
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Chen PWY, Olivia M, Gong GC, Jan S, Tsai AY. Viral Dynamics in the Tropical Pacific Ocean: A Comparison between Within and Outside a Warm Eddy. Viruses 2024; 16:937. [PMID: 38932229 PMCID: PMC11209615 DOI: 10.3390/v16060937] [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: 03/30/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In mesoscale eddies, the chemical properties and biological composition are different from those in the surrounding water due to their unique physical processes. The mechanism of physical-biological coupling in warm-core eddies is unclear, especially because no studies have examined the effects of environmental factors on bacteria and viruses. The purpose of the present study was to examine the influence of an anticyclonic warm eddy on the relationship between bacterial and viral abundances, as well as viral activity (viral production), at different depths. At the core of the warm eddy, the bacterial abundance (0.48 to 2.82 × 105 cells mL-1) fluctuated less than that outside the eddy (1.12 to 7.03 × 105 cells mL-1). In particular, there was a four-fold higher viral-bacterial abundance ratio (VBR) estimated within the eddy, below the layer of the deep chlorophyll maximum, than outside the eddy. An anticyclonic warm eddy with downwelling at its center may contribute to viruses being transmitted directly into the deep ocean through adsorption on particulate organic matter while sinking. Overall, our findings provide valuable insights into the interaction between bacterial and viral abundances and their ecological mechanisms within a warm eddy.
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Affiliation(s)
- Patrichka Wei-Yi Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Madeline Olivia
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Sen Jan
- Institute of Oceanography, National Taiwan University, Taipei 106319, Taiwan;
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
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Yu M, Zhang M, Zeng R, Cheng R, Zhang R, Hou Y, Kuang F, Feng X, Dong X, Li Y, Shao Z, Jin M. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun 2024; 15:3228. [PMID: 38622147 PMCID: PMC11018836 DOI: 10.1038/s41467-024-47600-1] [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: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
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Affiliation(s)
- Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Ruolin Cheng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Fangfang Kuang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xiyang Dong
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Yinfang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
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5
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Wei W, Tian Y, Cai L, Xu Y, Xiao X, Wang Q, Wang H, Dong C, Shao Z, Jiao N, Zhang R. Survival of surface bacteriophages and their hosts in in situ deep-sea environments. Microbiol Spectr 2024; 12:e0453422. [PMID: 38051228 PMCID: PMC10783000 DOI: 10.1128/spectrum.04534-22] [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: 11/08/2022] [Accepted: 10/27/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE The survival of the sinking prokaryotes and viruses in the deep-sea environment is crucial for deep-sea ecosystems and biogeochemical cycles. Through an in situ deep-sea long-term incubation device, our results showed that viral particles and infectivity had still not decayed completely after in situ incubation for 1 year. This suggests that, via infection and lysis, surface viruses with long-term infectious activity in situ deep-sea environments may influence deep-sea microbial populations in terms of activity, function, diversity, and community structure and ultimately affect deep-sea biogeochemical cycles, highlighting the need for additional research in this area.
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Affiliation(s)
- Wei Wei
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiong Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Haowen Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - 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, China
| | - 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, China
- Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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6
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Joffe N, Kuhlisch C, Schleyer G, Ahlers NS, Shemi A, Vardi A. Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga. THE ISME JOURNAL 2024; 18:wrae038. [PMID: 38452203 PMCID: PMC10980834 DOI: 10.1093/ismejo/wrae038] [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: 11/30/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Algal blooms drive global biogeochemical cycles of key nutrients and serve as hotspots for biological interactions in the ocean. The massive blooms of the cosmopolitan coccolithophore Emiliania huxleyi are often infected by the lytic E. huxleyi virus, which is a major mortality agent triggering bloom demise. This multi-annual "boom and bust" pattern of E. huxleyi blooms suggests that coexistence is essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from an E. huxleyi culture that recovered from viral infection. The recovered population coexists with the virus, as host cells continue to divide in parallel to viral production. By applying single-molecule fluorescence in situ hybridization (smFISH) to quantify the fraction of infected cells, and assessing infection-specific lipid biomarkers, we identified a small subpopulation of cells that were infected and produced new virions, whereas most of the host population could resist infection. To further assess population heterogeneity, we generated clonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to E. huxleyi virus infection. This unraveled substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, highlighting that infection outcome may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives the host-virus coexistence and demonstrate how the coexistence with a lytic virus provides an ecological advantage for the host by killing competing strains.
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Affiliation(s)
- Nir Joffe
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, 07745 Jena, Germany
| | - Nadia S Ahlers
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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7
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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [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: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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8
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Burian A, Gruber-Dorninger M, Schweichart J, Yasindi A, Bulling M, Jirsa F, Winter C, Muia AW, Schagerl M. Drivers of microbial food-web structure along productivity gradients. Proc Biol Sci 2023; 290:20231531. [PMID: 37876193 PMCID: PMC10598424 DOI: 10.1098/rspb.2023.1531] [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: 08/29/2022] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Ratios between viruses, heterotrophic prokaryotes and chlorophyll a are key indicators of microbial food structure and both virus-prokaryote and prokaryote-chlorophyll ratios have been proposed to decrease with system productivity. However, the mechanisms underlying these responses are still insufficiently resolved and their consistency across aquatic ecosystem types requires critical evaluation. We assessed microbial community ratios in highly productive African soda-lakes and used our data from naturally hypereutrophic systems which are largely underrepresented in literature, to complement earlier across-system meta-analyses. In contrast to marine and freshwater systems, prokaryote-chlorophyll ratios in African soda-lakes did not decrease along productivity gradients. High-resolution time series from two soda-lakes indicated that this lack of response could be driven by a weakened top-down control of heterotrophic prokaryotes. Our analysis of virus-prokaryote relationships, revealed a reduction of virus-prokaryote ratios by high suspended particle concentrations in soda-lakes. This effect, likely driven by the adsorption of free-living viruses, was also found in three out of four additionally analysed marine datasets. However, the decrease of virus-prokaryote ratios previously reported in highly productive marine systems, was neither detectable in soda-lakes nor freshwaters. Hence, our study demonstrates that system-specific analyses can reveal the diversity of mechanisms that structure microbial food-webs and shape their response to productivity increases.
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Affiliation(s)
- Alfred Burian
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
- Marine Ecology Department, Lurio University, Nampula, Mozambique
| | | | - Johannes Schweichart
- Biology Centre, University of South Bohemia in České, České Budějovice, Czech Republic
| | - Andrew Yasindi
- Department of Biological Sciences, Egerton University, Njoro, Kenya
| | - Mark Bulling
- Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Franz Jirsa
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Christian Winter
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Michael Schagerl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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9
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Zhang E, Zhang S, Li G, Zhang Z, Liu J. Identification and Verification of Candidate miRNA Biomarkers with Application to Infection with Emiliania huxleyi Virus. Genes (Basel) 2023; 14:1716. [PMID: 37761856 PMCID: PMC10531489 DOI: 10.3390/genes14091716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The interactions of Emiliania huxleyi and its specific lytic virus (EhV) have a profound influence on marine biogeochemical carbon-sulfur cycles and play a prominent role in global climate change. MicroRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential due to their role in virus-host interactions. However, the application of miRNA signatures as diagnostic markers in marine viral infection has made limited progress. Based on our previous small-RNA sequencing data, one host miRNA biomarker that is upregulated in early infection and seven viral miRNA biomarkers that are upregulated in late infection were identified and verified using qRT-PCR and a receiver operating characteristic curve analysis in pure culture, mixed culture, and natural seawater culture. The host ehx-miR20-5p was able to significantly differentiate infection groups from the control in the middle (24 h post-infection, hpi) and late infection (48 hpi) phases, while seven virus-derived miRNA biomarkers could diagnose the early and late stages of EhV infection. Functional enrichment analysis showed that these miRNAs participated in numerous essential metabolic pathways, including gene transcription and translation, cell division-related pathways, protein-degradation-related processes, and lipid metabolism. Additionally, a dual-luciferase reporter assay confirmed the targeted relationship between a viral ehv-miR7-5p and the host dihydroceramide desaturase gene (hDCD). This finding suggests that the virus-derived miRNA has the ability to inhibit the host sphingolipid metabolism, which is a specific characteristic of EhV infection during the late stage. Our data revealed a cluster of potential miRNA biomarkers with significant regulatory functions that could be used to diagnose EhV infection, which has implications for assessing the infectious activity of EhV in a natural marine environment.
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Affiliation(s)
| | | | | | | | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China; (E.Z.); (S.Z.); (G.L.); (Z.Z.)
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10
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Grazing on Marine Viruses and Its Biogeochemical Implications. mBio 2023; 14:e0192121. [PMID: 36715508 PMCID: PMC9973340 DOI: 10.1128/mbio.01921-21] [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] [Indexed: 01/31/2023] Open
Abstract
Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.
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11
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Isolation, characterization, and comparative genomic analysis of vB_BviS-A10Y, a novel bacteriophage from mangrove sediments. Arch Virol 2023; 168:54. [PMID: 36609927 DOI: 10.1007/s00705-022-05637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/24/2022] [Indexed: 01/09/2023]
Abstract
Mangrove is among the most carbon-rich biomes on earth, and viruses are believed to play a significant role in modulating local and global carbon cycling. However, few viruses have been isolated from mangrove sediments to date. Here, we report the isolation of a novel Bacillus phage (named phage vB_BviS-A10Y) from mangrove sediments. Phage vB_BviS-A10Y has a hexameric head with a diameter of ~ 79.22 nm and a tail with a length of ~ 548.56 nm, which are typical features of siphophages. vB_BviS-A10Y initiated host lysis at 3.5 h postinfection with a burst size of 25 plaque-forming units (PFU)/cell. The genome of phage vB_BviS-A10Y is 162,435 bp long with 225 predicted genes, and the GC content is 34.03%. A comparison of the whole genome sequence of phage vB_BviS-A10Y with those of other phages from the NCBI viral genome database showed that phage vB_BviS-A10Y has the highest similarity (73.7% identity with 33% coverage) to Bacillus phage PBC2. Interestingly, abundant auxiliary metabolic genes (AMGs) were identified in the vB_BviS-A10Y genome. The presence of a β-1,3-glucosyltransferase gene in the phage genome supported our previous hypothesis that mangrove viruses may manipulate carbon cycling directly through their encoded carbohydrate-active enzyme (CAZyme) genes. Therefore, our study will contribute to a better understanding of the diversity and potential roles of viruses in mangrove ecosystems.
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12
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Cai L, Feng C, Xie L, Xu B, Wei W, Jiao N, Zhang R. Ecological dynamics and impacts of viruses in Chinese and global estuaries. WATER RESEARCH 2022; 226:119237. [PMID: 36244143 DOI: 10.1016/j.watres.2022.119237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Estuaries are important ecosystems providing irreplaceable services for humankind and, in turn, are extensively influenced by human activities and climate changes. Microbial processes, which are largely controlled by viruses, are always responsible for the ecological function and environmental problems in estuaries. However, we know little about the ecology and importance of viruses in estuarine systems. Here, we investigated viral ecological dynamics in estuarine systems on local (four largest estuaries in China in different seasons) and global scales. Viral production varied by almost 20-fold in Chinese estuaries with significant seasonality, being responsible for the removal of 1.41%-21.45% of the bacterioplankton standing stock each day, and contributed directly to the organic carbon pool by releasing an average of 3.57 µg of cellular carbon per liter per day. By compiling data from 21 estuaries across the world, we found for the first time that viral population size peaked at mid-latitude and viral production increased towards the equator in estuarine ecosystems. The results indicated the higher viral impact on microbial mortality and dissolved organic matter cycling in tropical estuaries. Our field investigation and global synthesized analysis provide compelling evidence of spatiotemporal variations in estuarine viral dynamics. The global view of viral impacts on estuarine microbial mortality offers important insight for incorporating viruses into ecological models and understanding the environmental implications of the tropicalization of temperate aquatic ecosystems under a scenario of climate warming.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chao Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Le Xie
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China; Department of Ocean Science and Engineering, Southern University of Science and Technology, Guangdong, China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong, China.
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13
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Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean. THE ISME JOURNAL 2022; 16:1668-1675. [PMID: 35365738 PMCID: PMC9123201 DOI: 10.1038/s41396-022-01224-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 12/03/2022]
Abstract
Particle sinking is an important process in the ocean, influencing the biogeochemical cycle and driving the long-term preservation of carbon into the deep sea via the biological pump. However, as an important component of marine ecosystems, the role of viruses during sinking is still poorly understood. Therefore, we performed a series of transplantation experiments in the South China Sea to simulate environmental changes during sinking and investigate their effects on viral eco-dynamics and life strategy. Our study demonstrated increased viral production but decreased virus-mediated bacterial mortality after transplantation. A larger burst size and switch from the lysogenic to lytic strategy were shown to contribute to enhanced viral productivity. We provide experimental evidence that surface viral ecological characteristics changed dramatically after transplantation into deep-sea waters, indicating a potential importance of viruses during vertical sinking in the ocean. This effect probably provides positive feedback on the efficiency of the biological pump.
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14
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Ding W, Wang R, Liang Z, Zhang R, Qian PY, Zhang W. Expanding our understanding of marine viral diversity through metagenomic analyses of biofilms. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:395-404. [PMID: 37073293 PMCID: PMC10077207 DOI: 10.1007/s42995-020-00078-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/06/2020] [Indexed: 05/03/2023]
Abstract
Recent metagenomics surveys have provided insights into the marine virosphere. However, these surveys have focused solely on viruses in seawater, neglecting those associated with biofilms. By analyzing 1.75 terabases of biofilm metagenomic data, 3974 viral sequences were identified from eight locations around the world. Over 90% of these viral sequences were not found in previously reported datasets. Comparisons between biofilm and seawater metagenomes identified viruses that are endemic to the biofilm niche. Analysis of viral sequences integrated within biofilm-derived microbial genomes revealed potential functional genes for trimeric autotransporter adhesin and polysaccharide metabolism, which may contribute to biofilm formation by the bacterial hosts. However, more than 70% of the genes could not be annotated. These findings show marine biofilms to be a reservoir of novel viruses and have enhanced our understanding of natural virus-bacteria ecosystems.
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Affiliation(s)
- Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Ruojun Wang
- Department of Ocean Sciences, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhicong Liang
- Department of Mathematics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005 China
| | - Pei-Yuan Qian
- Department of Ocean Sciences, Hong Kong University of Science and Technology, Hong Kong, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
- Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266100 China
- Department of Ocean Sciences, Hong Kong University of Science and Technology, Hong Kong, China
- Fok Ying Tung Research Institute, Hong Kong University of Science and Technology, Guangzhou, 510000 China
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15
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Cook R, Hooton S, Trivedi U, King L, Dodd CER, Hobman JL, Stekel DJ, Jones MA, Millard AD. Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. MICROBIOME 2021; 9:65. [PMID: 33743832 PMCID: PMC7981956 DOI: 10.1186/s40168-021-01010-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. RESULTS Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. CONCLUSIONS The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.
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Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Steve Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Liz King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Andrew D Millard
- Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK.
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16
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Zhao Y, Zhao Y, Zheng S, Zhao L, Li X, Zhang W, Grégori G, Xiao T. Virioplankton distribution in the tropical western Pacific Ocean in the vicinity of a seamount. Microbiologyopen 2020; 9:1207-1224. [PMID: 32180355 PMCID: PMC7294315 DOI: 10.1002/mbo3.1031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 11/05/2022] Open
Abstract
The shallow Caroline Seamount is located in the tropical western Pacific Ocean. Its summit is 57 m below the surface and penetrates the euphotic zone. Therefore, it is ideal for the study of the influence of seamount on plankton distribution. Here, virioplankton abundance and distribution were investigated by flow cytometry (FCM) in the Caroline Seamount in August and September 2017. The total abundance of virus‐like particles (VLP) was in the range of 0.64 × 106–18.77 × 106 particles/ml and the average was 5.37 ± 3.75 × 106 particles/ml. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensities were identified. Above the deep chlorophyll maximum (DCM), two medium fluorescence virus (MFV) subclusters were discriminated. Between the DCM and the deeper layers, only one MFV subcluster was resolved. In general, low fluorescence viruses (LFV) comprised the most abundant subclusters. In the 75–150 m water column, however, the MFV abundance was higher than the LFV abundance. High fluorescence viruses (HFV) constituted the least abundant subcluster throughout the entire water column. Virioplankton abundance was significantly enhanced at the seamount stations. Environmental factors including water temperature and nitrate concentration were the most correlated with the variation in virioplankton abundance at the seamount stations. Interactions between shallow seamounts and local currents can support large virus standing stocks, causing a so‐called indirect “seamount effect” on the virioplankton.
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Affiliation(s)
- Yanchu Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shan Zheng
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Jiaozhou Bay Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wuchang Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Gérald Grégori
- Aix-Marseille University, Toulon University, CNRS, IRD, Mediterranean Institute of Oceanography UM110, Marseille, France
| | - Tian Xiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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17
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Wei W, Wang N, Cai L, Zhang C, Jiao N, Zhang R. Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary. MICROBIAL ECOLOGY 2019; 78:843-854. [PMID: 30972435 PMCID: PMC6842343 DOI: 10.1007/s00248-019-01362-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 106 viruses ml-1, 7.98 ± 2.33 to 16.27 ± 2.85% h-1 and 0.80 ± 0.23 to 3.74 ± 0.98% h-1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.
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Affiliation(s)
- Wei Wei
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nannan Wang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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18
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Chen X, Wei W, Wang J, Li H, Sun J, Ma R, Jiao N, Zhang R. Tide driven microbial dynamics through virus-host interactions in the estuarine ecosystem. WATER RESEARCH 2019; 160:118-129. [PMID: 31136846 DOI: 10.1016/j.watres.2019.05.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/11/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Microbes drive ecosystems and their viruses manipulate these processes, yet the importance of tidal functioning on the estuarine viruses and microbes remains poorly elucidated. Here, an integrative investigation on tidal patterns in viral and microbial communities and their inherent interactions over an entire spring-neap tidal cycle was conducted along a macrotidal subtropical estuary. The viral and microbial abundances oscillated significantly over the tidal cycle with relatively higher abundances observed at spring tide compared to neap tide. The distinct tidal dynamic patterns in bacterial production and community composition were tightly associated with the variations in viral infection, production and decay, revealing the tide-driven interactions between viruses and microbes. Concurrent with the higher viral decay but lower bacterial abundance and inhibited bacterial metabolism during the neap tide, lower gross viral production was coupled with a synchronous switching from viral lytic to lysogenic infection induced by the loss of viral infection efficiency and the transition from marine to freshwater bacterial populations triggered by tidal mixing. Our results highlighted the major tidal impact on the microbial dynamics through virus-host interactions, with cascading effects, neglected so far, on estuarine biogeochemical cycles.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China; College of the Environment and Ecology, Xiamen University, Xiamen, 361102, PR China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Hongbo Li
- National Marine Environmental Monitoring Center, State Oceanic Administration, Dalian, 116023, PR China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
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19
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He L, Yin K, Yuan X. Double Maximum Ratios of Viruses to Bacteria in the Water Column: Implications for Different Regulating Mechanisms. Front Microbiol 2019; 10:1593. [PMID: 31379770 PMCID: PMC6646418 DOI: 10.3389/fmicb.2019.01593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/26/2019] [Indexed: 11/13/2022] Open
Abstract
The viruses play an important role in limiting bacterial abundance in oceans and, hence, in regulating bacterial biogeochemical functions. A cruise was conducted in September 2005 along a transect in the deep South China Sea (SCS). The results showed the double maxima in the ratio of viral to bacterial abundance (VBR) in the water column: a deep maximum at 800–1000 m coinciding with the oxygen minimum zone (OMZ) and a subsurface maximum at 50–100 m near the subsurface chlorophyll maximum (SCM) layer. At the deep maximum of VBR, both viral and bacterial abundances were lower than those in the upper layer, but the former was reduced less than the latter. In contrast, at the subsurface maximum of VBR, both viral and bacterial abundances increased to the maximum, with viral abundance increasing more than bacterial abundance. The results suggest that two VBR maxima were formed due to different mechanisms. In the SCM, the VBR maximum is due to an abundant supply of organic matter, which increases bacterial growth, and stimulates viral abundance faster. In contrast, in the OMZ, organic matter is consumed and limits bacterial growth, but viruses are less limited by organic matter and continue to infect bacteria, leading to the maximum VBR. The OMZ in the deep-water column of oceans is over hundreds of years old and receives a constant supply of organic matter from the water above. However, the oxygen level cannot be depleted to anoxia. Bacterial respiration is largely responsible for oxygen consumption in the OMZ; and hence, any process that limits bacterial abundance and respiration contributes to the variation in the OMZ. Viral control of bacterial abundance can be a potential mechanism responsible for slowing down oxygen consumption to anoxia in the OMZ. Our finding provides preliminary evidence that viruses are an important player in controlling bacterial abundance when bacterial growth is limited by organic matter, and thus, regulates the decomposition of organic matter, oxygen consumption and nutrient re-mineralization in deep oceans.
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Affiliation(s)
- Lei He
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Kedong Yin
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Kedong Yin,
| | - Xiangcheng Yuan
- Key Laboratory of Marine Bio-Resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity. ISME JOURNAL 2019; 13:2551-2565. [PMID: 31227815 DOI: 10.1038/s41396-019-0449-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 02/01/2023]
Abstract
Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.
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Jin M, Guo X, Zhang R, Qu W, Gao B, Zeng R. Diversities and potential biogeochemical impacts of mangrove soil viruses. MICROBIOME 2019; 7:58. [PMID: 30975205 PMCID: PMC6460857 DOI: 10.1186/s40168-019-0675-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Mangroves are ecologically and economically important forests of the tropics. As one of the most carbon-rich biomes, mangroves account for 11% of the total input of terrestrial carbon into oceans. Although viruses are considered to significantly influence local and global biogeochemical cycles, little information is available regarding the community structure, genetic diversity and ecological roles of viruses in mangrove ecosystems. METHODS Here, we utilised viral metagenomics sequencing and virome-specific bioinformatics tools to study viral communities in six mangrove soil samples collected from different mangrove habitats in Southern China. RESULTS Mangrove soil viruses were found to be largely uncharacterised. Phylogenetic analyses of the major viral groups demonstrated extensive diversity and previously unknown viral clades and suggested that global mangrove viral communities possibly comprise evolutionarily close genotypes. Comparative analysis of viral genotypes revealed that mangrove soil viromes are mainly affected by marine waters, with less influence coming from freshwaters. Notably, we identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from mangrove viruses, most of which participate in biolysis of complex polysaccharides, which are abundant in mangrove soils and organism debris. Host prediction results showed that viral CAZyme genes are diverse and probably widespread in mangrove soil phages infecting diverse bacteria of different phyla. CONCLUSIONS Our results showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangrove ecosystems.
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Affiliation(s)
- Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xun Guo
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Wu Qu
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Boliang Gao
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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23
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Zhang C, Dang H, Azam F, Benner R, Legendre L, Passow U, Polimene L, Robinson C, Suttle CA, Jiao N. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwy074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.
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Affiliation(s)
- Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Benner
- Department of Biological Sciences and School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC 29208, USA
| | - Louis Legendre
- Sorbonne Université, Laboratoire d’Océanographie de Villefranche, LOV, 06230 Villefranche-sur-Mer, France
| | - Uta Passow
- Marine Science Institute, University of California Santa Barbara, CA 93106, USA
| | - Luca Polimene
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Carol Robinson
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Botany, and Microbiology and Immunology, and the Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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Liu L, Cai L, Zhang R. Co-existence of freshwater and marine T4-like myoviruses in a typical subtropical estuary. FEMS Microbiol Ecol 2018; 93:4584463. [PMID: 29099976 DOI: 10.1093/femsec/fix119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/13/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth and play an important role in microbial community dynamics and biogeochemical cycling, yet their ecological characteristics in estuarine ecosystems are unclear. Here, virioplankton communities in a typical subtropical estuary, the Jiulong River estuary (JRE) in China, were investigated. The abundance of virioplankton ranged from 1.01 ± 0.05 × 107 to 1.62 ± 0.09 × 107 particles mL-1 in JRE, and the population size of viruses was correlated with temperature and nutrient levels. Three tailed viral morphotypes (myovirus, siphovirus and podovirus) were observed. Phylogenetic analysis showed that most of the g23 sequences in the JRE fell into three previously established groups (Marine, Paddy and Lake Groups) and two potential Estuary Groups. This demonstrates the co-existence of typical freshwater and marine T4-like myoviruses in the estuarine ecosystem, suggesting the movement of viruses and their hosts among biomes. Additionally, the spatial variation of g23 sequences suggests a geographic distribution pattern of T4-like myoviruses in the JRE, which might be shaped by the environmental gradient and/or their host distribution. These results provide valuable insights into the abundance, diversity and distribution patterns of virioplankton, as well as the factors influencing them, in subtropical estuarine ecosystems.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiang'an, Xiamen, Fujian 361102, People's Republic of China
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiang'an, Xiamen, Fujian 361102, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiang'an, Xiamen, Fujian 361102, People's Republic of China
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Wei W, Zhang R, Peng L, Liang Y, Jiao N. Effects of temperature and photosynthetically active radiation on virioplankton decay in the western Pacific Ocean. Sci Rep 2018; 8:1525. [PMID: 29367730 PMCID: PMC5784127 DOI: 10.1038/s41598-018-19678-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/08/2018] [Indexed: 12/04/2022] Open
Abstract
In this study, we investigated virioplankton decay rates and their responses to changes in temperature and photosynthetically active radiation (PAR) in the western Pacific Ocean. The mean decay rates for total, high-fluorescence, and low-fluorescence viruses were 1.64 ± 0.21, 2.46 ± 0.43, and 1.57 ± 0.26% h−1, respectively. Higher temperatures and PAR increased viral decay rates, and the increases in the decay rates of low-fluorescence viruses were greater than those of high-fluorescence viruses. Our results revealed that low-fluorescence viruses are more sensitive to warming and increasing PAR than are high-fluorescence viruses, which may be related to differences in their biological characteristics, such as the density of packaged nucleic acid materials. Our study provided experimental evidence for the responses of natural viral communities to changes in global environmental factors (e.g., temperature and solar radiation).
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Affiliation(s)
- Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
| | - Lulu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Yantao Liang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.,Research Center for Marine Biology and Carbon Sequestration, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
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Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. mSphere 2017; 2:mSphere00366-17. [PMID: 28989970 PMCID: PMC5628290 DOI: 10.1128/msphere.00366-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume. The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.
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Chen JM, Legendre L, Benner R. A recent project shows that the microbial carbon pump is a primary mechanism driving ocean carbon uptake. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwy006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Louis Legendre
- Laboratoire d’Océanographie de Villefranche, Sorbonne Université, CNRS, France
| | - Ronald Benner
- Department of Biological Sciences and Marine Science Program, University of South Carolina, USA
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28
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Cai L, Zhang R, He Y, Feng X, Jiao N. Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China. Viruses 2016; 8:v8020035. [PMID: 26848678 PMCID: PMC4776190 DOI: 10.3390/v8020035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 11/24/2022] Open
Abstract
Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% ± 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361005, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361005, China.
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361005, China.
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