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Barno AR, Green K, Rohwer F, Silveira CB. Snow viruses and their implications on red snow algal blooms. mSystems 2024; 9:e0008324. [PMID: 38647296 PMCID: PMC11097641 DOI: 10.1128/msystems.00083-24] [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: 01/24/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024] Open
Abstract
Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We hypothesize that these algal blooms affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of double-stranded DNA virus communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Putative snow viruses encoded genes involved in energy metabolisms, such as NAD+ synthesis and salvage pathways. In model phages, these genes facilitate increased viral particle production and lysis rates. The frequency of temperate phages was positively correlated with microbial abundance in the snow samples. These results suggest the increased frequency of temperate virus-bacteria interactions as microbial densities increase during snowmelt. We propose that this virus-bacteria dynamic may facilitate the red snow algae growth stimulated by bacteria.IMPORTANCEMicrobial communities in red snow algal blooms contribute to intensifying snowmelt rates. The role of viruses in snow during this environmental shift, however, has yet to be elucidated. Here, we characterize novel viruses extracted from snow viral metagenomes and define the functional capacities of snow viruses in both white and red snow. These results are contextualized using the composition and functions observed in the bacterial communities from the same snow samples. Together, these data demonstrate the energy metabolism performed by viruses and bacteria in a snow algal bloom, as well as expand the overall knowledge of viral genomes in extreme environments.
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Affiliation(s)
- Adam R. Barno
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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Nweze JE, Schweichhart JS, Angel R. Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome. Environ Microbiol 2024; 26:e16586. [PMID: 38356108 DOI: 10.1111/1462-2920.16586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.
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Affiliation(s)
- Julius Eyiuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Johannes Sergej Schweichhart
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Roey Angel
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
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3
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Rihtman B, Torcello-Requena A, Mikhaylina A, Puxty RJ, Clokie MRJ, Millard AD, Scanlan DJ. Coordinated transcriptional response to environmental stress by a Synechococcus virus. THE ISME JOURNAL 2024; 18:wrae032. [PMID: 38431846 PMCID: PMC10976474 DOI: 10.1093/ismejo/wrae032] [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: 12/08/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon among cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that the production of infectious virus particles of such viruses is reduced in low P conditions. However, this reduction in progeny is not caused by impaired phage genome replication, thought to be a major sink for cellular phosphate. Instead, transcriptomic analysis showed that under low P conditions, a PstS-lacking cyanophage increased the expression of a specific gene set that included mazG, hli2, and gp43 encoding a pyrophosphatase, a high-light inducible protein and DNA polymerase, respectively. Moreover, several of the upregulated genes were controlled by the host's phoBR two-component system. We hypothesize that recycling and polymerization of nucleotides liberates free phosphate and thus allows viral morphogenesis, albeit at lower rates than when phosphate is replete or when phages encode pstS. Altogether, our data show how phage genomes, lacking obvious P-stress-related genes, have evolved to exploit their host's environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alberto Torcello-Requena
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alevtina Mikhaylina
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Martha R J Clokie
- Leicester Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Andrew D Millard
- Leicester Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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Lopez-Simon J, Vila-Nistal M, Rosenova A, De Corte D, Baltar F, Martinez-Garcia M. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles. Nat Commun 2023; 14:8295. [PMID: 38097581 PMCID: PMC10721903 DOI: 10.1038/s41467-023-44028-x] [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: 05/30/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, and metagenomic data to uncover the viral diversity, biogeography, activity, and their role as metabolic facilitators of microbes beneath the Ross Ice Shelf. This is the largest Antarctic ice shelf with a major impact on global carbon cycle. The viral community found in the cavity under the ice shelf mainly comprises endemic viruses adapted to polar and mesopelagic environments. The low abundance of genes related to lysogenic lifestyle (<3%) does not support a predominance of the Piggyback-the-Winner hypothesis, consistent with a low-productivity habitat. Our results indicate a viral community actively infecting key ammonium and sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting a "kill-the-winner" dynamic. Based on genome analysis, these viruses carry specific auxiliary metabolic genes potentially involved in nitrogen, sulfur, and phosphorus acquisition. Altogether, the viruses under Antarctic ice shelves are putatively involved in programming the metabolism of ecologically relevant microbes that maintain primary production in these chemosynthetically-driven ecosystems, which have a major role in global nutrient cycles.
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Affiliation(s)
- Javier Lopez-Simon
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Marina Vila-Nistal
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Aleksandra Rosenova
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, UK
| | - Federico Baltar
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassi-Platz 1, 1030, Vienna, Austria.
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain.
- Instituto Multidisciplinar para el Estudio del Medio Ramon Margalef, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain.
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Zorz J, Paquette AJ, Gillis T, Kouris A, Khot V, Demirkaya C, De La Hoz Siegler H, Strous M, Vadlamani A. Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. THE ISME JOURNAL 2023; 17:2403-2414. [PMID: 37914776 PMCID: PMC10689466 DOI: 10.1038/s41396-023-01545-3] [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: 05/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.
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Affiliation(s)
- Jackie Zorz
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada.
| | - Alexandre J Paquette
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Timber Gillis
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Angela Kouris
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
| | - Varada Khot
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Cigdem Demirkaya
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | | | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Agasteswar Vadlamani
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
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Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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7
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Tsiola A, Michoud G, Daffonchio D, Fodelianakis S, Giannakourou A, Malliarakis D, Pavlidou A, Pitta E, Psarra S, Santi I, Zeri C, Pitta P. Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters. Front Microbiol 2023; 14:1271535. [PMID: 38029212 PMCID: PMC10653327 DOI: 10.3389/fmicb.2023.1271535] [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: 08/02/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Marine viruses regulate microbial population dynamics and biogeochemical cycling in the oceans. The ability of viruses to manipulate hosts' metabolism through the expression of viral auxiliary metabolic genes (AMGs) was recently highlighted, having important implications in energy production and flow in various aquatic environments. Up to now, the presence and diversity of viral AMGs is studied using -omics data, and rarely using quantitative measures of viral activity alongside. Methods In the present study, four depth layers (5, 50, 75, and 1,000 m) with discrete hydrographic features were sampled in the Eastern Mediterranean Sea; we studied lytic viral community composition and AMG content through metagenomics, and lytic production rates through the viral reduction approach in the ultra-oligotrophic Levantine basin where knowledge regarding viral actions is rather limited. Results and Discussion Our results demonstrate depth-dependent patterns in viral diversity and AMG content, related to differences in temperature, nutrients availability, and host bacterial productivity and abundance. Although lytic viral production rates were similar along the water column, the virus-to-bacteria ratio was higher and the particular set of AMGs was more diverse in the bathypelagic (1,000 m) than the shallow epipelagic (5, 50, and 75 m) layers, revealing that the quantitative effect of viruses on their hosts may be the same along the water column through the intervention of different AMGs. In the resource- and energy-limited bathypelagic waters of the Eastern Mediterranean, the detected AMGs could divert hosts' metabolism toward energy production, through a boost in gluconeogenesis, fatty-acid and glycan biosynthesis and metabolism, and sulfur relay. Near the deep-chlorophyll maximum depth, an exceptionally high percentage of AMGs related to photosynthesis was noticed. Taken together our findings suggest that the roles of viruses in the deep sea might be even more important than previously thought as they seem to orchestrate energy acquisition and microbial community dynamics, and thus, biogeochemical turnover in the oceans.
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Affiliation(s)
- Anastasia Tsiola
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stilianos Fodelianakis
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Antonia Giannakourou
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Anavyssos, Attiki, Greece
| | | | - Alexandra Pavlidou
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Anavyssos, Attiki, Greece
| | - Elli Pitta
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Anavyssos, Attiki, Greece
| | - Stella Psarra
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| | - Ioulia Santi
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| | - Christina Zeri
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Anavyssos, Attiki, Greece
| | - Paraskevi Pitta
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes. THE ISME JOURNAL 2023; 17:1660-1670. [PMID: 37452097 PMCID: PMC10504331 DOI: 10.1038/s41396-023-01466-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
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Affiliation(s)
| | | | - Ashley G Bell
- School of Biosciences, University of Exeter, Exeter, UK
| | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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9
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Zhu X, Li Z, Tong Y, Chen L, Sun T, Zhang W. From natural to artificial cyanophages: Current progress and application prospects. ENVIRONMENTAL RESEARCH 2023; 223:115428. [PMID: 36746205 DOI: 10.1016/j.envres.2023.115428] [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: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
The over proliferation of harmful cyanobacteria and their cyanotoxins resulted in damaged aquatic ecosystem, polluted drinking water and threatened human health. Cyanophages are a kind of viruses that exclusively infect cyanobacteria, which is considered as a potential strategy to deal with cyanobacterial blooms. Nevertheless, the infecting host range and/or lysis efficiency of natural cyanophages is limited, rising the necessity of constructing non-natural cyanophages via artificial modification, design and synthesis to expand their host range and/or efficiency. The paper firstly reviewed representative cyanophages such as P60 with a short latent period of 1.5 h and S-CBS1 having a burst size up to 200 PFU/cell. To explore the in-silico design principles, we critically summarized the interactions between cyanophages and the hosts, indicating modifying the recognized receptors, enhancing the adsorption ability, changing the lysogeny and excluding the defense of hosts are important for artificial cyanophages. The research progress of synthesizing artificial cyanophages were summarized subsequently, raising the importance of developing genetic manipulation technologies and their rescue strategies in the future. Meanwhile, Large-scale preparation of cyanophages for bloom control is a big challenge. The application prospects of artificial cyanophages besides cyanobacteria bloom control like adaptive evolution and phage therapy were discussed at last. The review will promote the design, synthesis and application of cyanophages for cyanobacteria blooms, which may provide new insights for the related water pollution control and ensuring hydrosphere security.
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Affiliation(s)
- Xiaofei Zhu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Zipeng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yindong Tong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China.
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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10
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Puxty RJ, Millard AD. Functional ecology of bacteriophages in the environment. Curr Opin Microbiol 2023; 71:102245. [PMID: 36512900 DOI: 10.1016/j.mib.2022.102245] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.
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Affiliation(s)
- Richard J Puxty
- University of Warwick, School of Life Sciences, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.
| | - Andrew D Millard
- University of Leicester, Dept of Genetics and Genome Biology, University Road, Leicester, United Kingdom.
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11
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Wang Q, Cai L, Zhang R, Wei S, Li F, Liu Y, Xu Y. A Unique Set of Auxiliary Metabolic Genes Found in an Isolated Cyanophage Sheds New Light on Marine Phage-Host Interactions. Microbiol Spectr 2022; 10:e0236722. [PMID: 36190421 PMCID: PMC9602691 DOI: 10.1128/spectrum.02367-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/10/2022] [Indexed: 01/04/2023] Open
Abstract
Cyanophages, viruses that infect cyanobacteria, are abundant and widely distributed in aquatic ecosystems, playing important roles in regulating the abundance, activity, diversity, and evolution of cyanobacteria. A T4-like cyanophage, S-SCSM1, infecting Synechococcus and Prochlorococcus strains of different ecotypes, was isolated from the South China Sea in this study. For the first time, a mannose-6-phosphate isomerase (MPI) gene was identified in the cultured cyanophage. At least 11 phylogenetic clusters of cyanophage MPIs were retrieved and identified from the marine metagenomic data sets, indicating that cyanophage MPIs in the marine environment are extremely diverse. The existence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins in the S-SCSM1 genome emphasizes their potential importance and diverse functions in reprogramming host metabolism during phage infection. Novel cell wall synthesis and modification genes found in the S-SCSM1 genome indicate that diverse phenotypic modifications imposed by phages on cyanobacterial hosts remain to be discovered. Two noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome were predicted to be associated with host exopolysaccharide metabolism and photosynthesis. The isolation and genomic characterization of cyanophage S-SCSM1 provide more information on the genetic diversity of cyanophages and phage-host interactions in the marine environment. IMPORTANCE Cyanophages play important ecological roles in aquatic ecosystems. Genomic and proteomic characterizations of the T4-like cyanophage S-SCSM1 indicate that novel and diverse viral genes and phage-host interactions in the marine environment remain unexplored. The first identified mannose-6-phosphate isomerase (MPI) gene from a cultured cyanophage was found in the S-SCSM1 genome, although MPIs were previously found in viral metagenomes at high frequencies similar to those of the cyanophage photosynthetic gene psbA. The presence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins, novel cell wall synthesis and modification genes, a nonbleaching protein A gene, and 2 noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome as well as the presence of a virion-associated regulatory protein indicate the diverse functions that cyanophages have in reprogramming the metabolism and modifying the phenotypes of hosts during infection.
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Affiliation(s)
- Qiong Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People’s Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Fang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, People’s Republic of China
| | - Yuanfang Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
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12
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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13
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Howard-Varona C, Roux S, Bowen BP, Silva LP, Lau R, Schwenck SM, Schwartz S, Woyke T, Northen T, Sullivan MB, Floge SA. Protist impacts on marine cyanovirocell metabolism. ISME COMMUNICATIONS 2022; 2:94. [PMID: 37938263 PMCID: PMC9723779 DOI: 10.1038/s43705-022-00169-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 07/26/2023]
Abstract
The fate of oceanic carbon and nutrients depends on interactions between viruses, prokaryotes, and unicellular eukaryotes (protists) in a highly interconnected planktonic food web. To date, few controlled mechanistic studies of these interactions exist, and where they do, they are largely pairwise, focusing either on viral infection (i.e., virocells) or protist predation. Here we studied population-level responses of Synechococcus cyanobacterial virocells (i.e., cyanovirocells) to the protist Oxyrrhis marina using transcriptomics, endo- and exo-metabolomics, photosynthetic efficiency measurements, and microscopy. Protist presence had no measurable impact on Synechococcus transcripts or endometabolites. The cyanovirocells alone had a smaller intracellular transcriptional and metabolic response than cyanovirocells co-cultured with protists, displaying known patterns of virus-mediated metabolic reprogramming while releasing diverse exometabolites during infection. When protists were added, several exometabolites disappeared, suggesting microbial consumption. In addition, the intracellular cyanovirocell impact was largest, with 4.5- and 10-fold more host transcripts and endometabolites, respectively, responding to protists, especially those involved in resource and energy production. Physiologically, photosynthetic efficiency also increased, and together with the transcriptomics and metabolomics findings suggest that cyanovirocell metabolic demand is highest when protists are present. These data illustrate cyanovirocell responses to protist presence that are not yet considered when linking microbial physiology to global-scale biogeochemical processes.
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Affiliation(s)
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - Leslie P Silva
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Syft Technologies, Ltd, Christchurch, 8024, New Zealand
| | - Rebecca Lau
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cellular and Molecular Medicine and Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Samuel Schwartz
- Department of Biology, Wake Forest University, Winston Salem, NC, USA
| | - Tanja Woyke
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | - Trent Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston Salem, NC, USA.
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14
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Heyerhoff B, Engelen B, Bunse C. Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea. Front Microbiol 2022; 13:863620. [PMID: 35875520 PMCID: PMC9301287 DOI: 10.3389/fmicb.2022.863620] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Marine microbial communities are facing various ecosystem fluctuations (e.g., temperature, organic matter concentration, salinity, or redox regimes) and thus have to be highly adaptive. This might be supported by the acquisition of auxiliary metabolic genes (AMGs) originating from virus infections. Marine bacteriophages frequently contain AMGs, which allow them to augment their host’s metabolism or enhance virus fitness. These genes encode proteins for the same metabolic functions as their highly similar host homologs. In the present study, we analyzed the diversity, distribution, and composition of marine viruses, focusing on AMGs to identify their putative ecologic role. We analyzed viruses and assemblies of 212 publicly available metagenomes obtained from sediment and water samples across the Baltic Sea. In general, the virus composition in both compartments differed compositionally. While the predominant viral lifestyle was found to be lytic, lysogeny was more prevalent in sediments than in the pelagic samples. The highest proportion of AMGs was identified in the genomes of Myoviridae. Overall, the most abundantly occurring AMGs are encoded for functions that protect viruses from degradation by their hosts, such as methylases. Additionally, some detected AMGs are known to be involved in photosynthesis, 7-cyano-7-deazaguanine synthesis, and cobalamin biosynthesis among other functions. Several AMGs that were identified in this study were previously detected in a large-scale analysis including metagenomes from various origins, i.e., different marine sites, wastewater, and the human gut. This supports the theory of globally conserved core AMGs that are spread over virus genomes, regardless of host or environment.
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15
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Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes. Viruses 2022; 14:v14050887. [PMID: 35632629 PMCID: PMC9146016 DOI: 10.3390/v14050887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
As significant drivers of cyanobacteria mortality, cyanophages have been known to regulate the population dynamics, metabolic activities, and community structure of this most important marine autotrophic picoplankton and, therefore, influence the global primary production and biogeochemical cycle in aquatic ecosystems. In the present study, a lytic Synechococcus phage, namely S-SZBM1, was isolated and identified. Cyanophage S-SZBM1 has a double-stranded DNA genome of 177,834 bp with a G+C content of 43.31% and contains a total of 218 predicted ORFs and six tRNA genes. Phylogenetic analysis and nucleotide-based intergenomic similarity suggested that cyanophage S-SZBM1 belongs to a new genus under the family Kyanoviridae. A variety of auxiliary metabolic genes (AMGs) that have been proved or speculated to relate to photosynthesis, carbon metabolism, nucleotide synthesis and metabolism, cell protection, and other cell metabolism were identified in cyanophage S-SZBM1 genome and may affect host processes during infection. In addition, 24 of 32 predicted structural proteins were identified by a high-throughput proteome analysis which were potentially involved in the assembly processes of virion. The genomic and proteomic analysis features of cyanophage S-SZBM1 offer a valuable insight into the interactions between cyanophages and their hosts during infection.
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16
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Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nat Microbiol 2022; 7:570-580. [PMID: 35365792 PMCID: PMC8975747 DOI: 10.1038/s41564-022-01088-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
Abstract
The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2-4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10-100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans.
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17
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Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. THE ISME JOURNAL 2022; 16:972-982. [PMID: 34743175 PMCID: PMC8940887 DOI: 10.1038/s41396-021-01143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/08/2022]
Abstract
Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.
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18
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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19
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Zhang D, He Y, Gin KYH. Genomic Characterization of a Novel Freshwater Cyanophage Reveals a New Lineage of Cyanopodovirus. Front Microbiol 2022; 12:768868. [PMID: 35095789 PMCID: PMC8790148 DOI: 10.3389/fmicb.2021.768868] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.
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Affiliation(s)
- Dong Zhang
- NUS Environmental Research Institute (E2S2-CREATE), National University of Singapore, Singapore, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute (E2S2-CREATE), National University of Singapore, Singapore, Singapore.,Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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20
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Novel Freshwater Cyanophages Provide New Insights into Evolutionary Relationships between Freshwater and Marine Cyanophages. Microbiol Spectr 2021; 9:e0059321. [PMID: 34585945 PMCID: PMC8557907 DOI: 10.1128/spectrum.00593-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria and cyanophages are present widely in both freshwater and marine environments. However, freshwater cyanophages remain unknown largely due to the small numbers of cyanophage isolates despite their ecological and environmental significance. In this study, we present the characterization of two novel lytic freshwater cyanophages isolated from a tropical inland lake in Singapore, namely, cyanopodovirus S-SRP01 and cyanomyovirus S-SRM01, infecting two different strains of Synechococcus spp. Functional annotation of S-SRP01 and S-SRM01 genomes revealed a high degree of homology with marine cyanophages. Phylogenetic trees of concatenated genes and whole-genome alignment provided further evidence that S-SRP01 is close evolutionarily to marine cyanopodoviruses, while S-SRM01 is evolutionarily close to marine cyanomyoviruses. Few genetic similarities between freshwater and marine cyanophages have been identified in previous studies. The isolation of S-SRP01 and S-SRM01 expand current knowledge on freshwater cyanophages infecting Synechococcus spp. Their high degree of gene sharing provides new insights into the evolutionary relationships between freshwater and marine cyanophages. This relatedness is further supported by the discovery of similar phenomenon from other freshwater viral metagenomes. IMPORTANCE This study expands the current knowledge on freshwater cyanophage isolates and cyanophage genetic diversity, indicating that freshwater and marine cyanophages infecting Synechococcus spp. may share close genetic similarity and evolutionary relationships.
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21
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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22
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Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nat Commun 2021; 12:3503. [PMID: 34108477 PMCID: PMC8190135 DOI: 10.1038/s41467-021-23698-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.
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23
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Rihtman B, Puxty RJ, Hapeshi A, Lee YJ, Zhan Y, Michniewski S, Waterfield NR, Chen F, Weigele P, Millard AD, Scanlan DJ, Chen Y. A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. Curr Biol 2021; 31:3199-3206.e4. [PMID: 34033748 PMCID: PMC8323127 DOI: 10.1016/j.cub.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 01/27/2023]
Abstract
Marine bacterial viruses (bacteriophages) are abundant biological entities that are vital for shaping microbial diversity, impacting marine ecosystem function, and driving host evolution.1, 2, 3 The marine roseobacter clade (MRC) is a ubiquitous group of heterotrophic bacteria4,5 that are important in the elemental cycling of various nitrogen, sulfur, carbon, and phosphorus compounds.6, 7, 8, 9, 10 Bacteriophages infecting MRC (roseophages) have thus attracted much attention and more than 30 roseophages have been isolated,11, 12, 13 the majority of which belong to the N4-like group (Podoviridae family) or the Chi-like group (Siphoviridae family), although ssDNA-containing roseophages are also known.14 In our attempts to isolate lytic roseophages, we obtained two new phages (DSS3_VP1 and DSS3_PM1) infecting the model MRC strain Ruegeria pomeroyi DSS-3. Here, we show that not only do these phages have unusual substitution of deoxythymidine with deoxyuridine (dU) in their DNA, but they are also phylogenetically distinct from any currently known double-stranded DNA bacteriophages, supporting the establishment of a novel family (“Naomiviridae”). These dU-containing phages possess DNA that is resistant to the commonly used library preparation method for metagenome sequencing, which may have caused significant underestimation of their presence in the environment. Nevertheless, our analysis of Tara Ocean metagenome datasets suggests that these unusual bacteriophages are of global importance and more diverse than other well-known bacteriophages, e.g., the Podoviridae in the oceans, pointing to an overlooked role for these novel phages in the environment. Two new roseophages isolated from the marine environment They have an unusual deoxythymidine to deoxyuridine substitution in their genomes These dU genomes are resistant to a common method of metagenome library preparation These phages represent a new family and are globally distributed in the oceans
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Alexia Hapeshi
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Yuanchao Zhan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Slawomir Michniewski
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nicholas R Waterfield
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Peter Weigele
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Andrew D Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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24
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Laurenceau R, Raho N, Forget M, Arellano AA, Chisholm SW. Frequency of mispackaging of Prochlorococcus DNA by cyanophage. THE ISME JOURNAL 2021; 15:129-140. [PMID: 32929209 PMCID: PMC7852597 DOI: 10.1038/s41396-020-00766-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.
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Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nicolas Raho
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathieu Forget
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institut de Biologie de l'Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aldo A Arellano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. Proc Natl Acad Sci U S A 2020; 117:29738-29747. [PMID: 33172994 DOI: 10.1073/pnas.2010783117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.
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26
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The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities. Microorganisms 2020; 8:microorganisms8111677. [PMID: 33137872 PMCID: PMC7692377 DOI: 10.3390/microorganisms8111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/28/2022] Open
Abstract
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.
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27
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Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
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Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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28
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Wang M, Gao C, Jiang T, You S, Jiang Y, Guo C, He H, Liu Y, Zhang X, Shao H, Liu H, Liang Y, Wang M, McMinn A. Genomic analysis of Synechococcus phage S-B43 and its adaption to the coastal environment. Virus Res 2020; 289:198155. [PMID: 32941942 DOI: 10.1016/j.virusres.2020.198155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022]
Abstract
Synechococcus dominate picocyanobacterial communities in coastal environments. However, only a few Synechococcus phages have been described from the coastal seas of the Northwest Pacific Ocean. Here a new Synechococcus phage, S-B43 was isolated from the Bohai Sea, a semi-closed coastal sea of the Northwest Pacific Ocean. S-B43 is a member of Myoviridae, containing 275 predicted open reading frames. Fourteen auxiliary metabolic genes (AMG) were identified from the genome of S-B43, including five photosynthetic associated genes and several AMGs related to its adaption to the high turbidity and eutrophic coastal environment with a low ratio of phosphorus to nitrogen (HNLP). The occurrences of 31 AMGs among 34 cyanophage genomes indicates that AMGs zwf, gnd, speD, petF and those coding for FECH and thioredoxin were more common in coastal areas than in the open ocean and AMGs pebS and ho1 were more prevalent in the open ocean. The occurrence of cyanophage AMGs in different environments might be a reflection of the environmental adaption of their hosts. This study contributes to our understanding of the interactions between cyanobacteria and cyanophages and their environmental adaption to the coastal environment.
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Affiliation(s)
- Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Siyuan You
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Hongbin Liu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
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29
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Fuchsman CA, Carlson MCG, Garcia Prieto D, Hays MD, Rocap G. Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environ Microbiol 2020; 23:2782-2800. [PMID: 32869473 DOI: 10.1111/1462-2920.15219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 01/19/2023]
Abstract
Cyanophages encode host-derived genes that may increase their fitness. We examined the relative abundance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress (psbA, psbD and pstS in T4-like and psbA in T7-like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4-like, but not T7-like cyanophages. No additional host-derived genes were found in deep T7-like cyanophages, suggesting that T4-like and T7-like cyanophages have different host-derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4-like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low-light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.
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Affiliation(s)
- Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Michael C G Carlson
- School of Oceanography, University of Washington, Seattle, WA, USA.,Technion-Israel Institute of Technology, Haifa, Israel
| | - David Garcia Prieto
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA
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30
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Goldin S, Hulata Y, Baran N, Lindell D. Quantification of T4-Like and T7-Like Cyanophages Using the Polony Method Show They Are Significant Members of the Virioplankton in the North Pacific Subtropical Gyre. Front Microbiol 2020; 11:1210. [PMID: 32612586 PMCID: PMC7308941 DOI: 10.3389/fmicb.2020.01210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The North Pacific Subtropical Gyre (NPSG) is one of the largest biomes on Earth, with the cyanobacterium Prochlorococcus being the most abundant primary producer year-round. Viruses that infect cyanobacteria (cyanophages) influence cyanobacterial mortality, diversity and evolution. Two major cyanophage families are the T4-like cyanomyoviruses and T7-like cyanopodoviruses, yet their abundances and distribution patterns remain unknown due to difficulty in quantifying their populations. To address this limitation, we previously adapted the polony method (for PCR colony) to quantify T7-like cyanophages and applied it to spring populations in the Red Sea. Here, we further adapted the method for the quantification of T4-like cyanophages and analyzed the abundances of T4-like and T7-like cyanophage populations in the photic zone of the NPSG in summer 2015 and spring 2016. Combined, the peak abundances of these two cyanophage families reached 2.8 × 106 and 1.1 × 106 cyanophages ⋅ ml–1 in the summer and spring, respectively. They constituted between 3 and 16% of total virus-like particles (VLPs), comprising a substantial component of the virioplankton in the NPSG. While both cyanophage families were highly abundant, the T4-like cyanophages were generally 1.3–4.4 fold more so. In summer, cyanophages had similar and reproducible distribution patterns with depth. Abundances were relatively low in the upper mixed layer and increased to form a pronounced subsurface peak at 100 m (1.9 × 106 and 9.1 × 105 phages ⋅ ml–1 for the T4-like and T7-like cyanophages, respectively), coincident with the maximum in Prochlorococcus populations. Less vertical structure in cyanophage abundances was apparent in the spring profile, despite a subsurface peak in Prochlorococcus numbers. In the summer upper mixed layer, cyanophages constituted a smaller proportion of VLPs than below it and cyanophage to cyanobacteria ratios were considerably lower (1.3–2.8) than those of VLPs to bacteria (8.1–21.2). Differences in abundances between the two families and their contribution to VLPs with depth suggest differences in cyanophage production and/or decay processes relative to other members of the virioplankton in the upper mixed layer. These findings highlight the importance of quantifying distinct populations within the virioplankton to gain accurate understanding of their distribution patterns.
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Affiliation(s)
- Svetlana Goldin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yotam Hulata
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Nava Baran
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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31
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Campbell IJ, Olmos JL, Xu W, Kahanda D, Atkinson JT, Sparks ON, Miller MD, Phillips GN, Bennett GN, Silberg JJ. Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. J Biol Chem 2020; 295:10610-10623. [PMID: 32434930 DOI: 10.1074/jbc.ra120.013501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/15/2020] [Indexed: 01/13/2023] Open
Abstract
Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (-336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.
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Affiliation(s)
- Ian J Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Jose Luis Olmos
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, Texas, USA
| | | | | | | | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - George N Bennett
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA .,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA.,Department of Bioengineering, Rice University, Houston, Texas, USA
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32
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Focardi A, Ostrowski M, Goossen K, Brown MV, Paulsen I. Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System. Viruses 2020; 12:E317. [PMID: 32188136 PMCID: PMC7150976 DOI: 10.3390/v12030317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.
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Affiliation(s)
- Amaranta Focardi
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, 123 Broadway, Sydney, NSW 2007, Australia;
| | - Kirianne Goossen
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
| | - Mark V. Brown
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
- School of Environmental and Life Sciences, University of Newcastle, University Dr, Callaghan, NSW 2308, Australia
| | - Ian Paulsen
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
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33
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Gann ER, Gainer PJ, Reynolds TB, Wilhelm SW. Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a "giant virus". PLoS One 2020; 15:e0226758. [PMID: 31899921 PMCID: PMC6941929 DOI: 10.1371/journal.pone.0226758] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/03/2019] [Indexed: 11/18/2022] Open
Abstract
The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980's, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.
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Affiliation(s)
- Eric R. Gann
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - P. Jackson Gainer
- Department of Biology, Tennessee Wesleyan University, Athens, Tennessee, United States of America
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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34
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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35
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Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 2019; 11:v11080720. [PMID: 31390807 PMCID: PMC6722890 DOI: 10.3390/v11080720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 12/30/2022] Open
Abstract
Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.
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Flores-Uribe J, Philosof A, Sharon I, Fridman S, Larom S, Béjà O. A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus 'relic' prophage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:598-604. [PMID: 31125500 DOI: 10.1111/1758-2229.12773] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.
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Affiliation(s)
- José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
- Tel Hai College, Upper Galilee, 12210, Israel
| | - Svetlana Fridman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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37
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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38
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Abstract
To adapt to the daily light–dark cycle, diurnal rhythms are used by the photosynthetic cyanobacteria Prochlorococcus and Synechococcus, which are the most abundant photosynthetic organisms on earth. Field studies revealed that cyanobacterial virus (cyanophage) populations in the oceans showed transcriptional rhythms. To explore the underlying mechanism, we used cyanophage laboratory cultures to find that some showed adsorption rhythms and all showed transcriptional rhythms. We discovered that the cyanophage transcriptional rhythm is partially caused by the photosynthetic activity of host cells, explaining transcriptional rhythms of field cyanophage populations. Our study shows that cultured viruses have diurnal infection rhythms which are critical for understanding how light–dark cycles shape the interaction of cyanophages and their hosts in the oceans. As an adaptation to the daily light–dark (diel) cycle, cyanobacteria exhibit diurnal rhythms of gene expression and cell cycle. The light–dark cycle also affects the life cycle of viruses (cyanophages) that infect the unicellular picocyanobacteria Prochlorococcus and Synechococcus, which are the major primary producers in the oceans. For example, the adsorption of some cyanophages to the host cells depends on light, and the burst sizes of cyanophages are positively correlated to the length of light exposure during infection. Recent metatranscriptomic studies revealed transcriptional rhythms of field cyanophage populations. However, the underlying mechanism remains to be determined, as cyanophage laboratory cultures have not been shown to exhibit diurnal transcriptional rhythms. Here, we studied variation in infection patterns and gene expression of Prochlorococcus phages in laboratory culture conditions as a function of light. We found three distinct diel-dependent life history traits in dark conditions (diel traits): no adsorption (cyanophage P-HM2), adsorption but no replication (cyanophage P-SSM2), and replication (cyanophage P-SSP7). Under light–dark cycles, each cyanophage exhibited rhythmic transcript abundance, and cyanophages P-HM2 and P-SSM2 also exhibited rhythmic adsorption patterns. Finally, we show evidence to link the diurnal transcriptional rhythm of cyanophages to the photosynthetic activity of the host, thus providing a mechanistic explanation for the field observations of cyanophage transcriptional rhythms. Our study identifies that cultured viruses can exhibit diurnal rhythms during infection, which might impact cyanophage population-level dynamics in the oceans.
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Cheng K, Frenken T, Brussaard CPD, Van de Waal DB. Cyanophage Propagation in the Freshwater Cyanobacterium Phormidium Is Constrained by Phosphorus Limitation and Enhanced by Elevated pCO 2. Front Microbiol 2019; 10:617. [PMID: 30984143 PMCID: PMC6449453 DOI: 10.3389/fmicb.2019.00617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Intensification of human activities has led to changes in the availabilities of CO2 and nutrients in freshwater ecosystems, which may greatly alter the physiological status of phytoplankton. Viruses require hosts for their reproduction and shifts in phytoplankton host physiology through global environmental change may thus affect viral infections as well. Various studies have investigated the impacts of single environmental factors on phytoplankton virus propagation, yet little is known about the impacts of multiple factors, particularly in freshwater systems. We therefore tested the combined effects of phosphorus limitation and elevated pCO2 on the propagation of a cyanophage infecting a freshwater cyanobacterium. To this end, we cultured Phormidium in P-limited chemostats under ambient (400 μatm) and elevated (800 μatm) pCO2 at growth rates of 0.6, 0.3, and 0.05 d-1. Host C:P ratios generally increased with strengthened P-limitation and with elevated pCO2. Upon host steady state conditions, virus growth characteristics were obtained in separate infection assays where hosts were infected by the double-stranded DNA cyanophage PP. Severe P-limitation (host growth 0.05 d-1) led to a 85% decrease in cyanophage production rate and a 73% decrease in burst size compared to the 0.6 d-1 grown P-limited cultures. Elevated pCO2 induced a 96% increase in cyanophage production rate and a 57% increase in burst size, as well as an 85% shorter latent period as compared to ambient pCO2 at the different host growth rates. In addition, elevated pCO2 caused a decrease in the plaquing efficiency and an increase in the abortion percentage for the 0.05 d-1 P-limited treatment, while the plaquing efficiency increased for the 0.6 d-1 P-limited cultures. Together, our results demonstrate interactive effects of elevated pCO2 and P-limitation on cyanophage propagation, and show that viral propagation is generally constrained by P-limitation but enhanced with elevated pCO2. Our findings indicate that global change will likely have a severe impact on virus growth characteristics and thereby on the control of cyanobacterial hosts in freshwater ecosystems.
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Affiliation(s)
- Kai Cheng
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, China.,Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research and University of Utrecht, Texel, Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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40
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Robidart JC, Magasin JD, Shilova IN, Turk-Kubo KA, Wilson ST, Karl DM, Scholin CA, Zehr JP. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:374-387. [PMID: 30254320 DOI: 10.1038/s41396-018-0280-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.
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Affiliation(s)
- J C Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,National Oceanography Centre, Southampton, UK
| | - J D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - I N Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,Second Genome, South San Francisco, CA, USA
| | - K A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - S T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - D M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - C A Scholin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - J P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
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41
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Xu Y, Zhang R, Wang N, Cai L, Tong Y, Sun Q, Chen F, Jiao N. Novel phage-host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment. Environ Microbiol 2018; 20:2974-2989. [DOI: 10.1111/1462-2920.14326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/09/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- School of Life Science; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
| | - Rui Zhang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Nannan Wang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Lanlan Cai
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Feng Chen
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine and Environmental Technology; University of Maryland Center for Environmental Science; Baltimore MD USA
| | - Nianzhi Jiao
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
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42
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Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses. Trends Microbiol 2018; 26:955-965. [PMID: 29937307 DOI: 10.1016/j.tim.2018.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
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Affiliation(s)
- Felipe Hernandes Coutinho
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández (UMH), Alicante, Spain
| | | | - Juline Marta Walter
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Carneiro Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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