1
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Jang HB, Chittick L, Li YF, Zablocki O, Sanderson CM, Carrillo A, van den Engh G, Sullivan MB. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME COMMUNICATIONS 2022; 2:12. [PMID: 37938680 PMCID: PMC9723727 DOI: 10.1038/s43705-022-00093-9] [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: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 04/27/2023]
Abstract
Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.
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Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Alfonso Carrillo
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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2
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Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L. Resolving the structure of phage-bacteria interactions in the context of natural diversity. Nat Commun 2022; 13:372. [PMID: 35042853 PMCID: PMC8766483 DOI: 10.1038/s41467-021-27583-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.
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Affiliation(s)
- Kathryn M Kauffman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Oral Biology, The University at Buffalo, Buffalo, NY, 14214, USA
| | - William K Chang
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Julia M Brown
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Fatima A Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Joy Yang
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Gencay YE, Gambino M, Prüssing TF, Brøndsted L. The genera of bacteriophages and their receptors are the major determinants of host range. Environ Microbiol 2019; 21:2095-2111. [PMID: 30888719 DOI: 10.1111/1462-2920.14597] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
The host range of phages is a key to understand their impact on bacterial ecology and evolution. Because of the complexity of phage-host interactions, the variables that determine the breadth of a phage host range remain poorly understood. Here, we propose a novel holistic approach to identify the host range determinants of a new collection of phages infecting Salmonella, isolated from animal, environmental and wastewater samples that were able to infect 58 of the 71 Salmonella strains in our collection. By using a set of statistic approaches (non-metric dimensional scaling, Bray-Curtis distance, PERMANOVA), we analysed phenotypic (host range on wild-type and receptor mutants) and genetic data (taxonomic assignment and receptor binding proteins) to evaluate the impact of isolation strain and niche, phage receptor and genus on the host range. Statistical analysis revealed that two phage characteristics influence the host range by explaining the most variance: the receptor by 45% and the genus by 51%. Interestingly, phage genus and receptor in combination explained 79% of the variance, establishing these characteristics as the major determinants of the host range. This study demonstrates the power and the novelty of applying statistical approaches to phenotypic and genetic data to investigate the ecology of phage-host interactions.
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Affiliation(s)
- Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Tessa From Prüssing
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
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4
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Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB. Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept. Front Microbiol 2017; 8:1241. [PMID: 28729861 PMCID: PMC5498523 DOI: 10.3389/fmicb.2017.01241] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.
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Affiliation(s)
- Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann ArborMI, United States
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Simon Roux
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Nathan C Verberkmoes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El PasoTX, United States
| | - Antje Wichels
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine ResearchHelgoland, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, ColumbusOH, United States.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, ColumbusOH, United States
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5
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Lara E, Holmfeldt K, Solonenko N, Sà EL, Ignacio-Espinoza JC, Cornejo-Castillo FM, Verberkmoes NC, Vaqué D, Sullivan MB, Acinas SG. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea. PLoS One 2015; 10:e0114829. [PMID: 25587991 PMCID: PMC4294664 DOI: 10.1371/journal.pone.0114829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.
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Affiliation(s)
- Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Karin Holmfeldt
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Natalie Solonenko
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Elisabet Laia Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - J. Cesar Ignacio-Espinoza
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Nathan C. Verberkmoes
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Matthew B. Sullivan
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
- * E-mail:
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6
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Riemann L, Middelboe M. Viral lysis of marine bacterioplankton: Implications for organic matter cycling and bacterial clonal composition. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/00785236.2002.10409490] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Fontes MLS, Abreu PC. Spatiotemporal variation of bacterial assemblages in a shallow subtropical coastal lagoon in Southern Brazil. MICROBIAL ECOLOGY 2009; 58:140-152. [PMID: 18953593 DOI: 10.1007/s00248-008-9454-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/10/2008] [Indexed: 05/27/2023]
Abstract
A study on the bacterioplankton of Conceição Lagoon (27 degrees 34' S-48 degrees 27' W), Southern Brazil, was carried out in July 2005 (austral winter) and January 2006 (austral summer) to characterize the bacterial spatiotemporal distribution and to determine the heterotrophic and photoautotrophic bacterial dominance in hypoxic/oxic stratified waters. Bacterial abundance increased significantly (p < 0.05) in summer with averages of coccus cyanobacteria (CCY) ranging from 1.02 x 10(5) (winter) to 3.21 x 10(6) cells mL(-1) (summer), heterotrophic coccus/rod-shaped (HCR) cells from 7.00 x 10(4) to 3.60 x 10(6) cells mL(-1), and heterotrophic filamentous (HF) bacteria from 2.90 x 10(3) to 2.74 x 10(5) cells mL(-1). Bacterial biovolumes also increased in summer with mean biovolumes of CCY ranging from 0.38 to 1.37 microm3, HCR cells from 0.31 to 1.12 microm3, and HF from 3.32 to 11.34 microm3. Principal component analysis showed that salinity, temperature, and light were the abiotic factors that better explained the temporal variability of bacterial assemblages. Bacterial heterotrophy dominated in the lagoon, excepted by the southern and part of central sector in January 2006, when autotrophic-dominated microbial community occurred. Spatially, bacterial assemblages were influenced by nutrient gradient, oxygen, and salinity with a positive relationship between biovolumes and nutrients and a negative relationship between abundance of coccus cyanobacteria and nutrients. The stratified [corrected] area revealed a singular temporal pattern with hypoxic bottom waters in winter and oxygen-rich waters appearing in summer related with the availability of light and predominant microbes. Thus, oxygen consumption/production is likely to be regulated by the amount of light reaching the bottom, stimulating the production of oxygen by oxygenic phototrophs.
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Affiliation(s)
- Maria Luiza Schmitz Fontes
- Post-Graduation Course on Biological Oceanography, Institute of Oceanography, Federal University of Rio Grande (FURG), Av. Itália km 08, Rio Grande, RS 96201-900, Brazil.
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8
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Abstract
Since most of the phage genomes isolated from natural samples are previously unknown sequences, an isolation-independent approach is necessary to quantify the diversity of natural viral communities. Currently, two different methodological approaches are widely used to obtain genetic fingerprints of natural phage communities. While the separation of different viral genomes with pulsed field gel electrophoresis (PFGE) is based on the size of the genome, denaturing gradient gel electrophoresis (DGGE) uses minor differences in gene base composition to separate fragments of amplified DNA from natural viral communities. Finger printing techniques are a relatively fast and cheap tool to assess the diversity of environmental viruses. Together, PFGE and DGGE provide useful tools to study viral ecology in natural habitats.
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9
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Zemb O, Urios L, Coetsier C, Lebaron P. Efficient method to isolate and purify viruses of bacteria from marine environments. Lett Appl Microbiol 2008; 47:41-5. [DOI: 10.1111/j.1472-765x.2008.02381.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Guyader S, Burch CL. Optimal foraging predicts the ecology but not the evolution of host specialization in bacteriophages. PLoS One 2008; 3:e1946. [PMID: 18414655 PMCID: PMC2279161 DOI: 10.1371/journal.pone.0001946] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 02/26/2008] [Indexed: 11/21/2022] Open
Abstract
We explore the ability of optimal foraging theory to explain the observation among marine bacteriophages that host range appears to be negatively correlated with host abundance in the local marine environment. We modified Charnov's classic diet composition model to describe the ecological dynamics of the related generalist and specialist bacteriophages φX174 and G4, and confirmed that specialist phages are ecologically favored only at high host densities. Our modified model accurately predicted the ecological dynamics of phage populations in laboratory microcosms, but had only limited success predicting evolutionary dynamics. We monitored evolution of attachment rate, the phenotype that governs diet breadth, in phage populations adapting to both low and high host density microcosms. Although generalist φX174 populations evolved even broader diets at low host density, they did not show a tendency to evolve the predicted specialist foraging strategy at high host density. Similarly, specialist G4 populations were unable to evolve the predicted generalist foraging strategy at low host density. These results demonstrate that optimal foraging models developed to explain the behaviorally determined diets of predators may have only limited success predicting the genetically determined diets of bacteriophage, and that optimal foraging probably plays a smaller role than genetic constraints in the evolution of host specialization in bacteriophages.
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Affiliation(s)
- Sébastien Guyader
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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11
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Holmfeldt K, Middelboe M, Nybroe O, Riemann L. Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl Environ Microbiol 2007; 73:6730-9. [PMID: 17766444 PMCID: PMC2074958 DOI: 10.1128/aem.01399-07] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phages are a main mortality factor for marine bacterioplankton and are thought to regulate bacterial community composition through host-specific infection and lysis. In the present study we demonstrate for a marine phage-host assemblage that interactions are complex and that specificity and efficiency of infection and lysis are highly variable among phages infectious to strains of the same bacterial species. Twenty-three Bacteroidetes strains and 46 phages from Swedish and Danish coastal waters were analyzed. Based on genotypic and phenotypic analyses, 21 of the isolates could be considered strains of Cellulophaga baltica (Flavobacteriaceae). Nevertheless, all bacterial strains showed unique phage susceptibility patterns and differed by up to 6 orders of magnitude in sensitivity to the same titer of phage. The isolated phages showed pronounced variations in genome size (8 to >242 kb) and host range (infecting 1 to 20 bacterial strains). Our data indicate that marine bacterioplankton are susceptible to multiple co-occurring phages and that sensitivity towards phage infection is strain specific and exists as a continuum between highly sensitive and resistant, implying an extremely complex web of phage-host interactions. Hence, effects of phages on bacterioplankton community composition and dynamics may go undetected in studies where strain identity is not resolvable, i.e., in studies based on the phylogenetic resolution provided by 16S rRNA gene or internal transcribed spacer sequences.
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Affiliation(s)
- Karin Holmfeldt
- Department of Natural Sciences, Kalmar University, S-391 82 Kalmar, Sweden
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12
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Säwström C, Granéli W, Laybourn-Parry J, Anesio AM. High viral infection rates in Antarctic and Arctic bacterioplankton. Environ Microbiol 2007; 9:250-5. [PMID: 17227429 DOI: 10.1111/j.1462-2920.2006.01135.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The frequency of visibly phage-infected bacterial cells (FVIB) and the average number of phages per cell [i.e. burst size (BS)] were determined in Antarctic and Arctic ultra-oligotrophic freshwater environments. Water samples were collected from two Antarctic freshwater lakes and cryoconite holes from a glacier in the Arctic. Data from this bipolar study show the highest FVIB (average 26.1%, range 5.1% to 66.7%) and the lowest BS (average 4, range 2-15) ever reported in the literature. The bacterial density is low in these ultra-oligotrophic freshwater environments but a large proportion of the bacteria are visibly infected. Our results suggest that a constant virioplankton population can be maintained in these extreme environments even though host density is low and often slow growing.
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Affiliation(s)
- Christin Säwström
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden.
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13
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Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol 2005; 13:278-84. [PMID: 15936660 DOI: 10.1016/j.tim.2005.04.003] [Citation(s) in RCA: 473] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Revised: 04/12/2005] [Accepted: 04/21/2005] [Indexed: 11/21/2022]
Abstract
There are an estimated 10(31) viruses on Earth, most of which are phages that infect bacteria. Metagenomic analyses have shown that environmental viral communities are incredibly diverse. There are an estimated 5000 viral genotypes in 200 liters of seawater and possibly a million different viral genotypes in one kilogram of marine sediment. By contrast, some culturing and molecular studies have found that viruses move between different biomes. Together, these findings suggest that viral diversity could be high on a local scale but relatively limited globally. Also, by moving between environments, viruses can facilitate horizontal gene transfer.
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Affiliation(s)
- Mya Breitbart
- Biology Department, LS301, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182 USA
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14
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Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev 2004; 28:127-81. [PMID: 15109783 DOI: 10.1016/j.femsre.2003.08.001] [Citation(s) in RCA: 912] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2002] [Revised: 07/22/2003] [Accepted: 08/05/2003] [Indexed: 11/24/2022] Open
Abstract
The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.
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Affiliation(s)
- Markus G Weinbauer
- Department of Biological Oceanography, Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.
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15
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Wolf A, Wiese J, Jost G, Witzel KP. Wide geographic distribution of bacteriophages that lyse the same indigenous freshwater isolate (Sphingomonas sp. strain B18). Appl Environ Microbiol 2003; 69:2395-8. [PMID: 12676728 PMCID: PMC154766 DOI: 10.1128/aem.69.4.2395-2398.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An indigenous freshwater bacterium (Sphingomonas sp. strain B18) from Lake Plubetasee (Schleswig-Holstein, Germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. This bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. Phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction pattern. Some phages were widely distributed, while different types coexisted in the same sample. It was concluded that phages could be a major factor in shaping the structure of bacterial communities and maintaining a high bacterial diversity.
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Affiliation(s)
- Arite Wolf
- Max Planck Institute for Limnology, 24302 Plön, Germany
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16
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Abstract
Marine phages are the most abundant biological entities in the oceans. They play important roles in carbon cycling through marine food webs, gene transfer by transduction and conversion of hosts by lysogeny. The handful of marine phage genomes that have been sequenced to date, along with prophages in marine bacterial genomes, and partial sequencing of uncultivated phages are yielding glimpses of the tremendous diversity and physiological potential of the marine phage community. Common gene modules in diverse phages are providing the information necessary to make evolutionary comparisons. Finally, deciphering phage genomes is providing clues about the adaptive response of phages and their hosts to environmental cues.
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Affiliation(s)
- John H Paul
- College of Marine Sciences, University of South Florida, 140 Seventh Ave S, St Petersburg, FL 33701, USA.
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17
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Abstract
The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.
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Affiliation(s)
- K E Wommack
- Center of Marine Biotechnology, Baltimore, Maryland 21202, USA
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Wichels A, Biel SS, Gelderblom HR, Brinkhoff T, Muyzer G, Schütt C. Bacteriophage diversity in the North Sea. Appl Environ Microbiol 1998; 64:4128-33. [PMID: 9797256 PMCID: PMC106618 DOI: 10.1128/aem.64.11.4128-4133.1998] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years interest in bacteriophages in aquatic environments has increased. Electron microscopy studies have revealed high numbers of phage particles (10(4) to 10(7) particles per ml) in the marine environment. However, the ecological role of these bacteriophages is still unknown, and the role of the phages in the control of bacterioplankton by lysis and the potential for gene transfer are disputed. Even the basic questions of the genetic relationships of the phages and the diversity of phage-host systems in aquatic environments have not been answered. We investigated the diversity of 22 phage-host systems after 85 phages were collected at one station near a German island, Helgoland, located in the North Sea. The relationships among the phages were determined by electron microscopy, DNA-DNA hybridization, and host range studies. On the basis of morphology, 11 phages were assigned to the virus family Myoviridae, 7 phages were assigned to the family Siphoviridae, and 4 phages were assigned to the family Podoviridae. DNA-DNA hybridization confirmed that there was no DNA homology between phages belonging to different families. We found that the 22 marine bacteriophages belonged to 13 different species. The host bacteria were differentiated by morphological and physiological tests and by 16S ribosomal DNA sequencing. All of the bacteria were gram negative, facultatively anaerobic, motile, and coccoid. The 16S rRNA sequences of the bacteria exhibited high levels of similarity (98 to 99%) with the sequences of organisms belonging to the genus Pseudoalteromonas, which belongs to the gamma subdivision of the class Proteobacteria.
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Affiliation(s)
- A Wichels
- Biologische Anstalt Helgoland, D-27498 Helgoland, Germany.
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Bratbak G, Thingstad F, Heldal M. Viruses and the microbial loop. MICROBIAL ECOLOGY 1994; 28:209-221. [PMID: 24186448 DOI: 10.1007/bf00166811] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The abundance of viral-like particles in marine ecosystems ranges from <104 ml(-1) to >10(8) ml(-1). Their distribution in time and space parallels that of other biological parameters such as bacterial abundance and chlorophyll a. There is a lack of consensus between methods used to assess viral activity, i.e., rate of change in viral abundance (increase or decrease). The highest rates, 10-100 days(-1), are observed in experiments with short sampling intervals (0.2-2 h), while lower rates, on the order of 1 day(-1), are observed in experiments with longer sampling intervals (days). Few studies have been carried out, but viruses appear, at least in some cases, to have a significant impact on carbon and nutrient flow in microbial food webs. Viruses have also been demonstrated to exert a species specific control of both bacteria and phytoplankton populations in natural waters.
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Affiliation(s)
- G Bratbak
- Department of Microbiology, University of Bergen, Jahnebakken 5, N-5020, Bergen, Norway
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Moebus K. Laboratory investigations on the survival of marine bacteriophages in raw and treated seawater. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf02367098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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