1
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Mäkelä K, Laanto E, Sundberg LR. Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases. Environ Microbiol 2024; 26:e16670. [PMID: 38952172 DOI: 10.1111/1462-2920.16670] [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: 12/20/2023] [Accepted: 05/24/2024] [Indexed: 07/03/2024]
Abstract
The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.
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Affiliation(s)
- Kati Mäkelä
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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2
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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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3
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Fang Z, Xu M, Shen S, Sun W, Yu Q, Wu Q, Xiang L, Weng Q. Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages. Sci Rep 2023; 13:22941. [PMID: 38135742 PMCID: PMC10746704 DOI: 10.1038/s41598-023-50449-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: 04/27/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023] Open
Abstract
Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.
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Affiliation(s)
- Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Shan Shen
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Weiwei Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qing Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Lan Xiang
- Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China.
- Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, People's Republic of China.
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4
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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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5
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Nilsson E, Li K, Hoetzinger M, Holmfeldt K. Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium. Environ Microbiol 2022; 24:2270-2281. [PMID: 35049095 PMCID: PMC9305737 DOI: 10.1111/1462-2920.15904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/11/2022] [Indexed: 12/01/2022]
Abstract
Phages modulate bacterial metabolism during infection by regulating gene expression, which influences aquatic nutrient cycling. However, the effects of shifting nutrient regimes are less understood. Here, we analyzed transcriptomes of an ecologically relevant Gammaproteobacterium and its lytic phage in high (HNM) and low (LNM) nutrient medium. Despite different infection characteristics, including reduced burst size and longer latent period in LNM, the phage had a fixed expression profile. Bacterial transcription was instead different depending on nutrient regime, with HNM bacteria focusing on growth while LNM bacteria focused on motility and membrane transport. Additionally, phage infection had a larger effect on bacterial gene expression in LNM compared to HNM, e.g. suppressing increased iron uptake and altering expression of phosphorus uptake genes. Overall, phage infection influenced host metabolism more in LNM, which was more similar to natural conditions, emphasizing the importance of considering natural conditions to understand phage and host ecology.
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Affiliation(s)
- Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, SE-39231, Kalmar, Sweden
| | - Ke Li
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, SE-39231, Kalmar, Sweden
| | - Matthias Hoetzinger
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, SE-39231, Kalmar, Sweden
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, SE-39231, Kalmar, Sweden
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6
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Characterization of a New and Efficient Polyvalent Phage Infecting E. coli O157:H7, Salmonella spp., and Shigella sonnei. Microorganisms 2021; 9:microorganisms9102105. [PMID: 34683426 PMCID: PMC8540833 DOI: 10.3390/microorganisms9102105] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
Ongoing outbreaks of foodborne diseases remain a significant public health concern. Lytic phages provide promising attributes as biocontrol agents. This study characterized KFS-EC3, a polyvalent and lytic phage, which was isolated from slaughterhouse sewage and purified by cesium chloride density centrifugation. Host range and efficiency of plating analyses revealed that KFS-EC3 is polyvalent and can efficiently infect E. coli O157:H7, Salmonella spp., and Shigella sonnei. KFS-EC3 had a latent time of 20 min and burst size of ~71 phages/infected cell. KFS-EC3 was stable and infectious following storage at a pH range of 3 to 11 and a temperature range of -70 °C to 60 °C. KFS-EC3 could inhibit E. coli O157:H7 growth by 2 logs up to 52 h even at the lowest MOI of 0.001. Genomic analysis of KFS-EC3 revealed that it consisted of 167,440 bp and 273 ORFs identified as functional genes, without any genes associated with antibiotic resistance, virulence, allergenicity, and lysogenicity. This phage was finally classified into the Tequatrovirus genus of the Myoviridae family. In conclusion, KFS-EC3 could simultaneously infect E. coli O157:H7, S. sonnei, and Salmonella spp. with the lowest MOI values over long periods, suggesting its suitability for simultaneous pathogen control in foods.
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7
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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8
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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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9
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Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS. Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol 2021; 19:501-513. [PMID: 33762712 DOI: 10.1038/s41579-021-00530-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 02/01/2023]
Abstract
Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.
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Affiliation(s)
| | | | - Samantha R Coy
- BioSciences Department, Rice University, Houston, TX, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 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.
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
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10
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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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11
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - 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 for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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12
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Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078. mSystems 2020; 5:5/3/e00017-20. [PMID: 32371470 PMCID: PMC7205517 DOI: 10.1128/msystems.00017-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
C. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile. Insights into the interaction between phages and their bacterial hosts are crucial for the development of phage therapy. However, only one study has investigated global gene expression of Clostridioides (formerly Clostridium) difficile carrying prophage, and transcriptional reprogramming during lytic infection has not been studied. Here, we presented the isolation, propagation, and characterization of a newly discovered 35,109-bp phage, JD032, and investigated the global transcriptomes of both JD032 and C. difficile ribotype 078 (RT078) strain TW11 during JD032 infection. Transcriptome sequencing (RNA-seq) revealed the progressive replacement of bacterial host mRNA with phage transcripts. The expressed genes of JD032 were clustered into early, middle, and late temporal categories that were functionally similar. Specifically, a gene (JD032_orf016) involved in the lysis-lysogeny decision was identified as an early expression gene. Only 17.7% (668/3,781) of the host genes were differentially expressed, and more genes were downregulated than upregulated. The expression of genes involved in host macromolecular synthesis (DNA/RNA/proteins) was altered by JD032 at the level of transcription. In particular, the expression of the ropA operon was downregulated. Most noteworthy is that the gene expression of some antiphage systems, including CRISPR-Cas, restriction-modification, and toxin-antitoxin systems, was suppressed by JD032 during infection. In addition, bacterial sporulation, adhesion, and virulence factor genes were significantly downregulated. This study provides the first description of the interaction between anaerobic spore-forming bacteria and phages during lytic infection and highlights new aspects of C. difficile phage-host interactions. IMPORTANCEC. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage, JD032, and analyzed the global transcriptomic changes in the hypervirulent RT078 C. difficile strain, TW11, during phage JD032 infection. We found that bacterial host mRNA was progressively replaced with phage transcripts, three temporal categories of JD032 gene expression, the extensive interplay between phage-bacterium, antiphage-like responses of the host and phage evasion, and decreased expression of sporulation- and virulence-related genes of the host after phage infection. These findings confirmed the complexity of interactions between C. difficile and phages and suggest that phages undergoing a lytic cycle may also cause different phenotypes in hosts, similar to prophages, which may inspire phage therapy for the control of C. difficile.
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13
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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14
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Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects. ISME JOURNAL 2020; 14:1688-1700. [PMID: 32242083 PMCID: PMC7305329 DOI: 10.1038/s41396-020-0637-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 01/07/2023]
Abstract
Temperate phages engage in long-term associations with their hosts that may lead to mutually beneficial interactions, of which the full extent is presently unknown. Here, we describe an environmentally relevant model system with a single host, a species of the Roseobacter clade of marine bacteria, and two genetically similar phages (ɸ-A and ɸ-D). Superinfection of a ɸ-D lysogenized strain (CB-D) with ɸ-A particles resulted in a lytic infection, prophage induction, and conversion of a subset of the host population, leading to isolation of a newly ɸ-A lysogenized strain (CB-A). Phenotypic differences, predicted to result from divergent lysogenic-lytic switch mechanisms, are evident between these lysogens, with CB-A displaying a higher incidence of spontaneous induction. Doubling times of CB-D and CB-A in liquid culture are 75 and 100 min, respectively. As cell cultures enter stationary phase, CB-A viable counts are half of CB-D. Consistent with prior evidence that cell lysis enhances biofilm formation, CB-A produces twice as much biofilm biomass as CB-D. As strains are susceptible to infection by the opposing phage type, co-culture competitions were performed to test fitness effects. When grown planktonically, CB-A outcompeted CB-D three to one. Yet, during biofilm growth, CB-D outcompeted CB-A three to one. These results suggest that genetically similar phages can have divergent influence on the competitiveness of their shared hosts in distinct environmental niches, possibly due to a complex form of phage-mediated allelopathy. These findings have implications for enhanced understanding of the eco-evolutionary dynamics of host-phage interactions that are pervasive in all ecosystems.
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15
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Howard-Varona C, Lindback MM, Bastien GE, Solonenko N, Zayed AA, Jang H, Andreopoulos B, Brewer HM, Glavina Del Rio T, Adkins JN, Paul S, Sullivan MB, Duhaime MB. Phage-specific metabolic reprogramming of virocells. ISME JOURNAL 2020; 14:881-895. [PMID: 31896786 PMCID: PMC7082346 DOI: 10.1038/s41396-019-0580-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/25/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022]
Abstract
Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - G Eric Bastien
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - HoBin Jang
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Tijana Glavina Del Rio
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Joshua N Adkins
- Biological Science Division, PNNL, 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH, 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA. .,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH, 43210, USA. .,Center for RNA Biology, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, USA.
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA.
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16
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Mohanraj U, Wan X, Spruit CM, Skurnik M, Pajunen MI. A Toxicity Screening Approach to Identify Bacteriophage-Encoded Anti-Microbial Proteins. Viruses 2019; 11:E1057. [PMID: 31739448 PMCID: PMC6893735 DOI: 10.3390/v11111057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/23/2022] Open
Abstract
The rapid emergence of antibiotic resistance among many pathogenic bacteria has created a profound need to discover new alternatives to antibiotics. Bacteriophages, the viruses of microbes, express special proteins to overtake the metabolism of the bacterial host they infect, the best known of which are involved in bacterial lysis. However, the functions of majority of bacteriophage encoded gene products are not known, i.e., they represent the hypothetical proteins of unknown function (HPUFs). In the current study we present a phage genomics-based screening approach to identify phage HPUFs with antibacterial activity with a long-term goal to use them as leads to find unknown targets to develop novel antibacterial compounds. The screening assay is based on the inhibition of bacterial growth when a toxic gene is expression-cloned into a plasmid vector. It utilizes an optimized plating assay producing a significant difference in the number of transformants after ligation of the toxic and non-toxic genes into a cloning vector. The screening assay was first tested and optimized using several known toxic and non-toxic genes. Then, it was applied to screen 94 HPUFs of bacteriophage φR1-RT, and identified four HPUFs that were toxic to Escherichia coli. This optimized assay is in principle useful in the search for bactericidal proteins of any phage, and also opens new possibilities to understanding the strategies bacteriophages use to overtake bacterial hosts.
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Affiliation(s)
- Ushanandini Mohanraj
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (U.M.); (X.W.); (C.M.S.); (M.S.)
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Xing Wan
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (U.M.); (X.W.); (C.M.S.); (M.S.)
- Division Animal and Human Health Engineering, Kasteelpark Arenberg 21 - box 2462, 3001 Leuven, Belgium
| | - Cindy M. Spruit
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (U.M.); (X.W.); (C.M.S.); (M.S.)
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (U.M.); (X.W.); (C.M.S.); (M.S.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (U.M.); (X.W.); (C.M.S.); (M.S.)
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17
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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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18
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Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. Appl Environ Microbiol 2019; 85:AEM.01003-19. [PMID: 31324626 PMCID: PMC6715854 DOI: 10.1128/aem.01003-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring “kill-the-winner” oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems. Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of “unknowns” that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimera sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and mazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages’ replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring “kill-the-winner” oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.
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19
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Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa. Appl Environ Microbiol 2019; 85:AEM.01170-19. [PMID: 31324627 DOI: 10.1128/aem.01170-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II.IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.
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20
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Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nat Commun 2019; 10:752. [PMID: 30765709 PMCID: PMC6375957 DOI: 10.1038/s41467-019-08672-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2019] [Indexed: 01/04/2023] Open
Abstract
Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.
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21
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Warwick-Dugdale J, Buchholz HH, Allen MJ, Temperton B. Host-hijacking and planktonic piracy: how phages command the microbial high seas. Virol J 2019; 16:15. [PMID: 30709355 PMCID: PMC6359870 DOI: 10.1186/s12985-019-1120-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the ocean, marine microbes eke out a living under constant assault from predatory viruses. Viral concentrations exceed those of their bacterial prey by an order of magnitude in surface water, making these obligate parasites the most abundant biological entities in the ocean. Like the pirates of the 17th and 18th centuries that hounded ships plying major trade and exploration routes, viruses have evolved mechanisms to hijack microbial cells and repurpose their cargo and indeed the vessels themselves to maximise viral propagation. Phenotypic reconfiguration of the host is often achieved through Auxiliary Metabolic Genes - genes originally derived from host genomes but maintained and adapted in viral genomes to redirect energy and substrates towards viral synthesis. In this review, we critically evaluate the literature describing the mechanisms used by bacteriophages to reconfigure host metabolism and to plunder intracellular resources to optimise viral production. We also highlight the mechanisms used when, in challenging environments, a 'batten down the hatches' strategy supersedes that of 'plunder and pillage'. Here, the infecting virus increases host fitness through phenotypic augmentation in order to ride out the metaphorical storm, with a concomitant impact on host substrate uptake and metabolism, and ultimately, their interactions with their wider microbial community. Thus, the traditional view of the virus-host relationship as predator and prey does not fully characterise the variety or significance of the interactions observed. Recent advances in viral metagenomics have provided a tantalising glimpse of novel mechanisms of viral metabolic reprogramming in global oceans. Incorporation of these new findings into global biogeochemical models requires experimental evidence from model systems and major improvements in our ability to accurately predict protein function from sequence data.
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Affiliation(s)
- Joanna Warwick-Dugdale
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.,University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Holger H Buchholz
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.,University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ben Temperton
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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22
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Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions. Appl Environ Microbiol 2018; 85:AEM.01311-18. [PMID: 30367000 PMCID: PMC6293099 DOI: 10.1128/aem.01311-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/07/2018] [Indexed: 12/29/2022] Open
Abstract
While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.
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Howard-Varona C, Vik DR, Solonenko NE, Li YF, Gazitua MC, Chittick L, Samiec JK, Jensen AE, Anderson P, Howard-Varona A, Kinkhabwala AA, Abedon ST, Sullivan MB. Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection. Antibiotics (Basel) 2018; 7:E101. [PMID: 30453470 PMCID: PMC6315980 DOI: 10.3390/antibiotics7040101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
Hemolytic⁻uremic syndrome is a life-threating disease most often associated with Shiga toxin-producing microorganisms like Escherichia coli (STEC), including E. coli O157:H7. Shiga toxin is encoded by resident prophages present within this bacterium, and both its production and release depend on the induction of Shiga toxin-encoding prophages. Consequently, treatment of STEC infections tend to be largely supportive rather than antibacterial, in part due to concerns about exacerbating such prophage induction. Here we explore STEC O157:H7 prophage induction in vitro as it pertains to phage therapy-the application of bacteriophages as antibacterial agents to treat bacterial infections-to curtail prophage induction events, while also reducing STEC O157:H7 presence. We observed that cultures treated with strictly lytic phages, despite being lysed, produce substantially fewer Shiga toxin-encoding temperate-phage virions than untreated STEC controls. We therefore suggest that phage therapy could have utility as a prophylactic treatment of individuals suspected of having been recently exposed to STEC, especially if prophage induction and by extension Shiga toxin production is not exacerbated.
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Affiliation(s)
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - M Consuelo Gazitua
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jennifer K Samiec
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Aubrey E Jensen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Paige Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | | | | | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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24
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Guajardo-Leiva S, Pedrós-Alió C, Salgado O, Pinto F, Díez B. Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs. Front Microbiol 2018; 9:2039. [PMID: 30233525 PMCID: PMC6129581 DOI: 10.3389/fmicb.2018.02039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2018] [Indexed: 01/16/2023] Open
Abstract
Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), taxonomic composition (metagenomics), and active infectivity (metatranscriptomics) of viral communities over a thermal gradient in hot spring phototrophic mats from Northern Patagonia (Chile). The mats were dominated (up to 53%) by cosmopolitan thermophilic filamentous true-branching cyanobacteria from the genus Mastigocladus, the associated viral community was predominantly composed of Caudovirales (70%), with most of the active infections driven by cyanophages (up to 90% of Caudovirales transcripts). Metagenomic assembly lead to the first full genome description of a T7-like Thermophilic Cyanophage recovered from a hot spring (Porcelana Hot Spring, Chile), with a temperature of 58°C (TC-CHP58). This could potentially represent a world-wide thermophilic lineage of podoviruses that infect cyanobacteria. In the hot spring, TC-CHP58 was active over a temperature gradient from 48 to 66°C, showing a high population variability represented by 1979 single nucleotide variants (SNVs). TC-CHP58 was associated to the Mastigocladus spp. by CRISPR spacers. Marked differences in metagenomic CRISPR loci number and spacers diversity, as well as SNVs, in the TC-CHP58 proto-spacers at different temperatures, reinforce the theory of co-evolution between natural virus populations and cyanobacterial hosts. Considering the importance of cyanobacteria in hot spring biogeochemical cycles, the description of this new cyanopodovirus lineage may have global implications for the functioning of these extreme ecosystems.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fabián Pinto
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research, Santiago, Chile
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25
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de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends Microbiol 2018; 27:51-63. [PMID: 30181062 DOI: 10.1016/j.tim.2018.08.006] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/07/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023]
Abstract
The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands; Laboratory for Microbiology, Wageningen University, Stippeneng 4 6708 WE, Wageningen, The Netherlands; These authors made equal contributions
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions.
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26
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Šulčius S, Mazur-Marzec H, Vitonytė I, Kvederavičiūtė K, Kuznecova J, Šimoliūnas E, Holmfeldt K. Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena. HARMFUL ALGAE 2018; 78:69-74. [PMID: 30196926 DOI: 10.1016/j.hal.2018.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
The effect of cyanophage infection and lysis on the dynamics of the hepatotoxin nodularin (NOD) and other non-ribosomal peptides (NRPs) produced by cyanobacteria is poorly understood. In this study, changes in concentration of NOD and other NRPs during cyanophage infection of the filamentous cyanobacteria Nodularia spumigena were assessed using incubation experiments. Viral infection and lysis were associated with a significant reduction (93% at the 96 h post infection) of N. spumigena cell density. While no correlation between N. spumigena abundance and total concentration of NOD (ng mL-1) within the infected cells was observed, cellular NOD quota (ng cell-1) gradually increased in the remaining cyanophage resistant N. spumigena subpopulation. Lysis of N. spumigena cells resulted in a substantial increase (>57 times) of dissolved NOD concentration in the culture medium. The relative concentration of other cyclic (anabaenopeptins) and linear (aeruginosins, spumigins) NRPs produced by N. spumigena also increased in response to cyanophage addition. This study highlights the importance of cyanophage infection on the population toxicity of filamentous cyanobacteria and demonstrates a significant contribution of virus-mediated cell lysis on the conversion of NOD from the particulate to dissolved phase.
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Affiliation(s)
- Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos str. 2, LT-08412, Vilnius, Lithuania; Center for Ecology and Evolution in Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Barlastgatan 11, SE-39231, Kalmar, Sweden.
| | - Hanna Mazur-Marzec
- Department of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Marszałka Józefa Piłsudskiego 46, PL-81378, Gdynia, Poland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland
| | - Irma Vitonytė
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos str. 2, LT-08412, Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- MAP Kinase Resource, Melchiorstrasse 9, CH-3027, Bern, Switzerland; Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Jolita Kuznecova
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos str. 2, LT-08412, Vilnius, Lithuania
| | - Eugenijus Šimoliūnas
- Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Karin Holmfeldt
- Center for Ecology and Evolution in Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Barlastgatan 11, SE-39231, Kalmar, Sweden
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27
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Sacher JC, Flint A, Butcher J, Blasdel B, Reynolds HM, Lavigne R, Stintzi A, Szymanski CM. Transcriptomic Analysis of the Campylobacter jejuni Response to T4-Like Phage NCTC 12673 Infection. Viruses 2018; 10:E332. [PMID: 29914170 PMCID: PMC6024767 DOI: 10.3390/v10060332] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
Campylobacter jejuni is a frequent foodborne pathogen of humans. As C. jejuni infections commonly arise from contaminated poultry, phage treatments have been proposed to reduce the C. jejuni load on farms to prevent human infections. While a prior report documented the transcriptome of C. jejuni phages during the carrier state life cycle, transcriptomic analysis of a lytic C. jejuni phage infection has not been reported. We used RNA-sequencing to profile the infection of C. jejuni NCTC 11168 by the lytic T4-like myovirus NCTC 12673. Interestingly, we found that the most highly upregulated host genes upon infection make up an uncharacterized operon (cj0423⁻cj0425), which includes genes with similarity to T4 superinfection exclusion and antitoxin genes. Other significantly upregulated genes include those involved in oxidative stress defense and the Campylobactermultidrug efflux pump (CmeABC). We found that phage infectivity is altered by mutagenesis of the oxidative stress defense genes catalase (katA), alkyl-hydroxyperoxidase (ahpC), and superoxide dismutase (sodB), and by mutagenesis of the efflux pump genes cmeA and cmeB. This suggests a role for these gene products in phage infection. Together, our results shed light on the phage-host dynamics of an important foodborne pathogen during lytic infection by a T4-like phage.
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Affiliation(s)
- Jessica C Sacher
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Annika Flint
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Bob Blasdel
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven 3001, Belgium.
| | - Hayley M Reynolds
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven 3001, Belgium.
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Christine M Szymanski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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28
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Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol 2018; 3:754-766. [PMID: 29867096 DOI: 10.1038/s41564-018-0166-y] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
| | - Chelsea Bonnain
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kema Malki
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Natalie A Sawaya
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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29
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Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. THE ISME JOURNAL 2018; 12:1605-1618. [PMID: 29568113 PMCID: PMC5955906 DOI: 10.1038/s41396-018-0099-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 01/08/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022]
Abstract
Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.
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Affiliation(s)
| | | | | | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, 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.
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30
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Abstract
Prions are molecules characterized by self-propagation, which can undergo a conformational switch leading to the creation of new prions. Prion proteins have originally been associated with the development of mammalian pathologies; however, recently they have been shown to contribute to the environmental adaptation in a variety of prokaryotic and eukaryotic organisms. Bacteriophages are widespread and represent the important regulators of microbiota homeostasis and have been shown to be diverse across various bacterial families. Here, we examined whether bacteriophages contain prion-like proteins and whether these prion-like protein domains are involved in the regulation of homeostasis. We used a computational algorithm, prion-like amino acid composition, to detect prion-like domains in 370,617 publicly available bacteriophage protein sequences, which resulted in the identification of 5040 putative prions. We analyzed a set of these prion-like proteins, and observed regularities in their distribution across different phage families, associated with their interactions with the bacterial host cells. We found that prion-like domains could be found across all phages of various groups of bacteria and archaea. The results obtained in this study indicate that bacteriophage prion-like proteins are predominantly involved in the interactions between bacteriophages and bacterial cell, such as those associated with the attachment and penetration of bacteriophage in the cell, and the release of the phage progeny. These data allow the identification of phage prion-like proteins as novel regulators of the interactions between bacteriophages and bacterial cells.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, United States
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, United States
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31
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Thomas F, Bordron P, Eveillard D, Michel G. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Front Microbiol 2017; 8:1808. [PMID: 28983288 PMCID: PMC5613140 DOI: 10.3389/fmicb.2017.01808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/05/2017] [Indexed: 11/13/2022] Open
Abstract
Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans DsijT, originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.
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Affiliation(s)
- François Thomas
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffRoscoff, France
| | - Philippe Bordron
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, FR2424, Analysis and Bioinformatics for Marine Science, Station Biologique de RoscoffRoscoff, France.,Mathomics, Center for Mathematical Modeling, Universidad de ChileSantiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile
| | - Damien Eveillard
- Université de Nantes, Laboratoire des Sciences du Numérique de Nantes, Centre National de la Recherche Scientifique, ECN, IMTANantes, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffRoscoff, France
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32
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Two Synechococcus genes, Two Different Effects on Cyanophage Infection. Viruses 2017; 9:v9060136. [PMID: 28574452 PMCID: PMC5490813 DOI: 10.3390/v9060136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 12/12/2022] Open
Abstract
Synechococcus is an abundant marine cyanobacterium that significantly contributes to primary production. Lytic phages are thought to have a major impact on cyanobacterial population dynamics and evolution. Previously, an investigation of the transcriptional response of three Synechococcus strains to infection by the T4-like cyanomyovirus, Syn9, revealed that while the transcript levels of the vast majority of host genes declined soon after infection, those for some genes increased or remained stable. In order to assess the role of two such host-response genes during infection, we inactivated them in Synechococcus sp. strain WH8102. One gene, SYNW1659, encodes a domain of unknown function (DUF3387) that is associated with restriction enzymes. The second gene, SYNW1946, encodes a PIN-PhoH protein, of which the PIN domain is common in bacterial toxin-antitoxin systems. Neither of the inactivation mutations impacted host growth or the length of the Syn9 lytic cycle. However, the DUF3387 mutant supported significantly lower phage DNA replication and yield of phage progeny than the wild-type, suggesting that the product of this host gene aids phage production. The PIN-PhoH mutant, on the other hand, allowed for significantly higher Syn9 genomic DNA replication and progeny production, suggesting that this host gene plays a role in restraining the infection process. Our findings indicate that host-response genes play a functional role during infection and suggest that some function in an attempt at defense against the phage, while others are exploited by the phage for improved infection.
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33
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Blasdel BG, Chevallereau A, Monot M, Lavigne R, Debarbieux L. Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera. ISME JOURNAL 2017; 11:1988-1996. [PMID: 28498372 PMCID: PMC5563952 DOI: 10.1038/ismej.2017.63] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/22/2017] [Accepted: 03/22/2017] [Indexed: 12/11/2022]
Abstract
Although the evolution of tailed bacteriophages has increasingly been better understood through comparisons of their DNA sequences, the functional consequences of this evolution on phage infectious strategies have remained unresolved. In this study, we comprehensively compared the transcriptional strategies of two related myoviruses, PAK_P3 and PAK_P4, infecting the same Pseudomonas aeruginosa host strain. Outside of the conservation of their structural clusters, their highly syntenic genomes display only limited DNA similarity. Despite this apparent divergence, we found that both viruses follow a similar infection scheme, relying on a temporal regulation of their gene expression, likely involving the use of antisense transcripts, as well as a rapid degradation of 90% of the host non-ribosomal mRNA, as previously reported for PAK_P3. However, the kinetics of the mRNA degradation is remarkably faster during PAK_P4 infection. Moreover, we found that each virus has evolved specific adaptations, as exemplified by the distinct patterns of their core genes expression as well as the specific manipulation of the expression of iron-related host genes by PAK_P4. This study enhances our understanding of the evolutionary process of virulent phages, which relies on adjusting globally conserved ancestral infection mechanisms.
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Affiliation(s)
- Bob G Blasdel
- Laboratory of Gene Technology, Department of Biosystems, Leuven, Belgium
| | - Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Leuven, Belgium
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
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34
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Needham DM, Sachdeva R, Fuhrman JA. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME JOURNAL 2017; 11:1614-1629. [PMID: 28398348 DOI: 10.1038/ismej.2017.29] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/13/2017] [Accepted: 02/02/2017] [Indexed: 12/21/2022]
Abstract
Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplankton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spearman>0.65) and became stronger (0.61 vs 0.58, t-test: P<0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho=0.49 vs 0.27; these results are consistent with strain-specific interactions. Mantel correlations suggested >1 μm (attached/large) prokaryotes are a major myovirus source. Consideration of microdiversity improved observation of apparent host and virus networks, and provided insights into the ecological and evolutionary factors influencing the success of lineages, with important implications to ecosystem resilience and microbial function.
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Affiliation(s)
- David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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35
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Marston MF, Martiny JBH. Genomic diversification of marine cyanophages into stable ecotypes. Environ Microbiol 2016; 18:4240-4253. [DOI: 10.1111/1462-2920.13556] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Marcia F. Marston
- Department of Biology and Marine Biology; Roger Williams University; Bristol RI 02809 USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology; University of California; Irvine CA 92697 USA
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36
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Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 2016; 18:3949-3961. [PMID: 27235779 DOI: 10.1111/1462-2920.13392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/21/2015] [Indexed: 01/21/2023]
Abstract
Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.
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Affiliation(s)
- Karin Holmfeldt
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.,Department of Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Natalie Solonenko
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Mario Moreno
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | | | - Matthew B Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
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