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Viruses
Special Issues
Phage Ecology 2021
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Phage Ecology 2021

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 19836

Special Issue Editor

Prof. Dr. Stephen T. Abedon

E-Mail Website
Guest Editor
Department of Microbiology, The Ohio State University, Columbus, OH 44906, USA
Interests: phage ecology; phage evolutionary ecology; phage therapy; phage therapy pharmacology; phage history
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ecology is the study of the interactions of organisms with their environments. This can be with environmental abiotic (non-living) components, environmental biotic (living) components, or in terms of organism distribution over space and time. We can describe these various interactions in terms of organismal ecology, physiological ecology, evolutionary ecology, behavioral ecology, population ecology, community ecology, ecosystem ecology, landscape ecology, mathematical ecology, and biogeography. Bacteriophages (phages) are the viruses of bacteria. Along with the conceptually related viruses of domain Archaea (archaeal viruses), phages generally make a living by finding and then infecting either individual cells or instead clumps of cells, the latter as making up cellular arrangements, microcolonies, and/or biofilms. Our interest is in the ecology, variously considered, of such viruses.

I have been studying phage ecology for ~30 years, with over 100 publications, most of which touch on this subject. My specific interests have been on phage adaptations and tradeoffs, the ecology of phage interactions with biofilms, and the ecology of phage use as antibacterial agents, otherwise described as phage-therapy pharmacology. I have authored, edited, or co-edited roughly 10 monographs or edited volumes including The Bacteriophages 2/e (Oxford University Press, 2006), Bacteriophage Ecology (Cambridge University Press, 2008), The ‘Nuts and Bolts’ of Phage Therapy (Current Pharmaceutical Biotechnology, 2010), Bacteriophages and Biofilms (Nova Science Publishers, 2011), and Viruses of Microorganisms (Caister, 2018). In addition, I founded in 1996 and continue to maintain phage.org, i.e., the Bacteriophage Ecology Group. See also abedon.phage.org as well as facebook.com/Bacteriophage-Ecology-Group-111721928901953/.

In this Special Issue we are inviting submissions on all aspects of phage ecology, from the basic to the applied, from the study of individual viruses to the viromics of environments, and everything in between. Each submission will be given a quick read and editing by myself, consisting of a pre-peer review, prior to submission for actual peer review. We look forward in these submissions to experiencing your passion and enthusiasm for the subject of phage ecology.

Prof. Stephen T. Abedon
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phages
  • bacteriophages
  • archaeal viruses
  • growth parameters
  • modeling
  • adaptation
  • population dynamics
  • predator-prey dynamics
  • antagonistic coevolution
  • transduction
  • trophic interactions
  • biogeochemistry
  • carbon cycle
  • productivity
  • viromics
  • metagenomics
  • microbiomes
  • environmental microbiology
  • biogeography
  • distribution

Related Special Issue

Published Papers (5 papers)

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12 pages, 2380 KiB  
Article
Phi 6 Bacteriophage Inactivation by Metal Salts, Metal Powders, and Metal Surfaces
by Katja Molan, Ramin Rahmani, Daniel Krklec, Miha Brojan and David Stopar
Viruses 2022, 14(2), 204; https://doi.org/10.3390/v14020204 - 21 Jan 2022
Cited by 12 | Viewed by 3276
Abstract
The interaction of phages with abiotic environmental surfaces is usually an understudied field of phage ecology. In this study, we investigated the virucidal potential of different metal salts, metal and ceramic powders doped with Ag and Cu ions, and newly fabricated ceramic and [...] Read more.
The interaction of phages with abiotic environmental surfaces is usually an understudied field of phage ecology. In this study, we investigated the virucidal potential of different metal salts, metal and ceramic powders doped with Ag and Cu ions, and newly fabricated ceramic and metal surfaces against Phi6 bacteriophage. The new materials were fabricated by spark plasma sintering (SPS) and/or selective laser melting (SLM) techniques and had different surface free energies and infiltration features. We show that inactivation of Phi6 in solutions with Ag and Cu ions can be as effective as inactivation by pH, temperature, or UV. Adding powder to Ag and Cu ion solutions decreased their virucidal effect. The newly fabricated ceramic and metal surfaces showed very good virucidal activity. In particular, 45%TiO2 + 5%Ag + 45%ZrO2 + 5%Cu, in addition to virus adhesion, showed virucidal and infiltration properties. The results indicate that more than 99.99% of viruses deposited on the new ceramic surface were inactivated or irreversibly attached to it. Full article
(This article belongs to the Special Issue Phage Ecology 2021)
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13 pages, 1159 KiB  
Article
Mycelia-Assisted Isolation of Non-Host Bacteria Able to Co-Transport Phages
by Xin You, Niclas Klose, René Kallies, Hauke Harms, Antonis Chatzinotas and Lukas Y. Wick
Viruses 2022, 14(2), 195; https://doi.org/10.3390/v14020195 - 20 Jan 2022
Cited by 4 | Viewed by 2659
Abstract
Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based [...] Read more.
Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90–95% for hydrophobic T4 and 30–95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments. Full article
(This article belongs to the Special Issue Phage Ecology 2021)
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15 pages, 3676 KiB  
Article
Interactions between the Prophage 919TP and Its Vibrio cholerae Host: Implications of gmd Mutation for Phage Resistance, Cell Auto-Aggregation, and Motility
by Na Li, Yigang Zeng, Bijie Hu, Tongyu Zhu, Sine Lo Svenningsen, Mathias Middelboe and Demeng Tan
Viruses 2021, 13(12), 2342; https://doi.org/10.3390/v13122342 - 23 Nov 2021
Cited by 1 | Viewed by 2604
Abstract
Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from [...] Read more.
Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (φ919TP cI-). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP cI-. Further, the comparative genomic analysis of wild-type and φ919TP cI--resistant mutant predicted that phage φ919TP cI- selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in V. cholerae. The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control. Full article
(This article belongs to the Special Issue Phage Ecology 2021)
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17 pages, 3911 KiB  
Article
Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage
by Karin R. H. Biggs, Clayton L. Bailes, LuAnn Scott, Holly A. Wichman and Elissa J. Schwartz
Viruses 2021, 13(7), 1389; https://doi.org/10.3390/v13071389 - 17 Jul 2021
Cited by 7 | Viewed by 2449
Abstract
In microbial communities, viruses compete with each other for host cells to infect. As a consequence of competition for hosts, viruses evolve inhibitory mechanisms to suppress their competitors. One such mechanism is superinfection exclusion, in which a preexisting viral infection prevents a secondary [...] Read more.
In microbial communities, viruses compete with each other for host cells to infect. As a consequence of competition for hosts, viruses evolve inhibitory mechanisms to suppress their competitors. One such mechanism is superinfection exclusion, in which a preexisting viral infection prevents a secondary infection. The bacteriophage ΦX174 exhibits a potential superinfection inhibition mechanism (in which secondary infections are either blocked or resisted) known as the reduction effect. In this auto-inhibitory phenomenon, a plasmid containing a fragment of the ΦX174 genome confers resistance to infection among cells that were once permissive to ΦX174. Taking advantage of this plasmid system, we examine the inhibitory properties of the ΦX174 reduction effect on a range of wild ΦX174-like phages. We then assess how closely the reduction effect in the plasmid system mimics natural superinfection inhibition by carrying out phage–phage competitions in continuous culture, and we evaluate whether the overall competitive advantage can be predicted by phage fitness or by a combination of fitness and reduction effect inhibition. Our results show that viral fitness often correctly predicts the winner. However, a phage’s reduction sequence also provides an advantage to the phage in some cases, modulating phage–phage competition and allowing for persistence where competitive exclusion was expected. These findings provide strong evidence for more complex dynamics than were previously thought, in which the reduction effect may inhibit fast-growing viruses, thereby helping to facilitate coexistence. Full article
(This article belongs to the Special Issue Phage Ecology 2021)
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19 pages, 1861 KiB  
Opinion
Improving Phage-Biofilm In Vitro Experimentation
by Stephen T. Abedon, Katarzyna M. Danis-Wlodarczyk, Daniel J. Wozniak and Matthew B. Sullivan
Viruses 2021, 13(6), 1175; https://doi.org/10.3390/v13061175 - 19 Jun 2021
Cited by 17 | Viewed by 7493
Abstract
Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a [...] Read more.
Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting. Full article
(This article belongs to the Special Issue Phage Ecology 2021)
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