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Viruses
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Diversity and Evolution of Viruses in Ecosystem 2025
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Diversity and Evolution of Viruses in Ecosystem 2025

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1229

Special Issue Editor

Dr. René Kallies

E-Mail Website
Guest Editor
German Environment Agency, Section II 1.4 Microbial Risks, Corrensplatz 1, 14195 Berlin, Germany
Interests: environmental virology; viral metagenomics; viral metatranscriptomics; phage genomics; virus evolution and phylogeny
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses are highly abundant in ecosystems and have a high degree of diversity, often with high evolution rates, enabling them to quickly adapt to (changing) environmental conditions. They influence (micro)organisms of higher trophic levels. For example, they are one key factor for microbial mortality and drive the diversification and evolution of microbes. Viruses are involved in gene transfer, and they are key contributors to the mineralization of nutrients since they solubilize microorganisms by lysis. As a result, they are important drivers of bio(geo)chemical cycles. Viruses affect host interactions and, as a result, can drive the structure and composition of populations and ecosystems. Consequently, viruses impact ecosystem health, resilience, and function, and it has been suggested that viruses are integral components of ecosystems.

This Special Issue invites submissions that involve studies about virus diversity in different types of ecosystems, such as environmental (e.g., marine, freshwater, and terrestrial ecosystems) and host-associated (e.g., microorganisms and animals including humans and plants) ecosystems. Manuscripts concerning the evolutionary aspects of how viruses respond to the ecosystem in which they exist, their impact on other organisms, and the possible effects of these organisms on viral communities and their contribution to ecosystem services are welcome. We will also consider manuscripts describing emerging pathogenic viruses, disease transmission after biodiversity loss, and/or altered ecosystem functions.

Dr. René Kallies
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

  • environmental virology
  • viral metagenomics
  • viral metatranscriptomics
  • phage genomics
  • virus evolution and phylogeny

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Related Special Issue

Published Papers (2 papers)

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Research

15 pages, 3201 KiB  
Article
Distinguishing Lytic and Temperate Infection Dynamics in the Environment
by Isha Tripathi, Naomi Barber-Choi, Lauren Woodward, Natalie Falta, Natalia Shahwan, Nickie Yang and Ben Knowles
Viruses 2025, 17(4), 513; https://doi.org/10.3390/v17040513 - 1 Apr 2025
Viewed by 334
Abstract
Viral infection and lysis drive bacterial diversity and abundances, ultimately regulating global biogeochemical cycles. Infection can follow lytic or temperate routes, with lytic dynamics suppressing bacterial population growth and temperate infection enhancing it. Given that bacterial over-proliferation is a pervasive threat to ecosystems, [...] Read more.
Viral infection and lysis drive bacterial diversity and abundances, ultimately regulating global biogeochemical cycles. Infection can follow lytic or temperate routes, with lytic dynamics suppressing bacterial population growth and temperate infection enhancing it. Given that bacterial over-proliferation is a pervasive threat to ecosystems, determining which infection dynamic dominates a given ecosystem is a central question in viral ecology. However, the fields that describe and test the rules of viral infection—theoretical ecology and environmental microbiology, respectively—remain disconnected. To address this, we simulated common empirical approaches to analyze and distinguish between the predictions of three theoretical models mechanistically representing lytic to temperate infection dynamics. By doing so, we found that the models have remarkably similar predictions despite their mechanistic differences, as shown by PCA and correlation analyses. Essentially, the models are only discernable under simulated nutrient addition, where lytic models become less stable with no increase in host densities while the temperate model remains stable and has elevated host abundances. Highlighting this difference between the models, we present a dichotomous key illustrating how researchers can determine whether lytic or temperate infection dynamics dominate their ecosystem of interest using common metrics and empirical approaches. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem 2025)
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15 pages, 2497 KiB  
Article
Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages
by Cristina Howard-Varona, Natalie E. Solonenko, Marie Burris, Marion Urvoy, Courtney M. Sanderson, Bejamin Bolduc and Matthew B. Sullivan
Viruses 2025, 17(3), 365; https://doi.org/10.3390/v17030365 - 3 Mar 2025
Viewed by 677
Abstract
Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages—ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist [...] Read more.
Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages—ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)—when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage–host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem 2025)
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