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

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

Deadline for manuscript submissions: 25 September 2024 | Viewed by 6973

Special Issue Editor

Dr. René Kallies

E-Mail Website
Guest Editor
Helmholtz Zentrum für Umweltforschung, Leipzig, 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, animals including humans and plants). 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.

Published Papers (7 papers)

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Research

17 pages, 13057 KiB  
Article
Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake
by Yu Zheng, Zihao Gao, Shuai Wu and Aidong Ruan
Viruses 2024, 16(4), 590; https://doi.org/10.3390/v16040590 - 11 Apr 2024
Viewed by 392
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving [...] Read more.
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus–host interaction systems, and the overarching influence of viruses on global biogeochemical cycling. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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14 pages, 2114 KiB  
Article
A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants
by Haozhe Zhao, Mingfei Yang, Xiang Fan, Qian Gui, Hao Yi, Yigang Tong and Wei Xiao
Viruses 2024, 16(4), 535; https://doi.org/10.3390/v16040535 - 29 Mar 2024
Viewed by 689
Abstract
The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well [...] Read more.
The concentration of viruses in sewage sludge is significantly higher (10–1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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13 pages, 3308 KiB  
Article
A Novel Podophage StenR_269 Suggests a New Family in the Class Caudoviricetes
by Vyacheslav I. Yakubovskij, Vera V. Morozova, Yuliya N. Kozlova, Artem Y. Tikunov, Igor V. Babkin, Alevtina V. Bardasheva, Elena V. Zhirakovskaya, Ivan K. Baykov, Galina B. Kaverina and Nina V. Tikunova
Viruses 2023, 15(12), 2437; https://doi.org/10.3390/v15122437 - 15 Dec 2023
Viewed by 826
Abstract
Stenotrophomonas rhizophila was first discovered in soil; it is associated with the rhizosphere and capable of both protecting roots and stimulating plant growth. Therefore, it has a great potential to be used in biocontrol. The study of S. rhizophila phages is important for [...] Read more.
Stenotrophomonas rhizophila was first discovered in soil; it is associated with the rhizosphere and capable of both protecting roots and stimulating plant growth. Therefore, it has a great potential to be used in biocontrol. The study of S. rhizophila phages is important for a further evaluation of their effect on the fitness and properties of host bacteria. A novel phage StenR_269 and its bacterial host S. rhizophila were isolated from a soil sample in the remediation area of a coal mine. Electron microscopy revealed a large capsid (~Ø80 nm) connected with a short tail, which corresponds to the podovirus morphotype. The length of the genomic sequence of the StenR_269 was 66,322 bp and it contained 103 putative genes; 40 of them encoded proteins with predicted functions, 3 corresponded to tRNAs, and the remaining 60 were identified as hypothetical ones. Comparative analysis indicated that the StenR_269 phage had a similar genome organization to that of the unclassified Xanthomonas phage DES1, despite their low protein similarity. In addition, the signature proteins of StenR_269 and DES1 had low similarity and these proteins clustered far from the corresponding proteins of classified phages. Thus, the StenR_269 genome is orphan and the analyzed data suggest a new family in the class Caudoviricetes. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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15 pages, 1994 KiB  
Article
Identification of Huge Phages from Wastewater Metagenomes
by René Kallies, Die Hu, Nafi’u Abdulkadir, Michael Schloter and Ulisses Rocha
Viruses 2023, 15(12), 2330; https://doi.org/10.3390/v15122330 - 28 Nov 2023
Viewed by 1013
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual [...] Read more.
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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16 pages, 4352 KiB  
Article
A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations
by Rachel E. Loney, Véronique A. Delesalle, Brianne E. Chaudry, Megan Czerpak, Alexandra A. Guffey, Leo Goubet-McCall, Michael McCarty, Madison S. Strine, Natalie T. Tanke, Albert C. Vill and Greg P. Krukonis
Viruses 2023, 15(11), 2267; https://doi.org/10.3390/v15112267 - 17 Nov 2023
Viewed by 1016
Abstract
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses [...] Read more.
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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20 pages, 3488 KiB  
Article
Genomic Analysis of Two Cold-Active Pseudoalteromonas Phages Isolated from the Continental Shelf in the Arctic Ocean
by Chung Yeon Hwang, Byung Cheol Cho, Jin Kyeong Kang, Jihye Park and Stephen C. Hardies
Viruses 2023, 15(10), 2061; https://doi.org/10.3390/v15102061 - 07 Oct 2023
Cited by 2 | Viewed by 1030
Abstract
Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage–host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, [...] Read more.
Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage–host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, ACA1 and ACA2, were isolated from sediment core samples of the continental shelf in the western Arctic Ocean. These phages exhibited successful propagation at a low temperature of 1 °C and displayed typical myovirus morphology with isometric icosahedral heads and contractile tails. The complete genome sequences of phages ACA1 and ACA2 were 36,825 bp and 36,826 bp in size, respectively, sharing almost the same gene content. These are temperate phages encoding lysogeny-related proteins such as anti-repressor, immunity repressor and integrase. The absence of cross-infection between the host strains, which were genomically distinct Pseudoalteromonas species, can likely be attributed to heavy divergence in the anti-receptor apparently mediated by an associated diversity-generating retroelement. HHpred searching identified genes for all of the structural components of a P2-like phage (family Peduoviridae), although the whole of the Peduoviridae family appeared to be divided between two anciently diverged tail modules. In contrast, Blast matching and whole genome tree analysis are dominated by a nonstructural gene module sharing high similarity with Pseudoalteromonas phage C5a (founder of genus Catalunyavirus). This study expands the knowledge of diversity of P2-like phages known to inhabit Peudoalteromonas and demonstrates their presence in the Arctic niche. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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20 pages, 20752 KiB  
Article
Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden
by Shaheen Nourinejhad Zarghani, Rim Al Kubrusli, Serghei Iancev, Risto Jalkanen, Carmen Büttner and Susanne von Bargen
Viruses 2023, 15(8), 1678; https://doi.org/10.3390/v15081678 - 01 Aug 2023
Viewed by 1268
Abstract
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may [...] Read more.
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (–ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT–PCR–RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins. Full article
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)
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