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

Deadline for manuscript submissions: closed (25 September 2024) | Viewed by 19752

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Dr. René Kallies

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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
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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.

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Diversity and Evolution of Viruses in Ecosystem 2025 in Viruses (2 articles)

Published Papers (10 papers)

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Research

13 pages, 2646 KiB

Open AccessArticle

Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6

by Marina Vila-Nistal, Ramiro Logares, Josep M. Gasol and Manuel Martinez-Garcia

Viruses 2024, 16(11), 1669; https://doi.org/10.3390/v16111669 - 24 Oct 2024

Viewed by 1509

Abstract

Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10³ copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses. Full article

(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)

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14 pages, 1845 KiB

Open AccessArticle

Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity

by Brian McDonnell, Elvina Parlindungan, Erika Vasiliauskaite, Francesca Bottacini, Keith Coughlan, Lakshmi Priyadarshini Krishnaswami, Tom Sassen, Gabriele Andrea Lugli, Marco Ventura, Felice Mastroleo, Jennifer Mahony and Douwe van Sinderen

Viruses 2024, 16(7), 1039; https://doi.org/10.3390/v16071039 - 27 Jun 2024

Cited by 2 | Viewed by 1977

Abstract

Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations. Full article

(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)

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14 pages, 2157 KiB

Open AccessArticle

Viral Dynamics in the Tropical Pacific Ocean: A Comparison between Within and Outside a Warm Eddy

by Patrichka Wei-Yi Chen, Madeline Olivia, Gwo-Ching Gong, Sen Jan and An-Yi Tsai

Viruses 2024, 16(6), 937; https://doi.org/10.3390/v16060937 - 11 Jun 2024

Viewed by 1159

Abstract

In mesoscale eddies, the chemical properties and biological composition are different from those in the surrounding water due to their unique physical processes. The mechanism of physical–biological coupling in warm-core eddies is unclear, especially because no studies have examined the effects of environmental factors on bacteria and viruses. The purpose of the present study was to examine the influence of an anticyclonic warm eddy on the relationship between bacterial and viral abundances, as well as viral activity (viral production), at different depths. At the core of the warm eddy, the bacterial abundance (0.48 to 2.82 × 10⁵ cells mL⁻¹) fluctuated less than that outside the eddy (1.12 to 7.03 × 10⁵ cells mL⁻¹). In particular, there was a four-fold higher viral–bacterial abundance ratio (VBR) estimated within the eddy, below the layer of the deep chlorophyll maximum, than outside the eddy. An anticyclonic warm eddy with downwelling at its center may contribute to viruses being transmitted directly into the deep ocean through adsorption on particulate organic matter while sinking. Overall, our findings provide valuable insights into the interaction between bacterial and viral abundances and their ecological mechanisms within a warm eddy. Full article

(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem)

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17 pages, 13057 KiB

Open AccessArticle

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

Cited by 7 | Viewed by 1525

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 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

Open AccessArticle

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

Cited by 2 | Viewed by 2382

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 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

Open AccessArticle

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 1567

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 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

Open AccessArticle

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

Cited by 3 | Viewed by 2232

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 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

Open AccessArticle

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 1847

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 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

Open AccessArticle

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 - 7 Oct 2023

Cited by 4 | Viewed by 1969

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, 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

Open AccessArticle

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 - 1 Aug 2023

Cited by 1 | Viewed by 1996

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 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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