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Viruses
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Viruses in the Environment
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Viruses in the Environment

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

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 19611

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:

Environmental viruses are one key factor for microbial mortality, drive diversification and evolution of microbes through gene transfer and are key contributors to the mineralization of nutrients since they solubilize microorganisms by lysis. As a result, they a are important drivers of global biogeochemical cycles. It is thought that most environmental viruses are bacteriophages, i.e. viruses that infect bacteria. However, it is quite possible that viruses that infect (micro)eukaryotes and archaea also play an important role in various ecosystems. Environmental changes may influence virus abundance and the composition of viral communities. These changes may in turn affect population dynamics and the diversity of host organisms that are of importance for many ecosystem functions.

This special issue invites submissions that involve studies about viruses in the environment (e.g. marine, freshwater and soil ecosystems), including virus discovery, virus-host interactions and the consequences of virus infection on ecosystem services.

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

  • viruses in the environment
  • ecosystems
  • microbes
  • bacteriophages
  • virus-host interactions

Published Papers (5 papers)

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Research

16 pages, 2259 KiB  
Communication
A Novel Freshwater Cyanophage Mae-Yong1326-1 Infecting Bloom-Forming Cyanobacterium Microcystis aeruginosa
by Fei Wang, Dengfeng Li, Ruqian Cai, Lingting Pan, Qin Zhou, Wencai Liu, Minhua Qian and Yigang Tong
Viruses 2022, 14(9), 2051; https://0-doi-org.brum.beds.ac.uk/10.3390/v14092051 - 16 Sep 2022
Cited by 3 | Viewed by 1588
Abstract
Microcystis aeruginosa is a major harmful cyanobacterium causing water bloom worldwide. Cyanophage has been proposed as a promising tool for cyanobacterial bloom. In this study, M. aeruginosa FACHB-1326 was used as an indicator host to isolate cyanophage from Lake Taihu. The isolated Microcystis [...] Read more.
Microcystis aeruginosa is a major harmful cyanobacterium causing water bloom worldwide. Cyanophage has been proposed as a promising tool for cyanobacterial bloom. In this study, M. aeruginosa FACHB-1326 was used as an indicator host to isolate cyanophage from Lake Taihu. The isolated Microcystis cyanophage Mae-Yong1326-1 has an elliptical head of about 47 nm in diameter and a slender flexible tail of about 340 nm in length. Mae-Yong1326-1 could lyse cyanobacterial strains across three orders (Chroococcales, Nostocales, and Oscillatoriales) in the host range experiments. Mae-Yong1326-1 was stable in stability tests, maintaining high titers at 0–40 °C and at a wide pH range of 3–12. Mae-Yong 1326-1 has a burst size of 329 PFU/cell, which is much larger than the reported Microcystis cyanophages so far. The complete genome of Mae-Yong1326-1 is a double-stranded DNA of 48, 822 bp, with a G + C content of 71.80% and long direct terminal repeats (DTR) of 366 bp, containing 57 predicted ORFs. No Mae-Yong1326-1 ORF was found to be associated with virulence factor or antibiotic resistance. PASC scanning illustrated that the highest nucleotide sequence similarity between Mae-Yong1326-1 and all known phages in databases was only 17.75%, less than 70% (the threshold to define a genus), which indicates that Mae-Yong1326-1 belongs to an unknown new genus. In the proteomic tree based on genome-wide sequence similarities, Mae-Yong1326-1 distantly clusters with three unclassified Microcystis cyanophages (MinS1, Mwe-Yong1112-1, and Mwes-Yong2). These four Microcystis cyanophages form a monophyletic clade, which separates at a node from the other clade formed by two independent families (Zierdtviridae and Orlajensenviridae) of Caudoviricetes class. We propose to establish a new family to harbor the Microcystis cyanophages Mae-Yong1326-1, MinS1, Mwe-Yong1112-1, and Mwes-Yong2. This study enriched the understanding of freshwater cyanophages. Full article
(This article belongs to the Special Issue Viruses in the Environment)
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12 pages, 307 KiB  
Article
SARS-CoV-2 in Environmental Samples of Quarantined Households
by Manuel Döhla, Bianca Schulte, Gero Wilbring, Beate Mareike Kümmerer, Christin Döhla, Esther Sib, Enrico Richter, Patrick Frank Ottensmeyer, Alexandra Haag, Steffen Engelhart, Anna Maria Eis-Hübinger, Martin Exner, Nico Tom Mutters, Ricarda Maria Schmithausen and Hendrik Streeck
Viruses 2022, 14(5), 1075; https://0-doi-org.brum.beds.ac.uk/10.3390/v14051075 - 17 May 2022
Cited by 44 | Viewed by 2390
Abstract
The role of environmental transmission of SARS-CoV-2 remains unclear. Thus, the aim of this study was to investigate whether viral contamination of air, wastewater, and surfaces in quarantined households result in a higher risk for exposed persons. For this study, a source population [...] Read more.
The role of environmental transmission of SARS-CoV-2 remains unclear. Thus, the aim of this study was to investigate whether viral contamination of air, wastewater, and surfaces in quarantined households result in a higher risk for exposed persons. For this study, a source population of 21 households under quarantine conditions with at least one person who tested positive for SARS-CoV-2 RNA were randomly selected from a community in North Rhine-Westphalia in March 2020. All individuals living in these households participated in this study and provided throat swabs for analysis. Air and wastewater samples and surface swabs were obtained from each household and analysed using qRT-PCR. Positive swabs were further cultured to analyse for viral infectivity. Out of all the 43 tested adults, 26 (60.47%) tested positive using qRT-PCR. All 15 air samples were qRT-PCR-negative. In total, 10 out of 66 wastewater samples were positive for SARS-CoV-2 (15.15%) and 4 out of 119 surface samples (3.36%). No statistically significant correlation between qRT-PCR-positive environmental samples and the extent of the spread of infection between household members was observed. No infectious virus could be propagated under cell culture conditions. Taken together, our study demonstrates a low likelihood of transmission via surfaces. However, to definitively assess the importance of hygienic behavioural measures in the reduction of SARS-CoV-2 transmission, larger studies should be designed to determine the proportionate contribution of smear vs. droplet transmission. Full article
(This article belongs to the Special Issue Viruses in the Environment)
13 pages, 1677 KiB  
Article
Bacteriophages Roam the Wheat Phyllosphere
by Laura Milena Forero-Junco, Katrine Wacenius Skov Alanin, Amaru Miranda Djurhuus, Witold Kot, Alex Gobbi and Lars Hestbjerg Hansen
Viruses 2022, 14(2), 244; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020244 - 26 Jan 2022
Cited by 11 | Viewed by 4571
Abstract
The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried [...] Read more.
The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria. Full article
(This article belongs to the Special Issue Viruses in the Environment)
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16 pages, 5057 KiB  
Article
Phage Biocontrol of Pseudomonas aeruginosa in Water
by Ari Kauppinen, Sallamaari Siponen, Tarja Pitkänen, Karin Holmfeldt, Anna Pursiainen, Eila Torvinen and Ilkka T. Miettinen
Viruses 2021, 13(5), 928; https://0-doi-org.brum.beds.ac.uk/10.3390/v13050928 - 17 May 2021
Cited by 16 | Viewed by 4462
Abstract
Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two [...] Read more.
Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50–55 min) and burst size (124–134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log10 reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log10) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments. Full article
(This article belongs to the Special Issue Viruses in the Environment)
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15 pages, 17260 KiB  
Article
Evaluation of Potential ARG Packaging by Two Environmental T7-Like Phage during Phage-Host Interaction
by Junlin Liu, Peng Liu, Fenglin Feng, Junxuan Zhang, Fulin Li, Mianzhi Wang and Yongxue Sun
Viruses 2020, 12(10), 1060; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101060 - 23 Sep 2020
Cited by 11 | Viewed by 2613
Abstract
The increase in antimicrobial resistance is a threat to both human and animal health. The transfer of antibiotic resistance genes (ARG) via plasmids has been studied in detail whereas the contribution of bacteriophage-mediated ARG transmission is relatively little explored. We isolated and characterized [...] Read more.
The increase in antimicrobial resistance is a threat to both human and animal health. The transfer of antibiotic resistance genes (ARG) via plasmids has been studied in detail whereas the contribution of bacteriophage-mediated ARG transmission is relatively little explored. We isolated and characterized two T7-like lytic bacteriophages that infected multidrug-resistant Escherichia coli hosts. The morphology and genomic analysis indicated that both phage HZP2 and HZ2R8 were evolutionarily related and their genomes did not encode ARGs. However, ARG-like raw reads were detected in offspring sequencing data with a different abundance level implying that potential ARG packaging had occurred. PCR results demonstrated that six fragments of genes (qnrS, cmlA, tetM, blaTEM, sul3, mcr-1) were potentially packaged by phage HZP2 and four (qnrS, cmlA, blaTEM, mcr-1) by phage HZ2R8. Further quantitative results showed that ARG abundance hierarchies were similar. The gene blaTEM was the most abundant (up to 1.38 × 107 copies/mL) whereas cmlA and qnrS were the least. Moreover, the clinically important mcr-1 gene was the second most abundant ARG indicating a possibility for spread through generalized transduction. Together, our results indicated that these structurally similar phage possessed similar characteristics and potential packaging during phage-host interaction displayed an ARG preference rather than occurring randomly. Full article
(This article belongs to the Special Issue Viruses in the Environment)
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