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Viruses
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Viruses of Microbes V: Biodiversity and Future Applications
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Viruses of Microbes V: Biodiversity and Future Applications

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

Deadline for manuscript submissions: closed (30 September 2018) | Viewed by 95516

Special Issue Editors

Dr. Heather E. Allison

E-Mail Website
Guest Editor
University of Liverpool, Liverpool, UK
Interests: phage biology; lysogen phenotypes; prophages; viral ecology
Prof. Dr. David Prangishvili

E-Mail Website
Guest Editor
Head of the research group "Viruses of Archaea", Department of Microbiology, Institut Pasteur, Paris, France
Interests: diversity of archaeal viruses: virion structures, genome organisation, structure and function of viral proteins; molecular aspects of virus host interactions in Archaea; biotechnological applications of archaeal viruses and their proteins
Prof. Dr. Ruth-Anne Sandaa

E-Mail Website
Guest Editor
University of Bergen, Department of Biological Sciences, Bergen, Norway
Interests: community dynamics and diversity of viruses infecting photosynthetic organisms like Cyanobacteria (cyanophages) and Phytoplankton (algal viruses); viral-host interactions of cyanophages and algal viruses in the marine environment
Dr. Dann Turner

E-Mail Website
Guest Editor
Department of Applied Sciences, University of the West of England, Bristol, UK
Interests: bacteriophage research; Acinetobacter bacteriophages; bacteriophage genomics; biotechnology; taxonomy; phage-host interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The central theme of this Special Issue will focus on 'Biodiversity and Future Applications' of viruses infecting microbes (algae, archaea, bacteria, fungi, protozoa and viruses). Viruses have always been a key element of microbial diversity and evolution, as well as a tool for a molecular biologist to learn more about how the host-cell functions. This information has also been put to productive use in recent days to control infections and fouling in many areas in our society.

The issue gathers articles covering key areas of ecology, host-virus dynamics, biotechnological, medical aspects, and structural biology. A main objective is to introduce a new understanding of the role that viruses of microbes play in ecosystems and in the sustainable development of human technologies.

Dr. Heather E. Allison
Prof. Dr. David Prangishvili
Prof. Dr. Ruth-Anne Sandaa
Dr. Dann Turner
Guest Editors

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

  • bacteriophages
  • archaeal viruses
  • cyanophages
  • algal and fungi viruses
  • viral-host interactions
  • structure and function of viral proteins
  • biotechnological applications

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Published Papers (16 papers)

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Research

Jump to: Review

15 pages, 2192 KiB  
Article
Sediments from Arctic Tide-Water Glaciers Remove Coastal Marine Viruses and Delay Host Infection
by Douwe S. Maat, Maarten A. Prins and Corina P. D. Brussaard
Viruses 2019, 11(2), 123; https://doi.org/10.3390/v11020123 - 30 Jan 2019
Cited by 18 | Viewed by 4926
Abstract
Over the past few decades, the Arctic region has been strongly affected by global warming, leading to increased sea surface temperatures and melting of land and sea ice. Marine terminating (tide-water) glaciers are expected to show higher melting and calving rates, with an [...] Read more.
Over the past few decades, the Arctic region has been strongly affected by global warming, leading to increased sea surface temperatures and melting of land and sea ice. Marine terminating (tide-water) glaciers are expected to show higher melting and calving rates, with an increase in the input of fine sediment particles in the coastal marine environment. We experimentally investigated whether marine viruses, which drive microbial interactions and biogeochemical cycling are removed from the water column through adsorption to glacier-delivered fine sediments. Ecologically relevant concentrations of 30, 100 and 200 mg·L−1 sediments were added to filtered lysates of 3 cultured algal viruses and to a natural marine bacterial virus community. Total virus removal increased with sediment concentration whereby the removal rate depended on the virus used (up to 88% for an Arctic algal virus), suggesting a different interaction strength with the sediment. Moreover, we observed that the adsorption of viruses to sediment is a reversible process, and that desorbed viruses are still able to infect their respective hosts. Nonetheless, the addition of sediment to infection experiments with the Arctic prasinovirus MpoV-45T substantially delayed host lysis and the production of progeny viruses. We demonstrate that glacier-derived fine sediments have the potency to alter virus availability and consequently, host population dynamics. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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22 pages, 5272 KiB  
Article
Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host–Viral Relationships in an Arctic Marine Ecosystem
by Ruth-Anne Sandaa, Julia E. Storesund, Emily Olesin, Maria Lund Paulsen, Aud Larsen, Gunnar Bratbak and Jessica Louise Ray
Viruses 2018, 10(12), 715; https://doi.org/10.3390/v10120715 - 14 Dec 2018
Cited by 18 | Viewed by 5170
Abstract
The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from [...] Read more.
The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from the surface to 1000 m in depth. We employed metabarcoding analysis of major capsid protein g23 and mcp genes in order to investigate T4-like myoviruses and large dsDNA viruses infecting prokaryotic and eukaryotic picophytoplankton, respectively. Microbial abundances were assessed using flow cytometry. Metabarcoding results demonstrated that seasonality was the key mediator shaping virus communities, whereas depth exerted a diversifying effect within seasonal virus assemblages. Viral diversity and virus-to-prokaryote ratios (VPRs) dropped sharply at the commencement of the spring bloom but increased across the season, ultimately achieving the highest levels during the winter season. These findings suggest that viral lysis may be an important process during the polar winter, when productivity is low. Furthermore, winter viral communities consisted of Operational Taxonomic Units (OTUs) distinct from those present during the spring-summer season. Our data provided a first insight into the diversity of viruses in a hitherto undescribed marine habitat characterized by extremes in light and productivity. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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17 pages, 6932 KiB  
Article
Identification of Dual Receptor Binding Protein Systems in Lactococcal 936 Group Phages
by Stephen Hayes, Yoan Duhoo, Horst Neve, James Murphy, Jean-Paul Noben, Charles M. A. P. Franz, Christian Cambillau, Jennifer Mahony, Arjen Nauta and Douwe Van Sinderen
Viruses 2018, 10(12), 668; https://doi.org/10.3390/v10120668 - 27 Nov 2018
Cited by 11 | Viewed by 4120
Abstract
Siphoviridae of the lactococcal 936 group are the most commonly encountered bacteriophages in the dairy processing environment. The 936 group phages possess a discrete baseplate at the tip of their tail—a complex harbouring the Receptor Binding Protein (RBP) which is responsible for host [...] Read more.
Siphoviridae of the lactococcal 936 group are the most commonly encountered bacteriophages in the dairy processing environment. The 936 group phages possess a discrete baseplate at the tip of their tail—a complex harbouring the Receptor Binding Protein (RBP) which is responsible for host recognition and attachment. The baseplate-encoding region is highly conserved amongst 936 phages, with 112 of 115 publicly available phages exhibiting complete synteny. Here, we detail the three exceptions (Phi4.2, Phi4R15L, and Phi4R16L), which differ from this genomic architecture in possessing an apparent second RBP-encoding gene upstream of the “classical” rbp gene. The newly identified RBP possesses an elongated neck region relative to currently defined 936 phage RBPs and is genetically distinct from defined 936 group RBPs. Through detailed characterisation of the representative phage Phi4.2 using a wide range of complementary techniques, we demonstrated that the above-mentioned three phages possess a complex and atypical baseplate structure. Furthermore, the presence of both RBPs in the tail tip of the mature virion was confirmed, while the anticipated host-binding capabilities of both proteins were also verified. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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14 pages, 3313 KiB  
Article
Genomic Analysis of the Recent Viral Isolate vB_BthP-Goe4 Reveals Increased Diversity of φ29-Like Phages
by Tobias Schilling, Michael Hoppert and Robert Hertel
Viruses 2018, 10(11), 624; https://doi.org/10.3390/v10110624 - 13 Nov 2018
Cited by 12 | Viewed by 4817
Abstract
We present the recently isolated virus vB_BthP-Goe4 infecting Bacillus thuringiensis HD1. Morphological investigation via transmission electron microscopy revealed key characteristics of the genus Phi29virus, but with an elongated head resulting in larger virion particles of approximately 50 nm width and 120 nm [...] Read more.
We present the recently isolated virus vB_BthP-Goe4 infecting Bacillus thuringiensis HD1. Morphological investigation via transmission electron microscopy revealed key characteristics of the genus Phi29virus, but with an elongated head resulting in larger virion particles of approximately 50 nm width and 120 nm height. Genome sequencing and analysis resulted in a linear phage chromosome of approximately 26 kb, harbouring 40 protein-encoding genes and a packaging RNA. Sequence comparison confirmed the relation to the Phi29virus genus and genomes of other related strains. A global average nucleotide identity analysis of all identified φ29-like viruses revealed the formation of several new groups previously not observed. The largest group includes Goe4 and may significantly expand the genus Phi29virus (Salasvirus) or the Picovirinae subfamily. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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12 pages, 1002 KiB  
Article
Effects of Staphylococcus aureus Bacteriophage K on Expression of Cytokines and Activation Markers by Human Dendritic Cells In Vitro
by Helen R. Freyberger, Yunxiu He, Amanda L. Roth, Mikeljon P. Nikolich and Andrey A. Filippov
Viruses 2018, 10(11), 617; https://doi.org/10.3390/v10110617 - 08 Nov 2018
Cited by 18 | Viewed by 4127
Abstract
A potential concern with bacteriophage (phage) therapeutics is a host-versus-phage response in which the immune system may neutralize or destroy phage particles and thus impair therapeutic efficacy, or a strong inflammatory response to repeated phage exposure might endanger the patient. Current literature is [...] Read more.
A potential concern with bacteriophage (phage) therapeutics is a host-versus-phage response in which the immune system may neutralize or destroy phage particles and thus impair therapeutic efficacy, or a strong inflammatory response to repeated phage exposure might endanger the patient. Current literature is discrepant with regard to the nature and magnitude of innate and adaptive immune response to phages. The purpose of this work was to study the potential effects of Staphylococcus aureus phage K on the activation of human monocyte-derived dendritic cells. Since phage K acquired from ATCC was isolated around 90 years ago, we first tested its activity against a panel of 36 diverse S. aureus clinical isolates from military patients and found that it was lytic against 30/36 (83%) of strains. Human monocyte-derived dendritic cells were used to test for an in vitro phage-specific inflammatory response. Repeated experiments demonstrated that phage K had little impact on the expression of pro- and anti-inflammatory cytokines, or on MHC-I/II and CD80/CD86 protein expression. Given that dendritic cells are potent antigen-presenting cells and messengers between the innate and the adaptive immune systems, our results suggest that phage K does not independently affect cellular immunity or has a very limited impact on it. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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15 pages, 5763 KiB  
Article
Comparative Genomics and Characterization of the Late Promoter pR’ from Shiga Toxin Prophages in Escherichia coli
by Ling Xiao Zhang, David J. Simpson, Lynn M. McMullen and Michael G. Gänzle
Viruses 2018, 10(11), 595; https://doi.org/10.3390/v10110595 - 31 Oct 2018
Cited by 8 | Viewed by 3509
Abstract
Shiga-toxin producing Escherichia coli (STEC) causes human illness ranging from mild diarrhea to death. The bacteriophage encoded stx genes are located in the late transcription region, downstream of the antiterminator Q. The transcription of the stx genes is directly under the control of [...] Read more.
Shiga-toxin producing Escherichia coli (STEC) causes human illness ranging from mild diarrhea to death. The bacteriophage encoded stx genes are located in the late transcription region, downstream of the antiterminator Q. The transcription of the stx genes is directly under the control of the late promoter pR’, thus the sequence diversity of the region between Q and stx, here termed the pR’ region, may affect Stx toxin production. Here, we compared the gene structure of the pR’ region and the stx subtypes of nineteen STECs. The sequence alignment and phylogenetic analysis suggested that the pR’ region tends to be more heterogeneous than the promoter itself, even if the prophages harbor the same stx subtype. Furthermore, we established and validated transcriptional fusions of the pR’ region to the DsRed reporter gene using mitomycin C (MMC) induction. Finally, these constructs were transformed into native and non-native strains and examined with flow cytometry. The results showed that induction levels changed when pR’ regions were placed under different regulatory systems. Moreover, not every stx gene could be induced in its native host bacteria. In addition to the functional genes, the diversity of the pR’ region plays an important role in determining the level of toxin induction. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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14 pages, 2206 KiB  
Article
Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine
by Eugenijus Šimoliūnas, Monika Šimoliūnienė, Laura Kaliniene, Aurelija Zajančkauskaitė, Martynas Skapas, Rolandas Meškys, Algirdas Kaupinis, Mindaugas Valius and Lidija Truncaitė
Viruses 2018, 10(11), 583; https://doi.org/10.3390/v10110583 - 25 Oct 2018
Cited by 16 | Viewed by 4015
Abstract
A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for [...] Read more.
A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNASer. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ0/preQ1 transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of Siphoviridae. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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13 pages, 1647 KiB  
Article
Controlled Disassembly and Purification of Functional Viral Subassemblies Using Asymmetrical Flow Field-Flow Fractionation (AF4)
by Katri Eskelin and Minna M. Poranen
Viruses 2018, 10(11), 579; https://doi.org/10.3390/v10110579 - 23 Oct 2018
Cited by 8 | Viewed by 3571
Abstract
Viruses protect their genomes by enclosing them into protein capsids that sometimes contain lipid bilayers that either reside above or below the protein layer. Controlled dissociation of virions provides important information on virion composition, interactions, and stoichiometry of virion components, as well as [...] Read more.
Viruses protect their genomes by enclosing them into protein capsids that sometimes contain lipid bilayers that either reside above or below the protein layer. Controlled dissociation of virions provides important information on virion composition, interactions, and stoichiometry of virion components, as well as their possible role in virus life cycles. Dissociation of viruses can be achieved by using various chemicals, enzymatic treatments, and incubation conditions. Asymmetrical flow field-flow fractionation (AF4) is a gentle method where the separation is based on size. Here, we applied AF4 for controlled dissociation of enveloped bacteriophage φ6. Our results indicate that AF4 can be used to assay the efficiency of the dissociation process and to purify functional subviral particles. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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20 pages, 4907 KiB  
Article
Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations
by Katherine Lavelle, Ines Martinez, Horst Neve, Gabriele A. Lugli, Charles M. A. P. Franz, Marco Ventura, Fabio Dal Bello, Douwe Van Sinderen and Jennifer Mahony
Viruses 2018, 10(10), 577; https://doi.org/10.3390/v10100577 - 22 Oct 2018
Cited by 25 | Viewed by 5090
Abstract
Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages [...] Read more.
Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages were classified into two groups (cos and pac groups), while more recently, two additional groups have been identified (5093 and 987 groups). This highlights the requirement for consistent monitoring of phage populations in the industry. Here, we report a survey of 35 samples of whey derived from 27 dairy fermentation facilities in ten countries against a panel of S. thermophilus strains. This culminated in the identification of 172 plaque isolates, which were characterized by multiplex PCR, restriction fragment length polymorphism analysis, and host range profiling. Based on this characterisation, 39 distinct isolates representing all four phage groups were selected for genome sequencing. Genetic diversity was observed among the cos isolates and correlations between receptor binding protein phylogeny and host range were also clear within this phage group. The 987 phages isolated within this study shared high levels of sequence similarity, yet displayed reduced levels of similarity to those identified in previous studies, indicating that they are subject to ongoing genetic diversification. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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13 pages, 1587 KiB  
Article
Roles of orf60a and orf61 in Development of Bacteriophages λ and Φ24B
by Aleksandra Dydecka, Bożena Nejman-Faleńczyk, Sylwia Bloch, Gracja Topka, Agnieszka Necel, Logan W. Donaldson, Grzegorz Węgrzyn and Alicja Węgrzyn
Viruses 2018, 10(10), 553; https://doi.org/10.3390/v10100553 - 11 Oct 2018
Cited by 11 | Viewed by 3497
Abstract
The exo-xis region of lambdoid bacteriophage genomes contains several established and potential genes that are evolutionarily conserved, but not essential for phage propagation under laboratory conditions. Nevertheless, deletion or overexpression of either the whole exo-xis region and important regulatory elements can significantly influence [...] Read more.
The exo-xis region of lambdoid bacteriophage genomes contains several established and potential genes that are evolutionarily conserved, but not essential for phage propagation under laboratory conditions. Nevertheless, deletion or overexpression of either the whole exo-xis region and important regulatory elements can significantly influence the regulation of phage development. This report defines specific roles for orf60a and orf61 in bacteriophage λ and Φ24B, a specific Shiga toxin-converting phage with clinical relevance. We observed that mutant phages bearing deletions of orf60a and orf61 impaired two central aspects of phage development: the lysis-versus-lysogenization decision and prophage induction. These effects were more pronounced for phage Φ24B than for λ. Surprisingly, adsorption of phage Φ24B on Escherichia coli host cells was less efficient in the absence of either orf60a or orf61. We conclude that these open reading frames (ORFs) play important, but not essential, roles in the regulation of lambdoid phage development. Although phages can propagate without these ORFs in nutrient media, we suggest that they may be involved in the regulatory network, ensuring optimization of phage development under various environmental conditions. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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19 pages, 3553 KiB  
Article
High Throughput Manufacturing of Bacteriophages Using Continuous Stirred Tank Bioreactors Connected in Series to Ensure Optimum Host Bacteria Physiology for Phage Production
by Francesco Mancuso, Jiahui Shi and Danish J. Malik
Viruses 2018, 10(10), 537; https://doi.org/10.3390/v10100537 - 01 Oct 2018
Cited by 23 | Viewed by 8173
Abstract
Future industrial demand for large quantities of bacteriophages e.g., for phage therapy, necessitates the development of scalable Good Manufacturing Practice compliant (cGMP) production platforms. The continuous production of high titres of E coli T3 phages (1011 PFU mL−1) was achieved [...] Read more.
Future industrial demand for large quantities of bacteriophages e.g., for phage therapy, necessitates the development of scalable Good Manufacturing Practice compliant (cGMP) production platforms. The continuous production of high titres of E coli T3 phages (1011 PFU mL−1) was achieved using two continuous stirred tank bioreactors connected in series, and a third bioreactor was used as a final holding tank operated in semi-batch mode to finish the infection process. The first bioreactor allowed the steady-state propagation of host bacteria using a fully synthetic medium with glucose as the limiting substrate. Host bacterial growth was decoupled from the phage production reactor downstream of it to suppress the production of phage-resistant mutants, thereby allowing stable operation over a period of several days. The novelty of this process is that the manipulation of the host reactor dilution rates (range 0.1–0.6 hr−1) allows control over the physiological state of the bacterial population. This results in bacteria with considerably higher intracellular phage production capability whilst operating at high dilution rates yielding significantly higher overall phage process productivity. Using a pilot-scale chemostat system allowed optimisation of the upstream phage amplification conditions conducive for high intracellular phage production in the host bacteria. The effect of the host reactor dilution rates on the phage burst size, lag time, and adsorption rate were evaluated. The host bacterium physiology was found to influence phage burst size, thereby affecting the productivity of the overall process. Mathematical modelling of the dynamics of the process allowed parameter sensitivity evaluation and provided valuable insights into the factors affecting the phage production process. The approach presented here may be used at an industrial scale to significantly improve process control, increase productivity via process intensification, and reduce process manufacturing costs through process footprint reduction. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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16 pages, 7694 KiB  
Article
Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters
by Yanze Li, Pascal Hingamp, Hiroyasu Watai, Hisashi Endo, Takashi Yoshida and Hiroyuki Ogata
Viruses 2018, 10(9), 496; https://doi.org/10.3390/v10090496 - 13 Sep 2018
Cited by 20 | Viewed by 8208
Abstract
“Megaviridae” is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due [...] Read more.
“Megaviridae” is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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Review

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16 pages, 1974 KiB  
Review
Ecological and Evolutionary Processes Shaping Viral Genetic Diversity
by Cas Retel, Hanna Märkle, Lutz Becks and Philine G. D. Feulner
Viruses 2019, 11(3), 220; https://doi.org/10.3390/v11030220 - 05 Mar 2019
Cited by 18 | Viewed by 6693
Abstract
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the [...] Read more.
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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15 pages, 717 KiB  
Review
Viruses of Polar Aquatic Environments
by Sheree Yau and Mansha Seth-Pasricha
Viruses 2019, 11(2), 189; https://doi.org/10.3390/v11020189 - 22 Feb 2019
Cited by 26 | Viewed by 6414
Abstract
The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions [...] Read more.
The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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14 pages, 1529 KiB  
Review
A Wake-Up Call: We Need Phage Therapy Now
by Karin Moelling, Felix Broecker and Christian Willy
Viruses 2018, 10(12), 688; https://doi.org/10.3390/v10120688 - 05 Dec 2018
Cited by 82 | Viewed by 11367
Abstract
The rise of multidrug-resistant bacteria has resulted in an increased interest in phage therapy, which historically preceded antibiotic treatment against bacterial infections. To date, there have been no reports of serious adverse events caused by phages. They have been successfully used to cure [...] Read more.
The rise of multidrug-resistant bacteria has resulted in an increased interest in phage therapy, which historically preceded antibiotic treatment against bacterial infections. To date, there have been no reports of serious adverse events caused by phages. They have been successfully used to cure human diseases in Eastern Europe for many decades. More recently, clinical trials and case reports for a variety of indications have shown promising results. However, major hurdles to the introduction of phage therapy in the Western world are the regulatory and legal frameworks. Present regulations may take a decade or longer to be fulfilled. It is of urgent need to speed up the availability of phage therapy. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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17 pages, 1237 KiB  
Review
RNA Phage Biology in a Metagenomic Era
by Julie Callanan, Stephen R. Stockdale, Andrey Shkoporov, Lorraine A. Draper, R. Paul Ross and Colin Hill
Viruses 2018, 10(7), 386; https://doi.org/10.3390/v10070386 - 21 Jul 2018
Cited by 39 | Viewed by 10443
Abstract
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, [...] Read more.
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies. Full article
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
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