Viruses of Microbes: From Basics to Biotechnological Application

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 14525

Special Issue Editor


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Guest Editor
Department of Microbiology, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
Interests: giant viruses; large viruses; viral genomics; virus evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Our planet is dominated by the most diverse microorganisms, from bacteria to fungi and protozoa. The diversity is enormous, second only to the viruses that are associated with them. A major part of the virosphere is composed of viruses of microbes, which play a fundamental role in the evolution of life and in the biological control of pathogens. In the past few years, new information has been obtained on the biology of these viruses, opening doors and paving the way for biotechnological innovations.

Protozoan viruses have drawn the attention of the scientific community, especially giant amoeba viruses, due to their unprecedented structural and genomic complexity, reviving debates about the origin of viruses and opening up possibilities for technological applications based on the study of genes never seen before. The study of microalgae viruses revealed fascinating characteristics, including complex glycosylation machinery, in addition to their crucial role in controlling bloom algae events. Biological control based on the use of viruses has also been explored by means of mycoviruses, especially those that affect phytopathogenic fungi. Plant pathogens are major concerns for agriculture, and their control using viruses has attracted much attention. Finally, prokaryotic viruses have been widely studied for decades, both in the virology field and as a model for other areas of knowledge, such as structural biochemistry and genetic engineering. Phages are ubiquitous in nature, and they have been conceived as an alternative to antibiotic therapy, especially at a time when we are experiencing a delicate situation with the emergence of antimicrobial-resistant microorganisms.

In this Special Issue we aim to compile the current research on viruses of different microbes, including algae, protozoa, fungi, and prokaryotic viruses. We welcome the submission of original research and review articles covering distinct aspects of the biology of these viruses, as well as those that focus on the possible biotechnological applications. We hope that this will result in a better comprehension of this extended part of the virosphere, and improve the discussion around the high potential for the biotechnological use of these viruses.

 

Prof. Rodrigo Rodrigues

Guest Editor

 

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Keywords

  • giant virus
  • algae virus
  • bacteriophages
  • archaeal virus
  • mycovirus
  • genomics
  • virus–host interaction
  • biotechnology

Published Papers (5 papers)

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Research

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22 pages, 5927 KiB  
Article
Uncovering a Complex Virome Associated with the Cacao Pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata
by Roy Bogardid Ardón Espinal, Sabrina Ferreira de Santana, Vinícius Castro Santos, Gabriela Nicolle Ramos Lizardo, Raner José Santana Silva, Ronan Xavier Corrêa, Leandro Lopes Loguercio, Aristóteles Góes-Neto, Carlos Priminho Pirovani, Paula Luize Camargos Fonseca and Eric Roberto Guimarães Rocha Aguiar
Pathogens 2023, 12(2), 287; https://doi.org/10.3390/pathogens12020287 - 9 Feb 2023
Cited by 4 | Viewed by 2545
Abstract
Theobroma cacao is one of the main crops of economic importance in the world as the source of raw material for producing chocolate and derivatives. The crop is the main source of income for thousands of small farmers, who produce more than 80% [...] Read more.
Theobroma cacao is one of the main crops of economic importance in the world as the source of raw material for producing chocolate and derivatives. The crop is the main source of income for thousands of small farmers, who produce more than 80% of the world’s cocoa supply. However, the emergence, re-emergence and proliferation of pathogens, such as Ceratocystis spp., the causative agent of Ceratocystis wilt disease and canker disease, have been affecting the sustainability of many crops. Fungal control is laborious, often depending on fungicides that are expensive and/or toxic to humans, prompting researchers to look for new solutions to counteract the proliferation of these pathogens, including the use of biological agents such as mycoviruses. In this study, we investigated the diversity of microorganisms associated with the T. cacao pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata with a focus on the virome using RNA sequencing data available in public databases. We used a comprehensive bioinformatics pipeline containing several steps for viral sequence enrichment and took advantage of an integrated assembly step composed of different assemblers followed by sequence similarity searches using NCBI nonredundant databases. Our strategy was able to identify four putative C. cacaofunesta viruses (hypovirus, sclerotimonavirus, alphapartitivirus and narnavirus) and six C. fimbriata viruses (three alphaendornaviruses, one victorivirus and two mitoviruses). All the viral sequences identified showed similarity to viral genomes in public databases only at the amino acid level, likely representing new viral species. Of note, we present the first report of viruses associated with the cacao pathogens C. cacaofunesta and C. fimbriata and the second report of viral species infecting members of the Ceratocystidaceae family. Our findings highlight the need for further prospective studies to uncover the real diversity of fungus-infecting viruses that can contribute to the development of new management strategies. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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18 pages, 8135 KiB  
Article
Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species
by Tulio Morgan, Rafael Reis de Rezende, Thamylles Thuany Mayrink Lima, Flávia de Oliveira Souza and Poliane Alfenas-Zerbini
Pathogens 2023, 12(1), 44; https://doi.org/10.3390/pathogens12010044 - 27 Dec 2022
Cited by 1 | Viewed by 3381
Abstract
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus [...] Read more.
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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19 pages, 1772 KiB  
Article
A Rapid Method for Performing a Multivariate Optimization of Phage Production Using the RCCD Approach
by Jessica Silva, Roberto Dias, José Ivo Junior, Maraísa Marcelino, Mirelly Silva, Adriele Carmo, Maira Sousa, Cynthia Silva and Sergio de Paula
Pathogens 2021, 10(9), 1100; https://doi.org/10.3390/pathogens10091100 - 29 Aug 2021
Cited by 3 | Viewed by 2748
Abstract
Bacteriophages can be used in various applications, from the classical approach as substitutes for antibiotics (phage therapy) to new biotechnological uses, i.e., as a protein delivery vehicle, a diagnostic tool for specific strains of bacteria (phage typing), or environmental bioremediation. The demand for [...] Read more.
Bacteriophages can be used in various applications, from the classical approach as substitutes for antibiotics (phage therapy) to new biotechnological uses, i.e., as a protein delivery vehicle, a diagnostic tool for specific strains of bacteria (phage typing), or environmental bioremediation. The demand for bacteriophage production increases daily, and studies that improve these production processes are necessary. This study evaluated the production of a T4-like bacteriophage vB_EcoM-UFV09 (an E. coli-infecting phage with high potential for reducing environmental biofilms) in seven types of culture media (Luria–Bertani broth and the M9 minimal medium with six different carbon sources) employing four cultivation variables (temperature, incubation time, agitation, and multiplicity of infection). For this purpose, the rotatable central composite design (RCCD) methodology was used, combining and comparing all parameters to determine the ideal conditions for starting to scale up the production process. We used the RCCD to set up the experimental design by combining the cultivation parameters in a specific and systematic way. Despite the high number of conditions evaluated, the results showed that when specific conditions were utilized, viral production was effective even when using a minimal medium, such as M9/glucose, which is less expensive and can significantly reduce costs during large-scale phage production. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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Review

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21 pages, 2131 KiB  
Review
Giant Viruses as a Source of Novel Enzymes for Biotechnological Application
by Ellen Gonçalves de Oliveira, João Victor Rodrigues Pessoa Carvalho, Bruna Barbosa Botelho, Clécio Alonso da Costa Filho, Lethícia Ribeiro Henriques, Bruna Luiza de Azevedo and Rodrigo Araújo Lima Rodrigues
Pathogens 2022, 11(12), 1453; https://doi.org/10.3390/pathogens11121453 - 1 Dec 2022
Cited by 5 | Viewed by 2526
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry [...] Read more.
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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17 pages, 1471 KiB  
Review
Comparative Analysis of Transcriptional Regulation Patterns: Understanding the Gene Expression Profile in Nucleocytoviricota
by Fernanda Gil de Souza, Jônatas Santos Abrahão and Rodrigo Araújo Lima Rodrigues
Pathogens 2021, 10(8), 935; https://doi.org/10.3390/pathogens10080935 - 24 Jul 2021
Cited by 3 | Viewed by 2322
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) possess unique characteristics that have drawn the attention of the scientific community, and they are now classified in the phylum Nucleocytoviricota. They are characterized by sharing many genes and have their own transcriptional apparatus, which provides [...] Read more.
The nucleocytoplasmic large DNA viruses (NCLDV) possess unique characteristics that have drawn the attention of the scientific community, and they are now classified in the phylum Nucleocytoviricota. They are characterized by sharing many genes and have their own transcriptional apparatus, which provides certain independence from their host’s machinery. Thus, the presence of a robust transcriptional apparatus has raised much discussion about the evolutionary aspects of these viruses and their genomes. Understanding the transcriptional process in NCLDV would provide information regarding their evolutionary history and a better comprehension of the biology of these viruses and their interaction with hosts. In this work, we reviewed NCLDV transcription and performed a comparative functional analysis of the groups of genes expressed at different times of infection of representatives of six different viral families of giant viruses. With this analysis, it was possible to observe a temporal profile of their gene expression and set of genes activated in specific phases throughout the multiplication cycle as a common characteristic of this group. Due to the lack of information regarding the transcriptional regulation process of this group of pathogens, we sought to provide information that contributes to and opens up the field for transcriptional studies of other viruses belonging to Nucleocytoviricota. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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