Viruses of Microorganisms | Book
Caister Academic Press
and Stephen T. Abedon2
1Department of Biology and Toxicology, Ashland University, Ashland, OH 44805, USA; 2Department of Microbiology, Ohio State University, Mansfield, OH 44903, USA
September 2018Buy book
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Viruses of microorganisms (VoMs) are the world's most abundant viruses. There are viruses for every known microbe and VoMs are usually described in terms of their hosts as algal viruses, archaeal viruses, bacteriophages, virophages, fungal viruses and protozoan viruses. A key feature of infection by VoMs is that they often kill the host. This allows VoMs to play a key role in modifying microbial communities and in nutrient cycling in various environments. When the host is itself a pathogen then VoMs may be exploited to create novel antimicrobial strategies. In fact phage therapy for a variety of antibiotic-resistant bacterial pathogens is currently at the clinical trial stage. When they don't kill the host, VoMs can still play important roles in the ecology and evolution of their hosts via various forms of virus-mediated horizontal gene transfer. Important in nature, these processes have also been used in the laboratory in genetic engineering techniques.
In this multi-authored volume, international experts review the genomics, ecology, comparative biology and biotechnological applications of these fascinating viruses. Chapters have extensive reference sections that should encourage readers to pursue each subject in greater detail.
This unique reference volume is a must-read for everyone working with VoMs, from the PhD student to the experienced scientist, in academia, the pharmaceutical or biotechnology industries and working in clinical environments.
Table of contents
1. Viruses of Microorganisms: What are They and Why Care?
Paul Hyman and Stephen T. Abedon
Like microorganisms generally, the notion of viruses of microorganisms, or VoMs, that is, viruses that infect cellular microorganisms, is an artificial concept, and particularly so from a phylogenetic perspective. Microorganisms are collectively defined by a single, somewhat primitive phenotype - their smallness even at maturity - rather than together making up a monophyletic taxon. There is, therefore, no clade Microorganisms. As individual viruses are more likely to infect organisms which in fact are members of the same clade, VoMs too do not collectively form a single viral clade, nor even a collection of distinct, only microorganism-infecting taxa. VoMs instead consist of viruses of domains Bacteria, Archaea, and Eukarya, with especially the viruses of Eukarya tending to be evolutionarily related between those that infect eukaryotic microorganisms and those that infect eukaryotic macroorganisms. By contrast, all viruses of domains Bacteria and Archaea represent VoMs. All members of those two domains in fact are microorganisms, though even here, these VoMs are far from being collectively monophyletic. The result, ultimately, is a great deal of diversity among both VoMs and their hosts. In this chapter we introduce the concept of viruses of microorganisms. We also offer a first-approximation introduction to what VoMs exist, as considered in great detail in subsequent chapters.
2. Genomics of Viruses of Microorganisms
Evelien M. Adriaenssens
Genomics, the study of the sequence and gene set making up the genome, of viruses of microorganisms is becoming increasingly important. It allows researchers to access the full sequence diversity of viruses, facilitates the discovery of previously unknown viral types and gives a better insight into evolutionary relationships. In this chapter, I review the current methods used in genomics of viruses of microorganisms, and highlight what is known about the major groups of viruses. I end with the impact genomics research has had on the study and understanding of higher-order genomic relationships.
3. Evolutionary Ecology of the Viruses of Microorganisms
Brian E. Ford, Marko Baloh and John J. Dennehy
With estimated numbers greater than 1031, viruses are the most abundant organisms on the planet, and occupy all habitats: aquatic, atmospheric and terrestrial. No cellular organisms - whether animal, plant or microbe - are free from viral parasitism. Consequently, the effects and influences of viruses are pervasive, directly or indirectly affecting all organisms, populations, communities and ecosystems. Here we consider the evolutionary ecology of the viruses of microorganisms (VoMs) which, due to the abundance of their hosts, outnumber all other types of viruses. Subfields of evolutionary ecology include life history evolution, population biology, biogeography, and community ecology. Like blind men describing an elephant, each approach only describes a facet of VoM evolutionary ecology. Here we describe some of the approaches used to describe VoM evolutionary ecology in hopes that a synthesis will allow some perception of the whole.
4. Viruses of Microorganisms in Soil Ecosystems
Kurt E. Williamson
Soils are extremely complex ecosystems that display fine-scale spatial and temporal heterogeneity. Depending on the soil type, total viral abundance in soils can range from as few as 10,000 (104) to over 109 virus particles per gram dry weight. While very limited data are available, comparative analyses suggest that soils contain a more genetically diverse array of viruses than either aquatic or sediment habitats. Viruses of Bacteria (bacteriophages) represent the most studied and best understood group of viruses of microorganisms in soils. They also are believed to be the most abundant virus type within soil viral communities and can have important impacts on host bacteria population dynamics as well as on biogeochemical processes. Bacteriophages can also impact bacterial genetic diversity through host selection, as well as host phenotypic conversion and gene transfer events. Fungi are important soil microbes and fungal viruses (mycoviruses) appear to be ubiquitous in nature as well, as most fungal lineages show evidence of viral infections. Virus-mediated lysis of fungal hosts is exceptionally rare, however, and most mycoviruses establish persistent, asymptomatic infections of their hosts. The significance of mycovirus infections therefore may lie in subtle modulations of host gene regulation but also can affect host secretion of toxins, hypovirulence, and thermotolerance. Protozoa are key players in soil microbial food webs and viruses of the protozoa, especially viruses of amoeba, have touched off a revolution in modern virology as recently discovered "giant viruses" have been found to exceed the 0.22 μm operational size cutoff that had been historically applied to viruses. Since 2003, four novel giant virus families have been established, with two representatives isolated from soils, though the ecological impacts of these giant amoebal viruses have yet to be determined. In addition to these unknowns, almost nothing is known regarding the viruses of Archaea, cyanobacteria, algae, or diatoms with specific regard to soil habitats. These represent significant knowledge gaps and targets for future research endeavours. Soils remain an under-studied ecosystem in spite of their complexity and importance to human civilization.
5. Marine Viral Metagenomics with Emphasis on Coral Microbiomes
Rebecca L. Vega Thurber Jérôme P. Payet, Lu Wang and Alec O. Eastman
Methods for analysing the viromes associated with tropical marine waters and its abundant wildlife have rapidly progressed due to advances in molecular biology methodologies, nucleic acid sequencing technology, and computational analysis. The viruses of corals, the foundational organisms of shallow tropical reefs, have been one of the most well studied symbioses using these techniques. Reef building corals are known to play host to hundreds to thousands of bacterial taxa and upwards of two dozen viral families, including many viruses of microorganisms as well those infecting host tissues. Due to the lack of single marker genes to describe viruses in these systems, however, research on these two facets of coral reef viromes has required different approaches. Most coral bacterial analysis has come from amplicon analysis while few if any studies have used this approach to study coral viruses. Instead metagenomics and meta-transcriptomics have provided the necessary tools for scientists to catalogue, characterize, and compare the genetic diversity of viruses in coral systems. This review describes the history of this field with emphasis on how methods have evolved since its inception in the early 2000's. We describe some basic findings from the past 20 years and discuss the major limitations of past and current approaches. Finally, we provide some considerations for future work in this arena of viral metagenomics and marker gene analysis.
6. Virus Interactions in the Aquatic World
Stéphan Jacquet, Xu Zhong, Peter Peduzzi, T. Frede Thingstad, Kaarle J.Parikka and Markus G.Weinbauer
During the past 30 years, a vast amount of articles has been published on the importance - in terms of abundance, diversity and functional roles - of viruses inhabiting the aquatic world (either marine or freshwater), which include several excellent reviews. Our knowledge e.g. on the interactions of viruses with the living (organisms) and non-living compartments (i.e. dissolved organic matter/particles/nutrients/physical factors) in aquatic environments has considerably increased. Furthermore, recent new ideas, concepts and technologies have shed light on host-virus interactions and the diversity of viral species and functions as discussed in this book. This chapter highlights some of these current advances in the field of aquatic viral ecology. Recently developed models and concepts will also be discussed, further emphasising the role of defence mechanisms against viruses which appear to be important drivers in strain diversification of host species. Additionally, new environments such as anoxic and benthic sediments have received more attention and novel information has been gathered e.g. on archaeal and RNA viruses. Interactions within entire food webs, such as with heterotrophic dinoflagellates, oysters and even cascading effects up to cyanobacteria-consuming flamingo populations represent another aspect of looking at viruses and their role in the global biosphere. The chapter also discusses knowledge gaps and proposes future research avenues.
7. Bacteriophage Diversity
Susan M. Lehman
Over 100 years of research, our understanding of bacteriophage diversity has expanded from the hypothesis of a single, highly adaptable phage species to an appreciation for the tremendous diversity that can exist in a millilitre of seawater. This progression is evident from the way that phage taxonomy has changed over time, as new tools for studying phages were developed. Basic microbiological methods were joined by electron microscopy. Resolving the structure of DNA ushered in the genetics era that has ultimately led to rapid, inexpensive sequencing and the multi-faceted "-omics" approaches. The result has been an increasingly sophisticated understanding of phage diversity from a population level down to the dynamics of a single phage-host infection.
8. Viruses of Domain Archaea
Stephen T. Abedon
There are three cellular domains - Archaea, Bacteria, and Eukarya - each of which possesses its own distinct set of viruses. Of these viruses the least studied and, indeed, least appreciated are the archaeal viruses. This poor appreciation stems in part from the historical lateness of the recognition of domain Archaea as a distinct lineage but also the historical lateness of the isolation of the first archaeal virus, with both events occurring in the 1970s. In addition, Archaea tend to be relatively difficult to cultivate and for the most part are not responsible for diseases (with both statuses resulting in a relative lack of applied interest). Their viruses, however, seem to display a plethora of morphologies which are distinct to the Archaea. The study of archaeal viruses as a consequence of these factors is relatively new but nevertheless has become an exciting area of inquiry, with a promise of discovery of much novel biology. In this chapter I briefly consider the history of archaeal virus study, provide an overview of what archaeal virus hosts these viruses have been isolated against, and describe archaeal virus types. The intention overall is to provide an introduction to the idea of archaeal viruses, along with their history and characteristics, rather than, and in light of space limitations, an exhaustive overview of this otherwise still relatively new field.
9. Fungal Viruses
Eeva J. Vainio and Jarkko Hantula
Fungal viruses (mycoviruses) occur in all major fungal phyla. They are taxonomically highly diverse, and are currently classified into seven families that have mono- or multipartitite dsRNA genomes and six families with ssRNA genomes. One described mycovirus species, Sclerotinia gemycircularvirus 1, has a genome composed of circular ssDNA and resembles plant geminiviruses. Most mycoviruses are considered to form latent infections without major phenotypic alterations in their host fungi, but both detrimental and mutualistic associations are known. As an example, a mycovirus infection causes a disease in cultivated mushrooms resulting in crop losses. On the other hand, hypoviruses of the Chestnut blight fungus (Cryphonectria parasitica) can be used for biocontrol against their host, which is a devastating plant pathogen. There is even one mycovirus involved in a three-way symbiosis formed by a grass, its endophytic fungus, and the virus. Mycoviruses with RNA genomes are considered to be completely intracellular and to transmit laterally between fungal strains during cell-to-cell contact, and vertically via sexual or asexual spores. Most mycovirus species are regarded as host-specific, but there are also examples of horizontal virus transmission between host species. This contradicts the commonly held hypothesis of strict virus-host co-evolution. The evolution of mycoviruses has likely been shaped by events of horizontal transmission between plants and fungi.
10. Diversity of Viruses Infecting Eukaryotic Algae
Steven M. Short, Michael A. Staniewski, Y. V. Chaban, A. M. Long and D. Wang
Algae are photosynthetic organisms that drive aquatic ecosystems, e.g. fueling food webs or forming harmful blooms. The discovery of viruses that infect eukaryotic algae has raised many questions about their influence on aquatic primary production and their role in algal ecology and evolution. Although the full extent of algal virus diversity is still being discovered, this review summarizes current knowledge of this topic. Where possible, formal taxonomic classifications are referenced from the International Committee on Taxonomy of Viruses (ICTV); since the pace of virus discovery has far surpassed the rate of formal classification, however, numerous unclassified viruses are discussed along with their classified relatives. In total, we recognized 61 distinct algal virus taxa with highly variable morphologies that include dsDNA, ssDNA, dsRNA, and ssRNA genomes ranging from approximately 4.4 to 560 kb, with virion sizes from approximately 20 to 210 nm in diameter. These viruses infect a broad range of algae and, although there are a few exceptions, they are generally lytic and highly species or strain specific. Dedicated research efforts have led to the appreciation of algal viruses as diverse, dynamic, and ecologically important members of the biosphere, and future investigations will continue to reveal the full extent of their diversity and impact.
11. Protozoal Giant Viruses
Dorine G. I. Reteno, Leena H. Bajrai, Sarah Aherfi, Philippe Colson and Bernard La Scola
Giant viruses that infect protists have been discovered during the past decade. They are named giant viruses due to the large size of their viral particle (over 100 nm in diameter but up to 1.5 μm) and to the extraordinary size of their genome, ranging from 150 kilobase pairs (kbp) to nearly 2.8 megabase pairs (Mbp). Their genomes, generally in the form of double-stranded DNA, may be linear or circular. They have been grouped into the nucleocytoplasmic large DNA virus (NCLDV) superfamily. The NCLDVs are divided into six families. Among these six viral families, three infect protozoa: the Mimiviridae and Marseilleviridae families infect amoebae and algae, and the newly discovered Pandoravirus salinus and P. dulcis, infect amoebae.
12. The Virophage Family Lavidaviridae
Matthias G. Fischer
Double-stranded (ds) DNA viruses of the family Lavidaviridae, commonly known as virophages, are a fascinating group of eukaryotic viruses that depend on a coinfecting giant dsDNA virus of the Mimiviridae for their propagation. Instead of replicating in the nucleus, virophages multiply in the cytoplasmic virion factory of a coinfecting giant virus inside a phototrophic or heterotrophic protistal host cell. Virophages are parasites of giant viruses and can inhibit their replication, which may lead to increased survival rates of the infected host cell population. The genomes of virophages are 17 to 33 kilobase pairs (kbp) long and encode 16 to 34 proteins. Genetic signatures of virophages can be found in metagenomic datasets from various saltwater and freshwater environments around the planet. Most virophages share a set of conserved genes that code for a major and a minor capsid protein, a cysteine protease, a genome-packaging ATPase, and a superfamily 3 helicase, although the genomes are otherwise diverse and variable. Lavidaviruses share genes with other mobile genetic elements, suggesting that horizontal gene transfer and recombination have been major forces in shaping these viral genomes. Integrases are occasionally found in virophage genomes and enable these DNA viruses to persist as provirophages in the chromosomes of their viral and cellular hosts. As we watch the genetic diversity of this new viral family unfold through metagenomics, additional isolates are still lacking and critical questions regarding their infection cycle, host range, and ecology remain to be answered.
13. Viruses of Microorganisms and Biotechnology
A large part of biotechnology in the sense of genetic engineering developed in parallel to increasing knowledge of the molecular biology of bacteria and their viruses, the bacteriophages. Many of the enzymes used were ones evolved by bacteriophages. While in principle, enzymes and other components of other viruses of other microbes could be used, historically, knowledge of bacteriophages predates the viruses of other microorganisms. In this chapter I present an overview of some of the technological methods that have been created using whole bacteriophages or bacteriophage components for: the creation of materials and molecules with novel selected properties (phage display); detection of bacterial pathogens (biosensors); and next-generation vaccines. In considering these, I will both define the technological approaches as well as discuss some of the challenges of taking these technologies from the laboratory to the marketplace.
14. Viruses as Biocontrol Agents of Microorganisms
Diana R. Alves, Jason Clark and Stephen T. Abedon
Biocontrol is the application of organisms, or substances that organisms produce, to reduce or eliminate populations of unwanted species. Within the context of environments, this application is equivalent to the use of pesticides, with the unwanted organism serving as the pest. Within the context of medicine, this application is equivalent to that of, especially, the use of antimicrobial drugs. Typically, for any such agents, the application of greater amounts will result in a greater negative impact on target organisms, but levels of application will be limited by costs, convenience, or potential to cause harm to the environment or to the patient being treated. Biocontrol agents thus may be deemed superior, for example versus the use of synthetic pesticides or antimicrobials, should biocontrol agents supply some combination of greater efficacy potential, lower cost, greater convenience, or lower potential to cause various forms of harm. In terms of viruses as biocontrol agents, we can distinguish between whole viruses versus their products or derivatives. Potential targets can be further differentiated in terms of what can be described as the six kingdoms: Bacteria, Archaea, Fungi, Protista, Animalia, and Plantae. In this chapter we touch upon all of these kingdoms as possessing potential targets for virus-mediated biocontrol; nevertheless, consistent with the theme of this monograph we focus particularly on the virus-mediated biocontrol of microorganisms. Given its substantial domination of the overall area of study, much of the review is derived from consideration of bacteriophage use against members of domain Bacteria. This is seen within the context of either phage-mediated biocontrol or instead the sub-category of such biocontrol known as phage therapy.
15. Methods and Technologies to Assess Viral Interactions in the Aquatic World
Stéphan Jacquet, Xu Zhong, Peter Peduzzi, T.Frede Thingstad, Kaarle J.Parikka and Markus G. Weinbauer
In this chapter, we summarize and discuss methods used to study viral interactions in aquatic environments. These methods to assess interactions between viruses, hosts and the environment (including other viruses) are operationally separated into interactions at the molecular, single-cell, and community levels. Many of these methods benefit from the methodological advancements in the field of molecular biology including the 'Omics area'. There are, however, numerous methods from other fields. We also present examples of unanswered questions along with problems solved by these questions. Finally, we conclude that viral interactions with the abiotic environment have received surprisingly little attention, so far, from a methodological perspective.
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(EAN: 9781910190852 9781910190869 Subjects: [environmental microbiology] [medical microbiology] [microbiology] [molecular microbiology] [virology] )