Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses—bacteriophages and archaeal viruses—influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage–host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth’s ecosystems.
Highlights
In the last few decades, it has been proven that viruses represent the most abundant components in Earth’s ecosystems [1]
We demonstrated above that there exists a plethora of literature on studying viruses in environmental samples using microscopy, only a limited number of studies applied both environmental genomics of viral communities and respective microscopy techniques [124,145]
Research to date has consistently shown that viruses can be detected with various imaging techniques
Summary
In the last few decades, it has been proven that viruses represent the most abundant components in Earth’s ecosystems [1]. Was set out with the aim of investigating microbial interactions, their evolution, and viral infections [15] in the sea ecosystem This project was based on an extraordinarily large dataset containing millions of newly discovered sequences from various oceanic microbes and viruses [15], and—along with the Pacific Ocean Virome (POV) [16,17] project and the Malaspina expedition [18]—revolutionized our view of genetic diversity of prokaryotic and eukaryotic viruses on Earth. Such datasets represent the best current means of documenting the taxonomic compositions of uncultivated and unknown viral communities [16]. We summarize the current state of the art of visualization techniques for (cultivated) viruses and discuss their potential linkage to sequencing data in order to explore viruses directly in ecosystems
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