Exploring the Archaeal Virosphere by Metagenomics -- From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool -- Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses -- Discovery and Identification of Viruses Infecting Oomycetes -- Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction using Improved Assemble Tools -- Determination of the Mycovirome of a Necrotrophic Fungus -- From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species -- SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters -- Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples -- Exploration and Retrieval of Virus-Related Molecular Data using ExTaxsI: The Monkeypox Use Case -- Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics -- Targeted Whole Genome Sequencing of the Capripoxvirus Genome from Clinical Tissue Samples and Lyophilized Vaccine Batches -- Viromes of Plants Determined by High-Throughput Sequencing of Virus Derived siRNAs -- Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids -- Identification of DNA Viruses in Ancient DNA from Herbarium Samples -- The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses -- Detection of Plant Viruses using Nanopore Sequencing Based Metagenomic Approach -- Application of Nanopore-Based Sequencing to Identify Virus Infections in Woody Plants -- Distribution of Small RNAs Along Transposable Elements in Vitis vinifera during Somatic Embryogenesis.

This second edition volume expands on the previous edition with discussions about the latest viral metagenomics aspects covering a range of different specimens such as soil, freshwater, wastewater, fecal samples, blood plasma, clinical tissues, fungi, and herbarium samples. Chapters also look at different viral groups including archaeal viruses, eukaryotic viruses, phages, mycoviruses, and circular DNA viruses. Techniques required for studying the three viral metagenomic steps of samples processing, library construction, and analysis of data are also discussed. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Vital Metagenomics: Methods and Protocols, Second Edition is a valuable resourcefor researchers who are interested in learning more about this important and developing field.

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