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Review
. 2019 Oct 18;10:2403.
doi: 10.3389/fmicb.2019.02403. eCollection 2019.

A Review on Viral Metagenomics in Extreme Environments

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Free PMC article
Review

A Review on Viral Metagenomics in Extreme Environments

Sonia Dávila-Ramos et al. Front Microbiol. .
Free PMC article

Abstract

Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.

Keywords: extreme environment; extremophile virome; metagenomic; viral gene bioprospection; virosphere.

Figures

FIGURE 1
FIGURE 1
Global distribution of metagenomics studies from extreme environments from public databases. Circles represent metagenomes deposited in Metavir database, stars in IMG/VR, triangles in Virome and squares in NCBI.
FIGURE 2
FIGURE 2
Comparison of the 10 most abundant virus families according to the Metavir database. The taxonomic composition is expressed in relative abundance at the virus family level. The families Siphoviridae, Podovirididae, and Myoviridae are ubiquitous in extreme environments. The figure was constructed from an abundance matrix, using the number of sequences reported in the Metavir database, from which the relative abundance was obtained; using the R program.
FIGURE 3
FIGURE 3
Comparison of families with lower abundance in the Metavir database. Unclassified phages predominate in all environments, compared with other virus families. However, greater diversity is observed in the sediments, hyperthermophile and hypersaline environments compared to deep waters, Oxygen Minimum Zones (OMZ) or saline environments.
FIGURE 4
FIGURE 4
Composition of Podoviridae family at genus level. Metagenomes from OMZ and deep-sediments were considered in the analysis.
FIGURE 5
FIGURE 5
Composition of Poxviridae family at genus level. Metagenomes from OMZ and deep-sediments were considered in the analysis.
FIGURE 6
FIGURE 6
Clustering dendrogram based on the abundance of virus families present in the metagenomes from extreme environments. Virus families are represented by presence or absence; the green color indicates the presence while the white color indicates absence. Families of the order of Caudovirales are present in all environments. The figure was constructed using a presence and absence matrix, using the heatmap library on R.
FIGURE 7
FIGURE 7
Multidimensional scaling (NMDS) to visualize the degree of overall similarity between the metagenomes. Metagenomes from different habitats are shown: deep-sea (pink), OMZ (green), hyperarid (red), hypersaline (blue), psychrophile (orange), hyperthermophile (yellow). Hypersaline metagenomes have a strong clustering compared to other metagenomes. The figure was constructed from an abundance matrix, where the multidimensional scaling algorithm was applied to observe the general similarity of metagenomes, using the R software.
FIGURE 8
FIGURE 8
Progress in function-based metagenomics. Functional bioprospections from extreme environments performed in the last years are summarized. Underexplored enzymes from extremophile viromes are listed.

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