Niche-dependent genetic diversity in Antarctic metaviromes

Zablocki, Olivier; Zyl, Leonardo Joaquim van; Adriaenssens, Evelien M.; Rubagotti, Enrico; Tuffin, Marla; Cary, S. Craig; Cowan, Don A.

doi:10.4161/21597081.2014.980125

Cited by 12 publications

(10 citation statements)

References 21 publications

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“…50 °C mean annual temperature difference) and substantial spatial separation (approx. 55 degrees of latitude), suggesting that aridity and not temperature may be the dominant driver of host and viral diversity 22 , 65 . Interestingly, soil related metaviromes (from Kogelberg Biosphere Reserve fynbos soil, Peruvian rainforest soil and Antarctic Dry Valley desert soil) clustered together and were clearly distinct from soils which were geographically much closer.…”

Section: Resultsmentioning

confidence: 99%

Exploring Viral Diversity in a Unique South African Soil Habitat

Segobola

Adriaenssens

Tsekoa

et al. 2018

Sci Rep

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The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.

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Section: Resultsmentioning

confidence: 99%

Exploring Viral Diversity in a Unique South African Soil Habitat

Segobola

Adriaenssens

Tsekoa

et al. 2018

Sci Rep

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“…Dinucleotide frequencies within metaviromes have shown distinct virus community clustering within single habitat types such as desert soils. Although reported from a single study which analyzed two sets of pooled samples, cluster analysis of hypolith and opensoil metaviromes from Antarctic and Namib Desert soil samples has shown that the two hypolith metaviromes clustered at a single node whereas, in contrast, the two open-soil metaviromes displayed identical patterns (65). Despite great geographic distances or differing environmental conditions, similar habitat types harbored more closely related viral communities.…”

Section: Factors Shaping Viral Community Structures In Desert Soilsmentioning

confidence: 99%

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Zablocki

Adriaenssens

Cowan

2016

Appl Environ Microbiol

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In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ϳ33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.

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“…In addition, because particle yields are typically low, most soil virome studies have amplified extracted viral DNA using multiple displacement amplification, which renders the data sets both stochastically and systematically biased and nonquantitative ( 54 , 58 – 63 ). The few polar soil viromes have been from Antarctic soils and further demonstrated the genetic novelty of this gene pool while suggesting that resident viral communities were dominated by tailed viruses, had high habitat specificity, and were structured by pH ( 51 , 64 , 65 ).…”

Section: Introductionmentioning

confidence: 97%

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

et al. 2018

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This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870–880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.

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Niche-dependent genetic diversity in Antarctic metaviromes

Cited by 12 publications

References 21 publications

Exploring Viral Diversity in a Unique South African Soil Habitat

Exploring Viral Diversity in a Unique South African Soil Habitat

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

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