Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA

Srinivasiah, Sharath; Lovett, Jacqueline; Polson, Shawn W.; Bhavsar, Jaysheel; Ghosh, Debasish; Roy, Krishnakali; Fuhrmann, Jeffry J.; Radosevich, Mark; Wommack, K. Eric

doi:10.1128/aem.00268-13

Cited by 30 publications

(24 citation statements)

References 71 publications

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“…The RAPD PCR in this study utilized primer SP2 (5'-CGC AAC AGG G-3'), which was designed by Shawn Polson by identifying the most common decamers in the 80 m viral metagenome from the Sargasso Sea (Angly et al 2006, Srinivasiah et al 2013. Each 50 µl reaction contained 2 U of Apex Taq DN A polymerase (Genesee Scientific), 1 × Apex reaction buffer, 1.5 mM Apex MgCl 2 , 4 µM of primer, 0.2 mM dNTPs, and 1 µl of template DNA.…”

Section: Rapd Pcr Amplification and Data Analysismentioning

confidence: 99%

Water column stratification structures viral community composition in the Sargasso Sea

Goldsmith¹,

Brum²,

Hopkins³

et al. 2015

Aquat. Microb. Ecol.

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Section: Rapd Pcr Amplification and Data Analysismentioning

confidence: 99%

Water column stratification structures viral community composition in the Sargasso Sea

Goldsmith¹,

Brum²,

Hopkins³

et al. 2015

Aquat. Microb. Ecol.

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“…Fertilizer applications to soil have been shown to increase virus abundance (Chen et al, 2014 ; Doan et al, 2014 ), and changes influencing the bacterial community in general also affect the abundance of viruses and the diversity of viral communities (Srinivasiah et al, 2013 , 2015 ; Doan et al, 2014 ). Viruses from forest soils are both more abundant and more diverse than viral communities from agricultural soils (Williamson et al, 2005 ), while different land use practices generally result in differing communities (Fierer et al, 2007 ; Srinivasiah et al, 2013 ). Still, time-series recording the temporal variability in different terrestrial ecosystems are needed to address questions regarding the temporal dynamics, the stability and responses of viral communities to changing environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

et al. 2017

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Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.

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“…In marine virus ecology, the use of conserved viral marker genes such as DNA polymerases (76), ribonucleotide reductases (77), and T4-related structural proteins (78,79) has provided detailed data on viral biodiversity, on intra-and interviral evolutionary relationships, and on oceanic viral turnover rates. The use of these methods to study virus diversity and biogeography in desert soils is relatively new and most commonly involves the sequencing of whole metaviromes (37)(38)(39). However, metaviromic approaches generally result in a large number of unknown sequences (43).…”

Section: Technical Recommendations and Future Researchmentioning

confidence: 99%

“…However, viral DNA was not specifically enriched in this study, and this may have resulted in an underestimation of viral diversity. The spatial composition and dynamics of viral communities along an Antarctic soil transect have been recently reported (37). Using random amplified polymorphic DNA (RAPD-PCR) assays, viral community fingerprints were used to assess short-term changes in the composition of viral communities.…”

Section: Diversity and Abundance Of Viruses 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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Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA

Cited by 30 publications

References 71 publications

Water column stratification structures viral community composition in the Sargasso Sea

Water column stratification structures viral community composition in the Sargasso Sea

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

Diversity and Ecology of Viruses in Hyperarid Desert Soils

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