A simple method for enumerating bacteriophages in soil

Yin, Xiaoming; Zeph, Lawrence R.; Stotzky, G.

doi:10.1139/m97-065

Cited by 8 publications

(3 citation statements)

References 23 publications

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“…There are an estimated 10 30 prokaryotes in the biosphere, the vast majority of which are in the subsurface terrestrial, sediments, and the oceans [18]. Generally, there are $1-10 phage particles per prokaryotic cell in environmental samples [19][20][21][22]. Therefore, most of the world's phages are probably found in these biomes as well.…”

Section: Resultsmentioning

confidence: 99%

Global distribution of nearly identical phage-encoded DNA sequences

Breitbart

2004

FEMS Microbiology Letters

101

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Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition. However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems. Here, we report that T7-like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan-associated. The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates. Some identical T7-like phage-encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7-like phages may be smaller than previously hypothesized.

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Section: Resultsmentioning

confidence: 99%

Global distribution of nearly identical phage-encoded DNA sequences

Breitbart

2004

FEMS Microbiology Letters

101

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“…There are an estimated 10 30 prokaryotes in the biosphere, the vast majority of which are in the subsurface terrestrial, sediments, and the oceans [18]. Generally, there are ∼1–10 phage particles per prokaryotic cell in environmental samples [19–22]. Therefore, most of the world's phages are probably found in these biomes as well.…”

Section: Resultsmentioning

confidence: 99%

Global distribution of nearly identical phage-encoded DNA sequences

Breitbart

Miyake

Rohwer

2004

FEMS Microbiology Letters

195

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Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition. However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems. Here, we report that T7‐like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan‐associated. The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates. Some identical T7‐like phage‐encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7‐like phages may be smaller than previously hypothesized.

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“…As recently as 2003, the abundance of autochthonous viruses in soil was unknown (5,57). Previous assessments of viral abundance in soils were based on determination of PFU by using susceptible indicator strains (64), microscopic enumeration of optically active viruses such as baculoviruses (53), or PCR amplification of viral nucleic acids by using specific primers (43). These approaches are unsatisfactory for determining the abundance of autochthonous soil viruses, since each method targets only a specific fraction of the total viral community.…”

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confidence: 99%

Abundance and Diversity of Viruses in Six Delaware Soils

Williamson

Radosevich

Wommack

2005

Appl Environ Microbiol

258

199

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The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 ؋ 10 9 to 4.17 ؋ 10 9 g ؊1 dry weight) than in agricultural soils (8.7 ؋ 10 8 to 1.1 ؋ 10 9 g ؊1 dry weight). Soil VLP abundance was significantly correlated to moisture content (r ‫؍‬ 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r ‫؍‬ 0.885) and viral (r ‫؍‬ 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.

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A simple method for enumerating bacteriophages in soil

Cited by 8 publications

References 23 publications

Global distribution of nearly identical phage-encoded DNA sequences

Global distribution of nearly identical phage-encoded DNA sequences

Global distribution of nearly identical phage-encoded DNA sequences

Abundance and Diversity of Viruses in Six Delaware Soils

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