TABLE 1.
Medium-to-high-throughput soil-based studies pertaining to viral ecology since 2005
| Authors, yr of publication (reference no.) | Soil type(s) | Location(s) of sample collection | Method(s) useda |
|---|---|---|---|
| Prigent et al., 2005 (29) | Hot desert surface sand | Sahara Desert in Morocco and Tunisia | EM, PFGE, lytic induction |
| Williamson et al., 2005 (16) | Agricultural, forest | Delaware, USA | Epifluorescence microscopy, EM |
| Fierer et al., 2007 (30) | Hot arid desert, tallgrass prairie, tropical rainforest | USA, Peru | Sanger sequencing of random viral metagenomics clones |
| Williamson et al., 2007 (17) | Loamy and sandy soils, agricultural, forested wetlands | Antarctica (Tom and Obelisk Pond); USA (Delaware) | Induction assays, epifluorescence counting |
| Prestel et al., 2008 (31) | Surface sand | Namib Desert | EM, PFGE, Sanger sequencing of cloned DNA fragments (LASL) |
| Swanson et al., 2009 (32) | Dystric-fluvic Cambisol soil | Dundee, Scotland | EM, epifluorescence counting |
| Meiring et al., 2012 (33) | Soil under hypoliths | Miers Valley, Antarctica | Lytic induction, EM, phage isolation from culture |
| Pearce et al., 2012 (34) | Surface soil | Alexander Island, Antarctica | Shotgun metagenome pyrosequencing |
| Swanson et al., 2012 (35) | Surface soil (Antarctica) | Antarctica | EM, lytic induction, phage isolation |
| Prestel et al., 2013 (36) | Dune surface sand | Mojave Desert, USA | EM, random amplification for viral DNA (Sanger) |
| Srinivasiah et al., 2013 (37) | Surface soil (Antarctica); silt loamy soil (USA) | Antarctica (Tom and Obelisk pond); Delaware, USA | RAPD viral community fingerprinting |
| Adriaenssens et al., 2015 (38) | Soil-associated rocks (hypoliths) | Namib Desert | Shotgun viral metagenome sequencing (Illumina) |
| Zablocki et al., 2014 (39) | Antarctic surface soil and hypoliths | Miers Valley, Antarctica | Shotgun viral metagenome sequencing (Illumina) |
| Srinivasiah et al., 2015 (40) | Silt loamy soil | Delaware, USA | Microcosms, RAPD viral community fingerprinting, epifluorescence counting |
a
EM, electron microscopy; PFGE, pulse field gel electrophoresis; LASL, linker amplified shotgun library; RAPD, random amplified polymorphic DNA.