Table 1.
Examples of belowground studies using PCR-based methods for agricultural systems.
| Agricultural area/field experiment/material employed | Ecological measurement | Organisms involved | PCR-based method | References |
|---|---|---|---|---|
| Winter wheat in an arable field (Germany) | Community structure | Fungi | DGGE | Hagn et al., 2003 |
| Grazed grassland (UK) | Community structure | Bacteria | TRFLP and DGGE | Nunan et al., 2005 |
| Arable soil (UK) | Community structure | Nematode | Clone and sequencing | Griffiths et al., 2006 |
| Grassland (Kansas, USA) | Community structure | Free-living bacterivorous nematodes | Multiplex qPCR | Jones et al., 2006a,b |
| — | Community structure | Nematode | DGGE | Sato and Toyota, 2006 |
| Arable soil, dune sand, coniferous forest, pasture, and moorland (UK) | Community structure | Nematode | TRFLP | Donn et al., 2007 |
| Maize crops (USA) | Predator-prey | Insects | qPCR | Lundgren et al., 2009 |
| Natural restoration and cropping management (China) | Community structure | Bacteria | DGGE | Wang et al., 2009 |
| Grazer pasture and forest (South Carolina, USA) | Community structure | Bacteria | Clone and sequencing | Hamilton et al., 2009 |
| Agroecosystems | Predator-prey | Beetles as predators; earthworms as prey | qPCR | King et al., 2010 |
| Agroecosystems | Predator-prey | Mite as predator; nematode as prey | qPCR | Heidemann et al., 2011 |
| Maize crops (USA) | Community structure | Insects (and plant damage linked) | Lundgren and Fergen, 2011 | |
| Citrus groves (Florida, USA) | Predator-prey; food webs | Entomopathogenic nematodes, nematophagous fungi, ectoparasitic bacteria, free-living nematodes | qPCR and nested | Campos-Herrera et al., 2011b, 2012; Pathak et al., 2012 |
| Tillage trial (UK) | Community structure | Nematode | d-TRFLP | Griffiths et al., 2012 |
| Agricultural field (Japan) | Community structure | Nematode | Next generation sequencing | Morise et al., 2012 |
| Abandon field (Netherlands) | Community structure | Nematode | qPCR | Vervoort et al., 2012 |
| Tillage and nutrient additions in wheat cropping experiment (Australia) | Community structure | Bacteria | TRFLP | Bissett et al., 2013 |
| Oilseed rape fiel trial (UK) | Community structure | Fungi and bacteria | TRFLP | Hilton et al., 2013 |
Note that we have excluded references corresponding to the development of new molecular methods for particular species, without establishing relationship among other (structure or food web).