Table 3.

Selected meta-organism-based methods and other complementary methods used to engineer the rhizosphere microbiome.

Method	Mechanisms/examples	Advantages	Disadvantages	Reference
Meta-organism-based
Selecting and managing complementary plants and microbiomes	Crop Rotation	Induction of suppressive soils by managing soil diversity. Higher level of nutrients cycling and increase of organic carbon. Improvement of physico-chemical soil characteristics.	Mechanisms are not fully understood	Mazzola (2002, 2007), Ryan et al. (2009)
Engineering plants to produce one or more compounds and engineering the inoculated bacteria to degrade these compounds.	Opine producing plants co-inoculated with opine utilizing bacteria	Establishing a direct trophic link between the two partners of the interaction.		Savka and Farrand (1997), Dessaux et al. (1998), Savka et al. (2002)
Other methods
Agricultural Inputs	Mineral fertilizers: urea, ammonium nitrate, sulfates, and phosphates.	Indirectly enhance soil biological activity via increases in system productivity, crop residue return, and soil organic matter.	N fertilization generates soil acidification and P fertilization affect root colonization of AMF.	Savka et al. (2002), Bünemann et al. (2006), Mazzola (2007)
	Organic fertilizers: animal manures, composts, and biosolids.	Increase in soil organic matter increase soil biological activity (organic fertilizers).	Biosolids: possible presence of toxic substances for the soil microflora. Inability to predictably reproduce compost composition.