Table 2.

Selected plant based methods used to engineer the rhizosphere microbiome.

Method	Mechanisms/examples	Advantages	Disadvantages	Reference
Plant breeding and cultivar selection.	Enhancing exudates production of stimulatory or inhibitory factors.	Influence microbial populations by inhibiting or enhancing the growth of selected microbial members of the rhizosphere community. It does not require change in infrastructure or management in the field.	Need for deeper knowledge on the impact of diversity, quantity, and consistency of exudation shaping the microbiome. There is no control over the variability across environments, soil types, and microbial communities. There is no breeding program that evaluates plant lines for interactions with the soil microbiome.	Lemanceau et al. (1995), Hartmann et al. (2009), Ryan et al. (2009), An et al. (2011), Bakker et al. (2012)
	Alteration of plant resistance to disease and environmental factors.	Improved ability to resist to adverse environmental conditions (climatic, edaphic, and biological).	May produce unexpected or undesirable outcomes.	O’Connell et al. (1996), Lynch et al. (2004)
	Selection of mutants with enhanced capacity to form mutual symbiosis	Improved access to nutrient	Could be deleterious under high nutrient conditions Higher percentage of carbon allocated to symbionts	Solaiman et al. (2000)
Genetic modification: change in the amount and/or quality of the organic exudates, signal molecules, and residues entering the soil.	Engineering plants to produce exudates to favor specific diversity or beneficial services.	Plant induction of microbiome beneficial functional traits such as nodulation, siderophore, anti-microbial, anti-fungal, or biological control compounds. Improve resistance to adverse environments. Use in bioremediation of toxic compounds.	Inter-species plant-microbe gene transfers. When a desired trait has been engineered successfully into a plant, the compounds might be rapidly degraded, inactivated in the soil, or the rate of exudation might be too small to influence the rhizosphere as predicted.	Truchet et al. (1991), Downie (1994), O’Connell et al. (1996), Zupan et al. (2000), Brussaard et al. (2007), Broeckling et al. (2008), Bakker et al. (2012), Sharma et al. (2013)
	Engineering plants to produce exudates to modify soil properties (acidic pH, anion efflux from roots).	Improve plant growth at low pH, salinity resistance, and water deficit. Enhance plant Al3+ resistance. Improve ability to acquire insoluble P. Larger roots, longer root hairs, and greater shoot biomass.	Enzyme activities do not necessarily lead to anion accumulation and enhanced efflux, and suggest that metabolic or environmental factors can influence the effectiveness of this approach. The gene TaALMT1 (malate release in the rhizosphere) needs to be activated by Al3+.	Koyama et al. (1999), Koyama et al. (2000), Tesfaye et al. (2001), Anoop et al. (2003), Li et al. (2005), Brussaard et al. (2007), Delhaize et al. (2007), Gévaudant et al. (2007), Yang et al. (2007), Ryan et al. (2009)
	Generation of transgenic plants producing quorum sensing signal molecules N-acyl-homoserine lactone (AHL).	May lead to an increase in plant disease resistance by blocking communication among members of the plant-associated bacterial community.	Blocking communication among members of the beneficial plant associated bacterial community.	Teplitski et al. (2000), Savka et al. (2002), Bakker et al. (2012)
	Engineering plants to produce an enzyme responsible for degradation of the quorum sensing signal (lactonases, acylases).	Prevention of bacterial infection.	Rhizosphere populations would be able to capture and stably integrate transgenic plant DNA, in particular antibiotic resistance genes used in the selection of successful transgenic plants.	Dong et al. (2001), Braeken et al. (2008), Zhang et al. (2015)