Table 1.

Overview of factors impeding organism establishment, potential engineering solutions. A comprehensive source of examples of studies which illustrate barriers to establishment and solutions is provided in Table S1.

Ecological principle	Factor impeding establishment	Potential engineering goal
Propagule pressure
• Dose	a. Stochastic extinction b. Density-dependent competitiveness	a. Add a higher dose of the inoculant b. Add a lower dose of the inoculant
• Frequency	a. Succession makes niche ephemeral b. Biotic disturbance (i.e., inoculation) is needed to open a niche	a. Add inoculant more frequently b. Add inoculant at certain timepoint(s)
• Delivery mode	a. Inoculants do not reach or do not stay in intended location	a. Alter delivery mode b. Increase dose
Environmental filtering
• Disturbance	High-turnover of organisms (low residence time)	a. Persistent delivery of inoculant is necessary b. Create a protected physical space c. Inoculant with characteristics resistant to disturbance
• Niche Breadth	Inoculated organism requires a specific resource that is absent	a. Engineer inoculant that has a larger niche breadth b. Pre-adapt inoculant to available environment c. Add resource specific to inoculant (‘pre-biotic’)
Biotic interactions
• Antagonism via Competition	Direct competition exists between resident organisms and inoculants	a. Remove/disturb resident microbes b. Increase “competitive” trait of inoculation (e.g., antibiotic production, biofilm formation) c. Both a & b d. Add resources to support the inoculant during establishment period or beyond e. Pre-adapt inoculant to available environment f. Create a protected space
• Antagonism via Antibiotics	Antibiotic-producing residents debilitate the inoculant	a. Make inoculant resistant b. Disrupt resident(s) (reduce antibiotic(s) production) c. Create a protected space
• Antagonism via Predation	Predation by resident microbes	a. Make the inoculant resistant b. Remove predators prior to inoculation c. Create a protected space
• Facilitation	Inoculant requires ‘services’ provided by another organism which is not present	a. Add in an additional organism serving as a ‘keystone’ species to modify interactions of the target inoculant and other organisms and/or modify the environment