Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

Fig. 1. Barriers to organism establishment and a path forward for microbiome engineering.

A The current state of research focused on inoculum establishment. Without quantitative prioritization, potential barriers like the illustrated examples are investigated randomly. B Path forward to improve establishment success. Prioritization of barriers includes quantifying their relative impact in order to create decision trees that can simultaneously rank barriers and summarize the potential impact of overcoming each barrier in a multi-factor solution path. Values in parentheses on the decision tree illustrate an example of percentage impact of a barrier on inoculum establishment, guiding microbiome engineering investments.