Reconciling Ecological and Engineering Design Principles for Building Microbiomes

Abstract

Simplified microbial communities, or “benchtop microbiomes,” enable us to manage the profound complexity of microbial ecosystems. Widespread activities aiming to design and control communities result in novel resources for testing ecological theories and also for realizing new biotechnologies. There is much to be gained by reconciling engineering design principles with ecological processes that shape microbiomes in nature. In this short Perspective, I will address how natural processes such as environmental filtering, the establishment of priority effects, and community “blending” (coalescence) can be harnessed for engineering microbiomes from complex starting materials. I will also discuss how future microbiome architects may draw inspiration from modern practices in synthetic biology. This topic is based on an important overarching research goal, which is to understand how natural forces shape microbial communities and interspecies interactions such that new engineering design principles can be extracted to promote human health or energy and environmental sustainability.

Repeated introduction of micropollutants enhances microbial succession despite stable degradation patterns

“…Although our microcosms represent an ideal system which is removed from in situ conditions, our experimental findings are valuable in at least three aspects, that is : i) the prediction of microbial responses to persistent micropollutants, ii) the harnessing of ecological principles and microbiomes in pollution management [80][81][82], and (iii) the development of a conceptual model to be used to predict when and how stochastic and deterministic processes contribute to community assembly after the exposure of persistent micropollutants. Our results suggest that strong ecological drift drives random community changes at the early stage of the exposure (Fig.…”

Innovating carbon-capture biotechnologies through ecosystem-inspired solutions

“…As we collectively identify connectivity between genomeencoded functions and carbon cycling for natural ecosystems, we often reveal new biotechnological insights. 6 We encourage ecologists to help engineers identify where accessible ecological/biological control points of CO 2 and/or CH 4 cycling occur within major biospheres. We use the term ''accessible control point'' to define the existence of current or future opportunities for technology to interface with these biomes.…”

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering

“…The community coalescence framework builds on earlier models of immigration dynamics by considering a distinct set of assembly processes that involves fusing whole communities along with the respective environments ( 1 ). Although this framework was developed to provide a mechanistic understanding of community assembly processes in natural systems, recent work highlights its utility to the ecological principles of optimizing community coalescence in engineering-based management ( 4 , 34 ). For example, the harnessing of environmental filtering (environments select certain species) and priority effects (early colonizer impacts on the success of subsequent arrivals) ( 35 ) can inform the design and construction of target microbial consortia.…”