Cooperation in microbial communities and their biotechnological applications

Abstract

SummaryMicrobial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross‐feeding, which can be understood in the general framework of ecological and evolutionary (eco‐evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of ‘cheating’ cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.

Bacillus licheniformis escapes from Myxococcus xanthus predation by deactivating myxovirescin A through enzymatic glucosylation

“…The enzymatic modification of antibiotics is both a deactivation mechanism that confers bacterial resistance (Blair et al, 2015) and a cooperative behaviour that can allow resistant cells to protect sensitive cells from antibiotics (Yurtsev et al, 2016). The presence of cooperative interactions among microorganisms is now recognized as an important factor in the function and evolutionary dynamics of microbial communities (Asfahl and Schuster, 2017;Cavaliere et al, 2017). Understanding how microbial cooperation can enable microbes to survive antibiotic exposure in environments is important both clinically and ecologically (Yurtsev et al, 2016).…”

Is “Wolf‐Pack” Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin

“…It is certainly not straightforward to apply the lessons learned from animal cooperativity to microbial systems. Although a thorough treatment of this subject is beyond our word limit, some excellent reviews and discussions are available …”

2038 – When microbes rule the Earth

“…More generally, the field of synthetic community ecology, the rational design and control of microbial communities, is gaining momentum in biotechnology and in addressing fundamental ecological questions (De Roy et al, 2014). Broader application of rationally designed communities will develop over the next 20 years with a more mechanistic understanding of crossfeeding and syntrophic interactions and the production of public goods (such as extracellular polymeric substances or extracellular enzymes), as well as with improved analysis of metabolites (Cavaliere et al, 2017). Understanding and minimizing the switch from cooperative to competitive behaviour, and in particular how to limit 'cheating' by members of a consortium, will make the functioning of consortia more reliable (Lindemann et al, 2016;Cavaliere et al, 2017).…”

“…Broader application of rationally designed communities will develop over the next 20 years with a more mechanistic understanding of crossfeeding and syntrophic interactions and the production of public goods (such as extracellular polymeric substances or extracellular enzymes), as well as with improved analysis of metabolites (Cavaliere et al, 2017). Understanding and minimizing the switch from cooperative to competitive behaviour, and in particular how to limit 'cheating' by members of a consortium, will make the functioning of consortia more reliable (Lindemann et al, 2016;Cavaliere et al, 2017). Several approaches are being used to make consortia more productive, manageable and predictable for bioengineers, for example, by optimizing spatial organization of species so that they can grow under ideal conditions while allowing metabolite exchange with their partner species, all of which is aided by developments in microfluidics, microfabrication and microsensors (Ben Said & Or, 2017;Seymour et al, 2017).…”

“…Cyanobacteria, for example, produce hydrocarbons that could sustain populations of hydrocarbonoclastic bacteria and contribute to a potentially large-scale cryptic hydrocarbon cycle in the oceans (Lea-Smith et al, 2015), and microalgal phototrophs in general enhance hydrocarbon biodegradation by supplying oxygen and other compounds to associated bacteria (McGenity et al, 2012). The next 20 years will see an accelerated move toward biotechnological processes using mixed cultures of diverse constellations, both bottom-up designed and topdown tamed, underpinned by an improved understanding of how microbial molecular cocktails influence social behaviour and by predictive models to provide efficient and stable processes (Richter et al, 2018;Cavaliere et al, 2017;Widder et al, 2016;Hays et al, 2015).…”