Interkingdom microbial consortia mechanisms to guide biotechnological applications.

Shu Zhang,Akihiro Okamoto,Phillip Gedalanga,Nancy Merino

doi:10.1111/1751-7915.13300

Abstract

SummaryMicrobial consortia are capable of surviving diverse conditions through the formation of synergistic population‐level structures, such as stromatolites, microbial mats and biofilms. Biotechnological applications are poised to capitalize on these unique interactions. However, current artificial co‐cultures constructed for societal benefits, including biosynthesis, agriculture and bioremediation, face many challenges to perform as well as natural consortia. Interkingdom microbial consortia tend to be more robust and have higher productivity compared with monocultures and intrakingdom consortia, but the control and design of these diverse artificial consortia have received limited attention. Further, feasible research techniques and instrumentation for comprehensive mechanistic insights have only recently been established for interkingdom microbial communities. Here, we review these recent advances in technology and our current understanding of microbial interaction mechanisms involved in sustaining or developing interkingdom consortia for biotechnological applications. Some of the interactions among members from different kingdoms follow similar mechanisms observed for intrakingdom microbial consortia. However, unique interactions in interkingdom consortia, including endosymbiosis or interkingdom‐specific cell–cell interactions, provide improved mitigation to external stresses and inhibitory compounds. Furthermore, antagonistic interactions among interkingdom species can promote fitness, diversification and adaptation, along with the production of beneficial metabolites and enzymes for society. Lastly, we shed light on future research directions to develop study methods at the level of metabolites, genes and meta‐omics. These potential research methods could lead to the control and utilization of highly diverse microbial communities.

Highlights

These competitive interactions can be an attractive factor in the biotechnological applications of interkingdom consortia with the potential to improve product yields and further expand the possible metabolites produced when co-culturing diverse microorganisms (Hailei et al, 2013; Marmann et al, 2014)
When selecting microorganisms to partake in competitive interactions for biotechnological applications, long-term maintenance of the consortia structure could be affected by the synthesis of unwanted defensive products [e.g. diatoms produce fatty acids and esters that impact algicidal bacteria and affect the bacterial composition in the consortia (Amin et al, 2012)]
Interkingdom microbial interactions between archaea, bacteria, fungi and algae provide societal benefits in natural and engineered systems that are unlikely to be achieved in monocultures or intrakingdom consortia due to a lack of promoting symbiotic or competitive functions

Summary

Microbial consortia are capable of surviving diverse conditions through the formation of synergistic population-level structures, such as stromatolites, microbial mats and biofilms. Competition can be split into two categories: interference competition to negatively impact other species by producing harmful products and exploitative competition to compete for scarce resources These competitive interactions can be an attractive factor in the biotechnological applications of interkingdom consortia with the potential to improve product yields and further expand the possible metabolites produced when co-culturing diverse microorganisms (Hailei et al, 2013; Marmann et al, 2014). These interactions are known to promote fitness, diversification and niche adaptations as each species evolves to survive within the community (Watanabe et al, 1982; Michie et al, 2016). A combination of such tools—stable isotope analysis, microscopy and molecular biological techniques—can be utilized to reveal the microbial consortia physiology and the source and requirements for the biosynthesis of novel natural compounds

Potential methods to control the interkingdom interactions

Concluding remarks

Conflict of interest