Microbe-driven chemical ecology: past, present and future

Abstract

Recent developments in microbiome biology and chemical analytics have revealed the relevance of microbial chemical communication and its networks for microbial ecology. Deciphering chemical interactions, however, is challenging and our understanding of Microbial Chemical Ecology (MCE) under natural conditions still remains fragmented. Here, we aim to summarize what is currently known in the field of MCE. We highlight new tools and methodological challenges and discuss future perspectives of this emerging field. We describe the factors affecting the production and environmental transport of signalling molecules, evaluate their metabolic and ecological functions, and discuss approaches to address future challenges in MCE. Our summary commends that future developments in the field of MCE will need to include studies involving organisms of all levels, and consider mechanisms underlying the communication including viruses, micro and macro-organisms in their natural environments. 3 Background Chemical ecology first appeared as a keystone discipline in the early 1950's, advancing our understanding of insect communication and plant chemical defenses [1]. However, chemical communication is not restricted to plant-insect and plant-plant interactions. In fact, chemically mediated relationships are now being recognized as common in the microbial world across terrestrial and aquatic ecosystems (Figure 1). Bonnie Bassler is one of the pioneers of microbial chemical communication being amongst the first to discover bacterial intra-specific quorum sensing via autoinducing chemical compounds. This mechanism is now proving to play a fundamental role in both intraspecific and interspecific interactions [2, 3]. Prof. Bassler coined the term "microbial language" and it was her initial work and the numerous follow-up studies that brought chemical communication between microbes into the spotlight. Researchers in the field of microbial ecology are recognizing the important roles that chemical communication and interactions play across all ecosystems (reviewed in [4]). In fact, the oldest form of communication is probably the chemical communication between microorganisms and only later evolved in plants, insects and other higher organisms [5]. Thus, by deciphering the chemical language, we will be able to better understand how species interact in their ecosystems. However, understanding the theoretical foundations of chemical language (its origin and diversity) is challenging and has been rarely studied. Until now, the topic of Microbial Chemical Ecology (MCE) has been largely neglected by microbiologists. The reason stems from methodological constraints concerning the analysis of microbiological communities under natural conditions. Furthermore, most of the research for natural products is focused on chemical and biochemical approaches and drug discovery with a less of an emphasis on ecological aspects. The traditional separation of disciplines limits our

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