Microbe-driven chemical ecology: past, present and future

Abstract

In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.

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Acknowledgements

The authors would like to thank all participants of the roundtable session “Microbial chemical ecology: intraspecies and interspecies communication” at ISME 17 for the fruitful discussion. We acknowledge funding from the Education, Culture, Sports, Science, and Technology Ministry of Japan special project costs Four-Dimensional Kuroshio Marine Science (4D-KMS) Project and Japan Society for the Promotion of Science (JSPS KAKENHI Grant Number 16K18678) to DU. HBB acknowledges support from the State of Hesse for the LOEWE TBG research center. LYW acknowledges support from the Collaborative Research Centre AquaDiva (CRC 1076 AquaDiva) at the Friedrich Schiller University Jena and the Helmholtz Centre for Environmental Research—UFZ, funded by the Deutsche Forschungsgemeinschaft (DFG). PG acknowledges the Netherlands Organization for Scientific Research (NWO), VIDI personal grant (864.11.015). This is publication 6750 of the NIOO-KNAW.

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Correspondence to Paolina Garbeva.

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