Efforts to meet the steadily increasing global need for plant products without continuously expanding the environmental footprint of crop production face several convoluted challenges. One challenge is minimizing crop loss due to diseases and pests without heavily relying on synthetic pesticides. Microorganisms secrete diverse molecules to influence surrounding organisms and environments. Research on these molecules has uncovered diverse mechanisms underpinning both beneficial and harmful microbial interactions and has also resulted in new crop protection strategies. However, compared with rapid advances in research on secreted proteins, research on metabolites, particularly volatile compounds, considerably lags. Diverse roles of secreted metabolites are highlighted here to underscore the need for systematically exploring microbial chemical ecology. This review focuses on how genomics, especially metabolomics, can enlighten the nature and mechanism of diverse microbial chemical ecology processes crucial for plant health and how to translate resulting insights into environment-friendly and sustainable crop protection strategies. Metabolomics entails comprehensive and rapid profiling of an entire measurable set of compounds in complex mixtures derived from organisms or environments using a growing array of analytical instruments. Metabolomics has expediated discoveries of novel bioactive compounds and subsequent studies on their mode of action. We review a variety of metabolomics tools and how they can be integrated with other tools to study and harness microbial chemical ecology.

Original languageEnglish (US)
Pages (from-to)195-210
Number of pages16
JournalPhytobiomes Journal
Issue number3
StatePublished - Jul 2020

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agronomy and Crop Science
  • Plant Science
  • Ecology


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