Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe-microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.

Past medicinal plant research primarily focused on bioactive phytochemicals, however, the focus is currently shifting due to the recognition that a significant number of phytotherapeutic compounds are actually produced by associated microbes or through interaction with their host. Medicinal plants provide an enormous bioresource of potential use in modern medicine and agriculture, yet their microbiome is largely unknown. The objective of this review is (i) to introduce novel insights into the plant microbiome with a focus on medicinal plants, (ii) to provide details about plant- and microbe-derived ingredients of medicinal plants, and (iii) to discuss possibilities for plant growth promotion and plant protection for commercial cultivation of medicinal plants. In addition, we also present a case study performed both to analyse the microbiome of three medicinal plants (Matricaria chamomilla L., Calendula officinalis L., and Solanum distichum Schumach. and Thonn.) cultivated on organically managed Egyptian desert farm and to develop biological control strategies. The soil microbiome of the desert ecosystem was comprised of a high abundance of Gram-positive bacteria of prime importance for pathogen suppression under arid soil conditions. For all three plants, we observed a clearly plant-specific selection of the microbes as well as highly specific diazotrophic communities that overall identify plant species as important drivers in structural and functional diversity. Lastly, native Bacillus spec. div. strains were able to promote plant growth and elevate the plants’ flavonoid production. These results underline the numerous links between the plant-associated microbiome and the plant metabolome.

There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal–bacterial interactions.

The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteria.Interactions and communication among organisms are central to understanding any ecosystem. The essential role of volatile organic compounds (VOCs) in the communication with other organisms, also known as infochemicals, has been acknowledged for more than 30 years 1 . However, their ecological functions have been mainly studied for aboveground plant-plant and plant-insect interactions 2, 3 . In recent years, VOCs are becoming increasingly important in the field of microbial ecology. Due to their unique nature (low molecular mass, high vapor pressure, low boiling point and a lipophilic moiety) VOCs play important roles in the long-distance interactions and communication within the microbial world 4 . In soil and in the rhizosphere, VOCs readily diffuse under atmospheric pressure and travel throughout the abundant air-and liquid-filled pockets of the soil 4, 5 .Several soil-associated bacteria were shown to have positive effects on plant growth and resistance 6-8 , as well as to have the ability to control plant diseases via production of VOCs 9 . Various studies have documented that VOCs can have diverse roles in the interaction between physically separated microorganisms, ranging from infochemical molecules affecting the behavior, population dynamics and gene expression in responding microorganisms to interference competition tools suppressing or eliminating potential enemies 4, 10-13 . Interestingly, most studies have only examined the role of bacterial VOCs and their effect on plants and fungi. However, the role and function of fungal VOCs on bacteria remains largely unknown. Only few studies demonstrated that the growth of some bacterial species was suppressed by fungal VOCs 14 . For example, VOCs produced by the oyster mushroom Pleurotus ostreatus showed inhibitory effects on Bacillus cereus and Bacillus subtilis 15 . Another study by Lutz et al. 16 demonstrated that VOCs emitted by T. atroviride increased the expression of a biocontrol gene (phlA) of P. fluorescens.Previous...

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