Most plant-associated microbes and particularly bacteria are beneficial for the growth and health of plants as well as for crop yield. This makes plant and soil microbes a crucial factor for sustainable agriculture, which is increasingly necessary to secure global food availability and nutritious crops while protecting biodiversity.
A recent review by Marks et al highlights microbial secondary metabolites as a promising solution to strengthen soil health, increase plant resistance, withstand weather conditions and improve nutrient availability. The authors outline the molecular and biological basics of microbial secondary metabolites, the technical approaches to produce and isolate them, as well as their actual and potential applications in agriculture and the current challenges in achieving these.
About microbial secondary metabolites
Microorganisms produce secondary metabolites when they have energy available after maintaining their primary metabolism required for growth and reproduction. Depending on the environmental conditions, chemicals available and the genetic repertoire, they shift their metabolic pathways to store the excessive energy. Based on this shift, they often produce complex molecules from metabolites or intermediates from primary pathways. While these secondary metabolites themselves are not essential for the survival of the producing microorganism, they have substantial impacts on the microbes’ ecology, especially on the interactions with other organisms and plants.
The review outlines the five main categories of microbial secondary metabolites based on their chemical skeletons and partly on their biological functions: peptides, polyketides, volatile compounds, terpenoids/steroids and growth regulators. For example, soil bacteria from the Bacillus species produce a wide range of secondary metabolites. Produced antibiotics suppress the growth of phytopathogens while auxins, cytokinins, gibberellins, ethylene and abscisic acid promote plant growth via facilitating nitrogen fixation and phosphate solubilisation.
Other plant-growth promoting bacteria producing beneficial secondary metabolites contain species from the Pseudomonas and Azospirillum genus and Rhizobia bacteria. The latter symbiotically associate with non-leguminous plant roots, where they produce growth regulators like lipochitooligosaccharides. These play a role both in nodule formation essential for the plant-bacteria symbiosis and in plant growth and stress resistance.
Upscaling microbial secondary metabolite production
As the authors emphasise the potential of microbial secondary metabolites in sustainable agriculture, they highlight that industrial-scale production and commercialisation remain challenging. To produce microbial secondary metabolites, both liquid and solid-state fermentation methods are suitable. Furthermore, several extraction and analysis methods, such as thin-layer chromatography, high-performance liquid chromatography, gas chromatography-mass spectrometry, spectroscopic and metabolomics approaches, are available to isolate the molecules.
Yet bottlenecks exist related to the scalability of the fermentation culture, the optimal conditions for the microbes to produce high amounts of the metabolites, the costs and complexity of the extraction and purification processes and waste management. Hence, the authors discuss approaches such as strain improvement, optimisation of fermentation parameters and implementing circular economy principles. Applying these would profoundly increase yield, extraction and purification rates and optimise waste handling.
This excellent and comprehensive review lastly emphasises that partnerships between academia and industry are mandatory to leverage microbial secondary metabolites for developing sustainable agricultural practices. As these molecules have the potential to address food security in the face of climate change, the authors expect increased research, government support and financial incentives. This would massively grow the number of products containing microbial secondary metabolites and contribute to establishing more sustainable agricultural systems.
2 Responses
Thanks a lot for the comments. Indeed, the search for new bio-inputs based on microbial metabolites is increasing a lot and we hope that this review will contribute to clarify some points regarding these metabolites.
We would like to sincerely thank the authors of this article for highlighting our recent publication. Our research group dedicated significant effort to this work, and we are pleased to see it gaining visibility. We hope our study can meaningfully contribute to the ongoing discussion on the use of microbial secondary metabolites (MSMs) at an industrial scale for sustainable agricultural applications.