Linking microbial community structure with function using functional amplicon sequencing of the NRPS genes around wheat roots during drought stress
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Secondary metabolites are an important group of compounds, mediating interactions between microorganisms and plants. One class of these secondary metabolites includes cyclic lipopeptides and siderophores produced by nonribosomal peptide synthetases (NRPSs) are essential for bacterial root colonization. However, due to the vast array of secondary metabolites, there are still a lot of compounds for which their role in plant root colonization is unknown. This is even more noticeable during drought. To unravel some of these secondary metabolites’ role, we used functional amplicon sequencing of the adenylation domain of the NRPSs and linked this with amplicon sequencing of the 16S rRNA gene from roots of wheat in controlled conditions or under drought stressed. Drought had a transient impact on the bacterial community composition, which was also seen for the NRPS composition. We found that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought selected for a Pseudomonas NRPS gene encoding the cyclic lipopepeptide viscosin hinting towards this compound providing a competitive advantage in root colonization during drought. We confirmed this by a follow up experiment using the viscosin producing P. fluorescens SBW25 and its Δ viscA mutant. In summary, our work demonstrates the potential for functional amplicon sequencing of NRPS genes coupled with in planta experiment to elucidate their importance in root colonization.
Importance
To exploit beneficial plant-microbe interactions for improved plant growth under drought stress, we need to improve our understanding of factors important for successful root colonization. Functional amplicon sequencing can leverage our understanding of plant- microbe interactions and provide the background knowledge for experimental testing. Secondary metabolites (SM) are important in plant-microbe interactions, and thus, targeting these genes provide the potential to increase translational power from lab experiments to field testing. Here, we show that a group of secondary metabolites, the siderophores, respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization during drought. This work demonstrates that the resolution provided by functional amplicon sequencing can be used to identify key genes in plant-microbe interactions around the roots.
