TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions

Abstract

Understanding the molecular mechanisms underlying plant–microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the complexity of natural microbial communities remains challenging. Such challenges can be addressed by employing synthetic microbial communities (SynComs) derived from well characterized microbial culture collections. Despite their importance, plant-associated microbial collections from major agricultural crops remain scarce. To bridge this gap, we established TriMic, a taxonomically and functionally representative culture collection of wheat root–associated bacteria. Complementing this collection, we include high quality genome sequences and an overview of genes involved in plant colonization, nutrient cycling, and plant growth promotion. Furthermore, we expanded this experimental toolkit by designing a reduced complexity SynCom that enables controlled dissection of plant-microbe interactions. Together, these resources lay the groundwork for mechanistic studies of plant-microbe interactions to accelerate biostimulant development aimed at enhancing agricultural productivity and sustainability. The TriMic collection and whole genomes are publicly available at the DSMZ (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/trimic) and NCBI. Graphical abstract Overview of the workflow for development of the wheat root bacterial collection and SynCom. (a) Bacterial isolates were recovered from roots of wheat grown in natural soil using two strategies after a root slurry was prepared: directly plating or host-mediated, which involved producing a secondary root slurry from wheat roots inoculated with the original root slurry (Ben Niu et al. 2017). Both root slurries were diluted and then plated onto four different types of media (1/10 R2A, 1/20 R2A, 1/100 R2A, and VxylG). Colonies were picked based on morphology and time of appearance. (b) Non-redundant strains of 88 purified isolates were made publicly available at the German Collection of Microorganisms and Cell cultures GmbH (DSMZ). (c) A 15-species synthetic community (SynCom) was developed after evaluating community dynamics in wheat roots inoculated with a 27-member consortium selected across genera in the collection. (d) Isolate genomes were sequenced using either short-read or hybrid assemblies with long-reads. Following functional annotation, genomes were screened for traits associated with plant-microbe interactions and secondary metabolite production.