Ploemacher, H. | bioRxiv Science

bioRxiv2026

Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant microbe interactions

O_LIPlant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes presents a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. C_LIO_LIWe designed 4 distinct, reduced-complexity variants of SynCom SRC1 and assessed their capacities for colonization, stability, and plant growth promotion. To understand the impact on plant performance of our highest performing SynCom variant, we characterized the hosts longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. C_LIO_LIThe top performing SynCom stably colonized sorghum roots and rhizospheres, elicited plant growth promotion, and induced dynamic spatiotemporal gene transcription in sorghum roots and shoots defined by modulation of growth-defense tradeoff machinery and enhanced flavonoid production. C_LIO_LIThe resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization. C_LI

plant biology↗

bioRxiv2025

Uncovering the hidden diversity and functional roles of root endophytic Streptomyces under drought stress

The genus Streptomyces has consistently been found to be enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment of Streptomyces in field-grown sorghum roots and identified five closely related but distinct ASVs belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought-versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that drought enrichment (DE) scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified gene clusters involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces enrichment under drought is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, enrichment in the root microbiome does not predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress. ImportanceUnderstanding how beneficial microbes respond to drought is critical for developing microbiome-based strategies to enhance crop resilience. The Streptomyces genus is consistently enriched in drought-stressed root microbiomes, yet our study reveals that this enrichment is not a uniform isolate-level response. Instead, we show that drought enrichment is highly strain-specific and functionally diverse, with key associated traits like osmotic stress tolerance and siderophore production varying independently of phylogeny. Importantly, enrichment does not predict a microbes ability to promote plant growth under stress. By integrating high-resolution taxonomic, genomic, and metabolomic approaches, we uncover the ecological and functional complexity underlying Streptomyces responses to drought. These findings emphasize the importance of resolving microbial function at the strain level and caution against assuming functional traits based on taxonomic identity itself.

microbiology↗