Biology subjects

Garcia, C. F.

Publications and source records attributed to Garcia, C. F..

3 recordsLinked to original sources

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↗

bioRxiv2023

Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion

Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals and humans and is used for bioethanol production. Its root tips exude large amounts of a lipophilic benzoquinone called sorgoleone. Sorgoleone is an allelochemical that suppresses the growth of competing plant seedlings and is mineralized by microbes in soil. As an avenue to understand how sorghum and its root microbiome may be connected through root exudates, we identified the molecular determinants of microbial sorgoleone degradation and the distribution of this trait among microbes. We isolated and studied from sorghum-associated soils, three bacterial strains classified as Acinetobacter, Burkholderia, and Pseudomonas species that grow with sorgoleone as a sole carbon and energy source. The genomes of these strains were sequenced and subjected to transcriptomic and gene fitness analyses to identify candidate sorgoleone degradation genes. Follow up mutational analysis showed that sorgoleone catabolism is dependent on four contiguous genes that are conserved among the species we sequenced. Phylogenetic analysis of the sorgoleone degradation gene cluster showed that sorgoleone catabolism is enriched in sorghum-associated Streptomyces strains. The discovery of bacteria that grow on a compound like sorgoleone that is plant specific and not widely distributed in the environment, provides an opportunity to study how a plant exudate can enforce the development of a rhizosphere specific microbiome for the mutual benefit of plant and microbe. SignificanceThe grain crop sorghum exudes an herbicidal compound called sorgoleone from its root tips, which inhibits the growth of other plants. We isolated bacteria that grow on sorogleone and identified a cluster of bacterial genes required for sorogleone degradation that can be used as a biomarker for this trait. An approach to improve the production of crops in stressful conditions such as drought, is to encourage their association with plant growth promoting bacteria. Our discovery of sorgoleone degradation genes opens the door to engineering bacteria that receive benefit from sorghum in the form of a plant-specific growth substrate, and in return promote the growth of this crop.

microbiology↗

bioRxiv2018

Neighbor signals perceived by phytochrome B increase thermotolerance in Arabidopsis

Due to the preeminence of reductionist approaches, our understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighboring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low red / far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight. Shade reduces the activity of phytochrome B (phyB) and the phyB mutant showed high tolerance to heat stress even under simulated sunlight. The enhanced heat tolerance under low red / far-red ratios failed in a multiple mutant of PHYTOCHROME INTERACTING FACTORs. The phyB mutant showed reduced expression of several fatty acid desaturase (FAD) genes, proportion of fully unsaturated fatty acids and electrolyte leakage of membranes exposed to a heat shock. Activation of phyB by red light also reduced thermotolerance of dark-grown (etiolated) seedlings but not via changes in FAD gene expression and membrane stability. We propose that the reduced photosynthetic capacity linked to thermotolerant membranes would be less costly under shade, where the light input itself limits photosynthesis.

plant biology↗