Improving rice drought tolerance through host-mediated microbiome selection

Styer, A.; Pettinga, D.; Caddell, D. F.; Coleman-Derr, D.

doi:10.1101/2024.02.03.578672

Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.02.03.578672

Improving rice drought tolerance through host-mediated microbiome selection

Styer, A.·Pettinga, D.·Caddell, D. F.·Coleman-Derr, D.

View original source ↗Export metadata ↓

Abstract

Plant microbiome engineering remains a significant challenge due to challenges associated with accurately predicting microbiome assembly and function in complex, heterogeneous soil environments. However, host-mediated selection can simplify the process by using plant host phenotype as a reporter of microbiome function; by iteratively selecting microbiomes from hosts with desired phenotypes and using them to inoculate subsequent cohorts of hosts, artificial selection can steer the microbiome towards a composition producing optimized plant phenotypes. In this study, we inoculated rice with wild microbial communities from fallow rice field, desert, and serpentine seep field soils. By challenging these plants with drought and iteratively selecting microbiomes from the least drought stressed plants across multiple generations, we derived simplified microbiomes that enhanced both the growth and drought tolerance of rice. Across selection cycles, microbiomes within and between soil treatments became increasingly similar, implicating both dispersal and selection as drivers of community composition. With amplicon sequencing data we identified specific bacterial taxa associated with improved rice drought phenotypes; while many of these taxa have been previously described as plant growth promoters, we also identified novel taxa exhibiting strong positive correlation with improved drought performance. Lastly, we resolved 272 metagenome-assembled genomes (MAGs) and used these MAGs to identify functions enriched in bacteria driving enhanced drought tolerance. The most significantly enriched functions--particularly glycerol-3-phosphate and iron transport--have been previously implicated as potential mediators of plant-microbe interactions during drought. Altogether, these data demonstrate that host-mediated selection provides an efficient framework for microbiome engineering through the identification of both individual taxa and simplified communities associated with enhanced plant phenotypes.

Explore related subjects

plant biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Styer, A., Pettinga, D., Caddell, D. F., Coleman-Derr, D.. 2024-02-05. Improving rice drought tolerance through host-mediated microbiome selection. https://doi.org/10.1101/2024.02.03.578672

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Melanoidins Suppress Cucumber and Tomato Diseases Incited by Pathogens that are Oomycetes, Bacteria and a Virus

We recently reported that solutions of the nitrogenous compounds melanoidins (M), that are formed during the final stages of the Maillard Reaction, are inducers of plant resistance (Elad et al. 2026). M promoted immunity and induced disease resistance through an effect on the transcriptome, primarily through the salicylic acid pathway. Here we tested the effect of M on plant diseases that are caused by Oomycetes, bacteria and a tobamovirus. Drench and spray of M suppressed Pythium aphanidermatum damping off in cucumber, cucumber downy mildew (Pseudoperonospera cubensis), tomato late blight (Phytophthora infestans), bacterial speck (Pseudomonas syringae pv. tomato), bacterial canker (Clavibacter michiganensis subsp. michiganensis) and the Tobamovirus Tomato brown rugose fruit virus (ToBRFV) in tomato. In various experiments control was achieved by concentrations of 0.03 and 0.1% and on older and younger leaves and even in long term experiments where the M was applied for ca 11 weeks. It can be concluded that the disease resistance inducer M can suppress soilborne and foliar diseases that are caused by Oomycetes, bacteria and a virus of the genus Tobamovirus, in addition to the fungal pathogen Botrytis cinerea reported earlier.

plant biology↗

bioRxiv2026

Expansion and Comprehensive Evaluation of the Peacock Eye Disease Management (PedMan) System across Olive Cultivars Differing in Susceptibility to Venturia oleaginea

Peacock eye disease, caused by Venturia oleaginea , is an important foliar disease of olive that is primarily managed through fungicide applications. Integrating host resistance into disease-warning systems could improve spray timing and reduce unnecessary fungicide use. PedMan (Peacock eye disease Manager) was previously developed and validated for highly susceptible olive cultivars. The objectives of the present study were to expand PedMan to cultivars differing in susceptibility to V. oleaginea and to evaluate the expanded system under commercial grove conditions. A sensitivity analysis of the rainfall and temperature criteria used for highly susceptible cultivars was conducted to establish criteria for moderately susceptible and moderately resistant cultivars. The rainfall threshold of [≥]15 mm was retained, whereas the temperature range triggering an infection alert was narrowed from 12-18 {degrees}C for highly susceptible cultivars to 13-17 {degrees}C for moderately susceptible and 14-16 {degrees}C for moderately resistant cultivars. The expanded system was subsequently evaluated in 33 field trials and observations under natural infection conditions. PedMan recommendations were classified as correct or incorrect based on statistical comparisons of leaf abscission between fungicide-treated and untreated trees. Overall, 30 of 33 recommendations were correct, resulting in an accuracy of 90.9%. Sensitivity was 87.0%, while specificity and positive predictive value were both 100%. These results demonstrate that incorporating cultivar susceptibility into PedMan broadens its applicability and provides reliable cultivar-specific fungicide recommendations. The system has potential to reduce unnecessary fungicide applications while maintaining effective management of peacock eye disease across olive cultivars differing in susceptibility.

plant biology↗

bioRxiv2026

Large seed size accompanying GmSDP1 suppression is linked to cellular remodeling and phytohormone regulation

Soybean (Glycine max) seeds contain approximately 20% oil and 40% protein and are important for food, feed, and biofuel. Improving soybean productivity and seed quality requires optimizing carbon partitioning during seed development. Previously, seed-specific suppression of the lipase-encoding gene Sugar-Dependent 1 (SDP1) increased seed oil content by approximately 5% while slightly reducing raffinose family oligosaccharides without compromising protein content. Seed-specific SDP1 suppression also increased seed size by 18-25% without affecting seed number, resulting in greater seed biomass per plant. To determine the developmental basis of the increased seed size, we investigated the cellular and molecular mechanisms underlying this phenotype. Microscopy and biochemical analyses showed that larger seeds were associated with increased seed cell size and enhanced lignocellulosic cell wall accumulation. Temporal biochemical and transcriptomic analyses further revealed coordinated changes in hormone homeostasis, including altered levels of abscisic acid, 12-oxo-phytodienoic acid, and jasmonoyl-isoleucine, together with differential expression of F-box and RING/U-box family genes. The results indicate that the enhanced seed size resulting from SDP1 suppression is associated with coordinated changes in cellular development, cell wall accumulation, hormone homeostasis, and regulation of gene expression during seed development. Developmental and metabolic changes associated with the increased seed size phenotype support SDP1 manipulation as a potential strategy for improving soybean seed yield and quality.

plant biology↗