Biology subjects

Mortimer, J. C.

Publications and source records attributed to Mortimer, J. C..

7 recordsLinked to original sources

bioRxiv2026

Leaf movements as a quantitative metric for early stress detection

Early, precise, and non-destructive stress detection is essential for maintaining crop productivity, particularly in high-density plant growth systems like controlled environment agriculture (CEA), where manual monitoring is often impractical. Using plant motion as a proxy for growth and plant health, we demonstrate a method for early, non-invasive stress detection through quantitative leaf-movement analysis in lettuce and five other CEA relevant crops. Leaf-movement dynamics under stress were imaged with a low-cost, scalable Raspberry Pi imaging setup and quantified using a repurposed open-source motion estimation algorithm; Tracking Rhythms in Plants (TRiP). Our system detected stress-induced changes in leaf-movement within 1 hour of stress, with the timing dependent on the nature of the stress. Sustained reductions in leaf-movement coincide with decreased biomass accumulation. This approach offers a non-invasive, rapid, scalable, and cost-effective solution for continuous crop monitoring, with potential for application in both terrestrial and space farming CEA systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/732190v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@19ee20eorg.highwire.dtl.DTLVardef@b0804org.highwire.dtl.DTLVardef@3b3fa8org.highwire.dtl.DTLVardef@1d04026_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Quantification of leaf-movement dynamics as a high-throughput proxy for plant physiological status, enabling early stress detection and timely intervention to mitigate yield penalties in CEA settings (image made with biorender.org). C_FIG

plant biology↗

bioRxiv2025

Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome

Lignin is a key component of the plant cell wall and a barrier to microbial interaction and biomass digestibility. While lignin biosynthesis has been engineered in grasses to reduce recalcitrance for agroindustrial applications, the consequences for root-associated microbial communities remain poorly understood. Here, we show in the model grass species Brachypodium distachyon that genetic modification of lignin biosynthetic genes, particularly caffeic acid O-methyltransferase (COMT), alters root lignin syringyl/guaiacyl (S/G) ratios, root exudate composition, and significantly reshapes the rhizosphere microbiome. Using a synthetic microbial community (SYNCOM) in controlled fabricated ecosystem (EcoFAB) environments, we observed a distinct reduction in Burkholderia colonization and enrichment of Rhodococcus in COMT mutant lines. LC-MS/MS profiling of root exudates revealed increased p-coumaric acid, caffeic acid and hydroxycinnamic acid amides in these lines, potentially linked to both metabolic remodeling and plant stress responses. These findings demonstrate that altering lignin composition can have profound, genotype-specific impacts on rhizosphere microbiome assembly, with implications for plant-microbe interactions, nutrient cycling, and biomass conversion strategies in bioenergy crops.

plant biology↗

bioRxiv2023

Identification of a putative rhamnogalacturonan-II CMP-beta-Kdo transferase through a callus-based gene editing method which overcomes embryo lethality.

Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate crosslinking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect crosslinking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here we developed a method using CRISPR/Cas9-mediated gene to generate callus carrying loss-of-function mutations in the MPG2 gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We show that in the callus mutant cell walls, RG-II does not crosslink normally because it lacks 3-deoxy-D-manno- octulosonic acid (Kdo) and thus cannot form the -L-Rhap-(1[->]5)--D-kdop-(1[->] sidechain. We suggest that MGP2 encodes an inverting CMP-{beta}-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization.

plant biology↗

bioRxiv2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

plant biology↗

bioRxiv2022

Extensive plant use of exometabolites

Root exudation has been extensively studied due to its importance in soil carbon cycling and in supporting growth of soil microbes. However, the extent and dynamics of plant uptake of exogenous metabolites is poorly understood. To gain new insights into these processes we used 13C-tracing to characterize plant uptake of exometabolites across a panel of diverse plant species (Arabidopsis thaliana, Brachypodium distachyon, Lotus japonicus, Panicum virgatum, and Kalanchoe fedtschenkoi) grown in sterile hydroponic cultures. The uptake of exometabolites accounted for 23% of the overall B. distachyon carbon budget, and we identified 33 metabolites that were taken up by plants. Counterintuitively, many metabolites had higher uptake rates during the day vs. night. Thirteen of the metabolites from root exudates were found to promote root growth in A. thaliana, including hydroxybenzoate, threonate, N-acetyl-glucosamine, and uracil. Together these results indicate that the root uptake of organics can account for a significant portion of the plant carbon budget and that exogenous small molecules used by plants alter root growth with implications for plant nutrition, organic farming, soil nutrient cycling, and rhizosphere community dynamics.

plant biology↗

bioRxiv2019

Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol

Plants emit high rates of methanol (meOH), generally assumed to derive from pectin demethylation, and this increases during abiotic stress. In contrast, less is known about the emission and source of acetic acid (AA). In this study, Populus trichocarpa (California poplar) leaves in different developmental stages were desiccated and quantified for total meOH and AA emissions together with bulk cell wall acetylation and methylation content. While young leaves showed high emissions of meOH (140 mol m-2) and AA (42 mol m-2), emissions were reduced in mature (meOH: 69%, AA: 60%) and old (meOH: 83%, AA: 76%) leaves. In contrast, the ratio of AA/meOH emissions increased with leaf development (young: 35%, mature: 43%, old: 82%), mimicking the pattern of O-acetyl/methyl ester ratios of leaf bulk cell walls (young: 35%, mature: 38%, old: 51%), which is driven by an increase in O-acetyl and decrease in methyl ester content with age. The results are consistent with meOH and AA emission sources from cell wall de-esterification, with young expanding tissues producing highly methylated pectin that is progressively demethyl-esterified. We highlight the quantification of AA/meOH emission ratios as a potential tool for rapid phenotype screening of structural carbohydrate esterification patterns.

plant biology↗

bioRxiv2019

Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies.

ObjectivesSorghum is one of the most recalcitrant species for transformation. Considering the time and effort required for stable transformation in sorghum, establishing a transient system to screen the efficiency and full functionality of vector constructs is highly desirable.\n\nResultsHere, we report an Agrobacterium-mediated transient transformation assay with intact sorghum leaves using green fluorescent protein as marker. It also provides a good monocot alternative to tobacco and protoplast assays with a direct, native and more reliable system for testing single guide RNA (sgRNA) expression construct efficiency. Given the simplicity and ease of transformation, high reproducibility, and ability to test large constructs, this method can be widely adopted to speed up functional genomic and genome editing studies.

plant biology↗