Biology subjects

Northen, T.

Publications and source records attributed to Northen, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Distinct Strategies for Engineering Bioenergy Traits in Sorghum Drive Divergent Functional Shifts in the Rhizosphere Microbiome

Engineering bioenergy crops for enhanced biomass digestibility and high-value co-products is a promising approach to sustainable biofuel production. However, the impact of these engineered crops on the belowground microbiome remains poorly understood. In this study, we characterized the composition and functional responses of the belowground microbiome associated with transgenic sorghum lines: one with reduced cell wall crosslinking (AT10) and another with elevated protocatechuic acid (PCA) production (Qsub). The lines were grown under field conditions with four irrigation levels, and samples were collected twice during the growing season. We found that the two transgenic types drove a subtle but significant divergence in bacterial communities, both compositionally and functionally. Community-wide functional profiling showed that AT10 rhizospheres were consistently depleted in genes associated with mobile genetic elements, while Qsub rhizospheres were enriched in TonB-dependent transport and vanillate monooxygenase, an enzyme that funnels lignin-derived monomers toward PCA degradation, alongside reduced pectin- and cellulose-degradation genes. Genome-resolved analysis linked these community-level shifts to specific taxa: in Qsub, the enriched MAGs were taxonomically diverse, ranging from genome-reduced Patescibacteria with an episymbiotic lifestyle to taxa enriched in lignin-associated auxiliary activity enzymes. In AT10, the depleted Azospirillaceae MAGs carried unusually high mobile genetic element content, consistent with the community-wide pattern. Collectively, these findings offer new insights into how genetic modifications aimed at improving bioenergy traits shapes the composition and function of the rhizosphere microbiome, with potential downstream consequences for soil carbon cycling.

plant biology↗

bioRxiv2026

The Everything Bagel Feature Finder: Ultra-fast automated feature finding for untargeted metabolomics

Metabolomics studies are increasingly being applied with hundreds to thousands, even tens of thousands of samples that demand rapid, automated data processing while maintaining analytical sensitivity or quantitative accuracy. A major computational bottleneck is feature finding, which is the transformation of LC-MS and LC-MS/MS data into a set of analyte signals aligned and quantified across samples. Feature finding can be computationally intensive and often requires manual iterative parameter optimization. To accelerate this process, we present the Everything Bagel (EB) feature finder, an ultra-fast automated feature finding tool that integrates feature detection, retention-time alignment, and gap filling designed for run-time and memory efficiency. We benchmarked EB against two automated feature finding methods on eight benchmarking datasets. Specifically, we evaluated these three feature finding methods by measuring spike-in standard detection coverage, dilution series quantification accuracy, and yeast 12C/13C credentialed features. In this evaluation, the EB feature finder achieved performance comparable to, and often exceeding, existing methods while requiring up to 150-fold lower CPU hours and up to 113-fold lower wall time. We further demonstrated the bioanalytical validity of EB by reanalyzing published datasets used for biomarker discovery and reproduced biologically significant features that matched the published findings using manually tuned feature finding settings. Taken along with the speed improvements, we anticipate EB will enhance the ability to automatically analyze datasets with thousands to tens of thousands of samples for the community.

bioinformatics↗

bioRxiv2026

Signaling metabolites spatially organize a multispecies mutualism in the soil microbiome

A plant-independent avenue for N2-fixation takes place in desert topsoils through a "C-for-N" mutualism between heterodiazotrophs and the cyanobacterium Microcoleus vaginatus. These partners come together within a diverse soil microbiome under conditions of N-limitation for the phototroph and C limitation for the heterotrophs. We hypothesized that extracellular chemical signaling might enable partner selection and collocation, though infomolecules shaping inter-microbial architecture were unknown. We show that the complex chemical composition of M. vaginatus exometabolome depends on its N-limitation status, thus potentially offering information to mutualists. In chemotactic assays, the exometabolome effectively repelled most native soil bacteria, particularly intensely when under N-limitation. Bacterial assemblages circumventing the repulsion were enriched in species that are rare in the soil microbiome, and that functionally resemble mutualistic cyanospheres (showing high N2-fixation potential, secretion of urea, and copiotrophy), setting the stage for a working symbiosis. Further, we could reproduce the enrichment of copiotrophs and nitrogen-fixers using mixtures of N-acetylglutamic acid, N-acetylmethionine, indole-3-acetic acid, and 5'-methylthioadenosine, all preferentially released by M. vaginatus under N-limitation. These signaling molecules did not result in an enrichment of urea producers, however. The results demonstrate that trans-species communication through specific infochemicals, together with already known quorum-sensing-like intraspecific communication in M. vaginatus, act as a tool to organize microbiomes spatially and to attain mutualistic partner specificity in an open, crowded background.

microbiology↗

bioRxiv2026

Metagenome-guided substrate selection enriches Terriglobus, reveals co-occurring taxa, and enables isolation of a novel species

Microbes that remain uncultivated occupy nearly every ecosystem on the planet; this is particularly true in soils, where despite their prevalence, the roles of rarely cultivated microbes in driving biogeochemical cycles and ecosystem function remain poorly explored. We combine metagenome-informed substrate selection with enrichment sub-communities to generate reduced-complexity communities that preserve co-occurrence and expand experimental access to underrepresented soil lineages without requiring prior isolation of each member. Carbohydrate-active enzyme (CAZyme) profiles from soil-derived genomes were used to select carbon compounds predicted to enrich difficult to culture taxa, including members of the phylum Acidobacteriota. Based on 16S rRNA amplicon sequencing, we reproducibly enriched Terriglobus (Acidobacteriota) on multiple metagenome-guided substrates. Select communities with consistent presence and varying abundance of Terriglobus were passaged in a longitudinal design to generate 89 metagenomes; genus-level profiling revealed that community composition varied between biological replicates but remained consistent within replicates over time, providing diverse Acidobacteriota-containing configurations for downstream analysis. Association network inference identified a core set of co-occurring taxa that positively tracked with Terriglobus across the longitudinal series. In parallel, the substrate-guided approach led to isolation of a novel Terriglobus species, the first cultured representative of its GTDB species cluster. Together, these results establish a generalizable strategy for generating communities enriched with rarely cultivated taxa, yielding tractable systems for studying microbial interactions and community assembly in soil.

microbiology↗

bioRxiv2026

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

Synthetic microbial ecology aims at designing communities with desired properties based on mathematical models of individual organisms. It is unclear whether simplified models harbor enough detail to predict the composition of synthetic communities in metabolically complex environments. Here, we use longitudinal exometabolite data of monocultures for 15 rhizosphere bacteria to parametrize a consumer-resource model, which we use to predict pairwise co-cultures and higher order communities. The capacity to artificially "switch off" cross-feeding interactions in the model demonstrates their importance in ecosystem structure. Leave-one-out and leave-two-out experiments demonstrate that pairwise co-cultures do not necessarily capture inter-species interactions within larger communities and broadly highlight the nonlinearity of interactions. Finally, we demonstrate that our model can be used to identify new sub-communities of three strains with high likelihood of coexistence. Our results establish hybrid mechanistic and data-driven metabolic models as a promising and extendable framework for predicting and engineering microbial communities.

systems biology↗

bioRxiv2025

Dopamine biosynthesis in plants

Dopamine, an essential human neurotransmitter, also plays important roles in plant-microbe interactions and abiotic stress tolerance. While dopamine biosynthesis is well-characterized in mammals, it remains largely unclear in plants. Through metabolite-based genome-wide association studies, we identified two putative polyphenol oxidase genes for dopamine biosynthesis in Brachypodium distachyon, located in the same chromosomal region as two tyrosine decarboxylase genes. Biochemical and knockout mutant analyses demonstrated that dopamine biosynthesis proceeds primarily via tyramine as an intermediate and contributes to plant tissue browning. Homology searches and functional assays indicate that this dopamine biosynthetic pathway is conserved across diverse plant species. This discovery provides valuable insights into plant dopamine biosynthesis with potential applications in reducing food browning, improving stress resilience, and bioengineering valuable compounds.

plant biology↗

bioRxiv2025

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central metabolic regulator in eukaryotes that integrates carbon and nitrogen to maintain homeostasis and promote growth and development through protein synthesis. While TOR regulatory mechanisms of amino acid accumulation are well known in yeast and mammals, they remain unknown in photosynthetic organisms. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler model system for understanding TOR function. Multiomics experiments showed that TOR inhibition leads to an increase in amino acid levels independent of hexokinase-mediated glucose signaling. We observed upregulation of selective amino acid biosynthesis pathways at the transcript and protein levels as potential mechanisms driving the increase in amino acids. Transcriptomics and proteomics experiments identified a basic helix-loop-helix (bHLH) transcription factor with rapid upregulation during TOR inhibition. DAP-seq analysis demonstrated that bHLH can bind directly to the promoters of amino acid biosynthesis genes, potentially regulating their transcription in response to TOR inhibition. We found high conservation of the bHLH-binding motif in the genomes of other green algae and plants, suggesting a conserved regulatory mechanism for amino acid biosynthesis across Viridiplantae. Phosphoproteomics experiments also revealed novel conserved targets that are not currently recognized as part of the TOR pathway. Altogether, our findings elucidate the transcriptional regulation of amino acid metabolism and explain how TOR regulates nitrogen metabolism to support growth and development in photosynthetic organisms. Significance StatementCarbon and nitrogen metabolism play key roles in enhancing plant yield and reducing fertilizer use. Thus, improving nitrogen utilization can significantly boost crop productivity and algal biotechnology. From yeast to plants to mammals, the protein target of rapamycin (TOR) kinase is an essential metabolic regulator. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler system to study conserved mechanisms in TOR signaling. Using a multiomics approach, we showed transcriptional regulation of amino acid accumulation upon TOR inhibition and identified a transcription factor with evolutionarily conserved DNA binding sites in nitrogen metabolism genes. We also discovered novel conserved targets of TOR. Our study demonstrates the role of TOR in regulating nitrogen metabolism to support growth and development in photosynthetic organisms.

plant biology↗

bioRxiv2025

Microbiome Assembly in Zostera marina during early host development: An EcoFAB 2.0 Application for Aquatic Plant-Microbe Interactions

Seagrass restoration practices are evolving to leverage microbiome applications, similar to agricultural systems that have demonstrated how targeted microbial communities enhance crop resilience in challenging environments. While adult seagrass microbiome research has expanded significantly, research on the seed microbiome remains critically understudied. This gap is particularly important given that seeds represent a large portion of restoration efforts. Advancing seed microbiome research requires standardized experimental systems for controlled plant-microbe interaction studies, which are currently lacking in seagrass research. Here, we tested fabricated ecosystem devices (EcoFAB 2.0) as a standardized system for growing seedlings of Zostera marina (eelgrass), enabling a controlled study of aquatic plant-microbe interactions. Using these chambers, we addressed three key questions: (i) Can we reliably grow eelgrass in a controlled laboratory setting? (ii) Can we manipulate eelgrass microbiome assembly and its long-term trajectory? and (iii) Can we detect shifts in the microbiome during plant development (host filtering)? Host morphology measurements and 16S rRNA gene amplicon sequencing were used to track microbiome assembly across three early developmental stages of the host. We identified 143 ASVs that differed between plants from surface-sterilized versus intact seeds, highlighting the strong influence of epiphytic bacteria on microbiome assembly. We also identified 26 stage-specific indicator ASVs across eelgrass development, suggesting stage-specific microbial associations during seedling establishment. This work demonstrates the potential for targeted manipulation of the microbiome in seagrass for restoration efforts. ImportanceUsing the Fabricated Ecosystem 2.0 (EcoFAB 2.0), we were able to successfully control the microbial environment of Z. marina, resulting in the removal of epiphytes and maintaining low microbial diversity across plants without compromising the growth dynamics of the seedlings. Our findings advance the marine plant model system, Zostera marina, by identifying taxonomic indicators across life stages. This work lays the foundation for a targeted understanding and application of microbiomes for seagrass restoration, bridging the critical knowledge gap between agricultural seed microbiome success and marine restoration applications.

microbiology↗

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↗

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↗

bioRxiv2024

Hyperspectral Segmentation of Plants in Fabricated Ecosystems

Hyperspectral imaging provides a powerful tool for analyzing above-ground plant characteristics in fabricated ecosystems, offering rich spectral information across diverse wavelengths. This study presents an efficient workflow for hyperspectral data segmentation and subsequent data analytics, minimizing the need for user annotation through the use of ensembles of sparse mixed-scale convolution neural networks. The segmentation process leverages the diversity of ensembles to achieve high accuracy with minimal labeled data, reducing labor-intensive annotation efforts. To further enhance robustness, we incorporate image alignment techniques to address spatial variability in the dataset. Down-stream analysis focuses on using the segmented data for processing spectral data, enabling monitoring of plant health. This approach not only provides a scalable solution for spectral segmentation but also facilitates actionable insights into plant conditions in complex, controlled environments. Our results demonstrate the utility of combining advanced machine learning techniques with hyperspectral analytics for high-throughput plant monitoring.

plant biology↗

bioRxiv2024

Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi

Xylariales is one of the largest and most ecologically diverse fungal orders that is well-known for its chemical diversity. Enhanced secondary metabolism of Xylariales taxa is associated with increased gene duplication and horizontal gene transfer (HGT) of biosynthetic gene clusters (BGCs), especially in generalist taxa with both greater saprotrophic abilities and broader host ranges as foliar endophytic symbionts. Thus, one hypothesis for BGC diversification among more generalist fungi is that diverse competitive interactions--in both their free-living and symbiotic life stages with many hosts--may exert selective pressure for HGT and a diverse metabolic repertoire. Here, we used untargeted metabolomics to examine how competition (pairwise co-cultures) between seven xylarialean fungi influenced their metabolite production. Of the >9,000 total features detected, 6,115 and 2,071 were over-represented in co-cultures vs. monocultures, respectively. For each strain, each additional co-culture interaction resulted in an 11-14-fold increase in metabolite richness compared to monocultures, reflecting the limited amount of metabolite overlap among different co-culture combinations. Phylogenetic relatedness and BGC content did not impact the diversity of metabolites produced in co-culture; however, co-cultures between more ecologically distinct fungi elicited the strongest metabolic response. Overall, the diversity, specificity, and putative bioactivity of metabolites over-represented only in co-culture supports the role of widespread and diverse competitive fungal interactions to drive xylarialean metabolic diversification. Additionally, as fungal-produced plant hormones were only detected in co-culture, our results reveal the potential for in planta interactions among fungal endophytes to influence the host plant. ImportanceSaprotrophic and endophytic xylarialean fungi are among the most prolific producers of bioactive secondary metabolites, with numerous industrial uses as antibiotics, pharmaceuticals, and insecticidal toxins. Fungal secondary metabolites are typically encoded in biosynthetic gene clusters (sets of physically clustered genes), but the products of most clusters are unknown as the genes are not active in typical culture conditions. Co-cultures can help to "turn on" fungal secondary metabolite production, yet factors that can influence co-culture outcomes are largely unknown. Here, we used untargeted metabolomics to assess how differences in genomic content, ecology, and phylogenetic relatedness among seven diverse xylarialean fungal strains impact metabolic production in co-culture. As expected, co-culturing significantly increased metabolite diversity, as well as the abundance of putatively bioactive metabolites. Each new pairwise combination produced different metabolites, indicative of strain-specific responses to competitors. This new information will enable further characterization of the immense biotechnological potential of xylarialean fungi.

microbiology↗

bioRxiv2024

Label-free structural imaging of plant roots and microbes using third- harmonic generation microscopy

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF fluorescence signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.

plant biology↗

bioRxiv2024

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

Horizontal gene transfer (HGT) is a major process by which genes are transferred within microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provided the first demonstration of gene transfer via triparental conjugation system in the Brachypodium distachyon rhizosphere in the EcoFABs using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor having the mobilizable and non-self-transmissible plasmid. We also observed that the frequency of conjugal plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage, and composition and amount of root exudates. The frequency of conjugation also increased with higher numbers of donor cells. We have also shown the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. showing the possibility of HGT within a rhizosphere microbial community. Environmental stresses also influence the rate of HGT in the rhizosphere between species and genera. Additionally, we observed transfer of a non-self transmissible donor plasmid without the helper strain on agar plates when supplemented with environmental stressors, indicating reduced dependency on the helper plasmid under certain conditions. This study provides a robust workflow to evaluate conjugal transfer of engineered plasmids in the rhizosphere when such plasmids are introduced in a field or plant associated environment. ImportanceWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbial interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

microbiology↗

bioRxiv2024

Rendering the metabolic wiring powering wetland soil methane production

Accounting for only 8% of Earths land coverage, freshwater wetlands remain the foremost contributor to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more so than land coverage or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane cycling microorganisms, contrasting with theoretical expected responses to hydrological perturbations. Co-expression analyses coupled to depth resolved methane measurements exposed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production. ImportanceSoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.

microbiology↗

bioRxiv2023

Powdery mildew infection induces a non-canonical route to storage lipid formation at the expense of host thylakoid lipids to fuel its spore production

Powdery mildews are obligate biotrophic fungi that manipulate plant metabolism to supply lipids, particularly during fungal asexual reproduction when fungal lipid demand is extensive. The mechanism for host response to fungal lipid demand has not been resolved. We found storage lipids, triacylglycerols (TAGs), increase by 3.5-fold in powdery mildew-infected tissue. In addition, lipid bodies, not observable in uninfected mature leaves, are present in both cytosol and chloroplasts at the infection site. This is concurrent with decreased thylakoid membrane lipids and thylakoid disassembly. Together, these findings indicate that the powdery mildew induces localized thylakoid membrane degradation to promote storage lipid formation. Genetic analyses show the canonical ER pathway for TAG synthesis does not support powdery mildew spore production. Instead, Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 3 (DGAT3), shown to be chloroplast-localized and to be largely responsible for powdery mildew-induced chloroplast TAGs, promotes fungal asexual reproduction. Powdery mildew-induced leaf TAGs are enriched in thylakoid associated fatty acids, which are also present in the produced spores. This research provides new insights on obligate biotrophy and plant lipid metabolism plasticity and function. Furthermore, by understanding how photosynthetically active leaves can be converted into TAG producers, more sustainable and environmentally benign plant oil production could be facilitated.

plant biology↗

bioRxiv2023

Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem

Digital cameras have the ability to capture daily images of plant roots, allowing for the estimation of root biomass. However, the complexities of root structures and noisy image backgrounds pose challenges for advanced phenotyping. Manual segmentation methods are laborious and prone to errors, which hinders experiments involving several plants. This paper introduces Rhizonet, a supervised deep learning approach for semantic segmentation of plant root images. Rhizonet harnesses a Residual U-Net backbone to enhance prediction accuracy, incorporating a convex hull operation to precisely outline the largest connected component. The primary objective is to accurately segment the biomass of the roots and analyze their growth over time. The input data comprises color images of various plant samples within a hydroponic environment known as EcoFAB, subject to specific nutrition treatments. Validation tests demonstrate the robust generalization of the model across experiments. This research pioneers advances in root segmentation and phenotype analysis by standardizing processes and facilitating the analysis of thousands of images while reducing subjectivity. The proposed root segmentation algorithms contribute significantly to the precise assessment of the dynamics of root growth under diverse plant conditions.

plant biology↗

bioRxiv2023

Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls

Many insects have evolved the ability to manipulate plant growth to generate extraordinary structures called galls in which insect larva can develop while being sheltered within and feeding on the plant. In particular, Cynipid (Hymenoptera: Cynipidae) wasps have evolved to form some of the most morphologically complex galls known and generate an astonishing array of gall shapes, colors, and sizes. However, the biochemical basis underlying these remarkable cellular and developmental transformations remains poorly understood. A key determinant in plant cellular development is the deposition of the cell wall to dictate the physical form and physiological function of newly developing cells, tissues, and organs. However, it is unclear to what degree cell walls are restructured to initiate and support the formation of new gall tissue. Here, we characterize the molecular alterations underlying gall development using a combination of metabolomic, histological, and biochemical techniques to elucidate how leaf cells are reprogrammed to form galls. Strikingly, gall development involves an exceptionally coordinated spatial deposition of lignin and xylan to form de novo gall vasculature. Our results highlight how Cynipid wasps can radically change the metabolite profile and restructure the cell wall to enable the formation of galls, providing new insights into the mechanism of gall induction and the extent to which plants can be entirely reprogrammed to form novel structures and organs.

plant biology↗