Biology subjects

Swift, J. F.

Publications and source records attributed to Swift, J. F..

14 recordsLinked to original sources

bioRxiv2026

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

microbiology↗

bioRxiv2026

Disentangling blade and vasculature shape in grapevine leaves

The leaf blade and vasculature develop together within a shared morphological space. Despite shared molecular patterning pathways, it is unknown if developmental and evolutionary variation affect these tissues separately or together in a coordinated way. Grapevine leaves have a morphometric history and abundant data measuring the shape of the blade and vasculature together. Using a combination of topological data analysis and deep learning, we perform reciprocal semantic segmentation of leaf blade and vasculature. Each tissue contains sufficient information to predict the other. We hypothesize that this is due to a one-to-one relationship between blade and vein. Using thin plate splines to swap and warp different combinations of blade and vein shapes, we show that a set of leaves with a many-to-one relationship of blade and vein are distinguishable from true leaves. We also swap blade and vein across the developmental series and between species and show that only reversing the developmental series disrupts the relationship between blade and vasculature. We end by discussing the evolutionary and developmental implications that there is a unique, one-to-one mapping between blade and vein that allows each to be predicted from the other. Author summaryLeaves are made of two closely connected parts: the flat blade that captures light and the network of veins that transports water, nutrients, and developmental signals. Although these tissues grow together and share common molecular patterning pathways, it has remained unclear whether a particular blade shape is uniquely linked to a specific vein pattern. In this study, we use grapevine leaves as a model system and combine mathematical shape analysis with deep learning to examine this relationship. We show that the shape of the blade alone can accurately predict the vein network, and that the vein network can likewise predict the blade. This finding suggests a near one-to-one relationship between these two tissues. To test this idea, we created artificial leaves in which blade and vein shapes were deliberately mismatched. Although these synthetic leaves appeared realistic at a global level, a neural network was able to distinguish them from real leaves based on subtle differences. We further show that this tight coupling is maintained by the developmental sequence of leaf growth rather than by species identity, revealing a conserved constraint linking leaf form and internal structure.

plant biology↗

bioRxiv2026

Conserved Rhizosphere Microbiomes and Metabolic Functions Across Diverse Grapevine Rootstocks: Implications for Plant Elemental Composition

BackgroundWhile grapevine rootstocks are essential to commercial viticulture, researchers still lack a complete understanding of how these root systems and their associated microbiomes influence the vines mineral nutrition. Previous research has shown that rootstocks with similar pedigrees, reflecting the limited number of parental genotypes in the breeding pool, affect both the vines elemental profile and microbiome composition. Here, we extend this work by surveying a broader diversity of rootstock genotypes representing distinct parentage groups across multiple scions and by assessing both functional and taxonomic associations between the rhizosphere metagenome and vine elemental composition. ResultsWe used a rootstock diversity trial with ten rootstock genotypes grafted to one of two scions to simultaneously characterize the rhizosphere metagenome and elemental composition of both berries and roots. We found that elemental composition varied strongly among vine compartments, while scion and rootstock had comparatively minor effects. Berries of Cabernet Sauvignon contained higher concentrations of boron, potassium, and phosphorus than those of Chardonnay. Only three elements in root tissues differed among rootstock genotypes, and these differences were unrelated to genetic relatedness among rootstocks. Rhizosphere microbiome composition was also conserved across rootstocks, suggesting that diverse genotypes recruit a consistent microbial community with similar functional potential. By linking rhizosphere microbiome profiles with root elemental composition, we found that Streptomyces and Mesorhizobium were significantly associated with elemental patterns, showing negative correlations with a principal component heavily loaded for molybdenum, cadmium, potassium, and iron. ConclusionsOur findings suggest that vine compartment exerts a dominant influence on elemental composition, while rootstock genotypes have comparatively modest effects. Despite the overall conservation of the rhizosphere microbiome, specific microbial taxa were linked to elemental variation, highlighting potential microbe-element associations that may influence nutrient dynamics in the grapevine rhizosphere. These results provide a foundation for disentangling how root-associated microbes contribute to vine mineral nutrition, or vice versa, across diverse rootstock genotypes.

plant biology↗

bioRxiv2025

The Rapid Anatomics Tool (RAT): A low-cost root anatomical phenotyping pipeline reveals changes in root anatomy along the root axis

Root anatomical phenotyping has become a demonstrably essential part of investigating root physiology and in acquiring a holistic understanding of plant development. However, accessible high throughput methods for root anatomical analysis are still lacking. Here, we present the Rapid Anatomics Tool (RAT), a novel, low-cost system for high throughput root anatomical imaging with a shallow learning curve for obtaining high quality images suitable for comparative analysis across a number of plant species. Its efficiency comes from combining blockface-like imaging and stain-free imaging using near-ultraviolet (nUV) autofluorescence utilising a combination of low-cost commercial equipment, readily available mechanical components, and custom designed and 3D printed tools. Using this system, we investigated the anatomy of mature tissue along the axis of wheat crown roots, revealing a tendency of reduction in vascular complexity (expressed through a reduction in metaxylem number, area, and mean area per metaxylem file) from the basal to the distal region of the root. This study highlights the importance of thorough sampling strategies for investigating root anatomy in relation to organ function and introduces an accessible, relatively high-throughput method to support such research.

plant biology↗

bioRxiv2025

Between Two Extremes: Tripsacum dactyloides Root Anatomical Responses to Drought and Waterlogging

PremisePlant roots are the critical interface between plants, soil, and microorganisms, and respond dynamically to changes in water availability. Although anatomical adaptations of roots to water stress (e.g., the formation of root cortical aerenchyma) are well documented, it remains unclear whether these responses manifest along the length of individual roots under both water deficiency and water over-abundance. MethodsWe investigated the anatomical responses of Tripsacum dactyloides L. to both drought and flood stress at high spatial resolution. Nodal roots were segmented into one-centimeter sections from the tip to the base, allowing us to pinpoint regions of maximal anatomical change. ResultsBoth stressors increased the proportion of root cortical aerenchyma, but metaxylem responses differed: flooding increased vessel area whereas drought led to smaller vessels, with both showing a lower number of vessels. Drought also significantly increased root hair formation, but only within the first two centimeters. The most pronounced anatomical changes occurred 3-7 cm from the root tip, where cortical cell density declined as aerenchyma expanded. DiscussionThese findings highlight spatial variation in root anatomical responses to water stress and provide a framework integrating various other data types where sampling effort is limiting (e.g., microbiome, transcriptome, proteome).

plant biology↗

bioRxiv2024

Terroir and rootstock effects on leaf shape in California Central Valley vineyards

SummaryO_LIEmbedded in a single leaf shape are the latent signatures of genetic, developmental, and environmental effects. In viticulture, choice of location and rootstock are important decisions that affect the performance and production of the shoot. We hypothesize that these effects influence plant morphology, as reflected in leaf shape. C_LIO_LIWe sample 1879 leaves arising from scion and rootstock combinations from commercial vineyards in the Central Valley of California. Our design tests 20 pairwise contrasts between Cabernet Sauvignon and Chardonnay scions from San Joaquin, Merced, and Madera counties from vines grafted to Teleki 5C, 1103 Paulsen, and Freedom rootstocks. C_LIO_LIUsing geometric morphometric approaches, we visualize a morphospace in which, in addition to clear separation of Cabernet Sauvignon and Chardonnay scion leaf shapes, an orthogonal source of shape variation affects both varieties. Comparing the Procrustes distances to within and between group means, the additional source of variance is found to arise from location and rootstock effects. C_LIO_LIWe describe and visualize a specific shape feature, the angle of the proximal lobe to the midvein that defines the closure of the petiolar sinus, that is attributable to location and rootstock effects and orthogonal to and separate from genetic, developmental, or allometric effects attributable to leaf size. C_LI Societal Impact Statement (EN)The innumerable effects of terroir--including climate, soil, microbial environment, biotic interactions, and cultivation practice--collectively alter plant performance and production. A more direct agricultural intervention is grafting, in which genetically distinct shoot and root genotypes are surgically combined to create a chimera that alter shoot performance at a distance. Selection of location and rootstock are intentional decisions in viticulture to positively alter production outcomes. Here, we show that terroir and rootstock alter the shapes of grapevine leaves in commercial vineyards throughout the California Central Valley, documenting the profound effects of these agricultural interventions that alter plant morphology.

plant biology↗

bioRxiv2023

Grapevine bacterial communities across the Central Valley of California

Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences, and the microbial differences across site compose terroir, the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity. In order to understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA metabarcoding to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflect rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local microbiome in the Central Valley of California.

plant biology↗

bioRxiv2023

Legacy effects of precipitation and land use impact maize growth and microbiome assembly under drought stress

Background and AimsAs the climate changes, plants and their associated microbiomes face greater water limitation and increased frequency of drought. Historical environmental patterns can leave a legacy effect on soil and root-associated microbiomes, but the impact of this conditioning on future drought performance is poorly understood. Precipitation gradients provide a means to assess these legacy effects. MethodsWe collected soil microbiomes from four native prairies across a steep precipitation gradient in Kansas, USA. Seedlings of two Zea mays genotypes were inoculated with each soil microbiome in a factorial drought experiment. We investigated plant phenotypic and root microbiome responses to drought and modeled relationships between plant growth metrics and climatic conditions from the soil microbiome origin sites. ResultsDrought caused plants to accumulate shoot mass more slowly and achieve greater root/shoot mass ratios. Drought restructured the bacterial root-associated microbiome via depletion of Pseudomonadota and enrichment of Actinomycetota, whereas the fungal microbiome was largely unaffected. An environmental legacy effect on prairie soil microbiomes influenced plants drought responses: counterintuitively, prairie soil inocula from historically wetter locations increased shoot biomass under drought more than inocula from historically drier prairie soils. ConclusionWe demonstrated links between soil microbiome legacy effects and plant performance under drought, suggesting that future drying climates may condition soils to negatively impact plant performance.

plant biology↗

bioRxiv2022

Grapevine leaf size influences vine canopy temperature

PremiseGrapevine leaves have diverse shapes and sizes. Their shape and size is known to be influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. In order to determine the importance of grapevine leaf shape and size to canopy temperature, we examined the relationship in five seedling populations grown in a vineyard in California, USA. MethodsAll of the populations had one parent with compound leaves of the Vitis piasezkii type and each population had a different second parent with non-compound leaves. In previous work, we measured leaf shape and size using 21 homologous landmarks. Here, we paired these morphology data with measurements taken using an infrared thermometer to measure the temperature of the canopy. By recording time of sampling and canopy temperature, we were able to determine which vines were cooler or hotter than expected, using a linear model. ResultsWe established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. In contrast, leaf shape was not strongly correlated with variation in temperature. ConclusionsUltimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall vine canopy temperature, but further work is needed to determine if this is due to variation in leaf size, differences in the openness of the canopy, or other related traits.

plant biology↗

bioRxiv2022

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index

O_LIAnnual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were collected at the beginning and end of the lifetime of the vineyard. C_LIO_LIX-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number using a negative exponential model. Early and late wood ring widths, cambium width, and scion trunk radius were correlated with 27 traits. C_LIO_LIModeling of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay thereafter, consistently shortening ring width throughout the lifetime of the vine. The ratio of yield to vegetative growth, juice pH, photosynthetic assimilation and transpiration rates, and stomatal conductance are correlated with scion trunk radius. C_LIO_LIRootstocks modulate secondary growth over years, altering hydraulic conductance, physiology, and agronomic traits. Rootstocks act in similar but distinct ways from climate to modulate ring width, which borrowing techniques from dendrochronology, can be used to monitor both genetic and environmental effects in woody perennial crop species. C_LI

plant biology↗

bioRxiv2022

Increases in vein length compensate for leaf area lost to lobing in grapevine

PremiseThere is considerable variation in leaf lobing and leaf size, including among grapevines, some of the most well-studied leaves. We examined the relationship between leaf lobing and leaf size across grapevine populations which varied in extent of leaf lobing. MethodsWe used homologous landmarking techniques to measure 2,632 leaves across two years in 476 unique, genetically distinct grapevines from 5 biparental crosses which vary primarily in the extent of lobing. We determined to what extent leaf area could explain variation in lobing, vein length, and vein to blade ratio. ResultsAlthough lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and decreases as a function of vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. ConclusionsFor a given leaf area, more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.

plant biology↗

bioRxiv2020

Root system influence on high dimensional leaf phenotypes over the grapevine growing season

O_LIIn many perennial crops, grafting the root system of one individual to the shoot system of another individual has become an integral part of propagation performed at industrial scales to enhance pest, disease, and stress tolerance and to regulate yield and vigor. Grafted plants offer important experimental systems for understanding the extent and seasonality of root system effects on shoot system biology. C_LIO_LIUsing an experimental vineyard where a common scion Chambourcin is growing ungrafted and grafted to three different rootstocks, we explore associations between root system genotype and leaf phenotypes in grafted grapevines across a growing season. We quantified five high-dimensional leaf phenotyping modalities: ionomics, metabolomics, transcriptomics, morphometrics, and physiology and show that rootstock influence is subtle but ubiquitous across modalities. C_LIO_LIWe find strong signatures of rootstock influence on the leaf ionome, with unique signatures detected at each phenological stage. Moreover, all phenotypes and patterns of phenotypic covariation were highly dynamic across the season. C_LIO_LIThese findings expand upon previously identified patterns to suggest that the influence of root system on shoot system phenotypes is complex and broad understanding necessitates volumes of high-dimensional, multi-scale data previously unmet. C_LI

plant biology↗

bioRxiv2020

Grapevine microbiota reflect diversity among compartments and complex interactions within and among root and shoot systems

BackgroundWithin an individual plant, different compartments (e.g. roots, leaves, fruits) host distinct communities of microorganisms due to variation in structural characteristics and resource availability. Grafting, which joins the root system of one individual with the shoot system of a second genetically distinct individual, has the potential to bring the microbial communities of different genotypes together. An important question is the extent to which unique root system and shoot system genotypes, when grafted together, influence the microbiota of the graft partner. Our study sought to answer this question by utilizing an experimental vineyard composed of Chambourcin vines growing ungrafted and grafted to three different rootstocks, replicated across three irrigation treatments. We characterized bacterial and fungal communities in roots, leaves, and berries, as well as surrounding soil. Our objectives were to (1) characterize the microbiota of compartments within the root system (roots and adjacent soil) and the shoot system (leaves and berries), (2) determine the influence of rootstock genotypes, irrigation, and their interaction on the microbiota of aboveground and belowground compartments, and (3) investigate the distribution of microorganisms implicated in the late-season grapevine bunch rot disease sour rot (Acetobacterales and Saccharomycetes). ResultsCompartments were significantly differentiated in bacterial and fungal richness and composition. Abundance-based machine learning accurately predicted the compartment and differential abundance analysis showed a large portion of taxa differed significantly across compartments. Rootstock genotypes did not differ significantly in microbial community richness or composition; however, individual microbial taxa exhibited significant differences in abundance based on rootstock and irrigation treatment. The relative abundance of Acetobacterales and Saccharomycetes in the berry was influenced by complex interactions among rootstock genotype and irrigation. ConclusionOur results indicate that grapevine compartments retain distinct core microbiota regardless of the rootstock to which they are grafted. While rootstock genotype generally had a subtle impact on global patterns of microbial diversity, we found associations between rootstock genotypes and specific groups of microorganisms. Further experimental validation is needed in order to understand how associations with these microorganisms impacts a vines susceptibility to sour rot upon damage and whether the characteristics of wine are impacted.

plant biology↗

bioRxiv2020

Understanding how an amphicarpic species with a mixed mating system responds to fire: a population genetic approach

Amphicarphic species produce both aboveground and belowground seeds; the belowground seeds have been proposed to be an adaptation to disturbed sites because they are protected belowground, enabling them to persist and recolonize a site after disturbance. However, it is unknown whether such seeds indeed serve as the main colonizers after a disturbance. The amphicarpic species Polygala lewtonii is endemic to fire-prone Florida sandhill and scrub and is among only a few species with three flower types (aboveground chasmogamous flowers and both above and belowground cleistogamous flowers). The goal of this study was to understand whether recolonization of sites by P. lewtonii was accomplished primarily through germination of belowground seed. First, we quantified the outcrossing rate in seeds produced by aboveground chasmogamous flowers to determine whether we could detect differences in colonization of between seeds produced aboveground vs. belowground. Approximately 25% of seeds from aboveground chasmogamous flowers showed evidence of cross pollination and the seeds showed greater heterozygosity and lower inbreeding coefficients than pure selfing, indicating that it is possible to differentiate between selfed and non-selfed seed types in postfire colonization. Second, we analyzed genetic diversity, inbreeding, and genetic structure of the populations before and after a prescribed fire. If heterozygosity and admixture increased, and spatial population genetic structure and inbreeding decreased, this would indicate that fire promoted germination of outcrossed seed from aboveground flowers. However, inbreeding increased and spatial genetic structure and admixture decreased after fire, suggesting that selfed seed produced by belowground flowers predominantly recolonized the site after fire. Thus, amphicarpy is a powerful adaptation to fire-maintained environments by producing seeds that are well suited to the range of conditions presented by a highly variable, disturbance prone habitat.

plant biology↗