Biology subjects

Miller, A. J.

Publications and source records attributed to Miller, A. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Alfalfa intercropping maintains intermediate wheatgrass grain yield relative to nitrogen fertilization across site conditions and stand ages

Intermediate wheatgrass (IWG; Thinopyrum intermedium) is a promising perennial grain crop, but yield instability remains a major challenge. We compared effects of nitrogen fertilization and intercropping with alfalfa (Medicago sativa L.) on IWG biomass, grain yield, and root traits across three stand ages at two nearby sites in eastern Missouri differing in soil properties (Planthaven Farms and Danforth Center Field Research Site). Four treatments (unfertilized IWG, fertilized IWG, IWG-alfalfa intercrop, and alfalfa monoculture) were established in a randomized complete block design with four replications per site. Biomass and grain yield were evaluated at per-row and field scales, while roots were measured to 1 m depth during the second stand age. Alfalfa intercropping maintained IWG grain yield without synthetic N fertilizer, although treatment responses varied by site and stand age. At Planthaven, differences became more pronounced as stands matured, with intercropped IWG producing the greatest per-row biomass and grain yield in stand age three. At the Danforth Center Field Research Site, intercropped IWG produced greater per-row biomass and grain yield than monocultures, whereas fertilized IWG tended to produce greater field-scale biomass; grain yield declined across treatments with stand age. Across sites, nitrogen fertilization increased vegetative biomass more consistently than grain yield. Despite having fewer IWG rows, intercrops maintained field-scale grain yield comparable to fertilized IWG in several site-years. Root traits responded weakly to management and were structured primarily by soil depth. These findings highlight the importance of site conditions, and stand age, when evaluating management strategies for perennial grain production.

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↗

bioRxiv2026

A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells

Pulmonary neuroendocrine cells (PNECs) are rare chemosensory epithelial cells, facultative stem cells, and a cell-of-origin for neuroendocrine lung cancers, yet the mechanisms governing their differentiation and heterogeneity are poorly understood. Here we establish NEr-fAOs, a human fetal airway organoid platform that robustly enriches PNECs, and identify a cooperative requirement for dual GSK3 and NOTCH inhibition to drive directed PNEC differentiation. This strategy yields stable cultures with up to 60-fold expansion of PNECs whose transcriptomes closely match fetal and adult PNECs. In addition to PNEC-enrichment, NEr-fAOs retain diverse airway epithelial cell types, preserving epithelial complexity. Time-resolved single-cell transcriptomics maps PNEC trajectories in NEr-fAOs, resolving precursor and mature states. Comparative analyses further reveal a distal airway bias in NEr-fAOs and enrichment for lower-airway progenitors. NEr-fAOs thus provide a scalable, tractable platform to dissect human PNEC biology and distal airway progenitor hierarchies relevant to lung development, cancer, and disease.

developmental biology↗

bioRxiv2025

NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pH during nitrate uptake in Medicago truncatula

Nitrate is the primary source of nitrogen for plants in most environments. Nitrate uptake from the rhizosphere into root cells is mediated by Nitrate Transporter 2 (NRT2) and NRT1.1 proteins via proton symport, with the apoplast serving as an intermediate compartment. Using a simple root immersion system, we investigated the effects of NRT transporters on external media pH (pHmed) and apoplastic pH (pHapo) in M. truncatula nitrate transporter mutants. Monitoring of pHmed showed that loss of NRT2.1 largely prevented nitrate induced alkalization of the media, while loss of NRT1.1A/B reduced media alkalization only during the initial stages of nitrate uptake, suggesting they have fundamentally different physiological roles. Use of the pH sensitive dye HPTS showed that the pHapo of root cells initially decreased during nitrate uptake, and this required NRT1.1A/B. Unexpectedly, the observed changes in pHmed during nitrate uptake in WT and the mutants were not reflected in pHapo. To explain these discrepancies, we propose a model in which the depletion of protons in the media occurring during nitrate symport is offset by the buffering of protons in the cell wall and the activity of the H+-ATPase, allowing a lower pHapo to be maintained. Such a mechanism would enable efficient nitrate uptake across a range of external pH values.

plant biology↗

bioRxiv2025

Watering regime affects aboveground and belowground trait covariation in a hybrid Silphium population

Premise of the studyPerennial, herbaceous members of the sunflower family (Asteraceae) can provide valuable agronomic products from aboveground biomass, as well as ecosystem services belowground. Aboveground and belowground trait covariation can be affected by environmental conditions such as the location of available water. Here, we investigated the effects of watering regime on trait covariation in Silphium (Asteraceae), an emerging perennial oilseed crop. MethodsSilphium integrifolium Michx. and S. perfoliatum L. are native North American species adapted to well-drained and moist soils, respectively. Using a backcrossed F1 hybrid S. integrifolium x S. perfoliatum population, we conducted a greenhouse experiment where plants were either watered at the soil line ("top-watered") or from below using watering trays ("bottom-watered"). Aboveground biomass, root distribution, and root morphology (e.g., specific root length) were measured destructively. Key resultsCompared to top-watered plants, bottom-watered plants were smaller aboveground and belowground, with a higher proportion of roots in the upper portions of the pots and higher specific root length. Negative relationships between aboveground biomass and specific root length were steeper for bottom-watered than top-watered plants. ConclusionsThe location of available water impacts aboveground biomass, the distribution and morphology of the root system, and relationships between aboveground and belowground plant structures. This work suggests that resource allocation depends in part on the location of available water, and has relevance for ongoing efforts aimed at developing perennial, herbaceous species that offer both economically viable products as well as ecosystem services.

plant biology↗

bioRxiv2025

Depth-Sensitive Assessment of Cerebral Blood Flow and Low-Frequency Oscillations After Traumatic Brain Injury in Mice Using Time-Gated Diffuse Correlation Spectroscopy

Traumatic brain injury (TBI) can lead to long-lasting impairments in cerebral perfusion, making early detection of microvascular changes critical for guiding clinical interventions. In this study, we employed time-gated diffuse correlation spectroscopy (TG-DCS) at 1064 nm to non-invasively quantify depth-resolved cerebral blood flow (CBF) and low-frequency oscillations (LFOs) in a mouse model of closed-head injury. By analyzing early (superficial) and late (deeper) photon arrival times, we identified a significant drop in CBF shortly after injury, with a partial recovery observed at 2 hours post-trauma. Power spectral analysis of the blood flow index revealed significant alterations in LFO bands, particularly in slow-5 (0.01-0.027 Hz) and slow-3 (0.073-0.198 Hz) ranges, with p < 0.05 at both early and late gates. These changes were more pronounced than BFI alterations alone, indicating that LFOs may serve as sensitive biomarkers of neurovascular disruption. Our findings demonstrate the feasibility of TG-DCS for depth-specific monitoring of cerebral hemodynamics and oscillatory dynamics after TBI and suggest its potential utility in translational neurotrauma research.

bioengineering↗

bioRxiv2025

Unearthing the rhizosphere microbiome recruited by ancestral bread wheat landraces

Crop root traits that modulate the soil microbiome can turn the tide of reduced fertility in intensively farmed land by optimising nutrient availability and resilience to environmental stresses. Advantageous genetic diversity that allows adaptation to nutrient availability is present in historic crop genotypes. The Watkins collection of bread wheat landraces is an unexploited resource, carrying untapped phenotypic traits. Here, we show that the rhizosphere microbiome assembly of these landraces is distinct compared to elite varieties, specifically those that come from ancestral groups (AGs) not used in modern breeding. We used 16S rRNA sequencing to identify changes in microbial communities of rhizosphere soil collected from 81 landraces and two elite varieties. We found high similarity in microbiome recruitment between the elite cultivars and the two AGs genetically closest to the elite. The rhizosphere microbiome of five AGs genetically distant from the elite cultivars showed significant differences in the abundance of taxa involved in nitrogen and carbon turnover, keystone taxa and associations within the microbial network. Our findings suggest that genes to recruit or suppress microbial taxa in the rhizosphere are shared by landraces from these AGs. Selective breeding for traits to control microbial functions can enhance soil productivity and crop performance.

ecology↗

bioRxiv2025

A leaf phenomics approach to estimating below-ground traits in North American Licorice

Premise of the studyThousands of years of selective breeding has prioritized above-ground yield, with little regard for changes happening below-ground. Despite their central role in plant success and resilience, our knowledge of roots lags behind above-ground structures. Accurately phenotyping root traits is often labor-intensive, expensive, and destructive. In order to advance understanding of the fundamental biology underlying root systems, and to integrate hard-to-measure root traits into breeding programs, high-throughput non-destructive methods are required. MethodsThis study uses American licorice (Glycyrrhiza lepidota Pursh.), a perennial legume with a rich ethnobotanical history, as a model to investigate root system phenotypes. We assess root traits across multiple populations, analyze relationships between above- and below-ground phenotypes, and test the use of multidimensional leaf traits, including spectral reflectance, in predicting root traits. Key resultsAmerican licorice displays significant variation in root traits across source populations and strong correlations between above- and below-ground traits. Leaf spectral reflectance and elemental composition show promise in modeling below-ground traits, though the isometric relationship between plant size and root traits complicates model accuracy. ConclusionsThese findings demonstrate the use of high-dimensional leaf traits as a proxy for root traits, with potential applications for understanding foundational questions in plant biology and in breeding programs targeting the below-ground structures of perennial herbaceous species. Further optimization and larger studies are needed to improve predictive models.

plant biology↗

bioRxiv2023

BdNRT2A and BdNRT3.2 are the major components of the High-Affinity nitrate Transport System in Brachypodium distachyon

O_LIAn efficient nitrate uptake system contributes to the improvement of crop nitrogen use efficiency under low nitrogen availability. The High Affinity nitrate Transport System (HATS) in plants is active in low external nitrate and is mediated by a two-component system [high affinity transporters NRT2 associated to a partner protein NRT3 (NAR2)]. C_LIO_LIIn Brachypodium, the model plant for C3 cereals, we investigated the role of BdNRT2A and BdNRT3.2 through various experimental approaches including gene expression profiling, functional characterisation in heterologous system, intracellular localization by imaging, and reverse genetics via gene silencing. C_LIO_LIExpression of BdNRT2.A and BdNRT3.2 genes in response to nitrate availability fits with the characteristics of the HATS components. Co-expression of BdNRT2A and BdNRT3.2 is required for an effective nitrate transport in the heterologous expression system Xenopus oocytes. Functional interaction between BdNRT2A-GFP and BdNRT3.2-RFP fusion proteins has been observed at the plasma membrane in Arabidopsis protoplasts in transient expression experiments. BdNRT3.2 appeared to be necessary for the plasma membrane localization of BdNRT2A. 15Nitrate influx measurements with bdnrt2a mutants (two amiRNA mutants and one NaN3 induced mutant with a truncated NRT2A protein), confirmed that BdNRT2A is a major contributor of the HATS in Brachypodium. C_LIO_LIDirected mutagenesis in BdNRT2A of a conserved Ser residue (S461) specific to monocotyledons has been performed to mimic a non-phosphorylated S461A or a constitutively phosphorylated S461D, in order to evaluate its potential role in the BdNRT2A and BdNRT3.2 interaction leading to plasma membrane targeting. Interestingly, the phosphorylation status of S461 did not modify the interaction, suggesting on a more complex mechanism. C_LIO_LIIn conclusion, our data show that BdNRT2A and BdNRT3.2 are the main components of the nitrate HATS activity in Brachypodium (Bd21-3) and allow an optimal growth in low N conditions. C_LI

plant biology↗

bioRxiv2023

Reconciling land sharing and sparing: a conceptual model for land use

Since the introduction of the terms in the early 2000s, the land sharing versus land sparing dichotomy has sparked considerable discussion stemming from the relationship between food production and ecological function. The theory underpinning these approaches straddles disciplinary and ideological boundaries and is frequently outlined within a general economy versus ecology background. Both strategies have come up with competing models on the relationship linking agricultural production and ecological function. The present work introduces a conceptual synthesis to unify alternative models under a single coherent framework. A generalized model linking agricultural production with ecological function that can harmonize these conflicting views is presented. In addition, a conceptual shift of paradigm is suggested to approach the issue, moving from yield targets to preservation thresholds. This article provides the theoretical means to identify the environmental and policy conditions under which land sharing strategies, based on low inputs and low impact per unit of cultivated land, can compete with land sparing approaches for the combined goals of biodiversity preservation and food safety.

ecology↗

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

Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen

Animals have evolved two defense strategies to survive infections. Antagonistic strategies include mechanisms of immune resistance that operate to sense and kill invading pathogens. Cooperative or physiological defenses mediate host adaptation to the infected state, limiting physiological damage and disease, without killing the pathogen, and have been shown to cause asymptomatic carriage and transmission of lethal pathogens. Here we demonstrate that physiological defenses cooperate with the adaptive immune response to generate long-term asymptomatic carriage of the lethal enteric murine pathogen, Citrobacter rodentium. Asymptomatic carriage of genetically virulent C. rodentium provided immune resistance against subsequent infections. Host immune protection was dependent on systemic antibody responses and pathogen virulence behavior, rather than the recognition of specific virulent factor antigens. Finally, we demonstrate that an avirulent strain of C. rodentium in the field has background mutations in two genes that are important for LPS structure. Our work reveals novel insight into how asymptomatic infections can arise mechanistically with immune resistance, mediating exclusion of phenotypically virulent enteric pathogen to promote asymptomatic carriage.

immunology↗

bioRxiv2023

Grapevine scion gene expression is driven by rootstock and environment interaction

BACKGROUNDGrafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings. RESULTSIn the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment. CONCLUSIONSOur results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.

plant biology↗

bioRxiv2022

Distinct airway progenitor cells drive epithelial heterogeneity in the developing human lung

Recent advances using single cell genomic approaches have identified new epithelial cell types and uncovered cellular heterogeneity in the murine and human lung (1). Here, using scRNA-seq and microscopy we identify and describe a secretory-like cell that is enriched in the small airways of the developing human lung and identified by the unique co-expression of SCGB3A2/SFTPB/CFTR. To place these cells in the hierarchy of airway development, we apply a single cell barcode-based lineage tracing method track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro (2). Lineage tracing revealed that these cells have distinct developmental potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells (PNECs) and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. We conclude that SCGB3A2/SFTPB/CFTR cells act as a progenitor cell contributing to the cellular diversity and heterogeneity in the developing human airway. SIGNIFICANCE STATEMENTThe current study identifies a novel secretory cell type that is present predominantly in the small airway of the developing human lung. These secretory cells are defined by co-expression of SCGB3A2/SFTPB/CFTR, and functional studies show that this cell gives rise to pulmonary neuroendocrine cells and a sub-population of multiciliated cells, thereby leading to cellular heterogeneity.

developmental 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↗

bioRxiv2021

Comparative population genomics in two sympatric species of Strophostyles (Fabaceae) with contrasting life histories

PREMISE OF THE STUDYLife history is an important predictor of population genetic variation, although this link remains unexplored in numerous important plant lineages. One such lineage is the legume genus Strophostyles, which contains both annual and herbaceous perennial vines native to eastern North America. Specifically, it remains to be determined whether Strophostyles species with different life histories show different patterns of genetic differentiation and diversity, as well as if these species hybridize across their range. METHODSHere we sampled the perennial Strophostyles helvola and annual S. leiosperma in five sites across a latitudinal transect in the central United States, including three sites where the species occur in sympatry. Using genotyping-by-sequencing, we identified 5556 polymorphic SNPs across 166 individuals. KEY RESULTSThere is no evidence that Strophostyles helvola and S. leiosperma hybridize in the populations examined. Within species, Strophostyles helvola (perennial) displays admixture among populations, while S. leiosperma (annual) does not, although both species show more genetic diversity among rather than within populations. Patterns of genetic diversity are varied across populations of both species, with both heterozygote excess and deficiency. CONCLUSIONSThe complex patterns of genetic differentiation and diversity warrant further investigation of life history and population dynamics in Strophostyles, particularly mating system and modes of gene flow. This study exemplifies the diversity of population genetic patterns even within a small genus, and it reinforces the need to characterize such diversity in non-model systems to gain a more complete understanding of how life history contributes to population genetics.

plant biology↗

bioRxiv2021

R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development

Mammalian respiratory system development is regulated by complex reciprocal signaling events that take place between epithelial cells and the surrounding mesenchymal cells; however, mesenchymal heterogeneity and function in the developing human lung is poorly understood. We interrogated single cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonist R-SPONDIN2 (RSPO2), and we found that adjacent epithelial bud tip progenitors are enriched for the RSPO2 receptor LGR5. By carrying out functional experiments using organoid models, lung explant cultures, and FACS-isolated RSPO2+ mesenchyme, we show that RSPO2 is a critical niche cue that potentiates WNT signaling in human lung progenitors to maintain their multipotency.

developmental biology↗

bioRxiv2021

The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia (Fabaceae)

PREMISE OF THE STUDYAnnual and perennial life history transitions are abundant among angiosperms, and understanding the phenotypic variation underlying life span shifts is a key endeavor of plant evolutionary biology. Comparative analyses of trait variation and correlation networks among annual and perennial plants is increasingly important as new perennial crops are being developed in a predominately annual-based agricultural setting. However, it remains unclear how seed to vegetative growth trait relationships may correlate with life span. METHODSWe measured 29 annual and perennial congeneric species of three herbaceous legume genera (Lathyrus, Phaseolus, and Vicia) for seed size and shape, germination proportion, and early vegetative height and leaf growth over three months in order to assess relative roles of genus and life span in predicting phenotypic variation and correlation. KEY RESULTSGenus was the greatest predictor of seed size and shape variation, while life span consistently predicted static vegetative growth traits. Correlation networks revealed that annual species had significant associations between seed traits and vegetative traits, while perennials had no significant seed-vegetative associations. Each genus also differed in the extent of integration between seed and vegetative traits, as well as within-vegetative trait correlation patterns. CONCLUSIONSGenus and life span were important for predicting aspects of early life stage phenotypic variation and trait relationships. Differences in phenotypic correlation may indicate selection on seed size traits will impact vegetative growth differently depending on life span, which has important implications for nascent perennial breeding programs.

plant biology↗