Biology subjects

Wagner, M. R.

Publications and source records attributed to Wagner, M. R..

17 recordsLinked to original sources

bioRxiv2026

Heritable variation in root bacterial microbiomes alters natural selection on host plants

Heritable variation in microbiome composition could theoretically evolve in response to selection acting on hosts, but empirical evidence of this is scarce. We tested for effects of allelic variation in Boechera stricta on microbiome composition and downstream consequences for host fitness. In the greenhouse, near-isogenic lines with contrasting phytochemistry alleles differentially conditioned soil microbiota in ways that changed the relative fecundity of host genotypes. In the field, root microbiome differences mediated allelic effects on host fitness. Selection gradients on individual taxa and multivariate axes of root microbiome composition suggest that independent components of the bacterial community favor each allele, especially under drought. These results show that microbiota contribute to natural selection on a major-effect phytochemistry gene, empirically closing the loop between microbiome heritability and host trait evolution.

evolutionary biology↗

bioRxiv2026

Wild Luteibacter populations exhibit climate-associated divergence and distinct genomic strategies for osmotic stress tolerance

Soil bacteria play a crucial role in supporting ecosystem health, yet little is known about how wild populations adapt to abiotic stressors, like limited water availability. We used 186 Luteibacter isolates from maize roots grown in never-irrigated prairie soils collected from a steep precipitation gradient in Kansas, US to test whether climate history is associated with osmotic stress tolerance and genomic differentiation. In vitro, strains from semi-arid sites were more tolerant to osmotic-stress treatment than those from humid sites. Comparative genomics of a subset of 96 isolates identified four strongly biogeographically structured lineages and extensive accessory-genome diversity. Semi-arid climate-associated strains were enriched for genes involved in osmotic homeostasis, oxidative stress protection, motility, and type IV secretion. Humid climate-associated strains were enriched in environmental sensing, metabolic versatility, biofilm formation, iron acquisition, type VI secretion, and resource competition. GWAS identified 22 candidate genes associated with osmotic-stress tolerance, including those related to type IV pili, biofilm production, DNA repair, and phage. No candidates were shared between semi-arid and humid strains, suggesting distinct genetic mechanisms of osmotic tolerance. Predicted prophage composition was also geographically structured, although total prophage gene content did not predict osmotic-stress tolerance. Together, these results show that adaptation to long-term differences in water availability likely involves coordinated shifts in stress physiology, genome content, and ecological interactions in wild bacterial populations, providing insight into predicting microbial responses to changing climates.

microbiology↗

bioRxiv2026

Stromal and Neuronal Sources of Slit2/3 Ligands in the Adult Pancreas Exhibit Distinct Expression Patterns Independent of Robo2 Receptor Expression in the Islet

Pancreatic islets regulate blood glucose homeostasis. Although islet architecture is stable under homeostatic conditions, increased metabolic demand drives compensatory islet expansion. In mice, islets are organized as a {beta} cell core surrounded by a mantle of and {delta} cells. The formation of islet architecture during development requires expression of Roundabout receptors 1 and 2 (Robo1/2) in endocrine cells and of Slits 2 and 3 (Slit2/3) from islet-extrinsic sources. Furthermore, expression of Robo2 in endocrine cells is required to maintain islet architecture in the adult mouse. However, the cellular sources of Slit2/3 in the adult pancreas and their expression dynamics during islet expansion remain unknown. Here, we identify distinct stromal populations, including fibroblasts and pericytes, as well as neurons within intrapancreatic ganglia, as the sources of Slit2/3. We further show that Slit3 expression is increased in Ob/Ob mice, and that SLIT2 expression is elevated in stromal cell populations of humans with type 2 diabetes. The expression of neither Slit2 nor Slit3 was affected by deletion of Robo2 in {beta} cells. Together, these findings define the cellular origins of Slit2/3 and their expression dynamics in the adult pancreas, supporting a potential role for Slit signaling in the diabetic islet microenvironment.

developmental biology↗

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

Genome-wide cell type-specific and sex-specific transcriptional dysregulation in the islet of Langerhans underlies islet dysfunction in Down syndrome-related diabetes

Individuals with Down syndrome (trisomy of human chromosome 21) are at a significantly higher risk of developing type 2 diabetes (T2D) than the general population. Systemic metabolic defects in Down syndrome have been linked to gene expression dysregulation in peripheral tissues like the liver, muscle, brain, and adipose. However, the contribution of gene expression dysregulation in the islets of Langerhans to the increased risk of T2D in Down syndrome has not been explored. Here we show that trisomic Ts65Dn mice, a common Down syndrome mouse model, are glucose intolerant and display reduced {beta}-to- cell ratio compared to disomic controls. Using single cell RNA sequencing on islets from Ts65Dn mice we found genome-wide, cell type-specific, and sex-specific transcriptional dysregulation in trisomic islets compared to controls. The Down syndrome-associated transcriptional signature revealed important islet defects, both at the cell autonomous level and at the whole-islet level, increasing T2D susceptibility. Our results put forth innate islet defects as a central underlying cause of Down syndrome-related T2D, warranting additional studies.

developmental biology↗

bioRxiv2025

Differential metaproteomics of bacteria grown in vitro and in planta reveals functions used during growth on maize roots

Microbes are ubiquitous in the rhizosphere and play crucial roles in plant health, yet the metabolisms and physiologies of individual species in planta remain poorly understood. In this study, we examined microbial gene expression in response to the maize root environment for seven bacterial species originally isolated from maize roots. We grew each species individually, both in vitro in a minimal medium and in planta, and used differential proteomics to identify functions upregulated specifically when bacteria are grown on maize roots. We identified between 1,500 and 2,100 proteins from each species, with 20-60% of these proteins being differentially abundant between the two conditions. While we found that transporter proteins were upregulated in all species in planta, all other differentially abundant functions varied greatly between species, suggesting niche specialization in root-associated microbes. Indeed, in vitro assays confirmed that Curtobacterium pusillum likely degrades plant hemicellulose, Enterobacter ludwigii may benefit the plant by phosphate solubilization, and Herbaspirillum robiniae colonizes maize roots more effectively when both of its Type VI Secretion Systems are functional. Together, our findings highlight both conserved and species-specific bacterial strategies for growth in the root environment and lay a foundation for future work investigating the mechanisms underlying plant-microbiota interactions. ImportanceBacteria that live on and around plant roots are important for plant growth and health, yet we still know relatively little about how individual bacterial species behave in this environment. In this study, we looked at seven bacterial species originally isolated from maize roots to understand how they change their metabolism and physiology when grown on the plant versus when grown under laboratory conditions. By doing this, we identified key strategies bacteria use to survive and thrive in the root environment, including changes in nutrient uptake, metabolism, and secretion systems. We also substantiated some of these behaviors using lab experiments and bacterial mutants. Understanding these species-specific functions helps us learn how bacteria establish themselves on roots and interact with the plant. This knowledge is critical for future efforts to design effective microbial communities that improve crop performance and resilience.

microbiology↗

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↗

bioRxiv2025

Intraspecific plant-soil feedbacks alter root traits in a perennial grass

Drought is a common stressor faced by plants and their associated microbiomes. Projected climate data point toward an increase in the severity and frequency of extreme precipitation events, such as drought. Previous research has shown that long-term exposure to drought can shape plants genomes, resulting in genetic variation for drought tolerance. We hypothesized that these genetic changes also affect patterns of microbial colonization in the rhizosphere, potentially feeding back to influence plant drought responses. Here, we tested 33 rhizosphere soils conditioned by 33 genotypes of Tripsacum dactyloides (eastern gamagrass) that originated from native populations across a precipitation gradient in the southern plains of the United States. We used these 33 rhizosphere soils as inocula for a fully factorial experiment to test the responses of conspecific plants to the differentially conditioned soils under drought or well-watered conditions. Variation in aboveground traits such as shoot length, weight, and root-to-shoot ratios was primarily explained by watering treatment. However, many belowground traits, such as root anatomical and architectural traits, were more likely to be affected by the genotype of the conditioning plant. Of the traits we measured, only aerenchyma area was affected by the interaction between current watering treatment and genotype of the conditioning plant. Ultimately, both the current watering treatment and conditioning plant genotype altered plant physiological traits and the associated microbiome. The differential intraspecies plant-soil feedback dynamics driven by plant local adaptation will be key to understanding future plants responses to rapidly shifting climates, in both restoration projects and agricultural systems.

ecology↗

bioRxiv2024

The interaction between abiotic and biotic soil factors drive heterosis expression in maize

Heterosis or hybrid vigor refers to the superior phenotypes of hybrids relative to their parental inbred lines. Recently, soil microbes were identified as an environmental driver of maize heterosis. While manipulation of the soil microbial community consistently altered heterosis, the direction of the effect appeared to be dependent on the microbiome composition, environment, or both. Abiotic factors are well-known modifiers of heterosis expression, however, how the interactive effects between the soil microbial community and abiotic factors contribute to heterosis are poorly understood. To disentangle the proposed mechanisms by which microbes influence heterosis, we characterize the variation in heterosis expression when maize was grown in soil inocula derived from active maize farms or prairies. While we did not observe consistent differences in heterosis among plants grown in these inocula, our observations reaffirm that microbial effects on heterosis are likely specific to the local microbial community. The introduction of a nutrient amendment resulted in greater heterosis expression in the presence of an agricultural inoculum but not a prairie inoculum. We also observed an effect of soil inocula and nutrient treatment on the composition of bacterial and fungal communities in the root endosphere. In addition, the interaction between soil and nutrient treatment significantly affected bacterial community composition, whereas fungal community composition was only marginally affected by this interaction. These results further suggest that the soil microbial community plays a role in maize heterosis expression but that the abiotic environment is likely a larger driver.

plant biology↗

bioRxiv2024

Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought

Both chronic and acute drought alter the composition and physiology of soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Currently, little is known about how the resulting precipitation legacy effects manifest at the molecular and physiological levels and how they influence neighboring plants, especially in the context of subsequent drought. We characterized metagenomes of six prairie soils spanning a steep precipitation gradient in Kansas, USA. By statistically controlling for variation in soil porosity and elemental profiles, we identified bacterial taxa and functional gene categories associated with precipitation. This microbial precipitation legacy persisted through a 5-month-long experimental drought and mitigated the negative physiological effects of acute drought for a wild grass species that is native to the precipitation gradient, but not for the domesticated crop species maize. In particular, microbiota with a low-precipitation legacy altered transcription of a subset of host genes that mediate transpiration and intrinsic water use efficiency during drought. Our results show how long-term exposure to water stress alters soil microbial communities with consequences for the drought responses of neighboring plants.

microbiology↗

bioRxiv2023

Effective seed sterilization methods require optimization across maize genotypes

Studies of plant-microbe interactions using synthetic microbial communities (SynComs) often require the removal of seed-associated microbes by seed sterilization prior to inoculation to provide gnotobiotic growth conditions. A diversity of seed sterilization protocols have been developed in the past and have been used on different plant species with various amounts of validation. From these studies it has become clear that each plant species requires its own optimized sterilization protocol. It has, however, so far not been tested if the same protocol works equally well for different varieties and seed sources of one plant species. We evaluated six seed sterilization protocols on two different varieties (Sugar Bun & B73) of maize. All unsterilized maize seeds showed fungal growth upon germination on filter paper, highlighting the need for a sterilization protocol. A short sterilization protocol with hypochlorite and ethanol was sufficient to prevent fungal growth on Sugar Bun germinants, however a longer protocol with heat treatment and germination in fungicide was needed to obtain clean B73 germinants. This difference may have arisen from the effect of either genotype or seed source. We then tested the protocol that performed best for B73 on three additional maize genotypes from four sources. Seed germination rates and fungal contamination levels varied widely by genotype and geographic source of seeds. Our study shows that consideration of both variety and seed source is important when optimizing sterilization protocols and highlights the importance of including seed source information in plant-microbe interaction studies that use sterilized seeds.

microbiology↗

bioRxiv2023

Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization

Synthetic microbial communities (SynComs) are a valuable tool to study community assembly patterns, host-microbe interactions, and microbe-microbe interactions in a fully controllable setting. Constructing the SynCom inocula for plant-microbe experiments can be time consuming and difficult because a large number of isolates with different media requirements and growth rates are grown in parallel and mixed to appropriate titers. A potential workaround to assembling fresh SynCom inocula for every experiment could be to pre-make and freeze SynComs on a large scale, creating ready-to-use stock inocula. The objective of this study was to compare the reproducibility, stability, and colonization ability of freshly prepared versus frozen SynCom inocula. We used a community of seven species known to colonize maize roots. The results from inoculation with the frozen SynCom were as consistent as standardized de novo construction of fresh SynCom. Our results indicate that creating frozen SynCom inocula for repeated use in experiments not only saves time, but could also improve cross-experiment reproducibility. Although this approach was only validated with one SynCom, it demonstrates a principle that can be tested for improving approaches in constructing other SynComs. ImportanceSynthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increases enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to freshly constructued SynComs and thus allow for large time savings when working with SynComs.

microbiology↗

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

Soil variation among natural habitats alters glucosinolate content in a wild perennial mustard

Baseline levels of glucosinolates--important defensive phytochemicals in Brassicaceous plants--are determined by both genotype and the environment. However, the ecological causes of glucosinolate plasticity are not well characterized. Fertilization is known to alter glucosinolate content of Brassica crops, but the effect of naturally-occurring soil variation on glucosinolate content of wild plants is unknown. Here, we conduct greenhouse experiments using Boechera stricta to ask 1) whether soil variation among natural habitats shapes leaf and root glucosinolate profiles; 2) whether such changes are caused by abiotic soil properties, soil microbes, or both; and 3) whether soil-induced glucosinolate plasticity is genetically variable. Total glucosinolate quantity differed up to two-fold between soils from different natural habitats, while the relative amounts of different compounds was less responsive. This effect was due to physico-chemical soil properties rather than microbial communities. We detected modest genetic variation for glucosinolate plasticity in response to soil. In addition, glucosinolate composition, but not quantity, of field-grown plants could be accurately predicted from measurements from greenhouse-grown plants. In summary, soil alone is sufficient to cause plasticity of baseline glucosinolate levels in natural plant populations, which may have implications for the evolution of this important trait across complex landscapes.

plant biology↗

bioRxiv2020

Microbe-dependent heterosis in maize

Hybrids account for nearly all commercially planted varieties of maize and many other crop plants, because crosses between inbred lines of these species produce F1 offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research (1). The leading hypotheses--which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)--have been able to explain some but not all of the observed patterns of heterosis (2, 3). However, possible ecological drivers of heterosis have largely been ignored. Here we show that heterosis of root biomass and germination in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions, but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved vs. live soil slurries in a growth chamber, and for plants grown in fumigated vs. untreated soil in the field. Together, our results demonstrate a novel, ecological mechanism for heterosis whereby soil microbes generally impair the germination and early growth of inbred but not hybrid maize.

plant biology↗

bioRxiv2020

Microbiome composition differs in hybrid and inbred maize

O_LIMacroorganisms genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. C_LIO_LIWe take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. C_LIO_LIWe show that inbred lines and hybrids differ consistently in composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for non-microbial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. C_LIO_LIOur results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize. C_LI

plant biology↗

bioRxiv2019

Breeding for broad-spectrum disease resistance alters the maize leaf microbiome

O_LIPlant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesized that broad-spectrum disease resistance alleles also affect colonization by non-pathogenic symbionts.\nC_LIO_LIQuantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared to the microbiome of the disease-susceptible parent line at two timepoints in multiple fields.\nC_LIO_LIIntrogression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-week-old and 7-week-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected plants and uninfected plants.\nC_LIO_LIThese results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.\nC_LI

plant biology↗