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Chemistry assigns phosphorus and its most oxidized form, inorganic phosphate, unique roles for propelling bioenergetics and metabolism in all domains of life, possibly since its very origin on prebiotic Earth. For plants, access to the vital mineral nutrient profoundly affects growth, development and vigour, thus constraining net primary productivity in natural ecosystems and crop production in modern agriculture. Unlike other major biogenic elements, the low abundance and uneven distribution of phosphate in Earths crust result from the peculiarities of phosphorus cosmochemistry and geochemistry. Here, we trace the chemical evolution of the element, the geochemical phosphorus cycle and its acceleration during Earths history until the present (Anthropocene) as well as during the evolution and rise of terrestrial plants. We highlight the chemical and biological processes of phosphate mobilization and acquisition, first evolved in bacteria, refined in fungi and algae and expanded into powerful phosphate-prospecting strategies during land plant colonization. Furthermore, we review the evolution of the genetic and molecular networks from bacteria to terrestrial plants, which monitor intracellular and extracellular phosphate availabilities and coordinate the appropriate responses and adjustments to fluctuating phosphate supply. Lastly, we discuss the modern global phosphorus cycle deranged by human activity and the challenges imposed ahead. This article is part of the theme issue Evolution and diversity of plant metabolism.

Key messageSpecific combinations of LFY and WAPO1 natural alleles maximize spikelet number per spike in wheat. Spikelet number per spike (SNS) is an important yield component in wheat that determines the maximum number of grains that can be formed in a wheat spike. In wheat, loss-of-function mutations in LEAFY (LFY) or its interacting protein WHEAT ORTHOLOG OF APO1 (WAPO1) significantly reduce SNS by reducing the rate of formation of spikelet meristems. In previous studies, we identified a natural amino acid change in WAPO1 (C47F) that significantly increases SNS in hexaploid wheat. In this study, we searched for natural variants in LFY that were associated with differences in SNS and detected significant effects in the LFY-B region in a nested association mapping population. We generated a large mapping population and confirmed that the LFY-B polymorphism R80S is linked with the differences in SNS, suggesting that LFY-B is the likely causal gene. A haplotype analysis revealed two amino acid changes P34L and R80S, which were both enriched during wheat domestication and breeding suggesting positive selection. We also explored the interactions between the LFY and WAPO1 natural variants for SNS using biparental populations and identified significant interaction, in which the positive effect of the 80S and 34L alleles from LFY-B was only detected in the WAPO-A1 47F background but not in the 47C background. Based on these results, we propose that the allele combination WAPO-A1-47F/LFY-B 34L 80S can be used in wheat breeding programs to maximize SNS and increase grain yield potential in wheat.

California is the nation’s primary producer of almonds, pistachios, and walnuts, and an important producer of rice. Because of California’s diverse cropping systems, off-target herbicide drift can be a considerable problem, particularly from aerial applications that are commonly used in flooded rice production systems. Triclopyr is an auxin-mimic type herbicide that has been commonly used in rice for many years for control of broadleaf weeds and the industry is familiar with symptoms of off-target triclopyr drift. Florpyrauxifen-benzyl is a newly registered auxin-mimic herbicide in California rice with activity on key weeds and is being rapidly adopted. Although symptoms typically are similar among auxinic herbicides, it is important to understand subtle differences and risks among these herbicides as stewardship for newly registered products. This research was conducted in 2020 and 2021 to determine the relative sensitivity of almond, pistachio, and walnut trees to simulated drift rates of florpyrauxifen-benzyl and triclopyr as well as characterize and compare symptoms caused by these two herbicides. The fractional herbicide rates tested were 1/200X, 1/100X, 1/33X, and 1/10X of the florpyrauxifen-benzyl use rate of 29.4 g·ha21 a.i. and 1/200X, 1/100X, and 1/33X of the triclopyr use rate of 420.3 g·ha21 a.e. Florpyrauxifen-benzyl and triclopyr herbicides were applied directly to one side of the canopy of 1- to 2-year-old almond, pistachio, and walnut trees. The general symptoms of florpyrauxifen-benzyl and triclopyr were chlorosis, chlorotic spots, leaf curling, leaf narrowing, leaf distortion, leaf malformation, leaf crinkling, shoot curling, stem coloring, stunting, terminal bud death, and twisting. The florpyrauxifen-benzyl and triclopyr injury symptoms were compared at the same fractional rates and found to be similar to each other. The herbicide injury was observed on the entire pistachio canopy, particularly on developing leaves and terminal buds. In contrast, injury symptoms on almond and walnut were more apparent on the side of the canopy to which the herbicides were applied. Symptom severity peaked at 14 days after treatment with the 1/10X florpyrauxifen-benzyl rate, when the visible injury was 16%, 48%, and 78% on almond, walnut, and pistachio, respectively. Although almond and walnut symptoms from the 1/10X florpyrauxifen-benzyl rate remained visible longer than all other treatments, all trees gradually recovered throughout the growing season. In contrast, pistachio trees did not recover fully and had injury symptoms that persisted for the remainder of the treatment year and at leaf-out the following spring. When drift occurs, it is typically at rates below 1/100X up to 1/33X of herbicide use rates. This research suggested that proper herbicide drift management practices and application precautions are likely to minimize the risk of significant injury from florpyrauxifen-benzyl drift to almond and walnut because of low injury symptoms at the typical drift rates. However, extra precautions may be needed if there are nearby pistachio orchards.

Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

This article is a Commentary on Yu et al. (2024), 244: 1024–1040.

Faithful genome partition during cell division relies on proper congression of chromosomes to the spindle equator before sister chromatid segregation. Here we uncover a kinesin-7 motor, kinetochore-associated kinesin 1 (KAK1), that is required for mitotic chromosome congression in Arabidopsis. KAK1 associates dynamically with kinetochores throughout mitosis. Loss of KAK1 results in severe defects in chromosome congression at metaphase, yet segregation errors at anaphase are rarely observed. KAK1 specifically interacts with the spindle assembly checkpoint protein BUB3.3 and both proteins show interdependent kinetochore localization. Chromosome misalignment in BUB3.3-depleted plants can be rescued by artificial tethering of KAK1 to kinetochores but not vice versa, demonstrating that KAK1 acts downstream of BUB3.3 to orchestrate microtubule-based chromosome transport at kinetochores. Moreover, we show that KAK1's motor activity is essential for driving chromosome congression to the metaphase plate. Thus, our findings reveal that plants have repurposed BUB3.3 to interface with a specialized kinesin adapted to integrate proper chromosome congression and checkpoint control through a distinct kinetochore design.

Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.

Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO3- uptake and CO2 fixation in C. necator, providing new pathways for CO2-based biomanufacturing.

Hybridization is increasingly recognized as an important evolutionary process across the tree of life. In many clades, phylogenomic approaches have permitted unparalleled insight into the extent and frequency of hybridization. However, we continue to lack a deep understanding of the factors that limit and shape patterns of hybridization, especially in evolutionary radiations. In this study, we characterized patterns of introgression across Costus (Costaceae), a young evolutionary radiation of tropical understory plants that maintain widespread interfertility despite exhibiting strong prezygotic reproductive isolation. We analyzed a phylogenomic dataset of 756 genes from 54 Costus species using multiple complementary approaches - D-statistics, gene-tree-based tests, and phylogenetic network analyses - to detect and characterize introgression events throughout the evolutionary history of the radiation. Our results identified a moderate number of introgression events, including a particularly ancient, well-supported event spanning one of the deepest divergences in the clade. Most introgression events occurred between taxa or ancestral lineages that shared the same pollination syndrome (bee-pollinated or hummingbird-pollinated). These findings suggest that prezygotic barriers, including pollinator specialization, have been key to the balance between introgression and reproductive isolation in Costus.

Plants and mycorrhizal fungi form mutualistic relationships that affect how resources flow between organisms and within ecosystems. Common mycorrhizal networks (CMNs) could facilitate preferential transfer of carbon and limiting nutrients, but this remains difficult to predict. Do CMNs favour fungal resource acquisition at the expense of plant resource demands (a fungi-centric view), or are they passive channels through which plants regulate resource fluxes (a plant-centric view)? We used stable isotope tracers (13CO2 and 15NH3), plant traits, and mycorrhizal DNA to quantify above- and below-ground carbon and nitrogen transfer between 18 plant species along a 520-km latitudinal gradient in the Pacific Northwest, USA. Plant functional type and tissue stoichiometry were the most important predictors of interspecific resource transfer. Of ‘donor’ plants, 98% were 13C-enriched, but we detected transfer in only 2% of ‘receiver’ plants. However, all donors were 15N-enriched and we detected transfer in 81% of receivers. Nitrogen was preferentially transferred to annuals (0.26 ± 0.50 mg N per g leaf mass) compared with perennials (0.13 ± 0.30 mg N per g leaf mass). This corresponded with tissue stoichiometry differences. Synthesis Our findings suggest that plants and fungi that are located closer together in space and with stronger demand for resources over time are more likely to receive larger amounts of those limiting resources. Read the free Plain Language Summary for this article on the Journal blog.

This article focuses on screening the major secreted proteins by the ischemia-challenged cardiac stromal fibroblasts (CF), the assessment of their expression status and functional role in the post-ischemic left ventricle (LV) and in the ischemia-challenged CF culture and to phenotype CF at single cell resolution based on the positivity of the identified mediators. The expression level of CRSP2, HSP27, IL-8, Cofilin-1, and HSP90 in the LV tissues following coronary artery bypass graft (CABG) and myocardial infarction (MI) and CF cells followed the screening profile derived from the MS/MS findings. The histology data unveiled ECM disorganization, inflammation and fibrosis reflecting the ischemic pathology. CRSP2, HSP27, and HSP90 were significantly upregulated in the LV-CABG tissues with a concomitant reduction ion LV-MI whereas Cofilin-1, IL8, Nrf2, and Troponin I were downregulated in LV-CABG and increased in LV-MI. Similar trends were exhibited by ischemic CF. Single cell transcriptomics revealed multiple sub-phenotypes of CF based on their respective upregulation of CRSP2, HSP27, IL-8, Cofilin-1, HSP90, Troponin I and Nrf2 unveiling pathological and pro-healing phenotypes. Further investigations regarding the underlying signaling mechanisms and validation of sub-populations would offer novel translational avenues for the management of cardiac diseases.

Abstract: Many herbivorous insect species exhibit phenotypic plasticity when using multiple hosts, which facilitates survival in heterogeneous host environments. Physiological host acclimation is an important part of it, yet the effects of host acclimation on insect feeding behaviour are not well studied, particularly for insect vectors of plant pathogens. We studied the combined effects of host acclimation and infection with a plant pathogenic symbiont on feeding behaviour of Bactericera cockerelli, an oligophagous psyllid widespread in both crop and natural habitats that feed primarily on Solanaceae and transmit an economically important plant pathogen, Candidatus Liberibacter solanacearum (CLso). We used a factorial design and the electrical penetration graphing technique to disentangle the effects of host acclimation, CLso infection and psyllid haplotype on the within‐plant feeding behaviour of B. cockerelli during conspecific and heterospecific host switches. This approach allows to connect phenotypic plasticity with the role of B. cockerelli as a vector by quantifying the frequency and duration of behaviours involved in CLso transmission. We found significant reductions in multiple metrics of B. cockerelli feeding efficiency, exacerbated by infection with CLso, which could lead to reduced transmission of this pathogen. Psyllid genotype was also important; the Central haplotype exhibited less dramatic changes in feeding efficiency than the Western haplotype during heterospecific host switches. Our study shows that host acclimation and heterospecific host switching directly alter feeding behaviours underlying pathogen transmission, and that the magnitude of feeding efficiency reductions depends on both host genotype and infection status.

Traditional leaf gas exchange experiments have focused on net CO2 exchange (Anet). Here, using California poplar (Populus trichocarpa), we coupled measurements of net oxygen production (NOP), isoprene emissions and δ18O in O2 to traditional CO2/H2O gas exchange with chlorophyll fluorescence, and measured light, CO2 and temperature response curves. This allowed us to obtain a comprehensive picture of the photosynthetic redox budget including electron transport rate (ETR) and estimates of the mean assimilatory quotient (AQ = Anet/NOP). We found that Anet and NOP were linearly correlated across environmental gradients with similar observed AQ values during light (1.25 ± 0.05) and CO2 responses (1.23 ± 0.07). In contrast, AQ was suppressed during leaf temperature responses in the light (0.87 ± 0.28), potentially due to the acceleration of alternative ETR sinks like lipid synthesis. Anet and NOP had an optimum temperature (Topt) of 31°C, while ETR and δ18O in O2 (35°C) and isoprene emissions (39°C) had distinctly higher Topt. The results confirm a tight connection between water oxidation and ETR and support a view of light-dependent lipid synthesis primarily driven by photosynthetic ATP/NADPH not consumed by the Calvin-Benson cycle, as an important thermotolerance mechanism linked with high rates of (photo)respiration and CO2/O2 recycling.

Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.

Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.

Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.

Chlorosplenium is a small genus comprising five species of inoperculate discomycetes in the order Helotiales (Leotiomycetes) often recognizable by their bright yellowish-green colors and gregarious growth on wood. In this study, we describe five new species-C. aotearoa, C. australiense, C. cusucoense, C. epimorsicum, and C. hawaiiense-based on a combination of recent fieldwork and examination of previously collected fungarium specimens. We use an integrative taxonomic approach to support the distinction of new species, incorporating morphology and DNA sequence data with biogeography. Macro- and micromorphological features of apothecia for all species and culture characteristics for four of the five new species are documented. A multilocus phylogeny based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, partial large subunit nuc ribosomal DNA (28S nuc rDNA), and A-B regions of the largest subunit of RNA polymerase II (RPB1) gene is presented. Additionally, we report Chlorosplenium chlora from Europe for the first time and expand our knowledge of the diversity and distributions of species in this genus in America, Australia, and New Zealand.

Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants' pores for gas exchange, are expected to decrease in density following increased CO2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.

Adaptive responses to climate change, based on heritable variation in stress tolerance, may be important for plant population persistence. It is unclear which populations will mount the strongest future adaptive responses. It may be fruitful to identify populations that have escaped trade-offs among performance traits, which can hinder adaptation. Barring strong genetic constraints, the extent of trade-offs may depend on spatial relationships among climate variables shaping different traits. Here, we test for climate-driven ecotypic variation and trade-offs among drought and freezing sensitivity, and growth, for Lemmon's willow (Salix lemmonii) in a common garden study of 90 genotypes from 38 sites in the Sierra Nevada, USA. Salix lemmonii exhibits ecotypic variation in leaf turgor loss point, a measure of drought sensitivity, from -0.95 to -0.74 MPa along a gradient of spring snowpack. We also find variation in spring freezing sensitivity with minimum May temperature. However, we find no trade-off, as the climatic gradients shaping these traits are spatially uncorrelated in our study region, despite being negatively correlated across the Sierra Nevada. Species may escape adaptive trade-offs in geographic regions where climate variables are spatially decoupled. These regions may represent valuable reservoirs of heritable adaptive phenotypic variation.

Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.

Plant natural products (PNPs) hold significant pharmaceutical importance. The sessile nature of plants has led to the evolution of chemical defense mechanisms over millions of years to combat environmental challenges, making it a crucial and essential defense weapon. Despite their importance, the abundance of these bioactive molecules in plants is typically low, and conventional methods are time-consuming for enhancing production. Moreover, there is a pressing need for novel drug leads, exemplified by the shortage of antibiotics and anticancer drugs. Understanding how plants respond to stress and regulate metabolism to produce these molecules presents an opportunity to explore new avenues for discovering compounds that are typically under the detection limit or not naturally produced. Additionally, this knowledge can contribute to the advancement of plant engineering, enabling the development of new chassis for the biomanufacturing of these valuable molecules. In this perspective, we explore the intricate regulation of PNP biosynthesis in plants, and discuss the biotechnology strategies that have been and can be utilized for the discovery and production enhancement of PNPs in plants.

Abstract: RNA methylation plays a central regulatory role in plant biology and is a relatively new target for plant improvement efforts. In nearly all cases, perturbation of the RNA methylation machinery results in deleterious phenotypes. However, a recent landmark paper reported that transcriptome‐wide use of the human RNA demethylase FTO substantially increased the yield of rice and potatoes. Here, we have performed the first independent replication of those results and demonstrated broader transferability of the trait, finding increased flower and fruit count in the model species Arabidopsis thaliana. We also performed RNA‐seq of our FTO‐transgenic plants, which we analyzed in conjunction with previously published datasets to detect several previously unrecognized patterns in the functional and structural classification of the upregulated and downregulated genes. From these, we present mechanistic hypotheses to explain these surprising results with the goal of spurring more widespread interest in this promising new approach to plant engineering.

Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related species Schizophyllum fasciatum was sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes, in combination with the high phenotypic diversity, will provide a solid basis for functional genomics analyses of the strains of S. commune.

The red and far-red light photoreceptor phytochrome B (phyB) transmits light signals following cytosol-to-nuclear translocation to regulate transcriptional networks therein. This necessitates changes in protein-protein interactions of phyB in the cytosol, about which little is presently known. Via introduction of a nucleus-excluding G767R mutation into the dominant, constitutively active phyBY276H (YHB) allele, we explore the functional consequences of expressing a cytosol-localized YHBG767R variant in transgenic Arabidopsis seedlings. We show that YHBG767R elicits selective constitutive photomorphogenic phenotypes in dark-grown phyABCDE null mutants, wild type and other phy-deficient genotypes. These responses include light-independent apical hook opening, cotyledon unfolding, seed germination and agravitropic hypocotyl growth with minimal suppression of hypocotyl elongation. Such phenotypes correlate with reduced PIF3 levels, which implicates cytosolic targeting of PIF3 turnover or PIF3 translational inhibition by YHBG767R. However, as expected for a cytoplasm-tethered phyB, YHBG767R elicits reduced light-mediated signaling activity compared with similarly expressed wild-type phyB in phyABCDE mutant backgrounds. YHBG767R also interferes with wild-type phyB light signaling, presumably by formation of cytosol-retained and/or otherwise inactivated heterodimers. Our results suggest that cytosolic interactions with PIFs play an important role in phyB signaling even under physiological conditions.

Solar-induced fluorescence (SIF) is a proxy of ecosystem photosynthesis that often scales linearly with gross primary productivity (GPP) at the canopy scale. However, the mechanistic relationship between GPP and SIF is still uncertain, especially at smaller temporal and spatial scales. We deployed a ultra-hyperspectral imager over two grassland sites in California throughout a soil moisture dry down. The imager has high spatial resolution that limits mixed pixels, enabling differentiation between plants and leaves within one scene. We find that imager SIF correlates well with diurnal changes in leaf-level physiology and gross primary productivity under well-watered conditions. These relationships deteriorate throughout the dry down event. Our results demonstrate an advancement in SIF imaging with new possibilities in remotely sensing plant canopies from the leaf to the ecosystem. These data can be used to resolve outstanding questions regarding SIF's meaning and usefulness in terrestrial ecosystem monitoring.

Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided angstrom-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein-environment interactions will improve our capacity to engineer more productive crops.

Future climate presents conflicting implications for forest biomass. We evaluate how plant hydraulic traits, elevated CO2 levels, warming, and changes in precipitation affect forest primary productivity, evapotranspiration, and the risk of hydraulic failure. We used a dynamic vegetation model with plant hydrodynamics (FATES-HYDRO) to simulate the stand-level responses to future climate changes in a wet tropical forest in Barro Colorado Island, Panama. We calibrated the model by selecting plant trait assemblages that performed well against observations. These assemblages were run with temperature and precipitation changes for two greenhouse gas emission scenarios (2086-2100: SSP2-45, SSP5-85) and two CO2 levels (contemporary, anticipated). The risk of hydraulic failure is projected to increase from a contemporary rate of 5.7% to 10.1-11.3% under future climate scenarios, and, crucially, elevated CO2 provided only slight amelioration. By contrast, elevated CO2 mitigated GPP reductions. We attribute a greater variation in hydraulic failure risk to trait assemblages than to either CO2 or climate. Our results project forests with both faster growth (through productivity increases) and higher mortality rates (through increasing rates of hydraulic failure) in the neo-tropics accompanied by certain trait plant assemblages becoming nonviable.

Background and aimsMany agricultural areas are expected to face hotter, drier conditions from climate change. Understanding the mechanisms that crops use to mitigate these stresses can guide breeding for more tolerant plant material. We tested relationships between traits, physiological function in hot conditions and historical climate associations to evaluate these mechanisms for winegrapes. We expected a more negative leaf osmotic potential at full hydration (πo), which reduces leaf turgor loss during drought, and either a metabolically cheaper or more osmoprotectant leaf chemical composition, to allow cultivars associated with hot, dry regions to maintain greater gas exchange in hot growing conditions.MethodsWe measured πo, gas exchange and leaf chemistry for seven commercially important winegrape cultivars that vary widely in historical climate associations. Vines were grown in common-garden field conditions in a hot wine-growing region (Davis, CA, USA) and measured over the hottest period of the growing season (July-September).Key resultsThe value of πo varied significantly between cultivars, and all cultivars significantly reduced πo (osmotically adjusted) over the study period, although osmotic adjustment did not vary across cultivars. The value of πo was correlated with gas exchange and climate associations, but in the direction opposite to expected. Photosynthesis and πo were higher in the cultivars associated with hotter, less humid regions. Leaf chemical composition varied between cultivars but was not related to climate associations.ConclusionsThese findings suggest that maintenance of leaf turgor is not a primary limitation on grapevine adaptation to hot or atmospherically dry growing conditions. Thus, selecting for a more negative πo or greater osmotic adjustment is not a promising strategy to develop more climate-resilient grape varieties, contrary to findings for other crops. Future work is needed to identify the mechanisms increasing photosynthesis in the cultivars associated with hot, dry regions.

Tobacco mild green mosaic virus (TMGMV)-like nanocarriers were designed for gene delivery to plant cells. High aspect ratio TMGMVs were coated with a polycationic biopolymer, poly(allylamine) hydrochloride (PAH), to generate highly charged nanomaterials (TMGMV-PAH; 56.20 ± 4.7 mV) that efficiently load (1:6 TMGMV:DNA mass ratio) and deliver single-stranded and plasmid DNA to plant cells. The TMGMV-PAH were taken up through energy-independent mechanisms in Arabidopsis protoplasts. TMGMV-PAH delivered a plasmid DNA encoding a green fluorescent protein (GFP) to the protoplast nucleus (70% viability), as evidenced by GFP expression using confocal microscopy and Western blot analysis. TMGMV-PAH were inactivated (iTMGMV-PAH) using UV cross-linking to prevent systemic infection in intact plants. Inactivated iTMGMV-PAH-mediated pDNA delivery and gene expression of GFP in vivo was determined using confocal microscopy and RT-qPCR. Virus-like nanocarrier-mediated gene delivery can act as a facile and biocompatible tool for advancing genetic engineering in plants.

The unculturable bacterium 'Candidatus Liberibacter solanacearum' (CLso) is responsible for a growing number of emerging crop diseases. However, we know little about the diversity and ecology of CLso and its psyllid vectors outside of agricultural systems, which limits our ability to manage crop disease and understand the impacts this pathogen may have on wild plants in natural ecosystems. In North America, CLso is transmitted to crops by the native potato psyllid (Bactericera cockerelli). However, the geographic and host plant range of the potato psyllid and CLso beyond the borders of agriculture are not well understood. A recent study of historic herbarium specimens revealed that a unique haplotype of CLso was present infecting populations of the native perennial Solanum umbelliferum in California decades before CLso was first detected in crops. We hypothesized that this haplotype and other potentially novel CLso variants are still present in S. umbelliferum populations. To test this, we surveyed populations of S. umbelliferum in Southern California for CLso and potato psyllid vectors. We found multiple haplotypes of CLso and the potato psyllid associated with these populations, with none of these genetic variants having been previously reported in California crops. These results suggest that CLso and its psyllid vectors are much more widespread and diverse in North American natural plant communities than suggested by data collected solely from crops and weeds in agricultural fields. Further characterization of these apparently asymptomatic haplotypes will facilitate comparison with disease-causing variants and provide insights into the continued emergence and spread of CLso.

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

Spatiotemporal patterns of plant water uptake, loss, and storage exert a first-order control on photosynthesis and evapotranspiration. Many studies of plant responses to water stress have focused on differences between species because of their different stomatal closure, xylem conductance, and root traits. However, several other ecohydrological factors are also relevant, including soil hydraulics, topographically driven redistribution of water, plant adaptation to local climatic variations, and changes in vegetation density. Here, we seek to understand the relative importance of the dominant species for regional-scale variations in woody plant responses to water stress. We map plant water sensitivity (PWS) based on the response of remotely sensed live fuel moisture content to variations in hydrometeorology using an auto-regressive model. Live fuel moisture content dynamics are informative of PWS because they directly reflect vegetation water content and therefore patterns of plant water uptake and evapotranspiration. The PWS is studied using 21,455 wooded locations containing U.S. Forest Service Forest Inventory and Analysis plots across the western United States, where species cover is known and where a single species is locally dominant. Using a species-specific mean PWS value explains 23% of observed PWS variability. By contrast, a random forest driven by mean vegetation density, mean climate, soil properties, and topographic descriptors explains 43% of observed PWS variability. Thus, the dominant species explains only 53% (23% compared to 43%) of explainable variations in PWS. Mean climate and mean NDVI also exert significant influence on PWS. Our results suggest that studies of differences between species should explicitly consider the environments (climate, soil, topography) in which observations for each species are made, and whether those environments are representative of the entire species range.

Arsenic contamination of soils threatens the health of millions globally through accumulation in crops. While plants detoxify arsenic via phytochelatin (PC) complexation and efflux of arsenite from roots, arsenite efflux mechanisms are not fully understood. Here, white lupin (Lupinus albus) was grown in semi-hydroponics and exudation of glutathione (GSH) derivatives and PCs in response to arsenic was scrutinised using LC-MS/MS. Inhibiting synthesis of PC precursor GSH with L-buthionine sulfoximine (BSO) or ABC transporters with vanadate drastically reduced (>22%) GSH-derivative and PC2 exudation, but not PC3 exudation. This was accompanied by arsenic hypersensitivity in plants treated with BSO and moderate sensitivity with vanadate treatment. Investigating arsenic-phytochelatin (As-PC) complexation revealed two distinct As-PC complexes, As bound to GSH and PC2 (GS-As-PC2) and As bound to PC3 (As-PC3), in exudates of As-treated lupin. Vanadate inhibited As-PC exudation, while BSO inhibited both the synthesis and exudation of As-PC complexes. These results demonstrate a role of GSH-derivatives and PC exudation in lupin arsenic tolerance and reveal As-PC exudation as a new potential mechanism contributing to active arsenic efflux in plants. Overall, this study uncovers insight into rhizosphere arsenic detoxification with potential to help mitigate pollution and reduce arsenic accumulation in crops.

Very little is known about potential benefits of using AM inoculation as a tool to alleviate drought stress of trees grown under nursery conditions. There is some evidence that benefits of mycorrhiza on gas exchange parameters and growth of trees are proportionally greater when trees are subjected to drought stress. We hypothesized that inoculation with mycorrhiza would increase growth, nutrition, stem water potential and gas exchange of containerized almond (Prunus dulcis (Mill.) D.A. Webb) when young trees are grown under low water availability. In the spring of 2015 and 2016, forty containerized almond trees (Nonpareil scion grafted on Hansen 536, a peach/almond hybrid rootstock) were either inoculated or not with a commercially available arbuscular mycorrhizal inoculum and kept well-watered for 60 days in 2015 and 54 days in 2016, after which half of the plants were exposed to gradually reduced water availability over 38 days in 2015 and 61 days in 2016. Measurements included growth metrics, stem water potential, stomatal density, leaf NPK concentration, light saturated photosynthesis, and parameters calculated from CO2 response curves (Vcmax, J, TPU, Rd, gm, and stomatal limitation).The low-water treatment decreased stem water potential and reduced trunk diameter growth, light saturated photosynthesis (A), stomatal conductance (gs), Vcmax, J, TPU, gm, specific root length, leaf N and K concentration and total leaf N, P, and K content. Inoculation decreased root mass, increased leaf mass fraction, and decreased root mass fraction in 2015, but not in 2016. Neither stem water potential nor gas exchange were significantly altered by inoculation. Inoculation decreased leaf stomatal density, and slightly elevated leaf N and P concentrations in the low water treatments, although not consistently across years. Contrary to expectations we did not find substantially greater benefits from mycorrhizal inoculation in young drought stressed almond trees and conclude that the potential for mycorrhizal inoculant to alleviate drought stress in containerized trees is minimal.

Nitrate, the form of nitrogen often associated with kelp growth, is typically low in summer during periods of high macroalgal growth. More ephemeral, regenerated forms of nitrogen, such as ammonium and urea, are much less studied as sources of nitrogen for kelps, despite the relatively high concentrations of regenerated nitrogen found in the Southern California Bight, where kelps are common. To assess how nitrogen uptake by kelps varies by species and nitrogen form in southern California, USA, we measured uptake rates of nitrate, ammonium, and urea by Macrocystis pyrifera and Eisenia arborea individuals from four regions characterized by differences in nitrogen availability-Orange County, San Pedro, eastern Santa Catalina Island, and western Santa Catalina Island-during the summers of 2021 and 2022. Seawater samples collected at each location showed that overall nitrogen availability was low, but ammonium and urea were often more abundant than nitrate. We also quantified the internal %nitrogen of each kelp blade collected, which was positively associated with ambient environmental nitrogen concentrations at the time of collection. We observed that both kelp species readily took up nitrate, ammonium, and urea, with M. pyrifera taking up nitrate and ammonium more efficiently than E. arborea. Urea uptake efficiency for both species increased as internal percent nitrogen decreased. Our results indicate that lesser-studied, more ephemeral forms of nitrogen can readily be taken up by these kelps, with possible upregulation of urea uptake as nitrogen availability declines.

Environmental variation commonly drives functional trait diversity within species, among species, and across communities. Climate and shared evolutionary history can both influence trait–environment relationships. We studied variation in plant functional traits among closely related Costus species occurring across environmental gradients, the extent to which this variation occurs within single species, and how that variation may be influenced by shared evolutionary history. We measured leaf, aboveground stem, rhizome, and fine root traits of 17 species of Costus in eight sites in Costa Rica and Panama, which varied in elevation, temperature, and precipitation. We then assessed the relationships among traits and environmental variables and estimated the phylogenetic signal of the traits. We observed significant relationships between functional traits and climate. Stomatal conductance decreased, but stem density and rhizome dry matter content increased with decreasing mean annual temperature and precipitation seasonality in both cross-species and single-species analyses. This suggests that herbaceous species have a similar trade-off between plant hydraulic efficiency and safety as found in woody plants. Mean annual temperature was a stronger driver of trait variation than mean annual precipitation. We also found phylogenetic signal in leaf and stem structural traits (i.e., closely related species are more similar than distantly related species), but not in physiological or belowground traits. Our results demonstrate significant trait variation within and among species of Costus, a widespread understory and herbaceous genus in the tropics, which is driven by both climate and shared evolutionary history.

Understanding forest water limitation during droughts within a warming climate is essential for accurate predictions of forest-climate interactions. In hyperdiverse ecosystems like the Amazon forest, the mechanisms shaping hysteresis patterns in transpiration relative to environmental factors are not well understood. From this perspective, we investigated these dynamics by conducting in situ leaf-level measurements throughout and after the 2015 El Niño-Southern Oscillation (ENSO) drought. Our findings indicate a substantial increase in the hysteresis area (Harea) among transpiration (E), vapor pressure deficit (VPD), and stomatal conductance (gs) at canopy level during the ENSO peak, attributed to both temporal lag and differences in magnitude between gs and VPD peaks. Specifically, the canopy species Pouteria anomala exhibited an increased Harea, due to earlier maximum gs rates leading to a greater temporal lag with VPD compared to the post-drought period. Additionally, leaf water potential (ΨL) and canopy temperature (Tcanopy) showed larger Harea during the ENSO peak compared to post-drought conditions across all studied species, suggesting that stomatal closure, particularly during the afternoon, acts to minimize water loss and may explain the counterclockwise hysteresis observed between ΨL and Tcanopy. The pronounced Harea during the drought points to a potential imbalance between water supply and demand, underlining the role of stomatal behavior of isohydric species in response to drought.

Biomass allocation in plants is the foundation for understanding dynamics in ecosystem carbon balance, species competition, and plant-environment interactions. However, existing work on plant allometry has mainly focused on trees, with fewer studies having developed allometric equations for grasses. Grasses with different life histories can vary in their carbon investment by prioritizing the growth of specific organs to survive, outcompete co-occurring plants, and ensure population persistence. Further, because grasses are important fuels for wildfire, the lack of grass allocation data adds uncertainty to process-based models that relate plant physiology to wildfire dynamics. To fill this gap, we conducted a greenhouse experiment with 11 common California grasses varying in photosynthetic pathway and growth form. We measured plant sizes and harvested above- and belowground biomass throughout the life cycle of annual species, while for the establishment stage of perennial grasses to quantify allometric relationships for leaf, stem, and root biomass, as well as plant height and canopy area. We used basal diameter as a reference measure of plant size. Overall, basal diameter is the best predictor for leaf and stem biomass, height, and canopy area. Including height as another predictor can improve model accuracy in predicting leaf and stem biomass and canopy area. Fine root biomass is a function of leaf biomass alone. Species vary in their allometric relationships, with most variation occurring for plant height, canopy area, and stem biomass. We further explored potential trade-offs in biomass allocation across species between leaf and fine root, leaf and stem, and allocation to reproduction. Consistent with our expectation, we found that fast-growing plants allocated a greater fraction to reproduction. Additionally, plant height and specific leaf area negatively influenced the leaf-to-stem ratio. However, contrary to our hypothesis, there were no differences in root-to-leaf ratio between perennial and annual or C4 and C3 plants. Our study provides species-specific and functional-type-specific allometry equations for both above- and belowground organs of 11 common California grass species, enabling nondestructive biomass assessment in California grasslands. These allometric relationships and trade-offs in carbon allocation across species can improve ecosystem model predictions of grassland species interactions and environmental responses through differences in morphology.

Every fungal cell is encapsulated in a cell wall, essential for cell viability, morphogenesis, and pathogenesis. Most knowledge of the cell wall composition in fungi has focused on ascomycetes, especially human pathogens, but considerably less is known about early divergent fungal groups, such as species in the Zoopagomycota and Mucoromycota phyla. To shed light on evolutionary changes in the fungal cell wall, we studied the monosaccharide composition of the cell wall of 18 species including early diverging fungi and species in the Basidiomycota and Ascomycota phyla with a focus on those with pathogenic lifestyles and interactions with plants. Our data revealed that chitin is the most characteristic component of the fungal cell wall, and was found to be in a higher proportion in the early divergent groups. The Mucoromycota species possess few glucans, but instead have other monosaccharides such as fucose and glucuronic acid that are almost exclusively found in their cell walls. Additionally, we observed that hexoses (glucose, mannose and galactose) accumulate in much higher proportions in species belonging to Dikarya. Our data demonstrate a clear relationship between phylogenetic position and fungal cell wall carbohydrate composition and lay the foundation for a better understanding of their evolution and their role in plant interactions.

A central goal of photoprotective energy dissipation processes is the regulation of singlet oxygen (1O2*) and reactive oxygen species in the photosynthetic apparatus. Despite the involvement of 1O2* in photodamage and cell signaling, few studies directly correlate 1O2* formation to nonphotochemical quenching (NPQ) or lack thereof. Here, we combine spin-trapping electron paramagnetic resonance (EPR) and time-resolved fluorescence spectroscopies to track in real time the involvement of 1O2* during photoprotection in plant thylakoid membranes. The EPR spin-trapping method for detection of 1O2* was first optimized for photosensitization in dye-based chemical systems and then used to establish methods for monitoring the temporal dynamics of 1O2* in chlorophyll-containing photosynthetic membranes. We find that the apparent 1O2* concentration in membranes changes throughout a 1 h period of continuous illumination. During an initial response to high light intensity, the concentration of 1O2* decreased in parallel with a decrease in the chlorophyll fluorescence lifetime via NPQ. Treatment of membranes with nigericin, an uncoupler of the transmembrane proton gradient, delayed the activation of NPQ and the associated quenching of 1O2* during high light. Upon saturation of NPQ, the concentration of 1O2* increased in both untreated and nigericin-treated membranes, reflecting the utility of excess energy dissipation in mitigating photooxidative stress in the short term (i.e., the initial ∼10 min of high light).

This research addresses the presence of Elsinoë phaseoli in Kenya, where information on the biology of this pathogen remains scarce. Employing a multifaceted approach, the study demonstrates the steps taken to isolate, identify, and characterize E. phaseoli as the pathogen responsible for scab on common bean. Field observations confirmed scab symptoms, particularly the prominent pod lesions. Elsinoë phaseoli was isolated from common bean using a targeted streaking method on older acervulus-bearing lesions. Morphological examinations revealed a notable diversity within E. phaseoli colonies, consistent with the characteristics of the genus. Molecular identification through ITS-rDNA sequencing confirmed isolate AscoSK1 obtained in this study as belonging to E. phaseoli, offering a robust species differentiation method. Assessing conidium production required the implementation of five different culture methods. An adaptation of the Scheper et al. (2013) method yielded the highest quantity of conidia from 25 colonies spaced at 1 cm apart, with a conidial yield of 5.0 × 106 conidia per 9-cm-diameter Petri dish. A higher conidial yield was attained after the colonies were pre-incubated on potato dextrose agar in the dark at room temperature for 28 days, followed by a transfer to corn meal agar for an additional 2 days at 20°C. This emphasizes the pivotal influence of incubation duration and pre-culture conditions on the process. This research provides insights into the biology of E. phaseoli and introduces an improved method for enhancing in vitro sporulation of the pathogen, setting groundwork for future research and handling.

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Abstract: Selection for resistance to plant diseases is a continuous effort on the part of plant breeders. Sources of genetic resistance are often limited, despite considerable discovery efforts. Stem rust and stripe rust are two diseases of particular importance in barley (Hordeum vulgare L.) production. The present work aims to develop and deploy genotypes with resistance to these diseases that can be used in future breeding efforts. The Woodies, Woody‐1 (DH160733; Reg. no. GP‐218, PI 704479) and Woody‐2 (DH160754; Reg. no. GP‐219, PI 704480), are two doubled‐haploid genotypes produced via F1 anther culture named in honor of the late Lynn “Woody” Gallagher. These two‐row spring habit barley germplasm accessions were released by the Oregon Agricultural Experiment Station in 2023. These genotypes have demonstrated resistance to both stem and stripe rust at the seedling and adult plant stage in trials conducted between 2018 and 2023. The genetic basis of this resistance appears to be a novel quantitative trait locus conferring resistance to both diseases on chromosome 5H that is different from the known rpg4/Rpg5 complex for stem rust resistance found on the same chromosome. Seed can be requested from the Oregon State University Barley Breeding Program or from the NLGRP Germplasm repository.

Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Plant viruses are ubiquitous throughout plant communities, but research on viral impacts largely focuses on crops. Little is known about how viruses influence wild plants in their native habitats. To address this gap, we examined virus interactions with wild drought-tolerant perennials in California desert natural areas encroached upon by agriculture. We used metagenomics, targeted diagnostics, and phylogenetics to assess virus diversity and clade relationships, and experiments to investigate viral influence on hosts. We focused on three herbaceous perennials ( Cucurbita foetidissima, C. palmata, and Datura wrightii) and tested the hypothesis that these wild species accumulate virus infections typically found in crops and transmitted by polyphagous insects. We predicted that such infections might be retained across seasons and potentially impair plant performance. Virome profiling revealed a rich community of previously characterized virus species (12 total), with virus community structure varying by site and host species. The dominant viruses in the wild hosts were non-native crop pathogens, including cucurbit aphid-borne yellows virus (CABYV) and cucurbit yellow stunting disorder virus (CYSDV). Targeted testing revealed that CABYV infected as many as 88% of sampled wild Cucurbita individuals, with dual CABYV–CYSDV infections common in natural areas adjacent to desert agriculture. CABYV infections reduced shoot and root production in greenhouse experiments with the two wild Cucurbita species. Phylogenetic analyses suggest that CABYV was introduced to California multiple times from other continents. Our findings provide concerning evidence of ways in which human activities can alter virus pressure on wild plants and potentially contribute to plant decline.

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 and feeding on the plant. In particular, cynipid (Hymenoptera: Cynipidae) wasps have evolved to form morphologically complex galls 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 cell wall deposition that dictates 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 valley oak (Quercus lobata) 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 insights into the mechanism of gall induction and the extent to which plants can be entirely reprogrammed to form unique structures and organs.

Abstract: Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown, is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, ABA, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached ‘Turning’ (T) after dark-storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming), were compared to fresh-harvest fruit ‘FHT’. Fruit stored at 12.5°C, had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in ABA. Clear differentiation between postharvest-ripened and ‘FHT’ was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in ‘FHT’ fruit, pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.