The evolution of the duckweed ionome mirrors losses in structural complexity.

BACKGROUND AND AIMS: The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown. METHODS: We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. KEY RESULTS: We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale. CONCLUSIONS: These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.

Acute interstitial nephritis in patients with inflammatory bowel disease treated with vedolizumab: a systematic review.

BACKGROUND: Acute interstitial nephritis (AIN) is a complication of drugs that may cause permanent kidney injury. AIN has been reported in patients with inflammatory bowel disease (IBD) treated with the integrin inhibitor vedolizumab. Through systematic review of existing literature, we aimed to identify and describe cases of AIN in patients with IBD treated with vedolizumab. METHODS: We searched Medline, Embase, Cochrane, and Web of Science Core Collection between 1 January 2009 and 25 April 2023. The search yielded 1473 publications. Titles and abstracts were screened by two independent reviewers. Seventy publications were reviewed in full-text. Eight met the inclusion criteria. Clinical characteristics of AIN cases were extracted. Case causality assessment was performed according to two international adverse drug reaction probability assessment scales. Results were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. RESULTS: Nine biopsy-confirmed cases of AIN were reported in six patients with ulcerative colitis and three with Crohn's disease. Mean age at AIN onset was 36 years (range = 19-58) and the majority of patients were females (n = 6/9). Time from vedolizumab treatment initiation to AIN onset spanned from hours to 12 months. Common symptoms were fever and malaise. Creatinine levels were elevated in all patients. Five patients sustained permanent kidney injury. CONCLUSION: Our findings suggest that vedolizumab, although rarely, could cause AIN in patients with IBD. Awareness of laboratory findings and symptoms consistent with AIN, along with monitoring of the kidney function, could be warranted in patients with IBD treated with vedolizumab.

Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors.

Suberin is a hydrophobic biopolymer that can be deposited at the periphery of cells, forming protective barriers against biotic and abiotic stress. In roots, suberin forms lamellae at the periphery of endodermal cells where it plays crucial roles in the control of water and mineral transport. Suberin formation is highly regulated by developmental and environmental cues. However, the mechanisms controlling its spatiotemporal regulation are poorly understood. Here, we show that endodermal suberin is regulated independently by developmental and exogenous signals to fine-tune suberin deposition in roots. We found a set of four MYB transcription factors (MYB41, MYB53, MYB92, and MYB93), each of which is individually regulated by these two signals and is sufficient to promote endodermal suberin. Mutation of these four transcription factors simultaneously through genome editing leads to a dramatic reduction in suberin formation in response to both developmental and environmental signals. Most suberin mutants analyzed at physiological levels are also affected in another endodermal barrier made of lignin (Casparian strips) through a compensatory mechanism. Through the functional analysis of these four MYBs, we generated plants allowing unbiased investigation of endodermal suberin function, without accounting for confounding effects due to Casparian strip defects, and were able to unravel specific roles of suberin in nutrient homeostasis.

The influences of stomatal size and density on rice abiotic stress resilience.

A warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice (Oryza sativa) yields. Elevated temperatures combined with vapour pressure deficit (VPD) rises are causing stomatal closure, further reducing plant productivity and cooling. It is unclear what stomatal size (SS) and stomatal density (SD) will best suit all these environmental extremes. To understand how stomatal differences contribute to rice abiotic stress resilience, we screened the stomatal characteristics of 72 traditionally bred varieties. We found significant variation in SS, SD and calculated anatomical maximal stomatal conductance (gsmax ) but did not identify any varieties with SD and gsmax as low as transgenic OsEPF1oe plants. Traditionally bred varieties with high SD and small SS (resulting in higher gsmax ) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties assessed were as resilient to drought or salinity as low SD OsEPF1oe transgenic plants. High SD and small SS rice displayed faster stomatal closure during increasing temperature and VPD, but photosynthesis and plant cooling were reduced. Compromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses.

Transcriptional network underpinning ploidy-related elevated leaf potassium in neo-tetraploids.

Whole-genome duplication generates a tetraploid from a diploid. Newly created tetraploids (neo-tetraploids) of Arabidopsis (Arabidopsis thaliana) have elevated leaf potassium (K), compared to their diploid progenitor. Micro-grafting has previously established that this elevated leaf K is driven by processes within the root. Here, mutational analysis revealed that the K+-uptake transporters K+ TRANSPORTER 1 (AKT1) and HIGH AFFINITY K+ TRANSPORTER 5 (HAK5) are not necessary for the difference in leaf K caused by whole-genome duplication. However, the endodermis and salt overly sensitive and abscisic acid-related signaling were necessary for the elevated leaf K in neo-tetraploids. Contrasting the root transcriptomes of neo-tetraploid and diploid wild-type and mutants that suppress the neo-tetraploid elevated leaf K phenotype allowed us to identify a core set of 92 differentially expressed genes associated with the difference in leaf K between neo-tetraploids and their diploid progenitor. This core set of genes connected whole-genome duplication with the difference in leaf K between neo-tetraploids and their diploid progenitors. The set of genes is enriched in functions such as cell wall and Casparian strip development and ion transport in the endodermis, root hairs, and procambium. This gene set provides tools to test the intriguing idea of recreating the physiological effects of whole-genome duplication within a diploid genome.

Phosphorylated B6 vitamer deficiency in SALT OVERLY SENSITIVE 4 mutants compromises shoot and root development.

Stunted growth in saline conditions is a signature phenotype of the Arabidopsis SALT OVERLY SENSITIVE mutants (sos1-5) affected in pathways regulating the salt stress response. One of the mutants isolated, sos4, encodes a kinase that phosphorylates pyridoxal (PL), a B6 vitamer, forming the important coenzyme pyridoxal 5'-phosphate (PLP). Here, we show that sos4-1 and more recently isolated alleles are deficient in phosphorylated B6 vitamers including PLP. This deficit is concomitant with a lowered PL level. Ionomic profiling of plants under standard laboratory conditions (without salt stress) reveals that sos4 mutants are perturbed in mineral nutrient homeostasis, with a hyperaccumulation of transition metal micronutrients particularly in the root, accounting for stress sensitivity. This is coincident with the accumulation of reactive oxygen species, as well as enhanced lignification and suberization of the endodermis, although the Casparian strip is intact and functional. Further, micrografting shows that SOS4 activity in the shoot is necessary for proper root development. Growth under very low light alleviates the impairments, including salt sensitivity, suggesting that SOS4 is important for developmental processes under moderate light intensities. Our study provides a basis for the integration of SOS4 derived B6 vitamers into plant health and fitness.

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome.

The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere.

Targeted expression of the arsenate reductase HAC1 identifies cell type specificity of arsenic metabolism and transport in plant roots.

High Arsenic Concentration 1 (HAC1), an Arabidopsis thaliana arsenate reductase, plays a key role in arsenate [As(V)] tolerance. Through conversion of As(V) to arsenite [As(III)], HAC1 enables As(III) export from roots, and restricts translocation of As(V) to shoots. To probe the ability of different root tissues to detoxify As(III) produced by HAC1, we generated A. thaliana lines expressing HAC1 in different cell types. We investigated the As(V) tolerance phenotypes: root growth, As(III) efflux, As translocation, and As chemical speciation. We showed that HAC1 can function in the outer tissues of the root (epidermis, cortex, and endodermis) to confer As(V) tolerance, As(III) efflux, and limit As accumulation in shoots. HAC1 is less effective in the stele at conferring As(V) tolerance phenotypes. The exception is HAC1 activity in the protoxylem, which we found to be sufficient to restrict As translocation, but not to confer As(V) tolerance. In conclusion, we describe cell type-specific functions of HAC1 that spatially separate the control of As(V) tolerance and As translocation. Further, we identify a key function of protoxylem cells in As(V) translocation, consistent with the model where endodermal passage cells, above protoxylem pericycle cells, form a 'funnel' loading nutrients and potentially toxic elements into the vasculature.

Soil carbonate drives local adaptation in Arabidopsis thaliana.

High soil carbonate limits crop performance especially in semiarid or arid climates. To understand how plants adapt to such soils, we explored natural variation in tolerance to soil carbonate in small local populations (demes) of Arabidopsis thaliana growing on soils differing in carbonate content. Reciprocal field-based transplants on soils with elevated carbonate (+C) and without carbonate (-C) over several years revealed that demes native to (+C) soils showed higher fitness than those native to (-C) soils when both were grown together on carbonate-rich soil. This supports the role of soil carbonate as a driving factor for local adaptation. Analyses of contrasting demes revealed key mechanisms associated with these fitness differences. Under controlled conditions, plants from the tolerant deme A1(+C) native to (+C) soil were more resistant to both elevated carbonate and iron deficiency than plants from the sensitive T6(-C) deme native to (-C) soil. Resistance of A1(+C) to elevated carbonate was associated with higher root extrusion of both protons and coumarin-type phenolics. Tolerant A1(+C) also had better Ca-exclusion than sensitive T6(-C) . We conclude that Arabidopsis demes are locally adapted in their native habitat to soils with moderately elevated carbonate. This adaptation is associated with both enhanced iron acquisition and calcium exclusion.

Inventory of metal complexes circulating in plant fluids: a reliable method based on HPLC coupled with dual elemental and high-resolution molecular mass spectrometric detection.

Description of metal species in plant fluids such as xylem, phloem or related saps remains a complex challenge usually addressed either by liquid chromatography-mass spectrometry, X-ray analysis or computational prediction. To date, none of these techniques has achieved a complete and true picture of metal-containing species in plant fluids, especially for the least concentrated complexes. Here, we present a generic analytical methodology for a large-scale (> 10 metals, > 50 metal complexes) detection, identification and semiquantitative determination of metal complexes in the xylem and embryo sac liquid of the green pea, Pisum sativum. The procedure is based on direct injection using hydrophilic interaction chromatography with dual detection by elemental (inductively coupled plasma mass spectrometry) and molecular (high-resolution electrospray mass spectrometry) mass spectrometric detection. Numerous and novel complexes of iron(II), iron(III), copper(II), zinc, manganese, cobalt(II), cobalt(III), magnesium, calcium, nickel and molybdenum(IV) with several ligands including nicotianamine, citrate, malate, histidine, glutamine, aspartic acid, asparagine, phenylalanine and others are observed in pea fluids and discussed. This methodology provides a large inventory of various types of metal complexes, which is a significant asset for future biochemical and genetic studies into metal transport/homeostasis.

Ascorbate efflux as a new strategy for iron reduction and transport in plants.

Iron (Fe) is essential for virtually all living organisms. The identification of the chemical forms of iron (the speciation) circulating in and between cells is crucial to further understand the mechanisms of iron delivery to its final targets. Here we analyzed how iron is transported to the seeds by the chemical identification of iron complexes that are delivered to embryos, followed by the biochemical characterization of the transport of these complexes by the embryo, using the pea (Pisum sativum) as a model species. We have found that iron circulates as ferric complexes with citrate and malate (Fe(III)3Cit2Mal2, Fe(III)3Cit3Mal1, Fe(III)Cit2). Because dicotyledonous plants only transport ferrous iron, we checked whether embryos were capable of reducing iron of these complexes. Indeed, embryos did express a constitutively high ferric reduction activity. Surprisingly, iron(III) reduction is not catalyzed by the expected membrane-bound ferric reductase. Instead, embryos efflux high amounts of ascorbate that chemically reduce iron(III) from citrate-malate complexes. In vitro transport experiments on isolated embryos using radiolabeled (55)Fe demonstrated that this ascorbate-mediated reduction is an obligatory step for the uptake of iron(II). Moreover, the ascorbate efflux activity was also measured in Arabidopsis embryos, suggesting that this new iron transport system may be generic to dicotyledonous plants. Finally, in embryos of the ascorbate-deficient mutants vtc2-4, vtc5-1, and vtc5-2, the reducing activity and the iron concentration were reduced significantly. Taken together, our results identified a new iron transport mechanism in plants that could play a major role to control iron loading in seeds.

Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots.

Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes. With this approach, we also identify a strong accumulation of manganese in trichoblasts of iron-deficient roots. We demonstrate that confining manganese sequestration in trichoblasts but not in endodermal cells efficiently retains manganese in roots, therefore preventing toxicity in shoots. These results indicate the existence of cell type-specific constraints for efficient metal sequestration in roots. Thus, our approach opens an avenue to investigate element compartmentation and transport pathways in plants.

Loss of ancestral function in duckweed roots is accompanied by progressive anatomical reduction and a re-distribution of nutrient transporters.

Organ loss occurs frequently during plant and animal evolution. Sometimes, non-functional organs are retained through evolution. Vestigial organs are defined as genetically determined structures that have lost their ancestral (or salient) function.1,2,3 Duckweeds, an aquatic monocot family, exhibit both these characteristics. They possess a uniquely simple body plan, variably across five genera, two of which are rootless. Due to the existence of closely related species with a wide diversity in rooting strategies, duckweed roots represent a powerful system for investigating vestigiality. To explore this, we employed a panel of physiological, ionomic, and transcriptomic analyses, with the main goal of elucidating the extent of vestigiality in duckweed roots. We uncovered a progressive reduction in root anatomy as genera diverge and revealed that the root has lost its salient ancestral function as an organ required for supplying nutrients to the plant. Accompanying this, nutrient transporter expression patterns have lost the stereotypical root biased localization observed in other plant species. While other examples of organ loss such as limbs in reptiles4 or eyes in cavefish5 frequently display a binary of presence/absence, duckweeds provide a unique snapshot of an organ with varying degrees of vestigialization in closely related neighbors and thus provide a unique resource for exploration of how organs behave at different stages along the process of loss.

Genetic Characterization of Spring Wheat Germplasm for Macro-, Microelements and Trace Metals.

Wheat as a staple food crop is the main source of micro- and macronutrients for most people of the world and is recognized as an attractive crop for biofortification. This study presents a comprehensive investigation of genomic regions governing grain micro- and macroelements concentrations in a panel of 135 diverse wheat accessions through a genome-wide association study. The genetic diversity panel was genotyped using the genotyping-by-sequencing (GBS) method and phenotyped in two environments during 2017−2018. Wide ranges of variation in nutrient element concentrations in grain were detected among the accessions. Based on 33,808 high-quality single nucleotide polymorphisms (SNPs), 2997 marker-element associations (MEAs) with −log10(p-value) > 3.5 were identified, representing all three subgenomes of wheat for 15-grain concentration elements. The highest numbers of MEAs were identified for Mg (499), followed by S (399), P (394), Ni (381), Cd (243), Ca (229), Mn (224), Zn (212), Sr (212), Cu (111), Rb (78), Fe (63), Mo (43), K (32) and Co (19). Further, MEAs associated with multiple elements and referred to as pleiotropic SNPs were identified for Mg, P, Cd, Mn, and Zn on chromosomes 1B, 2B, and 6B. Fifty MEAs were subjected to validation using KASIB multilocational trial at six sites in two years using 39 genotypes. Gene annotation of MEAs identified putative candidate genes that potentially encode different types of proteins related to disease, metal transportation, and metabolism. The MEAs identified in the present study could be potential targets for further validation and may be used in marker-assisted breeding to improve nutrient element concentrations in wheat grain.

Variation of Macro- and Microelements, and Trace Metals in Spring Wheat Genetic Resources in Siberia.

Western Siberia is one of the major spring wheat regions of Russia, cultivating over 7 Mha. The objective of the study was to evaluate the variation of macro- and microelements, and of trace metals in four distinct groups of genetic resources: primary synthetics from CIMMYT (37 entries), primary synthetics from Japan (8), US hard red spring wheat cultivars (14), and material from the Kazakhstan-Siberian Network on Spring Wheat Improvement (KASIB) (74). The experiment was conducted at Omsk State Agrarian University, using a random complete block design with four replicates in 2017 and 2018. Concentrations of 15 elements were included in the analysis: macroelements, Ca, K, Mg, P, and S; microelements, Fe, Cu, Mn, and Zn; toxic trace elements, Cd, Co, Ni; and trace elements, Mo, Rb, and Sr. Protein content was found to be positively correlated with the concentrations of 11 of the elements in one or both years. Multiple regression was used to adjust the concentration of each element, based on significant correlations with agronomic traits and macroelements. All 15 elements were evaluated for their suitability for genetic enhancement, considering phenotypic variation, their share of the genetic component in this variation, as well as the dependence of the element concentration on other traits. Three trace elements (Sr, Mo, and Co) were identified as traits that were relatively easy to enhance through breeding. These were followed by Ca, Cd, Rb, and K. The important biofortification elements Mn and Zn were among the traits that were difficult to enhance genetically. The CIMMYT and Japanese synthetics had significantly higher concentrations of K and Sr, compared to the local check. The Japanese synthetics also had the highest concentrations of Ca, S, Cd, and Mo. The US cultivars had concentrations of Ca as high as the Japanese synthetics, and the highest concentrations of Mg and Fe. KASIB's germplasm had near-average values for most elements. Superior germplasm, with high macro- and microelement concentrations and low trace-element concentrations, was found in all groups of material included.

A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment.

Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles.

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis.

Plant roots and animal guts have evolved specialized cell layers to control mineral nutrient homeostasis. These layers must tolerate the resident microbiota while keeping homeostatic integrity. Whether and how the root diffusion barriers in the endodermis, which are critical for the mineral nutrient balance of plants, coordinate with the microbiota is unknown. We demonstrate that genes controlling endodermal function in the model plant Arabidopsis thaliana contribute to the plant microbiome assembly. We characterized a regulatory mechanism of endodermal differentiation driven by the microbiota with profound effects on nutrient homeostasis. Furthermore, we demonstrate that this mechanism is linked to the microbiota's capacity to repress responses to the phytohormone abscisic acid in the root. Our findings establish the endodermis as a regulatory hub coordinating microbiota assembly and homeostatic mechanisms.

Two chemically distinct root lignin barriers control solute and water balance.

Lignin is a complex polymer deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in response to endogenous and exogenous cues. In roots, a fine band of lignin, the Casparian strip encircles endodermal cells. This forms an extracellular barrier to solutes and water and plays a critical role in maintaining nutrient homeostasis. A signalling pathway senses the integrity of this diffusion barrier and can induce over-lignification to compensate for barrier defects. Here, we report that activation of this endodermal sensing mechanism triggers a transcriptional reprogramming strongly inducing the phenylpropanoid pathway and immune signaling. This leads to deposition of compensatory lignin that is chemically distinct from Casparian strip lignin. We also report that a complete loss of endodermal lignification drastically impacts mineral nutrients homeostasis and plant growth.

Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips.

Casparian strips (CSs) are cell wall modifications of vascular plants restricting extracellular free diffusion into and out of the vascular system [1]. This barrier plays a critical role in controlling the acquisition of nutrients and water necessary for normal plant development [2-5]. CSs are formed by the precise deposition of a band of lignin approximately 2 µm wide and 150 nm thick spanning the apoplastic space between adjacent endodermal cells [6, 7]. Here, we identified a copper-containing protein, Uclacyanin1 (UCC1), that is sub-compartmentalized within the CS. UCC1 forms a central CS nanodomain in comparison with other CS-located proteins that are found to be mainly accumulated at the periphery of the CS. We found that loss-of-function of two uclacyanins (UCC1 and UCC2) reduces lignification specifically in this central CS nanodomain, revealing a nano-compartmentalized machinery for lignin polymerization. This loss of lignification leads to increased endodermal permeability and, consequently, to a loss of mineral nutrient homeostasis.