Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

Zinc/Iron-Regulated Transporter-like Protein CsZIP4 Enhances Zinc and Nitrogen Uptake and Alleviates Zinc Stresses with Nitrogen Supply in Camellia sinensis

Zinc (Zn) and nitrogen (N) are the two crucial nutrients for tea plant growth and development and contribute to the quality formation of tea fresh leaves. In this study, a zinc/iron-regulated transporter-like protein 4 gene (i.e., CsZIP4) was functionally characterized. Expression profiling showed that CsZIP4 could be induced by Zn stresses and a N deficiency. Heterologous expression of CsZIP4 in yeast revealed that CsZIP4 possessed the capacity for Zn transport but not ammonium. Moreover, CsZIP4 overexpression in Arabidopsis thaliana promoted Zn and N uptake and transport and contributed to alleviate Zn stresses by collaborating with N supply, which might be interrelated to the expression of N or Zn metabolism-related genes, such as AtNRT1.1 and AtZIP4. Additionally, CsZIP4 was localized in the plasma membrane and chloroplast, which was helpful in maintaining cellular homeostasis under a Zn excess. Furthermore, silencing of CsZIP4 in tea plants by virus-induced gene silencing increased the chlorophyll content but decreased the Zn content. Finally, the yeast one-hybrid assay demonstrated that CsbZIP2 bound to the CsZIP4 promoter. These results will shed light on the functions of CsZIP4 in the N and Zn interaction in tea plants.

Root-based inorganic carbon uptake increases the growth of Arabidopsis thaliana and changes transporter expression and nitrogen and sulfur metabolism

Root-based uptake of inorganic carbon has been suggested as an additional carbon source. Our study aimed to characterize and understand the root-based uptake and fixation mechanisms and their impact on plant growth. 13C-labeled bicarbonate fed to Arabidopsis roots was assimilated into aspartic acid but mainly into sucrose, indicating that the added inorganic carbon was transported to the leaves. A hydroponic treatment was also established for A. thaliana using 2 mM NaHCO3 at pH 5.6, which enhanced the photosynthetic and growth parameters. According to transcriptome sequencing data, the observed enhancement in growth may be orchestrated by trehalose-6-phosphate signaling and supported by augmented nitrogen and sulfur assimilation. The analysis also revealed regulatory and transporter activities, including several nitrate (NRT2.1), and sulfate transporter (SULTR1;1 and SULTR1;2) candidates that could participate in bicarbonate uptake. Different transporters and carbon fixation mutants were assessed. Arabidopsis homologs of SLOW-TYPE ANION CHANNEL 1 (slah3) CARBONIC ANHYDRASE (βca4), and SULFATE TRANSPORTER (sultr1;2) mutants were shown to be inferior to the bicarbonate-treated wild types in several growth and root ultrastructural parameters. Besides, aquaporin genes PIP1;3 and PIP2;6 could play a negative role in the carbon uptake by venting carbon dioxide out of the plant. The findings support the hypothesis that the inorganic carbon is taken up by the root anion channels, mostly transported up to the shoots by the xylem, and fixed there by RuBisCo after the conversion to CO2 by carbonic anhydrases. The process boosts photosynthesis and growth by providing an extra carbon supply.

Carbohydrate distribution via SWEET17 is critical for Arabidopsis inflorescence branching under drought

Sugars Will Eventually be Exported Transporters (SWEETs) are the most recently discovered family of plant sugar transporters. By acting as uniporters, SWEETs facilitate the diffusion of sugars across cell membranes and play an important role in various physiological processes such as abiotic stress adaptation. AtSWEET17, a vacuolar fructose facilitator, was shown to be involved in the modulation of the root system during drought. In addition, previous studies have shown that overexpression of an apple homolog leads to increased drought tolerance in tomato plants. Therefore, SWEET17 might be a molecular element involved in plant responses to drought. However, the role and function of SWEET17 in above-ground tissues of Arabidopsis under drought stress remain elusive. By combining gene expression analysis and stem architecture with the sugar profiles of different above-ground tissues, we uncovered a putative role for SWEET17 in carbohydrate supply and thus cauline branch elongation, especially during periods of carbon limitation, as occurs under drought stress. Thus, SWEET17 seems to be involved in maintaining efficient plant reproduction under drought stress conditions.

Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana

Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.

The AT-hook protein AHL29 promotes Bacillus subtilis colonization by suppressing SWEET2-mediated sugar retrieval in Arabidopsis roots

Beneficial Bacillus subtilis (BS) symbiosis could combat root pathogenesis, but it relies on root-secreted sugars. Understanding the molecular control of sugar flux during colonization would benefit biocontrol applications. The SWEET (Sugar Will Eventually Be Exported Transporter) uniporter regulates microbe-induced sugar secretion from roots; thus, its homologs may modulate sugar distribution upon BS colonization. Quantitative polymerase chain reaction revealed that gene transcripts of SWEET2, but not SWEET16 and 17, were significantly induced in seedling roots after 12 h of BS inoculation. Particularly, SWEET2-β-glucuronidase fusion proteins accumulated in the apical mature zone where BS abundantly colonized. Yet, enhanced BS colonization in sweet2 mutant roots suggested a specific role for SWEET2 to constrain BS propagation, probably by limiting hexose secretion. By employing yeast one-hybrid screening and ectopic expression in Arabidopsis protoplasts, the transcription factor AHL29 was identified to function as a repressor of SWEET2 expression through the AT-hook motif. Repression occurred despite immunity signals. Additionally, enhanced SWEET2 expression and reduced colonies were specifically detected in roots of BS-colonized ahl29 mutant. Taken together, we propose that BS colonization may activate repression of AHL29 on SWEET2 transcription that would be enhanced by immunity signals, thereby maintaining adequate sugar secretion for a beneficial Bacillus association.

Kritzler U, Burslem DFRP. External aluminium supply regulates photosynthesis and carbon partitioning in the Al-accumulating tropical shrub Melastoma malabathricum

Aluminium (Al) is toxic to most plants, but recent research has suggested that Al addition may stimulate growth and nutrient uptake in some species capable of accumulating high tissue Al concentrations. The physiological basis of this growth response is unknown, but it may be associated with processes linked to the regulation of carbon assimilation and partitioning by Al supply. To test alternative hypotheses for the physiological mechanism explaining this response, we examined the effects of increasing Al concentrations in the growth medium on tissue nutrient concentrations and carbon assimilation in two populations of the Al-accumulator Melastoma malabathricum. Compared to seedlings grown in a control nutrient solution containing no Al, mean rates of photosynthesis and respiration increased by 46% and 27%, respectively, total non-structural carbohydrate concentrations increased by 45%, and lignin concentration in roots decreased by 26% when seedlings were grown in a nutrient solution containing 2.0 mM Al. The concentrations of P, Ca and Mg in leaves and stems increased by 31%, 22%, and 26%, respectively, in response to an increase in nutrient solution Al concentration from 0 to 2.0 mM. Elemental concentrations in roots increased for P (114%), Mg (61%) and K (5%) in response to this increase in Al concentration in the nutrient solution. Plants derived from an inherently faster-growing population had a greater relative increase in final dry mass, net photosynthetic and respiration rates and total non-structural carbohydrate concentrations in response to higher external Al supply. We conclude that growth stimulation by Al supply is associated with increases in photosynthetic and respiration rates and enhanced production of non-structural carbohydrates that are differentially allocated to roots, as well as stimulation of nutrient uptake. These responses suggest that internal carbon assimilation is up-regulated to provide the necessary resources of non-structural carbohydrates for uptake, transport and storage of Al in Melastoma malabathricum. This physiological mechanism has only been recorded previously in one other plant species, Camellia sinensis, which last shared a common ancestor with M. malabathricum more than 120 million years ago.

Understanding atrazine elimination via treatment of the enzyme-based Fenton reaction: Kinetics, mechanism, reaction pathway, and metabolites toxicity

The degradation kinetics and mechanism of atrazine (ATZ) via an enzyme-based Fenton reaction were investigated at various substrate concentrations and pH values. Toxicological assessment was conducted on ATZ and its degradation products, and the associated reaction pathway was examined. The in situ production of hydrogen peroxide (H2O2) was monitored within the range of 3-15 mM, depending on the increase in glucose concentration, while decreasing the pH to 3.2-5.1 (initial pH of 5.8) or 6.5-7.4 (initial pH of 7.7). The degradation efficiency of ATZ was approximately 2-3 times higher at an initial pH of 5.8 with lower glucose concentrations than at an initial pH of 7.7 with higher substrate concentrations during the enzyme-based Fenton reaction. The apparent pseudo-first-order rate constant for H2O2 decomposition under various conditions in the presence of ferric citrate was 1.9-6.3 × 10-5 s-1. The •OH concentration ([•OH]ss) during the enzyme-based Fenton reaction was 0.5-4.1 × 10-14 M, and the second-order rate constant for ATZ degradation was 1.5-3.3 × 109 M-1 s-1. ATZ intrinsically hinders the growth and development of Arabidopsis thaliana, and its inhibitory effect is marginal, depending on the reaction time of the enzyme-based Fenton process. The ATZ transformation during this process occurs through dealkylation, hydroxylation, and dechlorination via •OH-mediated reactions. The degradation kinetics, mechanism, and toxicological assessment in the present study could contribute to the development and application of enzyme-based Fenton reactions for in situ pollutant abatement. Moreover, the enzyme-based Fenton reaction could be an environmentally benign and applicable approach for eliminating persistent organic matter, such as herbicides, using diverse H2O2-producing microbes and ubiquitous ferric iron with organic complexes.

Co-cultures from Plants and Cyanobacteria: A New Way for Production Systems in Agriculture and Bioprocess Engineering

Due to the global increase in the world population, it is not possible to ensure a sufficient food supply without additional nitrogen input into the soil. About 30-50% of agricultural yields are due to the use of chemical fertilizers in modern times. However, overfertilization threatens biodiversity, such as nitrogen-loving, fast-growing species overgrow others. The production of artificial fertilizers produces nitrogen oxides, which act as greenhouse gases. In addition, overfertilization of fields also releases ammonia, which damages surface waters through acidification and eutrophication. Diazotrophic cyanobacteria, which usually form a natural, stable biofilm, can fix nitrogen from the atmosphere and release it into the environment. Thus, they could provide an alternative to artificial fertilizers. In addition to this, biofilms stabilize soils and thus protect against soil erosion and desiccation. This chapter deals with the potential of cyanobacteria as the use of natural fertilizer is described. Possible partners such as plants and callus cells and the advantages of artificial co-cultivation will be discussed later. In addition, different cultivation systems for studying artificial co-cultures will be presented. Finally, the potential of artificial co-cultures in the agar industry will be discussed.

Vacuolar sugar transporter EARLY RESPONSE TO DEHYDRATION6-LIKE4 affects fructose signaling and plant growth

Regulation of intracellular sugar homeostasis is maintained by regulation of activities of sugar import and export proteins residing at the tonoplast. We show here that the EARLY RESPONSE TO DEHYDRATION6-LIKE4 (ERDL4) protein, a member of the monosaccharide transporter family, resides in the vacuolar membrane in Arabidopsis (Arabidopsis thaliana). Gene expression and subcellular fractionation studies indicated that ERDL4 participates in fructose allocation across the tonoplast. Overexpression of ERDL4 increased total sugar levels in leaves due to a concomitantly induced stimulation of TONOPLAST SUGAR TRANSPORTER 2 (TST2) expression, coding for the major vacuolar sugar loader. This conclusion is supported by the finding that tst1-2 knockout lines overexpressing ERDL4 lack increased cellular sugar levels. ERDL4 activity contributing to the coordination of cellular sugar homeostasis is also indicated by 2 further observations. First, ERDL4 and TST genes exhibit an opposite regulation during a diurnal rhythm, and second, the ERDL4 gene is markedly expressed during cold acclimation, representing a situation in which TST activity needs to be upregulated. Moreover, ERDL4-overexpressing plants show larger rosettes and roots, a delayed flowering time, and increased total seed yield. Consistently, erdl4 knockout plants show impaired cold acclimation and freezing tolerance along with reduced plant biomass. In summary, we show that modification of cytosolic fructose levels influences plant organ development and stress tolerance.

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Background

Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions.

Methods

Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions.

Results

Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software.

Conclusions

The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.

Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids

BACKGROUND

Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we turn to hybrids, which provide a facile means for creating many novel allele combinations.

RESULTS

We focus on the interaction between alleles of the same locus, i.e., dominance, and perform a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive, dominant gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below the parental average. Unlike in the additive genes, regulatory rare-allele burden in the dominant gene set is strongly correlated with F1 rosette size, even though it only mildly covaries with the expression level of these genes.

CONCLUSIONS

Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.

Chloroplast magnesium transporters play essential but differential roles in maintaining magnesium homeostasis

Magnesium (Mg2+) is essential for photosynthesis in the chloroplasts of land plants and algae. Being the central ion of chlorophyll, cofactor and activator of many photosynthetic enzymes including RuBisCO, magnesium-deficient plants may suffer from leaf chlorosis symptoms and retarded growth. Therefore, the chloroplast Mg2+ concentration is tightly controlled by magnesium transport proteins. Recently, three different transporters from two distinct families have been identified in the chloroplast inner envelope of the model plant Arabidopsis thaliana: MGT10, MGR8, and MGR9. Here, we assess the individual roles of these three proteins in maintaining chloroplast Mg2+ homeostasis and regulating photosynthesis, and if their role is conserved in the model green alga Chlamydomonas reinhardtii. Phylogenetic analysis and heterologous expression revealed that the CorC-like MGR8 and MGR9 transport Mg2+ by a different mechanism than the CorA-like MGT10. MGR8 and MGT10 genes are highest expressed in leaves, indicating a function in chloroplast Mg2+ transport. MGR9 is important for chloroplast function and plant adaptation in conditions of deficiency or excess of Mg2+. Transmission electron microscopy indicated that MGT10 plays a differential role in thylakoid stacking than MGR8 and MGR9. Furthermore, we report that MGR8, MGR9, and MGT10 are involved in building up the pH gradient across the thylakoid membrane and activating photoprotection in conditions of excess light, however the mechanism has not been resolved yet. While there are no chloroplast MGR-like transporters in Chlamydomonas, we show that MRS4 is a homolog of MGT10, that is required for photosynthesis and cell growth. Taken together, our findings reveal that the studied Mg2+ transporters play essential but differential roles in maintaining chloroplast Mg2+ homeostasis.

Moonlighting Arabidopsis molybdate transporter 2 family and GSH-complex formation facilitate molybdenum homeostasis

Molybdenum (Mo) as essential micronutrient for plants, acts as active component of molybdenum cofactor (Moco). Core metabolic processes like nitrate assimilation or abscisic-acid biosynthesis rely on Moco-dependent enzymes. Although a family of molybdate transport proteins (MOT1) is known to date in Arabidopsis, molybdate homeostasis remained unclear. Here we report a second family of molybdate transporters (MOT2) playing key roles in molybdate distribution and usage. KO phenotype-analyses, cellular and organ-specific localization, and connection to Moco-biosynthesis enzymes via protein-protein interaction suggest involvement in cellular import of molybdate in leaves and reproductive organs. Furthermore, we detected a glutathione-molybdate complex, which reveals how vacuolar storage is maintained. A putative Golgi S-adenosyl-methionine transport function was reported recently for the MOT2-family. Here, we propose a moonlighting function, since clear evidence of molybdate transport was found in a yeast-system. Our characterization of the MOT2-family and the detection of a glutathione-molybdate complex unveil the plant-wide way of molybdate.

Production of, Factors Affecting, Gene Regulations, and Challenges in Tissue Cultured Plant through Soilless Culture

Soilless culture also known as water based culture and substrate based culture has immense potential to grow tissue cultured plants in a closed and controlled environment system. This review analyzes the various factors that affect the vegetative growth, reproductive growth, metabolic processes, and gene regulatory functions of tissue cultured plants and the suitability of soilless culture for tissue culture plants. Experiments show that morphological and reproductive abnormalities are mitigated in tissue cultured plants by gene regulation in a closed and controlled environment system. Various factors of a soilless culture influence gene regulation and enhance cellular, molecular, and biochemical processes and compensate constraints in tissue cultured plants in closed and controlled environment conditions. The soilless culture can be utilized to harden and grow tissue culture plants. The tissue cultured plants counter water logging problems and are supplied with nutrients at 7 day intervals in the water based culture. It is necessary to analyze the involvement of regulatory genes in detail in combating challenges of tissue cultured plants in soilless cultures under closed systems. Detailed studies are also required to determine anatomy, genesis, and function of microtuber cells in tissue cultured plants.

The Arabidopsis D27-LIKE1 is a cis/cis/trans-β-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level

The enzyme DWARF27 (D27) catalyzes the reversible isomerization of all-trans- into 9-cis-β-carotene, initiating strigolactone (SL) biosynthesis. Genomes of higher plants encode two D27-homologs, D27-like1 and -like2, with unknown functions. Here, we investigated the enzymatic activity and biological function of the Arabidopsis D27-like1. In vitro enzymatic assays and expression in Synechocystis sp. PCC6803 revealed an unreported 13-cis/15-cis/9-cis- and a 9-cis/all-trans-β-carotene isomerization. Although disruption of AtD27-like1 did not cause SL deficiency phenotypes, overexpression of AtD27-like1 in the d27 mutant restored the more-branching phenotype, indicating a contribution of AtD27-like1 to SL biosynthesis. Accordingly, generated d27 d27like1 double mutants showed a more pronounced branching phenotype compared to d27. The contribution of AtD27-like1 to SL biosynthesis is likely a result of its formation of 9-cis-β-carotene that was present at higher levels in AtD27-like1 overexpressing lines. By contrast, AtD27-like1 expression correlated negatively with the content of 9-cis-violaxanthin, a precursor of ABA, in shoots. Consistently, ABA levels were higher in shoots and also in dry seeds of the d27like1 and d27 d27like1 mutants. Transgenic lines expressing GUS driven by the AtD27LIKE1 promoter and transcript analysis of hormone-treated Arabidopsis seedlings revealed that AtD27LIKE1 is expressed in different tissues and affects ABA and auxin. Taken together, our work reports a cis/cis-β-carotene isomerase that affects the content of both cis-carotenoid-derived plant hormones, ABA and SLs.

Multi-cation exchanges involved in cesium and potassium sorption mechanisms on vermiculite and micaceous structures

Vermiculite and micaceous minerals are relevant Cs⁺ sorbents in soils and sediments. To understand the bioavailability of Cs⁺ in soils resulting from multi-cation exchanges, sorption of Cs⁺ onto clay minerals was performed in batch experiments with solutions containing Ca²⁺, Mg²⁺, and K⁺. A sequence between a vermiculite and various micaceous structures has been carried out by conditioning a vermiculite at various amounts of K. Competing cation exchanges were investigated as function of Cs⁺ concentration. The contribution of K⁺ on trace Cs⁺ desorption is probed by applying different concentrations of K⁺ on Cs-doped vermiculite and micaceous structures. Cs sorption isotherms at chemical equilibrium were combined with elemental mass balances in solution and structural analyses. Cs⁺ replaces easily Mg²⁺  > Ca²⁺ and competes scarcely with K⁺. Cs⁺ is strongly adsorbed on the various matrix, and a K/Cs ratio of about a thousand is required to remobilize Cs⁺. Cs⁺ is exchangeable as long as the clay interlayer space remains open to Ca²⁺. However, an excess of K⁺, as well as Cs⁺, in solution leads to the collapse of the interlayer spaces that locks the Cs into the structure. Once K⁺ and/or Cs⁺ collapse the interlayer space, the external sorption sites are then particularly involved in Cs sorption. Subsequently, Cs⁺ preferentially exchanges with Ca²⁺ rather than Mg²⁺. Mg²⁺ is extruded from the interlayer space by Cs⁺ and K⁺ adsorption, excluded from short interlayer space and replaced by Ca²⁺ as Cs⁺ desorbs.

Mucilaginibacter sp. K Improves Growth and Induces Salt Tolerance in Nonhost Plants via Multilevel Mechanisms

Soil salinity negatively modulates plant growth and development, contributing to severe decreases in the growth and production of crops. Mucilaginibacter sp. K is a root endophytic bacterium that was previously reported by our laboratory to stimulate growth and confer salt tolerance in Arabidopsis (Arabidopsis thaliana). The main purpose of the present study is to elucidate the physiological and molecular machinery responsible for the prospective salt tolerance as imparted by Mucilaginibacter sp. K. We first report that auxin, gibberellin, and MPK6 signalings were required for strain K-induced growth promotion and salt tolerance in Arabidopsis. Then, this strain was assessed as a remediation strategy to improve maize performance under salinity stress. Under normal growth conditions, the seed vigor index, nitrogen content, and plant growth were significantly improved in maize. After NaCl exposure, strain K significantly promoted the growth of maize seedlings, ameliorated decline in chlorophyll content and reduced accretion of MDA and ROS compared with the control. The possible mechanisms involved in salt resistance in maize could be the improved activities of SOD and POD (antioxidative system) and SPS (sucrose biosynthesis), upregulated content of total soluble sugar and ABA, and reduced Na⁺ accumulation. These physiological changes were then confirmed by induced gene expression for ion transportation, photosynthesis, ABA biosynthesis, and carbon metabolism. In summary, these results suggest that strain K promotes plant growth through increases in photosynthesis and auxin- and MPK6-dependent pathways; it also bestows salt resistance on plants through protection against oxidative toxicity, Na⁺ imbalance, and osmotic stress, along with the activation of auxin-, gibberellin-, and MPK6-dependent signaling pathways. This is the first detailed report of maize growth promotion by a Mucilaginibacter sp. strain from wild plant. This strain could be used as a favorable biofertilizer and a salinity stress alleviator for maize, with further ascertainment as to its reliability of performance under field conditions and in the presence of salt stress.

Precise Quantification of Molybdate In Vitro by the FRET-Based Nanosensor 'MolyProbe'

Molybdenum (Mo) is an essential trace element in all kingdoms of life. Mo is bioavailable as the oxyanion molybdate and gains biological activity in eukaryotes when bound to molybdopterin, forming the molybdenum cofactor. The imbalance of molybdate homeostasis results in growth deficiencies or toxic symptoms within plants, fungi and animals. Recently, fluorescence resonance energy transfer (FRET) methods have emerged, monitoring cellular and subcellular molybdate distribution dynamics using a genetically encoded molybdate-specific FRET nanosensor, named MolyProbe. Here, we show that the MolyProbe system is a fast and reliable in vitro assay for quantitative molybdate determination. We added a Strep-TagII affinity tag to the MolyProbe protein for quick and easy purification. This MolyProbe is highly stable, resistant to freezing and can be stored for several weeks at 4 °C. Furthermore, the molybdate sensitivity of the assay peaked at low nM levels. Additionally, The MolyProbe was applied in vitro for quantitative molybdate determination in cell extracts of the plant Arabidopsis thaliana, the fungus Neurospora crassa and the yeast Saccharomyces cerevisiae. Our results show the functionality of the Arabidopsis thaliana molybdate transporter MOT1.1 and indicate that FRET-based molybdate detection is an excellent tool for measuring bioavailable Mo.

Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances

The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.

Root-Specific Expression of Vitis vinifera VviNPF2.2 Modulates Shoot Anion Concentration in Transgenic Arabidopsis

Grapevines (Vitis vinifera L., Vvi) on their roots are generally sensitive to salt-forming ions, particularly chloride (Cl-) when grown in saline environments. Grafting V. vinifera scions to Cl--excluding hybrid rootstocks reduces the impact of salinity. Molecular components underlying Cl--exclusion in Vitis species remain largely unknown, however, various anion channels and transporters represent good candidates for controlling this trait. Here, two nitrate/peptide transporter family (NPF) members VviNPF2.1 and VviNPF2.2 were isolated. Both highly homologous proteins localized to the plasma membrane of Arabidopsis (Arabidopsis thaliana) protoplasts. Both were expressed primarily in grapevine roots and leaves and were more abundant in a Cl--excluding rootstock compared to a Cl--includer. Quantitative PCR of grapevine roots revealed that VviNPF2.1 and 2.2 expression was downregulated by high [NO3 -] resupply post-starvation, but not affected by 25 mM Cl-. VviNPF2.2 was functionally characterized using an Arabidopsis enhancer trap line as a heterologous host which enabled cell-type-specific expression. Constitutive expression of VviNPF2.2 exclusively in the root epidermis and cortex reduced shoot [Cl-] after a 75 mM NaCl treatment. Higher expression levels of VviNPF2.2 correlated with reduced Arabidopsis xylem sap [NO3 -] when not salt stressed. We propose that when expressed in the root epidermis and cortex, VviNPF2.2 could function in passive anion efflux from root cells, which reduces the symplasmic Cl- available for root-to-shoot translocation. VviNPF2.2, through its role in the root epidermis and cortex, could, therefore, be beneficial to plants under salt stress by reducing net shoot Cl- accumulation.

Physiological Importance of Molybdate Transporter Family 1 in Feeding the Molybdenum Cofactor Biosynthesis Pathway in Arabidopsis thaliana

Molybdate uptake and molybdenum cofactor (Moco) biosynthesis were investigated in detail in the last few decades. The present study critically reviews our present knowledge about eukaryotic molybdate transporters (MOT) and focuses on the model plant Arabidopsis thaliana, complementing it with new experiments, filling missing gaps, and clarifying contradictory results in the literature. Two molybdate transporters, MOT1.1 and MOT1.2, are known in Arabidopsis, but their importance for sufficient molybdate supply to Moco biosynthesis remains unclear. For a better understanding of their physiological functions in molybdate homeostasis, we studied the impact of mot1.1 and mot1.2 knock-out mutants, including a double knock-out on molybdate uptake and Moco-dependent enzyme activity, MOT localisation, and protein–protein interactions. The outcome illustrates different physiological roles for Moco biosynthesis: MOT1.1 is plasma membrane located and its function lies in the efficient absorption of molybdate from soil and its distribution throughout the plant. However, MOT1.1 is not involved in leaf cell imports of molybdate and has no interaction with proteins of the Moco biosynthesis complex. In contrast, the tonoplast-localised transporter MOT1.2 exports molybdate stored in the vacuole and makes it available for re-localisation during senescence. It also supplies the Moco biosynthesis complex with molybdate by direct interaction with molybdenum insertase Cnx1 for controlled and safe sequestering.

Plastid retrograde regulation of miRNA expression in response to light stress

BACKGROUND

MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play a pivotal role in the regulation of plant development and responses to the surrounding environment. Despite the efforts made to elucidate their function in the adaptation of plants to many abiotic and biotic stresses, their role in high light (HL) stress is still vague. HL stress often arises upon plant exposure to full sunlight. Subsequent changes in nuclear gene expression are triggered by chloroplast-derived retrograde signals.

RESULTS

In this study, we show that HL is involved in miRNA-dependent regulation in Arabidopsis thaliana rosettes. Microtranscriptomic screening revealed a limited number of miRNAs reacting to HL. To explain the miRNA regulation mechanisms at the different biogenesis stages, chemical and genetic approaches were applied. First, we tested the possible role of plastoquinone (PQ) redox changes using photosynthetic electron transport chain inhibitors. The results suggest that increased primary transcript abundance (pri-miRNAs) of HL-regulated miRNAs is dependent on signals upstream of PQ. This indicates that such signals may originate from photosystem II, which is the main singlet oxygen (¹O₂) source. Nevertheless, no changes in pri-miRNA expression upon a dark-light shift in the conditional fluorescent (flu) mutant producing ¹O₂ were observed when compared to wild-type plants. Thus, we explored the ¹O₂ signaling pathway, which is initiated independently in HL and is related to β-carotene oxidation and production of volatile derivatives, such as β-cyclocitral (β-CC). Pri-miRNA induction by β-CC, which is a component of this ¹O₂ pathway, as well as an altered response in the methylene blue sensitivity 1 (mbs1) mutant support the role of ¹O₂ signaling in miRNA regulation.

CONCLUSIONS

We show that light stress triggers changes in miRNA expression. This stress response may be regulated by reactive oxygen species (ROS)-related signaling. In conclusion, our results link ROS action to miRNA biogenesis, suggesting its contribution to inconsistent pri- and mature miRNA dynamics.

Cytidine Triphosphate Synthase Four From Arabidopsis thaliana Attenuates Drought Stress Effects

Cytidine triphosphate synthase (CTPS) catalyzes the final step in pyrimidine de novo synthesis. In Arabidopsis, this protein family consists of five members (CTPS1-5), and all of them localize to the cytosol. Specifically, CTPS4 showed a massive upregulation of transcript levels during abiotic stress, in line with increased staining of CTPS4 promoter:GUS lines in hypocotyl, root and to lesser extend leaf tissues. In a setup to study progressive drought stress, CTPS4 knockout mutants accumulated less fresh and dry weight at days 5-7 and showed impaired ability to recover from this stress after 3 days of rewatering. Surprisingly, a thorough physiological characterization of corresponding plants only revealed alterations in assimilation and accumulation of soluble sugars including those related to drought stress in the mutant. Bimolecular fluorescence complementation (BiFC) studies indicated the interaction of CTPS4 with other isoforms, possibly affecting cytoophidia (filaments formed by CTPS formation. Although the function of these structures has not been thoroughly investigated in plants, altered enzyme activity and effects on cell structure are reported in other organisms. CTPS activity is required for cell cycle progression and growth. Furthermore, drought can lead to the accumulation of reactive oxygen species (ROS) and by this, to DNA damage. We hypothesize that effects on the cell cycle or DNA repair might be relevant for the observed impaired reduced drought stress tolerance of CTPS4 mutants.

Oxylipin signaling in salt-stressed soybean is modulated by ligand-dependent interaction of Class II acyl-CoA-binding proteins with lipoxygenase

Plant lipoxygenases (LOXs) oxygenate linoleic and linolenic acids, creating hydroperoxy derivatives, and from these, jasmonates and other oxylipins are derived. Despite the importance of oxylipin signaling, its activation mechanism remains largely unknown. Here, we show that soybean ACYL-COA-BINDING PROTEIN3 (ACBP3) and ACBP4, two Class II acyl-CoA-binding proteins, suppressed activity of the vegetative LOX homolog VLXB by sequestering it at the endoplasmic reticulum. The ACBP4-VLXB interaction was facilitated by linoleoyl-CoA and linolenoyl-CoA, which competed with phosphatidic acid (PA) for ACBP4 binding. In salt-stressed roots, alternative splicing produced ACBP variants incapable of VLXB interaction. Overexpression of the variants enhanced LOX activity and salt tolerance in Arabidopsis and soybean hairy roots, whereas overexpressors of the native forms exhibited reciprocal phenotypes. Consistently, the differential alternative splicing pattern in two soybean genotypes coincided with their difference in salt-induced lipid peroxidation. Salt-treated soybean roots were enriched in C32:0-PA species that showed high affinity to Class II ACBPs. We conclude that PA signaling and alternative splicing suppress ligand-dependent interaction of Class II ACBPs with VLXB, thereby triggering lipid peroxidation during salt stress. Hence, our findings unveil a dual mechanism that initiates the onset of oxylipin signaling in the salinity response.

BrpNAC895 and BrpABI449 coregulate the transcription of the afflux-type Cd transporter BrpHMA2 in Brassica parachinensis

Brassica parachinensis is a popular leafy vegetable. It is able to accumulate high concentration of Cd, however, the molecular mechanism of Cd accumulation is unknown. This study investigated the function and regulatory mechanism of the Cd-responsive metal ion transporter gene BrpHMA2. BrpHMA2 was induced by Cd stress and specifically expressed in vascular tissues, and the protein was localized in the plasma membrane. Heterologous expression of BrpHMA2 enhanced Cd accumulation and Cd sensitivity in transgenic Arabidopsis and yeast. After Cd stress, the transcriptional factors BrpNAC895 and BrpABI449, which may recognize the ABREs in the BrpHMA2 promoter, were also differentially expressed. The transcriptional regulation of BrpHMA2 was further investigated using ChIP-qPCR, EMSA and LUC reporter activity analysis employing the transient expression system of Brassica parachinensis protoplasts and tobacco leaves and the E. coli expression system. By binding to the promoter, BrpNAC895 induced the transcription of BrpHMA2. BrpABI449 might bind to the BrpHMA2 promoter or interact with BrpNAC895 to interfere with the action of BrpNAC895. The findings suggest that BrpHMA2 is a membrane-based afflux-type Cd transporter involved in the Cd2+ uptake and long-distance transport in plants. BrpNAC895 and BrpABI449, which function as the transcription activator and repressor respectively, coregulate BrpHMA2 expression.

Removal of Pathogens from Domestic Wastewater Using Small-Scale Gradual Hydroponics Planted with Duranta erecta, Addis Ababa, Ethiopia

This study aimed to evaluate the treatment potential of gradual hydroponics planted with Duranta erecta in the removal of pathogens from domestic wastewater. Two experimental and control units were configured in series. Each unit contains three bioreactors and was arranged in a cascaded configuration. The two experimental units used both plant and media, but the two control units used only media to treat the wastewater. Gravel and polyester sponge were used as media. Experimental unit 1 and control unit 1 used gravel as media; however, experimental unit 2 and control unit 2 used polyester sponges as media. The experiment was operated at hydraulic retention times of 1, 3, 5, and 7 days in a continuous mode. The performance of the hydroponic system was evaluated by characterizing the influent and effluent quality using standard methods. At optimum hydraulic retention time (7 days), the average removal of experimental units 1 and 2 was 98.7% and 89.8% for heterotrophic bacteria, 96.2% and 86.8% for total coliform, and 92.9% and 84.0% for fecal coliform, respectively. Analysis of variance showed that there was a significant difference (P < 0.05) between the two experimental and control units in removing pathogens, but no significant difference (P > 0.05) was observed between the two experimental units and between the two control units. Heterotrophic bacteria and coliforms were satisfactorily removed from domestic wastewater via a gradual hydroponic system. Hence, the hydroponic treatment system planted with Duranta erecta has a promising potential in the removal of pathogens from domestic wastewater in developing countries including Ethiopia.

UCP1 and AOX1a contribute to regulation of carbon and nitrogen metabolism and yield in Arabidopsis under low nitrogen stress

Nitrogen (N) availability is a critical factor for plant development and crop yield, and it closely correlates to carbon (C) metabolism. Uncoupling protein (UCP) and alternative oxidase (AOX) exhibit a strong correlation with N and C metabolism. Here, we investigated the functions of UCP1 and AOX1a using their mutants and complementation lines in Arabidopsis adaptation to low N. Low N markedly increased AOX1a and UCP1 expression, alternative pathway capacity and UCP activity. Eight-day-old aox1a/ucp1 seedlings were more sensitive to low N than Col-0 and single mutants, exhibiting lower primary root length and higher anthocyanin accumulation. The net photosynthetic rate, electron transport rate, PSII actual photochemical efficiency, stomatal conductance and carboxylation efficiency were markedly decreased in ucp1 and aox1a/ucp1 compared to those in Col-0 and aox1a under low N stress; comparatively, chlorophyll content and non-photochemical quenching coefficient were the lowest and highest in aox1a/ucp1, respectively. Nitrate acquisition rate was accelerated in aox1a/ucp1, but its transport activity was decreased, which resulted in low nitrate content and nitrate reductase activity under low N condition. The C/N ratio in seeds, but not in leaves, is higher in aox1a/ucp1 than that in Col-0, aox1a and ucp1 under low N condition. RNA-seq analysis revealed that many genes involved in photosynthesis and C/N metabolism were markedly down-regulated in aox1a/ucp1 under low N stress. These results highlight the key roles of UCP1 and AOX1a in modulating photosynthetic capacity, C/N assimilation and distribution under low N stress.

Functional characterization of hydroxyproline-O-galactosyltransferases for Arabidopsis arabinogalactan-protein synthesis

BACKGROUND

Arabinogalactan-proteins (AGPs) are structurally complex hydroxyproline-rich cell wall glycoproteins ubiquitous in the plant kingdom. AGPs biosynthesis involves a series of post-translational modifications including the addition of type II arabinogalactans to non-contiguous Hyp residues. To date, eight Hyp-galactosyltransferases (Hyp-GALTs; GALT2-GALT9) belonging to CAZy GT31, are known to catalyze the addition of the first galactose residues to AGP protein backbones and enable subsequent AGP glycosylation. The extent of genetic redundancy, however, remains to be elucidated for the Hyp-GALT gene family.

RESULTS

To examine their gene redundancy and functions, we generated various multiple gene knock-outs, including a triple mutant (galt5 galt8 galt9), two quadruple mutants (galt2 galt5 galt7 galt8, galt2 galt5 galt7 galt9), and one quintuple mutant (galt2 galt5 galt7 galt8 galt9), and comprehensively examined their biochemical and physiological phenotypes. The key findings include: AGP precipitations with β-Yariv reagent showed that GALT2, GALT5, GALT7, GALT8 and GALT9 act redundantly with respect to AGP glycosylation in cauline and rosette leaves, while the activity of GALT7, GALT8 and GALT9 dominate in the stem, silique and flowers. Monosaccharide composition analysis showed that galactose was decreased in the silique and root AGPs of the Hyp-GALT mutants. TEM analysis of 25789 quintuple mutant stems indicated cell wall defects coincident with the observed developmental and growth impairment in these Hyp-GALT mutants. Correlated with expression patterns, galt2, galt5, galt7, galt8, and galt9 display equal additive effects on insensitivity to β-Yariv-induced growth inhibition, silique length, plant height, and pollen viability. Interestingly, galt7, galt8, and galt9 contributed more to primary root growth and root tip swelling under salt stress, whereas galt2 and galt5 played more important roles in seed morphology, germination defects and seed set. Pollen defects likely contributed to the reduced seed set in these mutants.

CONCLUSION

Additive and pleiotropic effects of GALT2, GALT5, GALT7, GALT8 and GALT9 on vegetative and reproductive growth phenotypes were teased apart via generation of different combinations of Hyp-GALT knock-out mutants. Taken together, the generation of higher order Hyp-GALT mutants demonstrate the functional importance of AG polysaccharides decorating the AGPs with respect to various aspects of plant growth and development.

Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations

Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax, isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.

Vacuolar fructose transporter SWEET17 is critical for root development and drought tolerance

Root growth and architecture are markedly influenced by both developmental and environmental cues. Sugars integrate different stimuli and are essential building blocks and signaling molecules for modulating the root system. Members from the SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET) family facilitate the transport of different sugars over cellular membranes and steer both inter and intracellular distribution of sugars. SWEET17 represents a fructose-specific sugar porter localized to the vacuolar membrane, the tonoplast. Here, we analyzed how SWEET17-dependent fructose released from vacuoles affects root growth during drought stress in Arabidopsis (Arabidopsis thaliana). We found that the SWEET17 gene was predominantly expressed in the root vasculature and in meristematic cells of the root tip. SWEET17 expression appeared markedly induced during lateral root (LR) outgrowth and under drought. Moreover, fructose repressed primary root growth but induced density and length of first order LRs. Consistently, sweet17 knock-out mutants exhibited reduced LR growth and a diminished expression of LR-development-related transcription factors during drought stress, resulting in impaired drought tolerance of sweet17 mutants. We discuss how SWEET17 activity integrates drought-induced cellular responses into fructose signaling necessary for modulation of the root system and maximal drought tolerance.

Diclofenac modified the root system architecture of Arabidopsis via interfering with the hormonal activities of auxin

Diclofenac, a pharmaceutical and personal care product, is accumulating in various environmental matrices worldwide. Increased irrigation has facilitated an influx of environmental diclofenac into agricultural products, which potentially threatens non-target living organisms. In this study, we demonstrated that diclofenac modified the growth and root developmental processes of plants by disturbing the activity of auxin, a group of major phytohormones. Exogenous diclofenac treatment retarded growth and induced oxidative stress in young seedlings of Arabidopsis thaliana. In the developmental perspective, diclofenac altered the root system architecture, which was also similarly observed under exogenous IAA (a natural form of phytoalexins) treatment. The effects of diclofenac on the root development of A. thaliana were mediated through canonical auxin signaling pathways. However, when diclofenac and IAA were treated in combination, diclofenac suppressed the activity of IAA in root system architecture. At the molecular level, diclofenac significantly inhibited the activity of IAA upregulating the expression of early auxin-responsive marker genes. In conclusion, diclofenac modified the root development of A. thaliana via interfering with the activities of natural auxin. These results indicate that diclofenac could potentially act as an environmental contaminant disturbing the natural developmental processes of plants.

An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development

Mass spectrometry is the predominant analytical tool used in the field of plant lipidomics. However, there are many challenges associated with the mass spectrometric detection and identification of lipids because of the highly complex nature of plant lipids. Studies into lipid biosynthetic pathways, gene functions in lipid metabolism, lipid changes during plant growth and development, and the holistic examination of the role of plant lipids in environmental stress responses are often hindered. Here, we leveraged a robust pipeline that we previously established to extract and analyze lipid profiles of different tissues and developmental stages from the model plant Arabidopsis thaliana. We analyzed seven tissues at several different developmental stages and identified more than 200 lipids from each tissue analyzed. The data were used to create a web-accessible in silico lipid map that has been integrated into an electronic Fluorescent Pictograph (eFP) browser. This in silico library of Arabidopsis lipids allows the visualization and exploration of the distribution and changes of lipid levels across selected developmental stages. Furthermore, it provides information on the characteristic fragments of lipids and adducts observed in the mass spectrometer and their retention times, which can be used for lipid identification. The Arabidopsis tissue lipid map can be accessed at http://bar.utoronto.ca/efp_arabidopsis_lipid/cgi-bin/efpWeb.cgi.

Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress

DSS1 is a small protein, highly conserved across different species. As a member of the intrinsically disordered protein family, DSS1 interacts with different protein partners, thus forming complexes involved in diverse biological mechanisms: DNA repair, regulation of protein homeostasis, mRNA export, etc. Additionally, DSS1 has a novel intriguing role in the post-translational protein modification named DSSylation. Oxidatively damaged proteins are targeted for removal with DSS1 and then degraded by proteasome. Yet, DSS1 involvement in the maintenance of genome integrity through homologous recombination is the only function well studied in Arabidopsis research. The fact that animal DSS1 shows wide multifunctionality imposes a need to investigate the additional roles of two Arabidopsis thaliana DSS1 homologs. Having in mind the universality of various biological processes, we considered the possibility of plant DSS1 involvement in cellular homeostasis maintenance during stress exposure. Using real-time PCR and immunoblot analysis, we investigated the profiles of DSS1 gene and protein expression under oxidative stress. We grew and selected the homozygous Arabidopsis mutant line, carrying the T-DNA intron insertion in the DSS1(V) gene. The mutant line was phenotypically described during plant development, and its sensitivity to oxidative stress was characterized. This is the first report which indicates that plant DSS1 gene expression has an altered profile under the influence of oxidative stress. dss1(V)^-/- plants showed an increased sensitivity to oxidative stress, germinated faster than WT, but generally showed developmental delay in further stages. Our results indicate that the DSS1 protein could be a crucial player in the molecular mechanisms underlying plant abiotic stress responses.

In situ Phenotyping of Grapevine Root System Architecture by 2D or 3D Imaging: Advantages and Limits of Three Cultivation Methods

The root system plays an essential role in the development and physiology of the plant, as well as in its response to various stresses. However, it is often insufficiently studied, mainly because it is difficult to visualize. For grapevine, a plant of major economic interest, there is a growing need to study the root system, in particular to assess its resistance to biotic and abiotic stresses, understand the decline that may affect it, and identify new ecofriendly production systems. In this context, we have evaluated and compared three distinct growing methods (hydroponics, plane, and cylindric rhizotrons) in order to describe relevant architectural root traits of grapevine cuttings (mode of grapevine propagation), and also two 2D- (hydroponics and rhizotron) and one 3D- (neutron tomography) imaging techniques for visualization and quantification of roots. We observed that hydroponics tubes are a system easy to implement but do not allow the direct quantification of root traits over time, conversely to 2D imaging in rhizotron. We demonstrated that neutron tomography is relevant to quantify the root volume. We have also produced a new automated analysis method of digital photographs, adapted for identifying adventitious roots as a feature of root architecture in rhizotrons. This method integrates image segmentation, skeletonization, detection of adventitious root skeleton, and adventitious root reconstruction. Although this study was targeted to grapevine, most of the results obtained could be extended to other plants propagated by cuttings. Image analysis methods could also be adapted to characterization of the root system from seedlings.

Interplay between Coumarin Accumulation, Iron Deficiency and Plant Resistance to Dickeya spp

Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.

The role of rhizofiltration and allelopathy on the removal of cyanobacteria in a continuous flow system

A continuous flow filtration system was designed to identify and quantify the removal mechanisms of Cyanobacteria (Microcystis aeruginosa) by hydroponic biofilters of Phalaris arundinacea compared to synthetic filters. The filtration units were continuously fed under plug-flow conditions with Microcystis grown in photobioreactors. Microcystis cells decreased at the two flow rates studied (1.2 ± 0.2 and 54 ± 3 cm³ min-¹) and results suggested physical and chemical/biological removal mechanisms were involved. Physical interception and deposition was the main removal mechanism with packing density of the media driving the extent of cell removal at high flow, whilst physical and chemical/biological mechanisms were involved at low flow. At low flow, the biofilters decreased Microcystis cell numbers by 70% compared to the controls. The decrease in cell numbers in the biofilters was accompanied by a chlorotic process (loss of green colour), suggesting oxidative processes by the release of allelochemicals from the biofilters.

Hormesis-Inducing Essential Oil Nanodelivery System Protects Plants against Broad Host-Range Necrotrophs

Botrytis cinerea, a broad host-range necrotrophic (BHN) phytopathogen, establishes compatible interactions with hosts by deploying multigene infection strategies, rendering simply inherited resistance ineffective to fight off this pathogen. Since essential oils (EOs) serve as intermediators during phytobiome communication, we hypothesize that they have the potential to enhance the quantitative disease resistance against BHN by eliciting the adaptive stress response (hormesis) in plants. However, using EOs is challenging due to their poor solubility in water. Nanoemulsification of EOs enhances not only the solubility of EOs but also their potency and stability. Here, we demonstrate the potential use of essential oil nanoemulsions (EONEs) to control infections caused by BHN. Using basic engineering principles of nanocarrier design, we demonstrate the efficacy of a robust EONEs design for controlling B. cinerea infection in a model plant, Arabidopsis thaliana. Our nanoemulsion delivery system significantly enhanced the disease resistance of the host by reducing the necrotic area by up to 50% compared to untreated plants. RNA-seq analysis indicated that successful treatments upregulated autophagy, ROS scavenging, and activation of the jasmonic acid signaling pathway.

TuMV triggers stomatal closure but reduces drought tolerance in Arabidopsis

Compatible plant viral infections are a common cause of agricultural losses worldwide. Characterization of the physiological responses controlling plant water management under combined stresses is of great interest in the current climate change scenario. We studied the outcome of TuMV infection on stomatal closure and water balance, hormonal balance and drought tolerance in Arabidopsis. TuMV infection reduced stomatal aperture concomitantly with diminished gas exchange rate, daily water consumption and rosette initial dehydration rate. Infected plants overaccumulated salicylic acid and abscisic acid and showed altered expression levels of key ABA homeostasis genes including biosynthesis and catabolism. Also the expression of ABA signalling gene ABI2 was induced and ABCG40 (which imports ABA into guard cells) was highly induced upon infection. Hypermorfic abi2-1 mutant plants, but no other ABA or SA biosynthetic, signalling or degradation mutants tested abolished both stomatal closure and low stomatal conductance phenotypes caused by TuMV. Notwithstanding lower relative water loss during infection, plants simultaneously subjected to drought and viral stresses showed higher mortality rates than mock-inoculated drought stressed controls, alongside downregulation of drought-responsive gene RD29A. Our findings indicate that despite stomatal closure triggered by TuMV, additional phenomena diminish drought tolerance upon infection.

GABA signalling modulates stomatal opening to enhance plant water use efficiency and drought resilience

The non-protein amino acid γ-aminobutyric acid (GABA) has been proposed to be an ancient messenger for cellular communication conserved across biological kingdoms. GABA has well-defined signalling roles in animals; however, whilst GABA accumulates in plants under stress it has not been determined if, how, where and when GABA acts as an endogenous plant signalling molecule. Here, we establish endogenous GABA as a bona fide plant signal, acting via a mechanism not found in animals. Using Arabidopsis thaliana, we show guard cell GABA production is necessary and sufficient to reduce stomatal opening and transpirational water loss, which improves water use efficiency and drought tolerance, via negative regulation of a stomatal guard cell tonoplast-localised anion transporter. We find GABA modulation of stomata occurs in multiple plants, including dicot and monocot crops. This study highlights a role for GABA metabolism in fine tuning physiology and opens alternative avenues for improving plant stress resilience.

Luxury zinc supply acts as antiaging agent and enhances reproductive fitness in Arabidopsis thaliana

Developmental senescence in plants is an age dependent process affected by phytohormones, nutrient status, and environmental factors, while the antiaging effects of zinc are recognized in humans. This study explores the possible influence of a high, non-toxic Zn-supply (12 μM) on senescence and reproductive fitness in A. thaliana. Auxin-resistance mutant, axr1-12, and auxin overexpressing YUCCA6 mutant, yuc6-1D, and their corresponding background genotypes were grown until complete rosette senescence to quantify the fruit biomass and seed number. Gene expression of different antioxidant, auxin and senescence-associated markers were analyzed after the onset of senescence. All mutants showed delayed developmental senescence. Luxury Zn delayed senescence in wild type, but not in the mutant genotypes. Excluding axr1-12 mutants, which showed very low expression of the auxin gene marker INDOLE-3-ACETIC ACID INDUCIBLE 2 (IAA2), enhanced expression of the senescence markers SENESCENCE-ASSOCIATED GENE 12 (SAG12) and AUXIN RESPONSE FACTOR 2 (ARF2) coincided with decreased expression of IAA2. Delayed senescence and total number of seeds per plant were related to higher expression of the peroxisomal antioxidant enzymes Cu/Zn superoxide dismutase (SOD3) and catalase (CAT2). These results evidence that high Zn-induced delayed senescence and improved reproductive fitness in Arabidopsis are related to an auxin-independent mechanism that retains antioxidant activity.

The role of PQL genes in response to salinity tolerance in Arabidopsis and barley

While soil salinity is a global problem, how salt enters plant root cells from the soil solution remains underexplored. Non-selective cation channels (NSCCs) are suggested to be the major pathway for the entry of sodium ions (Na+), yet their genetic constituents remain unknown. Yeast PQ loop (PQL) proteins were previously proposed to encode NSCCs, but the role of PQLs in plants is unknown. The hypothesis tested in this research is that PQL proteins constitute NSCCs mediating some of the Na+ influx into the root, contributing to ion accumulation and the inhibition of growth in saline conditions. We identified plant PQL homologues, and studied the role of one clade of PQL genes in Arabidopsis and barley. Using heterologous expression of AtPQL1a and HvPQL1 in HEK293 cells allowed us to resolve sizable inwardly directed currents permeable to monovalent cations such as Na+, K+, or Li+ upon membrane hyperpolarization. We observed that GFP-tagged PQL proteins localized to intracellular membrane structures, both when transiently over-expressed in tobacco leaf epidermis and in stable Arabidopsis transformants. Expression of AtPQL1a, AtPQL1b, and AtPQL1c was increased by salt stress in the shoot tissue compared to non-stressed plants. Mutant lines with altered expression of AtPQL1a, AtPQL1b, and AtPQL1c developed larger rosettes in saline conditions, while altered levels of AtPQL1a severely reduced development of lateral roots in all conditions. This study provides the first step toward understanding the function of PQL proteins in plants and the role of NSCC in salinity tolerance.

Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

Development of a robust hydroponic method for screening of sunflower (Helianthus annuus L.) accessions for tolerance to heat and osmotic stress

Hydroponic systems are known to provide a platform for uniform growth conditions until the reproductive stage. However, many plant species, including sunflower, show poor growth and survivability under conventional hydroponic systems due to poor nutrient availability, hypoxia and algal contamination. Thus, we tested various hydroponic systems to select a hydroponic system suitable for screening of sunflower germplasm. Sunflower accessions showed better growth and leaf gas exchange in newly-designed over conventional hydroponic systems. Selected hydroponic systems were further engaged in sunflower accession screening under heat and osmotic stress in a two-pan system (210 cm × 60 cm). Heat stress treatment was applied by growing sunflower germplasm at 42 °C and osmotic stress by adding polyethylene glycol 8000 which decreased the osmotic potential to - 0.6 MPa. There was significant variability among the sunflower accessions for their ability to survive under stress. Accessions such as C-2721 (43%), C-291 (46%) and D-14 (43%) had lower cell membrane injury percentage under osmotic stress and high seedling survivability (60‒80%) under heat stress when compared with susceptible accessions. Moreover, resistant accessions exhibited greater cuticular waxes and root length but lower transpiration losses. The newly designed hydroponic platform proved reliable for the selection of resistant sunflower accessions. Selected parental lines were validated by assessing their hybrids under field trials across two seasons under water and temperature stress during the reproductive phase (autumn). Hybrid H3 obtained by crossing drought and heat resistant parents had the highest seed yield and water use efficiency.

Identification of Metal Stresses in Arabidopsis thaliana Using Hyperspectral Reflectance Imaging

Industrial accidents, such as the Fukushima and Chernobyl disasters, release harmful chemicals into the environment, covering large geographical areas. Natural flora may serve as biological sensors for detecting metal contamination, such as cesium. Spectral detection of plant stresses typically employs a few select wavelengths and often cannot distinguish between different stress phenotypes. In this study, we apply hyperspectral reflectance imaging in the visible and near-infrared along with multivariate curve resolution (MCR) analysis to identify unique spectral signatures of three stresses in Arabidopsis thaliana: salt, copper, and cesium. While all stress conditions result in common stress physiology, hyperspectral reflectance imaging and MCR analysis produced unique spectral signatures that enabled classification of each stress. As the level of potassium was previously shown to affect cesium stress in plants, the response of A. thaliana to cesium stress under variable levels of potassium was also investigated. Increased levels of potassium reduced the spectral response of A. thaliana to cesium and prevented changes to chloroplast cellular organization. While metal stress mechanisms may vary under different environmental conditions, this study demonstrates that hyperspectral reflectance imaging with MCR analysis can distinguish metal stress phenotypes, providing the potential to detect metal contamination across large geographical areas.

A comprehensive comparison of four methods for extracting lipids from Arabidopsis tissues

BACKGROUND

The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken.

RESULTS

In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana.

CONCLUSION

While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.

Higher Atmospheric CO2 Levels Favor C3 Plants Over C4 Plants in Utilizing Ammonium as a Nitrogen Source

Photosynthesis of wheat and maize declined when grown with NH4 + as a nitrogen (N) source at ambient CO2 concentration compared to those grown with a mixture of NO3 - and NH4 +, or NO3 - as the sole N source. Interestingly, these N nutritional physiological responses changed when the atmospheric CO2 concentration increases. We studied the photosynthetic responses of wheat and maize growing with various N forms at three levels of growth CO2 levels. Hydroponic experiments were carried out using a C3 plant (wheat, Triticum aestivum L. cv. Chuanmai 58) and a C4 plant (maize, Zea mays L. cv. Zhongdan 808) given three types of N nutrition: sole NO3 - (NN), sole NH4 + (AN) and a mixture of both NO3 - and NH4 + (Mix-N). The test plants were grown using custom-built chambers where a continuous and desired atmospheric CO2 (C a ) concentration could be maintained: 280 μmol mol-1 (representing the pre-Industrial Revolution CO2 concentration of the 18th century), 400 μmol mol-1 (present level) and 550 μmol mol-1 (representing the anticipated futuristic concentration in 2050). Under AN, the decrease in net photosynthetic rate (P n ) was attributed to a reduction in the maximum RuBP-regeneration rate, which then caused reductions in the maximum Rubisco-carboxylation rates for both species. Decreases in electron transport rate, reduction of electron flux to the photosynthetic carbon [Je(PCR)] and electron flux for photorespiratory carbon oxidation [Je(PCO)] were also observed under AN for both species. However, the intercellular (C i ) and chloroplast (C c ) CO2 concentration increased with increasing atmospheric CO2 in C3 wheat but not in C4 maize, leading to a higher Je(PCR)/ Je(PCO) ratio. Interestingly, the reduction of P n under AN was relieved in wheat through higher CO2 levels, but that was not the case in maize. In conclusion, elevating atmospheric CO2 concentration increased C i and C c in wheat, but not in maize, with enhanced electron fluxes towards photosynthesis, rather than photorespiration, thereby relieving the inhibition of photosynthesis under AN. Our results contributed to a better understanding of NH4 + involvement in N nutrition of crops growing under different levels of CO2.

Phenylacetic Acid and Methylphenyl Acetate From the Biocontrol Bacterium Bacillus mycoides BM02 Suppress Spore Germination in Fusarium oxysporum f. sp. lycopersici

Bacillus mycoides strain BM02 originally isolated from the tomato rhizosphere was found to have beneficial functions in tomato by promoting plant growth and reducing the severity of Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol). Cytological experiments demonstrated B. mycoides BM02 reduced Fol invasion by reducing spore attachment and increasing hyphal deformation in hydroponics-grown tomato root tissues. Two volatile antifungal compounds, phenylacetic acid (PAA) and methylphenyl acetate (MPA), were identified from the culture filtrates of B. mycoides BM02 by GC-MS analysis. Chemically synthesized PAA, and to a lower extent MPA, suppressed spore germination but have no effects on the hyphal growth of Fol. Our results indicated that the biocontrol agent B. mycoides BM02 produced an array of bioactive compounds including PAA and MPA to suppress plant diseases caused by Fol and other pathogenic microorganisms.

Micronutrient homeostasis and chloroplast iron protein expression is largely maintained in a chloroplast copper transporter mutant

PAAI is a P-Type ATPase that functions to import copper (Cu) into the chloroplast. Arabidopsis thaliana (L.) Heynh. paa1 mutants have lowered plastocyanin levels, resulting in a decreased photosynthetic electron transport rate. In nature, iron (Fe) and Cu homeostasis are often linked and it can be envisioned that paa1 acclimates its photosynthetic machinery by adjusting expression of its chloroplast Fe-proteome, but outside of Cu homeostasis paa1 has not been studied. Here, we characterise paa1 ultrastructure and accumulation of electron transport chain proteins in a paa1 allelic series. Furthermore, using hydroponic growth conditions, we characterised metal homeostasis in paa1 with an emphasis on the effects of Fe deficiency. Surprisingly, the paa1 mutation does not affect chloroplast ultrastructure or the accumulation of other photosynthetic electron transport chain proteins, despite the strong decrease in electron transport rate. The regulation of Fe-related photosynthetic electron transport proteins in response to Fe status was maintained in paa1, suggesting that regulation of the chloroplast Fe proteins ignores operational signals from photosynthetic output. The characterisation of paa1 has revealed new insight into the regulation of expression of the photosynthetic electron transport chain proteins and chloroplast metal homeostasis and can help to develop new strategies for the detection of shoot Fe deficiency.

Ureide metabolism in Arabidopsis thaliana is modulated by C:N balance

Plants can respond and adapt to changes in the internal content of carbon and nitrogen by using organic compounds that widely differ in their carbon/nitrogen ratio. Among them, the amides asparagine and glutamine are believed to be preferred by most plants, including Arabidopsis. However, increases in the ureides allantoin and/or allantoate concentrations have been observed in different plant species under several environmental conditions. In this work, changes in the ratio between carbon skeletons and reduced nitrogen were investigated by varying the concentrations of nitrogen and sucrose in the growth media. Allantoin accumulation was observed when plants were grown in media with high ammonia concentrations. This increase was reverted by adding sucrose as additional carbon source. Moreover, mutant plants with a decreased capability to degrade allantoin showed a compromised growth compared to WT in ammonia supplemented media. Together, our results indicate that allantoin accumulation is induced by low carbon/nitrogen ratio and suggest that its degradation is critical for proper plant growth and development.

Nutrient solutions for Arabidopsis thaliana: a study on nutrient solution composition in hydroponics systems

BACKGROUND

There is little information on the effect of nutrient solutions composition on Arabidopsis growth. Therefore, we compared growth performance of Arabidopsis thaliana (Col-0) grown on the most commonly used nutrient solutions in deep water culture: Hoagland and Arnon, Murashige and Skoog, Tocquin, Hermans, and Conn. In addition to these nutrient solution composition experiments, we established Arabidopsis growth response curves for nutrient solution concentration and salt stress (NaCl).

RESULTS

Arabidopsis rosette fresh and dry weight showed an approximate linear decline with NaCl dose in deep water culture, i.e. 9% reduction relative to control per unit of electrical conductivity (EC in dS m-1, for scale comprehension 1 dS m-1 equals ~ 10 mM NaCl). The Tocquin, ½Hoagland and Conn nutrient solutions had equal and optimal growth performance. Optimal nutrient solution concentration for Tocquin and Hoagland was 0.8 to 0.9 dS m-1. Close to the EC of ½Hoagland (1.1 dS m-1), which is frequently used in Arabidopsis research. Conn solution showed optimal growth at much higher EC (2 dS m-1) indicating that it is a balanced nutrient solution that matches the needs of Arabidopsis. Full Murashige and Skoog solution (5.9 dS m-1) was lethal and diluted solutions (EC of 1.6 and 1.1 dS m-1) caused stress symptoms and severe growth retardation at later developmental stages.

CONCLUSIONS

Arabidopsis thaliana (Col-0) plants grown in deep water culture showed a sixfold growth difference when commonly used nutrient solutions were compared. Murashige and Skoog solution should not be used as nutrient solution in deep water culture. Conn, Tocquin and ½Hoagland are balanced nutrient solutions which result in optimal Arabidopsis growth in hydroponic systems.