An improved, low-cost, hydroponic system for growing Arabidopsis and other plant species under aseptic conditions

Rhizosphere microbiome influence on tomato growth under low-nutrient settings

Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.

Exploring Natural Variations in Arabidopsis thaliana: Plant Adaptability to Salt Stress

The increase in soil salinization represents a current challenge for plant productivity, as most plants, including crops, are mainly salt-sensitive species. The identification of molecular traits underpinning salt tolerance represents a primary goal for breeding programs. In this scenario, the study of intraspecific variability represents a valid tool for investigating natural genetic resources evolved by plants in different environmental conditions. As a model system, Arabidopsis thaliana, including over 750 natural accessions, represents a species extensively studied at phenotypic, metabolic, and genomic levels under different environmental conditions. Two haplogroups showing opposite root architecture (shallow or deep roots) in response to auxin flux perturbation were identified and associated with EXO70A3 locus variations. Here, we studied the influence of these genetic backgrounds on plant salt tolerance. Eight accessions belonging to the two haplogroups were tested for salt sensitivity by exposing them to moderate (75 mM NaCl) or severe (150 mM NaCl) salt stress. Salt-tolerant accessions were found in both haplogroups, and all of them showed efficient ROS-scavenging ability. Even if an exclusive relation between salt tolerance and haplogroup membership was not observed, the modulation of root system architecture might also contribute to salt tolerance.

Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation

As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/-) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI- modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response.

Production and N-glycan engineering of Varlilumab in Nicotiana benthamiana

N-glycan engineering has dramatically evolved for the development and quality control of recombinant antibodies. Fc region of IgG contains two N-glycans whose galactose terminals on Fc-glycan have been shown to increase the stability of CH2 domain and improve effector functions. Nicotiana benthamiana has become one of the most attractive production systems for therapeutic antibodies. In this study, Varlilumab, a CD27-targeting monoclonal antibody, was transiently produced in fresh leaves of soil-grown and hydroponic-grown N. benthamiana, resulted in the yield of 174 and 618 µg/gram, respectively. However, the IgG produced in wild-type N. benthamiana lacked the terminal galactose residues in its N-glycan. Therefore, N-glycan engineering was applied to fine-tune recombinant antibodies produced in plant platforms. We further co-expressed IgG together with murine β1,4-galactosyltransferase (β1,4-GALT) to modify plant N-glycan with β1,4-linked Gal residue(s) and Arabidopsis thaliana β1,3-galactosylatransferase (β1,3-GALT) to improve galactosylation. The co-expression of IgG with each of GALTs successfully resulted in modification of N-glycan structures on the plant-produced IgG. Notably, IgG co-expressed with murine β1,4-GALT in soil-grown N. benthamiana had 42.5% of N-glycans variants having galactose (Gal) residues at the non-reducing terminus and 55.3% of that in hydroponic-grown N. benthamiana plants. Concomitantly, N-glycan profile analysis of IgG co-expressed with β1,3-GALT demonstrated that there was an increased efficiency of galactosylation and an enhancement in the formation of Lewis a structure in plant-derived antibodies. Taken together, our findings show that the first plant-derived Varlilumab was successfully produced with biantennary β1,4-galactosylated N-glycan structures.

Plant growth-promoting properties of the phosphate-solubilizing red yeast Rhodosporidium paludigenum

Phosphorus (P) is one of the essential elements that are necessary for plant development and growth. However, the availability of soluble forms of P for plants in the soils is limited, because a large proportion of it is bound to soil constituents. Thus, the concentration of P available to plants at any time is very low and, moreover, its availability depends on the soil pH. As a solution, phosphate-solubilizing microorganisms (PSMs) are employed that render inorganic P available to plants in soluble form. Thus far, research into PSMs has been insufficient, and only few such organisms have been considered for exploitation as microbial fertilizer strains. The characteristics of plant growth promotion with the plant-PSMs coculture system remain to be elucidated. In the current study, we report on the isolate Rhodosporidium paludigenum JYC100 that exhibits good performance for solubilizing calcium phosphate. We found that it can be regulated by the amount of soluble phosphate. Furthermore, R. paludigenum JYC100 promotes plant growth under specific conditions (P deficiency, but with insoluble phosphate) in different media and soil pots. In contrast, the yeast Aureobasidium pullulans JYC104 exhibited weak phosphate-solubilizing capacities and no plant growth-promoting ability. Compared to control plants, the biomass, shoot height, and cellular inorganic P content of plants increased in plants cocultivated with R. paludigenum JYC100. In addition, histochemical GUS and qRT-PCR assays of phosphate starvation-induced (PSI) genes showed that the transcript levels of these PSI genes are decreased in the plants cocultured with R. paludigenum JYC100. These findings reflect the unique ability of R. paludigenum JYC100 to convert insoluble P compounds to plant-available P, thereby leading to growth promotion. Our study results highlight the use of yeasts as potential substitutes for inorganic phosphate fertilizers to meet the P demands of plants, which may eventually improve yields in sustainable agricultures.

Titanium nanoparticles activate a transcriptional response in Arabidopsis that enhances tolerance to low phosphate, osmotic stress and pathogen infection

Titanium is a ubiquitous element with a wide variety of beneficial effects in plants, including enhanced nutrient uptake and resistance to pathogens and abiotic stresses. While there is numerous evidence supporting the beneficial effects that Ti fertilization give to plants, there is little information on which genetic signaling pathways the Ti application activate in plant tissues. In this study, we utilize RNA-seq and ionomics technologies to unravel the molecular signals that Arabidopsis plants unleash when treated with Ti. RNA-seq analysis showed that Ti activates abscisic acid and salicylic acid signaling pathways and the expression of NUCLEOTIDE BINDING SITE-LEUCINE RICH REPEAT receptors likely by acting as a chemical priming molecule. This activation results in enhanced resistance to drought, high salinity, and infection with Botrytis cinerea in Arabidopsis. Ti also grants an enhanced nutritional state, even at suboptimal phosphate concentrations by upregulating the expression of multiple nutrient and membrane transporters and by modifying or increasing the production root exudates. Our results suggest that Ti might act similarly to the beneficial element Silicon in other plant species.

Enhanced Cd-Accumulation in Typha latifolia by Interaction with Pseudomonas rhodesiae GRC140 under Axenic Hydroponic Conditions

The Typha genus comprises plant species extensively studied for phytoremediation processes. Recently, Pseudomonas rhodesiae GRC140, an IAA-producing bacterium, was isolated from Typha latifolia roots. This bacterium stimulates the emergence of lateral roots of Arabidopsis thaliana in the presence and absence of cadmium. However, the bacterial influence on cadmium accumulation by the plant has not been determined. Moreover, the P. rhodesiae GRC140 effect in Cd phytoextraction by T. latifolia remains poorly understood. In this work, an axenic hydroponic culture of T. latifolia was established. The plants were used to evaluate the effects of cadmium stress in axenic plants and determine the effects of P. rhodesiae GRC140 and exogenous indole acetic acid (IAA) on Cd tolerance and Cd uptake by T. latifolia. Biomass production, total chlorophyll content, root electrolyte leakage, catalase activity, total glutathione, and Cd content were determined. The results showed that Cd reduces shoot biomass and increases total glutathione and Cd content in a dose-dependent manner in root tissues. Furthermore, P. rhodesiae GRC140 increased Cd translocation to the shoots, while IAA increased the Cd accumulation in plant roots, indicating that both treatments increase Cd removal by T. latifolia plants. These results indicate that axenic plants in hydroponic systems are adequate to evaluate the Cd effects in plants and suggest that T. latifolia phytoextraction abilities could be improved by P. rhodesiae GRC140 and exogenous IAA application.

Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes' ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes' existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes' ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis

As phosphorus is one of the most limiting nutrients in many natural and agricultural ecosystems, plants have evolved strategies that cope with its scarcity. Genetic approaches have facilitated the identification of several molecular elements that regulate the phosphate (Pi) starvation response (PSR) of plants, including the master regulator of the transcriptional response to phosphate starvation PHOSPHATE STARVATION RESPONSE1 (PHR1). However, the chromatin modifications underlying the plant transcriptional response to phosphate scarcity remain largely unknown. Here, we present a detailed analysis of changes in chromatin accessibility during phosphate starvation in Arabidopsis thaliana root cells. Root cells undergo a genome-wide remodeling of chromatin accessibility in response to Pi starvation that is often associated with changes in the transcription of neighboring genes. Analysis of chromatin accessibility in the phr1 phl2 double mutant revealed that the transcription factors PHR1 and PHL2 play a key role in remodeling chromatin accessibility in response to Pi limitation. We also discovered that PHR1 and PHL2 play an important role in determining chromatin accessibility and the associated transcription of many genes under optimal Pi conditions, including genes involved in the PSR. We propose that a set of transcription factors directly activated by PHR1 in Pi-starved root cells trigger a second wave of epigenetic changes required for the transcriptional activation of the complete set of low-Pi-responsive genes.

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.

Hydroponic approach to assess rhizodegradation by sudangrass (Sorghum x drummondii) reveals pH- and plant age-dependent variability in bacterial degradation of polycyclic aromatic hydrocarbons (PAHs)

Rhizodegradation of polycyclic aromatic hydrocarbons (PAHs) is a product of complex interactions between plant and bacteria. In this study, hydroponic culture of sudangrass was established in order to investigate the effects of the plant on PAHs degradation and vice versa through changes in rhizosphere bacterial community. Results showed a plant-induced variability in PAHs degradation dependent on a characteristic shift in bacterial community, with pH and plant age as driving factors. Moreover, bacterial communities with high diversity seemed to abate the phytotoxic effects of PAHs degradation as observed in the plant's gross health. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that regardless of plant age and culture conditions, the increase or decrease of Sphingobium sp. could dictate the PAHs degradation potential of the bacterial consortium. Overall, this study utilized hydroponic culture of sudangrass to show that plant even of same species can suppress, support, or enhance PAHs degradation of bacteria depending on specific factors.

A Flexible Low Cost Hydroponic System for Assessing Plant Responses to Small Molecules in Sterile Conditions

A wide range of studies in plant biology are performed using hydroponic cultures. In this work, an in vitro hydroponic growth system designed for assessing plant responses to chemicals and other substances of interest is presented. This system is highly efficient in obtaining homogeneous and healthy seedlings of the C3 and C4 model species Arabidopsis thaliana and Setaria viridis, respectively. The sterile cultivation avoids algae and microorganism contamination, which are known limiting factors for plant normal growth and development in hydroponics. In addition, this system is scalable, enabling the harvest of plant material on a large scale with minor mechanical damage, as well as the harvest of individual parts of a plant if desired. A detailed protocol demonstrating that this system has an easy and low-cost assembly, as it uses pipette racks as the main platform for growing plants, is provided. The feasibility of this system was validated using Arabidopsis seedlings to assess the effect of the drug AZD-8055, a chemical inhibitor of the target of rapamycin (TOR) kinase. TOR inhibition was efficiently detected as early as 30 min after an AZD-8055 treatment in roots and shoots. Furthermore, AZD-8055-treated plants displayed the expected starch-excess phenotype. We proposed this hydroponic system as an ideal method for plant researchers aiming to monitor the action of plant inducers or inhibitors, as well as to assess metabolic fluxes using isotope-labeling compounds which, in general, requires the use of expensive reagents.

An aerated axenic hydroponic system for the application of root treatments: exogenous pyruvate as a practical case

BACKGROUND

Hydroponic systems are a convenient platform for plant cultivation when treatments are applied to the roots because they provide precise control of the composition of the growth medium, ensuring the availability of different compounds. A problem arises when axenic conditions are needed but the treatment of choice (exogenous organic acids or sugars) promote the growth of unwanted microorganisms. Moreover, axenic conditions are usually applied in liquid and semi-liquid growing systems, where oxygen availability can be compromised, if no aeration is provided.

RESULTS

The driver for the development of this hydroponic system was the application of the organic acid pyruvate to the roots of plants grown under aerated axenic conditions. No contamination was detected in the nutrient solution, even after the addition of pyruvate. The system was validated in pea plants treated with either pyruvate or herbicides inhibiting amino acid biosynthesis. The effects on ethanol fermentation were compared by analysing the enzymatic activity, protein content and transcriptional levels in plants treated with either pyruvate or herbicides.

CONCLUSIONS

The developed system enables the study of the exogenous application of organic acids in the nutrient solution under axenic conditions and without oxygen limitation. This system allows the study of the effect of any type of treatments applied to roots under aerated axenic hydroponic systems at physiological and molecular levels. The role of pyruvate in the induction of fermentation by herbicides cannot be simply explained by an increase in substrate availability.

A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling

An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.

Improved axenic hydroponic whole plant propagation for rapid production of roots as transformation target tissue

BACKGROUND

Plant roots are used as an efficient target tissue for plant transformation assays. In root propagable species transformed roots are able to regenerate into whole plants without the addition of exogenous hormones, thus avoiding somaclonal variation associated with many plant transformation protocols. Plants grown in soil or soilless solid medium have roots that tend to be extremely delicate and are difficult to sterilize in advance of plant transformation experiments. Axenic tissue culture plants grown on semi-solid media are slow to produce large amounts of biomass compared to plants grown in solution-based media.

METHODS

Seeds were germinated and grown for 14 days on half-strength semi-solid Murashige and Skoog medium containing 1% sucrose. Seedlings were then transferred to Magenta™ GA7 vessels containing either liquid or semi-solid ½ MS medium with 0.25, 0.5, 1, 2 or 3% sucrose. In the hydroponics (liquid medium) treatments, expanded clay balls were used to anchor seedlings. Hydroponic vessels were fitted with a sterile air aeration hose and filled ¾ full (100 mL) with liquid ½ MS media. Liquid media were replaced after 7 days. All plants were grown under fluorescent lights for 14 days.

RESULTS

We have developed an improved axenic hydroponic propagation system for producing large quantities of plant roots for use in transformation assays using Taraxacum kok-saghyz as a model for root propagable species. Plants grew significantly faster in liquid media than on solid media. Addition of sucrose from 0.25 to 2% was correlated with an increase in biomass accumulation in plants grown in liquid media.

CONCLUSIONS

Our improved axenic hydroponic method yields sufficient quantities of roots for extensive plant transformation/molecular studies.

A flow cytometric method for estimating S-phase duration in plants

The duration of the DNA synthesis stage (S phase) of the cell cycle is fundamental in our understanding of cell cycle kinetics, cell proliferation, and DNA replication timing programs. Most S-phase duration estimates that exist for plants are based on indirect measurements. We present a method for directly estimating S-phase duration by pulse-labeling root tips or actively dividing suspension cells with the halogenated thymidine analog 5-ethynl-2'-deoxyuridine (EdU) and analyzing the time course of replication with bivariate flow cytometry. The transition between G₁ and G₂ DNA contents can be followed by measuring the mean DNA content of EdU-labeled S-phase nuclei as a function of time after the labeling pulse. We applied this technique to intact root tips of maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and wheat (Triticum aestivum L.), and to actively dividing cell cultures of Arabidopsis (Arabidopsis thaliana (L.) Heynh.) and rice. Estimates of S-phase duration in root tips were remarkably consistent, varying only by ~3-fold, although the genome sizes of the species analyzed varied >40-fold.

Hydroponics: A Versatile System to Study Nutrient Allocation and Plant Responses to Nutrient Availability and Exposure to Toxic Elements

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several crops, including lettuce and tomato. Within the plant research community, numerous hydroponic systems have been designed to study plant responses to biotic and abiotic stresses. Here we present a hydroponic protocol that can be easily implemented in laboratories interested in pursuing studies on plant mineral nutrition. This protocol describes the hydroponic system set up in detail and the preparation of plant material for successful experiments. Most of the materials described in this protocol can be found outside scientific supply companies, making the set up for hydroponic experiments less expensive and convenient. The use of a hydroponic growth system is most advantageous in situations where the nutrient media need to be well controlled and when intact roots need to be harvested for downstream applications. We also demonstrate how nutrient concentrations can be modified to induce plant responses to both essential nutrients and toxic non-essential elements.

Deciphering Phosphate Deficiency-Mediated Temporal Effects on Different Root Traits in Rice Grown in a Modified Hydroponic System

Phosphate (Pi), an essential macronutrient for growth and development of plant, is often limiting in soils. Plants have evolved an array of adaptive strategies including modulation of root system architecture (RSA) for optimal acquisition of Pi. In rice, a major staple food, RSA is complex and comprises embryonically developed primary and seminal roots and post-embryonically developed adventitious and lateral roots. Earlier studies have used variant hydroponic systems for documenting the effects of Pi deficiency largely on primary root growth. Here, we report the temporal effects of Pi deficiency in rice genotype MI48 on 15 ontogenetically distinct root traits by using easy-to-assemble and economically viable modified hydroponic system. Effects of Pi deprivation became evident after 4 days- and 7 days-treatments on two and eight different root traits, respectively. The effects of Pi deprivation for 7 days were also evident on different root traits of rice genotype Nagina 22 (N22). There were genotypic differences in the responses of primary root growth along with lateral roots on it and the number and length of seminal and adventitious roots. Notably though, there were attenuating effects of Pi deficiency on the lateral roots on seminal and adventitious roots and total root length in both these genotypes. The study thus revealed both differential and comparable effects of Pi deficiency on different root traits in these genotypes. Pi deficiency also triggered reduction in Pi content and induction of several Pi starvation-responsive (PSR) genes in roots of MI48. Together, the analyses validated the fidelity of this modified hydroponic system for documenting Pi deficiency-mediated effects not only on different traits of RSA but also on physiological and molecular responses.

An improved high-throughput screening assay for tunicamycin sensitivity in Arabidopsis seedlings

Tunicamycin (Tm) sensitivity assays are a useful method for studies of endoplasmic reticulum stress and the unfolded protein response in eukaryotic cells. While Tm sensitivity and Tm recovery assays have been previously described, these existing methods are time-consuming, labor intensive, and subjected to mechanical wounding. This study shows an improved method of testing Tm sensitivity in Arabidopsis using liquid Murashige and Skoog medium versus the traditional solid agar plates. Liquid medium bypasses the physical manipulation of seedlings, thereby eliminating the risk of potential mechanical damage and additional unwanted stress to seedlings. Seedlings were subjected to comparative treatments with various concentrations of Tm on both solid and liquid media and allowed to recover. Determination of fresh weight, chlorophyll contents analysis and qRT-PCR results confirm the efficacy of using liquid medium to perform quantitative Tm stress assays.