The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology

Time-resolved chemical monitoring of whole plant roots with printed electrochemical sensors and machine learning

Traditional single-point measurements fail to capture dynamic chemical responses of plants, which are complex, nonequilibrium biological systems. We report TETRIS (time-resolved electrochemical technology for plant root environment in situ chemical sensing), a real-time chemical phenotyping system for continuously monitoring chemical signals in the often-neglected plant root environment. TETRIS consisted of low-cost, highly scalable screen-printed electrochemical sensors for monitoring concentrations of salt, pH, and H2O2 in the root environment of whole plants, where multiplexing allowed for parallel sensing operation. TETRIS was used to measure ion uptake in tomato, kale, and rice and detected differences between nutrient and heavy metal ion uptake. Modulation of ion uptake with ion channel blocker LaCl3 was monitored by TETRIS and machine learning used to predict ion uptake. TETRIS has the potential to overcome the urgent "bottleneck" in high-throughput screening in producing high-yielding plant varieties with improved resistance against stress.

Presence and future of plant phenotyping approaches in biostimulant research and development

Commercial interest in biostimulants as a tool for sustainable green economics and agriculture concepts is on a steep rise, being followed by increasing demand to employ efficient scientific methods to develop new products and understand their mechanisms of action. Biostimulants represent a highly diverse group of agents derived from various natural sources. Regardless of their nutrition content and composition, they are classified by their ability to improve crop performance through enhanced nutrient use efficiency, abiotic stress tolerance, and quality of crops. Numerous reports have described modern, non-invasive sensor-based phenotyping methods in plant research. This review focuses on applying phenotyping approaches in biostimulant research and development, and maps the evolution of interaction of these two intensively growing domains. How phenotyping served to identify new biostimulants, the description of their biological activity, and the mechanism/mode of action are summarized. Special attention is dedicated to the indoor high-throughput methods using model plants suitable for biostimulant screening and developmental pipelines, and high-precision approaches used to determine biostimulant activity. The need for a complex method of testing biostimulants as multicomponent products through integrating other -omic approaches followed by advanced statistical/mathematical tools is emphasized.

The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria

Background

The 'Microphenotron' is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana.

Methods

In the present study, high-throughput screening based on 'Microphenotron' was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the 'Microphenotron' system and pot trials.

Results

Selected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, Enterobacter asburiae S-24 and B. thuringiensis S-26 used auxin signaling for plant growth promotion. Similarly, for ethylene insensitive mutant lines (ein2.5 and etr1), Prolinoborus fasciculus S-3, B. endophyticus S-6, Psy. alimenterius S-7, E. asburiae S-24, and B. thuringiensis S-26 showed the involvement of ethylene signaling. However, the growth promotion pattern for most of the strains indicated the involvement of other mechanisms in enhancing plant growth. The result of Microphenotron assays generally agreed with pot trials with mutant and wild type A. thaliana varieties. Bacterial strains that induced the highest growth response by these cultivars in the 'Microphenotron' promoted plant growth in pot trials. This suggests that Microphenotron can accelerate the evaluation of PGPR for agricultural applications.

Gnotobiotic Plant Systems for Reconstitution and Functional Studies of the Root Microbiota

Healthy plants host a multi-kingdom community of microbes, which is known as the plant microbiota. Amplicon sequencing technologies for microbial genomic markers were a milestone in revealing the taxonomic composition of the microbiota and its variation associated with a plant host in natural environments. However, this method alone does not allow conclusions to be drawn about functions of these microbial assemblages for the plant. The development of culture collections, which recapitulate natural microbial communities in their diversity, and multiple gnotobiotic plant systems therefore represent a breakthrough in plant-microbiota research such that plants can be inoculated with defined communities to study proposed microbiota functions. These systems provided, for the root microbiota, first insights into mechanisms underlying microbial community establishment and contributions of its microbial members to indirect pathogen protection and mineral nutrition of the host. We argue that the choice of a gnotobiotic system for microbiota reconstitution and subsequent functional analysis depends on the particular plant trait that is influenced by the microbiota. We start by discussing the advantages and limitations of using individual gnotobiotic systems and then describe the general procedures for preparing bacterial cultures from the Arabidopsis thaliana At-R-SPHERE culture collection for inoculation and cocultivation in two gnotobiotic plant growth systems using agar and perlite matrix. Additionally, a protocol for inoculation of plants with opportunistic Pseudomonas pathogens is provided. Lastly, we describe a high-throughput system for visual assessment of roots after inoculation with individual mutants of a transposon library generated from a root-derived bacterial commensal. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of bacterial cultures from At-R-SPHERE Support Protocol 1: Validation of strains by sequencing hypervariable regions of the 16S rRNA gene Basic Protocol 2: Coinoculation of plants grown on an agar matrix with microbial elicitor and a defined microbial community Alternate Protocol: Inoculation of plants cultivated in a perlite-based growth system Support Protocol 2: Surface sterilization of Arabidopsis thaliana seeds Basic Protocol 3: Inoculation using a Pseudomonas opportunistic pathogen Basic Protocol 4: Assessment of commensal-mediated root phenotypes using phytostrips.

High-Throughput Phenotyping: A Platform to Accelerate Crop Improvement

Development of high-throughput phenotyping technologies has progressed considerably in the last 10 years. These technologies provide precise measurements of desired traits among thousands of field-grown plants under diversified environments; this is a critical step towards selection of better performing lines as to yield, disease resistance, and stress tolerance to accelerate crop improvement programs. High-throughput phenotyping techniques and platforms help unraveling the genetic basis of complex traits associated with plant growth and development and targeted traits. This review focuses on the advancements in technologies involved in high-throughput, field-based, aerial, and unmanned platforms. Development of user-friendly data management tools and softwares to better understand phenotyping will increase the use of field-based high-throughput techniques, which have potential to revolutionize breeding strategies and meet the future needs of stakeholders.

Chitosan Plasma Chemical Processing in Beam-Plasma Reactors as a Way of Environmentally Friendly Phytostimulants Production

A novel technique of phytoactive water-soluble chitooligosaccharide (COS) production in low-temperature plasma is described. Design, operation, and control of plasma chemical reactors used to produce COS from the powder of high molecular weight chitosan are presented. The electron beam plasma is strongly non-equilibrium and chemically active; plasma was excited by injecting the scanning electron beam into reaction volume filled with aerosol, containing oxygen and chitosan powder. Plasma chemical processes, responsible for the raw chitosan destruction and techniques of these processes to obtain control of products of optimal molecular weight, are considered. COS, in amounts sufficient for laboratory tests with some plants, were produced. Tests showed that the addition of COS into the liquid growing medium at 0.25 and 1 mg/mL stimulates root growth in Arabidopsis thaliana seedlings (Col-0) by up to 40%, with respect to control plants. Foliar application of these COS formulations at 0.25 mg/mL on tomato plants (cv. Micro-Tom) also resulted in increases between 11.9% and 36% in two important plant productivity indicators (flower and fruit numbers) compared to the control plants. Being environmentally friendly (and resource saving) the electron beam plasma technology of renewable natural biopolymer processing can be considered as a competitive way to produce biostimulants for commercial agriculture.

Plant Leaf Position Estimation with Computer Vision

Autonomous analysis of plants, such as for phenotyping and health monitoring etc., often requires the reliable identification and localization of single leaves, a task complicated by their complex and variable shape. Robotic sensor platforms commonly use depth sensors that rely on either infrared light or ultrasound, in addition to imaging. However, infrared methods have the disadvantage of being affected by the presence of ambient light, and ultrasound methods generally have too wide a field of view, making them ineffective for measuring complex and intricate structures. Alternatives may include stereoscopic or structured light scanners, but these can be costly and overly complex to implement. This article presents a fully computer-vision based solution capable of estimating the three-dimensional location of all leaves of a subject plant with the use of a single digital camera autonomously positioned by a three-axis linear robot. A custom trained neural network was used to classify leaves captured in multiple images taken of a subject plant. Parallax calculations were applied to predict leaf depth, and from this, the three-dimensional position. This article demonstrates proof of concept of the method, and initial tests with positioned leaves suggest an expected error of 20 mm. Future modifications are identified to further improve accuracy and utility across different plant canopies.

The platform GrowScreen-Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants

BACKGROUND

Root system architecture and especially its plasticity in acclimation to variable environments play a crucial role in the ability of plants to explore and acquire efficiently soil resources and ensure plant productivity. Non-destructive measurement methods are indispensable to quantify dynamic growth traits. For closing the phenotyping gap, we have developed an automated phenotyping platform, GrowScreen-Agar, for non-destructive characterization of root and shoot traits of plants grown in transparent agar medium.

RESULTS

The phenotyping system is capable to phenotype root systems and correlate them to whole plant development of up to 280 Arabidopsis plants within 15 min. The potential of the platform has been demonstrated by quantifying phenotypic differences within 78 Arabidopsis accessions from the 1001 genomes project. The chosen concept 'plant-to-sensor' is based on transporting plants to the imaging position, which allows for flexible experimental size and design. As transporting causes mechanical vibrations of plants, we have validated that daily imaging, and consequently, moving plants has negligible influence on plant development. Plants are cultivated in square Petri dishes modified to allow the shoot to grow in the ambient air while the roots grow inside the Petri dish filled with agar. Because it is common practice in the scientific community to grow Arabidopsis plants completely enclosed in Petri dishes, we compared development of plants that had the shoot inside with that of plants that had the shoot outside the plate. Roots of plants grown completely inside the Petri dish grew 58% slower, produced a 1.8 times higher lateral root density and showed an etiolated shoot whereas plants whose shoot grew outside the plate formed a rosette. In addition, the setup with the shoot growing outside the plate offers the unique option to accurately measure both, leaf and root traits, non-destructively, and treat roots and shoots separately.

CONCLUSIONS

Because the GrowScreen-Agar system can be moved from one growth chamber to another, plants can be phenotyped under a wide range of environmental conditions including future climate scenarios. In combination with a measurement throughput enabling phenotyping a large set of mutants or accessions, the platform will contribute to the identification of key genes.

Virus-induced gene silencing: empowering genetics in non-model organisms

Virus-induced gene silencing (VIGS) is an RNA interference-based technology used to transiently knock down target gene expression by utilizing modified plant viral genomes. VIGS can be adapted to many angiosperm species that cover large phylogenetic distances, allowing the analysis of gene functions in species that are not amenable to stable genetic transformation. With a vast amount of sequence information already available and even more likely to become available in the future, VIGS provides a means to analyze the functions of candidate genes identified in large genomic or transcriptomic screens. Here, we provide a comprehensive overview of target species and VIGS vector systems, assess recent key publications in the field, and explain how plant viruses are modified to serve as VIGS vectors. As many reports on the VIGS technique are being published, we also propose minimal reporting guidelines for carrying out these experiments, with the aim of increasing comparability between experiments. Finally, we propose methods for the statistical evaluation of phenotypic results obtained with VIGS-treated plants, as analysis is challenging due to the predominantly transient nature of the silencing effect.

A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals

Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.

Novel Micro-Phenotyping Approach to Chemical Genetic Screening for Increased Plant Tolerance to Abiotic Stress

Studying the effects of small molecules on root system development in the context of a large-scale chemical genetic screen has previously been a technical challenge. The recent development of novel seedling growth devices ("Phytostrips"), used in combination with standard 96-well microtiter plates, has made it possible to perform detailed studies of changes in root morphology and root system architecture following the application of a library of chemical compounds. Phytostrips were originally designed to allow automated robotic capture of images of roots and shoots of the model species Arabidopsis thaliana, but can also be used for manual screens that are more laborious but do not require the investment in expensive robotics.Here we describe a protocol for the use of Phytostrips to perform chemical genetic screens that rely on clearly observable changes in root morphology or root system architecture. As an example, we describe the use of polyethylene glycol to impose an abiotic stress related to reduced water potential and the application of a chemical screen for small molecules that are able to rescue Arabidopsis root development from the disruptive effect of the polyethylene glycol treatment. The protocol we describe provides a template for the application of a multiplicity of other screens for compounds that can antagonize the effects of a range of abiotic stresses on root development.

Differential manipulation of leaf angle throughout the canopy: current status and prospects

Leaf angle is defined as the inclination between the midrib of the leaf blade and the vertical stem of a plant. This trait has been identified as a key component in the development of high-yielding varieties of cereal species, particularly maize, rice, wheat, and sorghum. The effect of leaf angle on light interception efficiency, photosynthetic rate, and yield has been investigated since the 1960s, yet, significant knowledge gaps remain in understanding the genetic control of this complex trait. Recent advances in physiology and modeling have proposed a plant ideotype with varying leaf angles throughout the canopy. In this context, we present historical and recent evidence of: (i) the effect of leaf angle on photosynthetic efficiency and yield; (ii) the hormonal regulation of this trait; (iii) the current knowledge on its quantitative genetic control; and (iv) the opportunity to utilize high-throughput phenotyping methods to characterize leaf angle at multiple canopy levels. We focus on research conducted on grass species of economic importance, with similar plant architecture and growth patterns. Finally, we present the challenges and strategies plant breeders will need to embrace in order to manipulate leaf angle differentially throughout the canopy and develop superior crops for food, feed, and fuel production.

AutoRoot: open-source software employing a novel image analysis approach to support fully-automated plant phenotyping

BACKGROUND

Computer-based phenotyping of plants has risen in importance in recent years. Whilst much software has been written to aid phenotyping using image analysis, to date the vast majority has been only semi-automatic. However, such interaction is not desirable in high throughput approaches. Here, we present a system designed to analyse plant images in a completely automated manner, allowing genuine high throughput measurement of root traits. To do this we introduce a new set of proxy traits.

RESULTS

We test the system on a new, automated image capture system, the Microphenotron, which is able to image many 1000s of roots/h. A simple experiment is presented, treating the plants with differing chemical conditions to produce different phenotypes. The automated imaging setup and the new software tool was used to measure proxy traits in each well. A correlation matrix was calculated across automated and manual measures, as a validation. Some particular proxy measures are very highly correlated with the manual measures (e.g. proxy length to manual length, r² > 0.9). This suggests that while the automated measures are not directly equivalent to classic manual measures, they can be used to indicate phenotypic differences (hence the term, proxy). In addition, the raw discriminative power of the new proxy traits was examined. Principal component analysis was calculated across all proxy measures over two phenotypically-different groups of plants. Many of the proxy traits can be used to separate the data in the two conditions.

CONCLUSION

The new proxy traits proposed tend to correlate well with equivalent manual measures, where these exist. Additionally, the new measures display strong discriminative power. It is suggested that for particular phenotypic differences, different traits will be relevant, and not all will have meaningful manual equivalent measures. However, approaches such as PCA can be used to interrogate the resulting data to identify differences between datasets. Select images can then be carefully manually inspected if the nature of the precise differences is required. We suggest such flexible measurement approaches are necessary for fully automated, high throughput systems such as the Microphenotron.