Plant Systems Biology at the Single-Cell Level

Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era

Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.

Towards single-cell ionomics: a novel micro-scaled method for multi-element analysis of nanogram-sized biological samples

BACKGROUND

To understand processes regulating nutrient homeostasis at the single-cell level there is a need for new methods that allow multi-element profiling of biological samples ultimately only available as isolated tissues or cells, typically in nanogram-sized samples. Apart from tissue isolation, the main challenges for such analyses are to obtain a complete and homogeneous digestion of each sample, to keep sample dilution at a minimum and to produce accurate and reproducible results. In particular, determining the weight of small samples becomes increasingly challenging when the sample amount decreases.

RESULTS

We developed a novel method for sampling, digestion and multi-element analysis of nanogram-sized plant tissue, along with strategies to quantify element concentrations in samples too small to be weighed. The method is based on tissue isolation by laser capture microdissection (LCM), followed by pressurized micro-digestion and ICP-MS analysis, the latter utilizing a stable µL min^-1 sample aspiration system. The method allowed for isolation, digestion and analysis of micro-dissected tissues from barley roots with an estimated sample weight of only ~ 400 ng. In the collection and analysis steps, a number of contamination sources were identified. Following elimination of these sources, several elements, including magnesium (Mg), phosphorus (P), potassium (K) and manganese (Mn), could be quantified. By measuring the exact area and thickness of each of the micro-dissected tissues, their volume was calculated. Combined with an estimated sample density, the sample weights could subsequently be calculated and the fact that these samples were too small to be weighed could thereby be circumvented. The method was further documented by analysis of Arabidopsis seeds (~ 20 µg) as well as tissue fractions of such seeds (~ 10 µg).

CONCLUSIONS

The presented method enables collection and multi-element analysis of small-sized biological samples, ranging down to the nanogram level. As such, the method paves the road for single cell and tissue-specific quantitative ionomics, which allow for future transcriptional, proteomic and metabolomic data to be correlated with ionomic profiles. Such analyses will deepen our understanding of how the elemental composition of plants is regulated, e.g. by transporter proteins and physical barriers (i.e. the Casparian strip and suberin lamellae in the root endodermis).

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression.

Root Plasticity in the Pursuit of Water

One of the greatest challenges of terrestrial vegetation is to acquire water through soil-grown roots. Owing to the scarcity of high-quality water in the soil and the environment's spatial heterogeneity and temporal variability, ranging from extreme flooding to drought, roots have evolutionarily acquired tremendous plasticity regarding their geometric arrangement of individual roots and their three-dimensional organization within the soil. Water deficiency has also become an increasing threat to agriculture and dryland ecosystems due to climate change. As a result, roots have become important targets for genetic selection and modification in an effort to improve crop resilience under water-limiting conditions. This review addresses root plasticity from different angles: Their structures and geometry in response to the environment, potential genetic control of root traits suitable for water-limiting conditions, and contemporary and future studies of the principles underlying root plasticity post-Darwin's 'root-brain' hypothesis. Our increasing knowledge of different disciplines of plant sciences and agriculture should contribute to a sustainable management of natural and agricultural ecosystems for the future of mankind.

Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress

Despite recent advancements in plant molecular biology and biotechnology, providing food security for an increasing world population remains a challenge. Drought (water scarcity), salinity, heat, and cold stress are considered major limiting factors that affect crop production both qualitatively and quantitatively. Therefore, the development of cost-effective and environmentally friendly strategies will be needed to resolve these agricultural problems. This will require a comprehensive understanding of transcriptomic alterations that occur in plants in response to varying levels of environmental stresses, singly and in combination. Here, we briefly discuss the current status and future challenges in plant research related to understanding transcriptional changes that occur in response to drought, salinity, heat, and cold stress.

Practical steps to digital organism models, from laboratory model species to 'Crops in silico

A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.

Lateral Root Primordium Morphogenesis in Angiosperms

Morphogenetic processes are the basis of new organ formation. Lateral roots (LRs) are the building blocks of the root system. After LR initiation and before LR emergence, a new lateral root primordium (LRP) forms. During this period, the organization and functionality of the prospective LR is defined. Thus, proper LRP morphogenesis is a decisive process during root system formation. Most current studies on LRP morphogenesis have been performed in the model species Arabidopsis thaliana; little is known about this process in other angiosperms. To understand LRP morphogenesis from a wider perspective, we review both contemporary and earlier studies. The latter are largely forgotten, and we attempted to integrate them into present-day research. In particular, we consider in detail the participation of parent root tissue in LRP formation, cell proliferation and timing during LRP morphogenesis, and the hormonal and genetic regulation of LRP morphogenesis. Cell type identity acquisition and new stem cell establishement during LRP morphogenesis are also considered. Within each of these facets, unanswered or poorly understood questions are identified to help define future research in the field. Finally, we discuss emerging research avenues and new technologies that could be used to answer the remaining questions in studies of LRP morphogenesis.

Transcriptomics of Arabidopsis sperm cells at single-cell resolution

We present a detailed protocol for isolation of single sperm cells and transcriptome analysis to study variation in gene expression between sperm cells. Male gametophyte development in flowering plants begins with a microspore mother cell, which upon two consecutive cell divisions forms a mature pollen grain containing a vegetative nucleus and two sperm cells. Pollen development is a highly dynamic process, involving changes at both the transcriptome and epigenome levels of vegetative nuclei and the pair of sperm cells that have their own cytoplasm and nucleus. While the overall transcriptome of Arabidopsis pollen development is well documented, studies at single-cell level, in particular of sperm cells, are still lacking. Such studies would be essential to understand whether and how the two sperm cells are transcriptionally different, in particular once the pollen tube grows through the transmitting tissue of the pistil. Here we describe a detailed protocol for isolation of single sperm cells from growing pollen tubes and analysis of their transcriptome.

Use of a duckweed species, Wolffiella hyalina, for whole-plant observation of physiological behavior at the single-cell level

We developed a new model system to analyze physiological behavior at the single-cell level in whole plants. Wolffiella hyalina is a species of rootless duckweed, which has a thin and very small structure and can grow rapidly on the surface of culture medium. Epidermal and mesophyll cells were transfected with a reporter gene using particle bombardment and were observed at the single-cell level in the whole living plant. An EM-CCD camera system with a macro zoom microscope was used to capture time-lapse images of bioluminescence, and we successfully detected circadian rhythms in individual cells that expressed a luciferase gene under the control of a circadian promoter. We also detected individual S-phase cells in meristematic tissues of intact W. hyalina plants by using a 5-ethynyl-2'-deoxyuridine (EdU)-labeling assay. Our observations indicated that low-molecular-weight compounds could access the inside of the plant body. Thus, W. hyalina showed the experimental characteristics suitable for single-cell analyses that could be combined with whole-plant observations and/or pharmacological analyses/chemical biology.

Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development

Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.

Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight

PREMISE OF THE STUDY

The root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA-Seq) to microarrays in characterizing genes that are relevant to spaceflight.

METHODS

Arabidopsis thaliana Columbia ecotype (Col-0) roots were sectioned into Zone 1 (0.5 mm; root cap and meristematic zone) and Zone 2 (1.5 mm; transition, elongation, and growth-terminating zone). Differential gene expression in each was compared.

RESULTS

Both microarrays and RNA-Seq proved applicable to the small samples. A total of 4180 genes were differentially expressed (with fold changes of 2 or greater) between Zone 1 and Zone 2. In addition, 771 unique genes and 19 novel transcriptionally active regions were identified by RNA-Seq that were not detected in microarrays. However, microarrays detected spaceflight-relevant genes that were missed in RNA-Seq.

DISCUSSION

Single root tip subsections can be used for transcriptome analysis using either RNA-Seq or microarrays. Both RNA-Seq and microarrays provided novel information. These data suggest that techniques for dealing with small, rare samples from spaceflight can be further enhanced, and that RNA-Seq may miss some spaceflight-relevant changes in gene expression.

Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development

The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.

Defining Cell Identity with Single-Cell Omics

Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.

Phyllosphere microbiology: at the interface between microbial individuals and the plant host

Contents Summary 1327 I. Introduction 1327 II. Individuality and the relevance of scales for the investigation of bacteria 1328 III. Bacterial aggregation and community patterning at the single-cell resolution 1329 IV. What are the effects on the plant host? 1330 V. Future directions and current questions 1331 Acknowledgements 1332 ORCID 1332 References 1332 SUMMARY: Leaf surfaces are home to diverse bacterial communities. Within these communities, every individual cell perceives its unique environment and responds accordingly. In this insight article, the perspective of the bacterial individual is assumed in an attempt to describe how the spatially heterogeneous leaf surface determines the fate of bacteria. To investigate behaviour at scales relevant to bacteria, single-cell approaches are essential. Single-cell studies provide important lessons about how current 'omics' approaches fail to give an accurate picture of the behaviour of bacterial populations in heterogeneous environments. Upcoming techniques will soon allow us to combine the power of single-cell and omics approaches.

Method for Ultrarapid High-Content Screening for Biologically Active Chemicals Using Plant Pollen

Chemical genomics attracts considerable attention by offering crucial tools for plant biology to regulate plant growth and development. However, most chemical screens are time consuming and laborious, and require a high input of resources. Here we describe a broadly applicable method for the ultrarapid high-content phenotypic screening of small chemical compound libraries for new plant growth regulators. The assay is based on determination of pollen tube growth and can be completed in less than 8 h. Using this method, we identified novel inhibitors and modulators of plant growth and showed that compounds selected using a Nicotiana tabacum-based assay were biologically active in other plants, such as Arabidopsis thaliana.

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets

Statistical and machine learning (ML)-based methods have recently advanced in construction of gene regulatory network (GRNs) based on high-throughput biological datasets. GRNs underlie almost all cellular phenomena; hence, comprehensive GRN maps are essential tools to elucidate gene function, thereby facilitating the identification and prioritization of candidate genes for functional analysis. High-throughput gene expression datasets have yielded various statistical and ML-based algorithms to infer causal relationship between genes and decipher GRNs. This review summarizes the recent advancements in the computational inference of GRNs, based on large-scale transcriptome sequencing datasets of model plants and crops. We highlight strategies to select contextual genes for GRN inference, and statistical and ML-based methods for inferring GRNs based on transcriptome datasets from plants. Furthermore, we discuss the challenges and opportunities for the elucidation of GRNs based on large-scale datasets obtained from emerging transcriptomic applications, such as from population-scale, single-cell level, and life-course transcriptome analyses.