3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam-scanning electron microscopy

The application and development of electron microscopy for three-dimensional reconstruction in life science: a review

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

Multiscale head anatomy of Megaphragma (Hymenoptera: Trichogrammatidae)

Methods of three-dimensional electron microscopy have been actively developed recently and open up great opportunities for morphological work. This approach is especially useful for studying microinsects, since it is possible to obtain complete series of high-resolution sections of a whole insect. Studies on the genus Megaphragma are especially important, since the unique phenomenon of lysis of most of the neuron nuclei was discovered in species of this genus. In this study we reveal the anatomical structure of the head of Megaphragma viggianii at all levels from organs to subcellular structures. Despite the miniature size of the body, most of the organ systems of M. viggianii retain the structural plan and complexity of organization at all levels. The set of muscles and the well-developed stomatogastric nervous system of this species correspond to those of larger insects, and there is also a well-developed tracheal system in the head of this species. Reconstructions of the head of M. viggianii at the cellular and subcellular levels were obtained, and of volumetric data were analyzed. A total of 689 nucleated cells of the head were reconstructed. The ultrastructure of M. viggianii is surprisingly complex, and the evolutionary benefits of such complexity are probably among the factors limiting the further miniaturization of parasitoid wasps.

Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning

Focused ion beam scanning electron microscopy is well suited for volumetric extractions and 3D reconstructions of plant cells and its organelles. The three-dimensional (3D) reconstruction of individual plant cells is an important tool to extract volumetric data of organelles and is necessary to fully understand ultrastructural changes and adaptations of plants to their environment. Methods such as the 3D reconstruction of cells based on light microscopical images often lack the resolution necessary to clearly reconstruct all cell compartments within a cell. The 3D reconstruction of cells through serial sectioning transmission electron microscopy (ssTEM) and focused ion beam scanning electron microscopy (FIB-SEM) are powerful alternatives but not widely used in plant sciences. Here, we present a method for the 3D reconstruction and volumetric extraction of plant cells based on FIB milling and compare the results with 3D reconstructions obtained with ssTEM. When compared to 3D reconstruction based on ssTEM, FIB-SEM delivered similar results. The data extracted in this study demonstrated that tobacco cells were larger (31410 µm³) than pumpkin cells (20697 µm³) and contained more chloroplasts (175 vs. 124), mitochondria (1317 vs. 291) and peroxisomes (745 vs. 79). While individual chloroplasts, mitochondria, peroxisomes were larger in pumpkin plants (25, 53, and 50%, respectively) they covered more total volume in tobacco plants (5390, 395, 374 µm³, respectively) due to their higher number per cell when compared to pumpkin plants (4762, 134, 59 µm³, respectively). While image acquisition with FIB-SEM was automated, software controlled, and less difficult than ssTEM, FIB milling was slower and sections could not be revised or re-imaged as they were destroyed by the ion beam. Nevertheless, the results in this study demonstrated that both, FIB-SEM and ssTEM, are powerful tools for the 3D reconstruction of and volumetric extraction from plant cells and that there were large differences in size, number, and organelle composition between pumpkin and tobacco cells.

Synchrotron Based X-ray Microtomography Reveals Cellular Morphological Features of Developing Wheat Grain

Wheat is one of the most important crops in the world, mainly used for human consumption and animal feed. To overcome the increasing demand in wheat production, it is necessary to better understand the mechanisms involved in the growth of the wheat grain. X-ray computed tomography is an efficient method for the non-destructive investigation of the 3D architecture of biological specimens, which does not require staining, sectioning, or inclusion. In particular, phase-contrast tomography results in images with better contrast and an increased resolution compared to that obtained with laboratory tomography devices. The aim of this study was to investigate the potential of phase-contrast tomography for the study of the anatomy of the wheat grain at early stages of development. We provided 3D images of entire grains at various development stages. The image analysis allowed identifying a large number of tissues, and to visualize individual cells. Using a high-resolution setup, finer details were obtained, making it possible to identify additional tissues. Three-dimensional rendering of the grain also revealed the pattern resulting from the epidermis cells. X-ray phase-contrast tomography appears as a promising imaging method for the study of the 3D anatomy of plant organs and tissues.

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography

Lignin is a heterogeneous aromatic polymer responsible for cell wall stiffness and protection from pathogen attack. However, lignin represents a bottleneck to biomass degradation due to its recalcitrance related to the natural cell wall resistance to release sugars for fermentation or further processing. A biological approach involving genetics and molecular biology was used to disrupt lignin pathway synthesis and decrease lignin deposition. Here, we imaged three-dimensional fragments of the petioles of wild type and C4H lignin mutant Arabidopsis thaliana plants by synchrotron cryo-ptychography. The three-dimensional images revealed the heterogeneity of vessels, parenchyma, and fibre cell wall morphologies, highlighting the relation between disturbed lignin deposition and vessel implosion (cell collapsing and obstruction of water flow). We introduce a new parameter to accurately define cell implosion conditions in plants, and we demonstrate how cryo-ptychographic X-ray computed tomography (cryo-PXCT) provides new insights for plant imaging in three dimensions to understand physiological processes.

Quantitative imaging of plants: multi-scale data for better plant anatomy

This article comments on: Staedler YM, Kreisberger T, Manafzadeh S, Chartier M, Handschuh S, Pamperl S, Sontag S, Paun O, Schönenberger J. 2017. Novel computed tomography-based tools reliably quantify plant reproductive investment. Journal of Experimental Botany 69, 525–535.

Unravelling the plant signalling machinery: an update on the cellular and genetic basis of plant signal transduction

Plant signalling is a set of phenomena that serves the transduction of external and internal signals into physiological responses such as modification of enzyme activity, cytoskeleton structure or gene expression. It operates at the level of cell compartments, whole cells, tissues, organs or even plant communities. To achieve this, plants have evolved a network of signalling proteins including plasma membrane receptors and ion transporters, cascades of kinases and other enzymes as well as several second messengers such as cytosolic calcium (Ca2+), reactive oxygen/nitrogen species (ROS/RNS), cyclic nucleotides (cAMP and cGMP) and others. Overall, these systems recognise and decode environmental signals and co-ordinate ontogeny programs. This paper summarises recent progress in the field of plant signalling, which was a major theme of the 4th International Symposium on Plant Signalling and Behaviour, 2016, in Saint Petersburg, Russia. Several novel hypotheses and concepts were proposed during this meeting. First, the concept of ROS-Ca2+ hubs has found further evidence and acceptance. This concept is based on reciprocal activation of NADPH oxidases by cytosolic Ca2+ on the one hand, and Ca2+-permeable channels that are activated by NADPH-produced ROS. ROS-Ca2+ hubs enhance the intensity and duration of originally weak Ca2+ and ROS signals. Hubs are directly involved in ROS- and Ca2+-mediated physiological reactions, such as stress response, growth, programmed cell death, autophagy and long-distance signalling. Second, recent findings have widened the list of cyclic nucleotide-regulated processes and strengthened the biochemical basis of cyclic nucleotide biochemistry by exploring cyclase activities of new receptors such as the Phytosulfokine Receptor 1, the pathogen peptide 1 receptor (atPepR1), the brassinosteroid BRI1 receptor and the cell wall-associated kinase like 10. cGMP and cAMP signalling has demonstrated strong link to Ca2+ signalling, via cyclic nucleotide-gated Ca2+-permeable ion channels (CNGCs), and to ROS and RNS via their nitrosylated forms. Third, a novel role for cytosolic K+ as a regulator of plant autophagy and programmed cell death has emerged. The cell death-associated proteases and endonucleases were demonstrated to be activated by a decrease of cytosolic K+ via ROS-induced stimulation of the plasma membrane K+ efflux channel GORK. Importantly, the origin of ROS for induction of autophagy and cell death varies in different tissues and comprises several pools, including NADPH oxidases, peroxidases, photosynthetic and respiratory electron-transporting chains and peroxisomal enzymes. The peroxisome pool is the 'latest' addition to established cellular ROS-producing machineries and is dependent on the state and abundance of catalase in this compartment. Finally, new aspects of phytohormone signalling, such as regulation of root hydraulic pressure by abscisic acid and rate of mitosis by cytokinins, as well as localising cytokinin receptors in endoplasmic reticulum, are reported. Other observations suggest that melatonin is a hormone-like substance in plants, because it targets Ca2+, ROS and RNS.

Spatial distribution of organelles in leaf cells and soybean root nodules revealed by focused ion beam-scanning electron microscopy

Analysis of cellular ultrastructure has been dominated by transmission electron microscopy (TEM), so images collected by this technique have shaped our current understanding of cellular structure. More recently, three-dimensional (3D) analysis of organelle structures has typically been conducted using TEM tomography. However, TEM tomography application is limited by sample thickness. Focused ion beam-scanning electron microscopy (FIB-SEM) uses a dual beam system to perform serial sectioning and imaging of a sample. Thus FIB-SEM is an excellent alternative to TEM tomography and serial section TEM tomography. Animal tissue samples have been more intensively investigated by this technique than plant tissues. Here, we show that FIB-SEM can be used to study the 3D ultrastructure of plant tissues in samples previously prepared for TEM via commonly used fixation and embedding protocols. Reconstruction of FIB-SEM sections revealed ultra-structural details of the plant tissues examined. We observed that organelles packed tightly together in Nicotiana benthamiana Domin leaf cells may form membrane contacts. 3D models of soybean nodule cells suggest that the bacteroids in infected cells are contained within one large membrane-bound structure and not the many individual symbiosomes that TEM thin-sections suggest. We consider the implications of these organelle arrangements for intercellular signalling.

Exploring the interior of cuticles and compressions of fossil plants by FIB-SEM milling and image microscopy

We present the first study of cuticles and compressions of fossil leaves by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Cavities preserved inside fossil leaf compressions corresponding to substomatal chambers have been observed for the first time and several new features were identified in the cross-section cuts. These results open a new way in the investigation of the three-dimensional structures of both micro- and nanostructural features of fossil plants. Moreover, the application of the FIB-SEM technique to both fossils and extant plant remains represent a new source of taxonomical, palaeoenvironmental and palaeoclimatic information.

Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM

BACKGROUND AND AIMS

Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction.

METHODS

Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software.

KEY RESULTS

The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other.

CONCLUSIONS

Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll cells enhance their CO 2 absorption with increased cell surface and sheet-shaped chloroplasts.