Root apical meristem diversity and the origin of roots: insights from extant lycophytes

Salinity survival: molecular mechanisms and adaptive strategies in plants

Soil salinity is a significant environmental challenge that threatens plant growth and development, adversely affecting global food crop production. This underscores the critical need to elucidate the molecular mechanisms underlying plant salt tolerance, which has profound implications for agricultural advancement. Recent progress in plant salt tolerance has greatly improved our understanding of the molecular mechanisms of plant responses to salt stress and precision design breeding as an effective strategy for developing new salt-tolerant crop varieties. This review focuses on the model plant species Arabidopsis thaliana and important crops, namely, wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa). It summarizes current knowledge on plant salt tolerance, emphasizing key aspects such as the perception and response to salt stress, Na+ transport, Na+ compartmentalization and clearance, changes in reactive oxygen species induced by salt stress, and regulation of plant stem cell development under salt stress conditions. The review might provide new and valuable information for understanding the molecular mechanisms of plant response and adaptation to salt stress.

Why can Palhinhaea cernua (lycophyte) grow closer to fumaroles in highly acidic solfatara fields?

Palhinhaea cernua, a lycophyte, and Dicranopteris linearis, a fern, are commonly observed in solfatara fields in Kyushu, Japan, but their distribution trends are different. The aim of this study was to determine why P. cernua is more abundant in areas closer to fumaroles from both a soil and plant perspective. Samples of P. cernua and D. linearis, as well as their respective growing soils, were collected, and the mineral properties, including the concentration of various mineral elements and inorganic anions and δ15N, were determined. P. cernua was better adapted to soil with lower pH, higher soluble aluminum concentrations, and poorer calcium and phosphorus concentrations than D. linearis. A positive correlation was observed between shoot nitrogen concentration and both shoot sulfur concentration and soil water-soluble sulfur concentration in P. cernua, implying the involvement of sulfur in nitrogen acquisition in P. cernua. The results also suggested that D. linearis mainly uses soil NO3-N, while P. cernua uses NH4-N, which is predominant and excessive in the solfatara fields, particularly near the fumaroles. This high preference for NH4-N in P. cernua was confirmed through a cultivation experiment. While D. linearis prefers NO3-N and distributes further from fumaroles, P. cernua may have survived in the solfatara fields by utilizing NH4-N and sulfur, which are abundant near fumaroles where competition from other plant species is minimal.

The role of fossils for reconstructing the evolution of plant development

Many of the developmental innovations that underpin the diversity of plant form alive today, such as those facilitating apical growth, branching, leaves, roots, wood and seeds, all evolved over 360 million years ago. Fossils, as our only direct record of plant form in the past, are thus essential for interpreting the origin and evolution of these innovations. The focus of this Spotlight is to showcase the rich plant fossil record open for developmental interpretation and to cement the role that fossils play at a time when increases in genome sequencing and new model species make tackling major questions in the area of plant evolution and development tractable for the first time.

The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.

Maintenance of stem cell activity in plant development and stress responses

Stem cells residing in plant apical meristems play an important role during postembryonic development. These stem cells are the wellspring from which tissues and organs of the plant emerge. The shoot apical meristem (SAM) governs the aboveground portions of a plant, while the root apical meristem (RAM) orchestrates the subterranean root system. In their sessile existence, plants are inextricably bound to their environment and must adapt to various abiotic stresses, including osmotic stress, drought, temperature fluctuations, salinity, ultraviolet radiation, and exposure to heavy metal ions. These environmental challenges exert profound effects on stem cells, potentially causing severe DNA damage and disrupting the equilibrium of reactive oxygen species (ROS) and Ca2+ signaling in these vital cells, jeopardizing their integrity and survival. In response to these challenges, plants have evolved mechanisms to ensure the preservation, restoration, and adaptation of the meristematic stem cell niche. This enduring response allows plants to thrive in their habitats over extended periods. Here, we presented a comprehensive overview of the cellular and molecular intricacies surrounding the initiation and maintenance of the meristematic stem cell niche. We also delved into the mechanisms employed by stem cells to withstand and respond to abiotic stressors.

Cellular and gene expression patterns associated with root bifurcation in Selaginella

The roots of lycophytes branch through dichotomy or bifurcation, during which the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, with LRs developing along the root axis at different distances from the apex. Although the process of root bifurcation is poorly understood, such knowledge can be important, because it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopic and transcriptomic level. Our results showed that, in contrast to previous assumptions, initial cells (ICs) in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages of root branching argues for the occurrence of a symmetric division of the single IC, resulting in two apical stem cells that initiate root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome that resulted in the delineation of a subset of core meristem genes. The occurrence of multiple putative orthologs of meristem genes in this dataset suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.

Shared body plans of lycophytes inferred from root formation of Lycopodium clavatum

Late Silurian to early Devonian lycophytes had prostrate aerial axes, while subordinate organs or subterranean axes were formed around the dichotomies of the axes. The subterranean axes are hypothesized to have evolved into root-bearing axes (rhizophores) and roots in extant Selaginellaceae and Lycopodiaceae, respectively. Consistent with this hypothesis, rhizophores are formed on the dichotomies of shoots in Selaginellaceae. However, it has remained unclear whether roots are borne in the same position in Lycopodiaceae. In addition, roots form endogenously in the stem, but no data are available regarding the tissues in stem from which they arise. In this study, we tracked the root development in the clubmoss, Lycopodium clavatum, based on anatomical sections and 3D reconstructed images. The vascular tissue of the stem is encircled by ground meristem, which supplies cortical cells outwardly by periclinal divisions. A linear parenchymatous tissue is present on the ventral side of vascular cylinder, which we call “ventral tissue” in this study. We found that root primordia are formed endogenously on the ventral side of stem, possibly from the ventral tissue. In addition, roots always initiate at positions close to dichotomies of stem. The root-initiating position supports the suggestion that Lycopodium roots share a body plan with the subterranean organs of the hypothesized ancestry.

Root Cap to Soil Interface: A Driving Force Toward Plant Adaptation and Development

Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has a specialized organ called the 'root cap'. The root cap assists the roots in penetrating the ground, absorbing water and minerals, avoiding heavy metals and regulating the rhizosphere microbiota. Furthermore, root-cap-derived auxin governs the lateral root patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aid in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphological and physiological characteristics for the root-soil interaction and their response toward various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type-enriched genes. We compiled root cap cell-type-enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor (TF) binding site enrichment. Further, the putative gene regulatory networks derived from root-cap-enriched genes and their TF regulators highlight the species-specific biological functions of root cap genes across the four plant species.

Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum

Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.

The quiescent centre of the root apical meristem: conceptual developments from Clowes to modern times

In this review we discuss the concepts of the quiescent centre (QC) of the root apical meristem (RAM) and their change over time, from their formulation by F.A.L. Clowes to the present. This review is dedicated to the 100th anniversary of the birth of Clowes, and we present his short biography and a full bibliography of Clowes' work. Over time, the concept of the QC proved to be useful for the understanding of RAM organization and behaviour. We focus specifically on conceptual developments, from the organization of the QC to understanding its functions in RAM maintenance and activity, ranging from a model species, Arabidopsis thaliana, to crops. Concepts of initial cells, stem cells, and heterogeneity of the QC cells in the context of functional and structural stem cells are considered. We review the role of the QC in the context of cell flux in the RAM and the nature of quiescence of the QC cells. We discuss the origin of the QC and fluctuation of its size in ontogenesis and why the QC cells are more resistant to stress. Contemporary concepts of the organizer and stem cell niche are also considered. We also propose how the stem cell niche in the RAM can be defined in roots of a non-model species.

WOX going on: CLE peptides in plant development

The development of plant tissues requires cell-cell communication facilitated by chemical and peptide hormones, including small signaling peptides in the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) family. The paradigmatic CLE signaling peptide CLAVATA3 regulates the size of the shoot apical meristem and the expression of the stem cell-promoting WUSCHEL transcription factor through an unknown mechanism. This review discusses recent advances in CLE signaling, showing that CLE pathways are conserved in bryophytes, that CLE peptides in Arabidopsis thaliana regulate stem cell identity and cell division in root tissues, and connections to auxin biosynthesis in regulating flower and leaf development. These advances shed light on potential WUSCHEL family-independent aspects of CLE signaling and the overlap between CLE and auxin signaling.

Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants

Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

Lycopodium root meristem dynamics supports homology between shoots and roots in lycophytes

Roots have played a pivotal role in the conquest of land by vascular plants, yet their origin has remained enigmatic. Palaeobotanical evidence suggests that roots may have originated from subterranean shoots in some lycophyte species. If this hypothesis is correct, it would follow that the roots and shoots of extant lycophytes share fundamental developmental mechanisms. We tracked meristem dynamics in root and shoot apices of Lycopodium clavatum using a thymidine analogue and expression patterns of histone H4, respectively. Then we compared the meristem dynamics of roots and shoots to identify developmental similarities. Both apical meristems contained a quiescent tissue characterised by a low frequency of cell division. Actively dividing cells appeared in the quiescent tissue during dichotomous branching of both roots and shoots. As a result, the parental meristem divides into two daughter meristems, which give rise to new root or shoot apices. These striking similarities in meristem dynamics provide new neobotanical data that support the shoot-origin hypothesis of lycophyte roots. Although Lycopodium roots may have originated from subterranean shoots of Devonian lycophytes, these shoots may have changed into root-bearing axes in other extant lycophyte lineages.

Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.