Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes

The fate and impact of Co3O4 nanoparticles in the soil environment: Observing the dose effect of nanoparticles on soybeans

The widespread presence and distribution of metal-based nanoparticles (NPs) in soil is threatening crop growth and food security. However, little is known about the fate of Co3O4 NPs in the soil-soybean system and their phytotoxicity. The study demonstrated the effects of Co3O4 NPs on soybean growth and yield in soil after 60 days and 140 days, and compared them with the phytotoxic effects of Co2+. The results showed that Co3O4 NPs (10-500 mg/kg) had no significant toxic effect on soybeans. Soil available Co content was significantly increased under 500 mg/kg Co3O4 NPs treatment. Compared with Co2+, Co3O4 NPs mainly accumulated in roots and had limited transport to the shoots, which was related to the particle size, surface charge and chemical stability of Co3O4 NPs. The significant accumulation of Co3O4 NPs in roots further led to a significant decrease in root antioxidant enzyme activity and changes in functional gene expression. Co3O4 NPs reduced soybean yield after 140 days, but interestingly, at specific doses, it increased grain nutrients (Fe content increased by 17.38% at 100 mg/kg, soluble protein and vitamin E increased by 14.34% and 16.81% at 10 mg/kg). Target hazard quotient (THQ) assessment results showed that consuming soybean seeds exposed to Co3O4 NPs (≥100 mg/kg) and Co2+ (≥10 mg/kg) would pose potential health risks. Generally, Co3O4 NPs could exist stably in the environment and had lower environmental risks than Co2+. These results help to better understand the environmental behavior and plant effect mechanisms of Co3O4 NPs in soil-plant systems.

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.

Molecular Regulation and Evolution of Cytokinin Signaling in Plant Abiotic Stresses

The sustainable production of crops faces increasing challenges from global climate change and human activities, which leads to increasing instances of many abiotic stressors to plants. Among the abiotic stressors, drought, salinity and excessive levels of toxic metals cause reductions in global agricultural productivity and serious health risks for humans. Cytokinins (CKs) are key phytohormones functioning in both normal development and stress responses in plants. Here, we summarize the molecular mechanisms on the biosynthesis, metabolism, transport and signaling transduction pathways of CKs. CKs act as negative regulators of both root system architecture plasticity and root sodium exclusion in response to salt stress. The functions of CKs in mineral-toxicity tolerance and their detoxification in plants are reviewed. Comparative genomic analyses were performed to trace the origin, evolution and diversification of the critical regulatory networks linking CK signaling and abiotic stress. We found that the production of CKs and their derivatives, pathways of signal transduction and drought-response root growth regulation are evolutionarily conserved in land plants. In addition, the mechanisms of CK-mediated sodium exclusion under salt stress are suggested for further investigations. In summary, we propose that the manipulation of CK levels and their signaling pathways is important for plant abiotic stress and is, therefore, a potential strategy for meeting the increasing demand for global food production under changing climatic conditions.

Development specifies, diversifies and empowers root immunity

Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.

Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.

Differential bioaccumulations and ecotoxicological impacts of metal-oxide nanoparticles, bulk materials, and metal-ions in cucumbers grown in sandy clay loam soil

Expanding applications of metal-oxide nanoparticles (NPs) and increased environmental deposition of NPs followed by their interactions with edible crops threaten yields. This study demonstrates the effects of aging (45 days in soil) of four NPs (ZnO, CuO, Al₂O₃, TiO₂; 3.9-34 nm) and their corresponding metal oxide bulk particles (BPs; 144-586 nm) on cucumbers (Cucumis sativus L.) cultivated in sandy-clay-loam field soil and compares these with the phytotoxic effects of readily soluble metal salts (Zn²⁺, Cu²⁺, and Al³⁺). Data revealed the cell-to-cell translocations of NPs, their attachments to outer and inner cell surfaces, nuclear membranes, and vacuoles, and their upward movements to aerial parts. Metal bioaccumulations in cucumbers were found in the order: (i) ZnO-NPs > ZnO-BPs > Zn²⁺, (ii) CuO-NPs > CuO-BPs > Cu²⁺, (iii) Al³⁺> Al₂O₃-NPs > Al₂O₃-BPs and (iv) TiO₂-NPs > TiO₂-BPs. Aging of NPs in soil for 45 days significantly enhanced metal uptake (P ≤ 0.05), for instance aged ZnO-NPs at 1 g kg^-1 increased the uptake by 20.7 % over non-aged ZnO-NPs. Metal uptakes inhibited root (RDW) and shoot (SDW) dry weight accumulations. For Cu species, maximum negative impact (%) was exhibited by Cu²⁺ (RDW:SDW = 94:65) followed by CuO-NPs (RDW:SDW = 78:34) and CuO-BPs (RDW:SDW = 27:22). Aging of NPs/BPs at 1-4 g kg^-1 further enhanced the toxic impact of tested materials on biomass accumulations and chlorophyll formation. NPs also induced membrane damage of root tissues and enhanced levels of antioxidant enzymes. The results of this study suggest that care is required when aged metal-oxide NPs of both essential (Zn and Cu) and non-essential (Al and Ti) metals interact with cucumber plants, especially, when they are used for agricultural purposes.

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.

Molecular Evolution of Auxin-Mediated Root Initiation in Plants

The root originated independently in euphyllophytes (ferns and seed plants) and lycophytes; however, the molecular evolutionary route of root initiation remains elusive. By analyses of the fern Ceratopteris richardii and seed plants, here we show that the molecular pathway involving auxin, intermediate-clade WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes, and WUSCHEL-clade WOX (WC-WOX) genes could be conserved in root initiation. We propose that the "auxin>IC-WOX>WC-WOX" module in root initiation might have arisen in the common ancestor of euphyllophytes during the second origin of roots, and that this module has further developed during the evolution of different root types in ferns and seed plants.

Molecular oxygen as a signaling component in plant development

While traditionally hypoxia has been studied as a detrimental component of flooding stress, the last decade has flourished with studies reporting the involvement of molecular oxygen availability in plant developmental processes. Moreover, proliferating and undifferentiated cells from different plant tissues were found to reside in endogenously generated hypoxic niches. Thus, stress-associated acute hypoxia may be distinguished from constitutively generated chronic hypoxia. The Cys/Arg branch of the N-degron pathway assumes a central role in integrating oxygen levels resulting in proteolysis of transcriptional regulators that control different aspects of plant growth and development. As a target of this pathway, group VII of the Ethylene Response Factor (ERF-VII) family has emerged as a hub for the integration of oxygen dynamics in root development and during seedling establishment. Additionally, vegetative shoot meristem activity and reproductive transition were recently associated with oxygen availability via two novel substrates of the N-degron pathways: VERNALISATION 2 (VRN2) and LITTLE ZIPPER 2 (ZPR2). Together, these observations support roles for molecular oxygen as a signalling molecule in plant development, as well as in essential metabolic reactions. Here, we review recent findings regarding oxygen-regulated development, and discuss outstanding questions that spring from these discoveries.

Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?

Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.

Shedding the Last Layer: Mechanisms of Root Cap Cell Release

The root cap, a small tissue at the tip of the root, protects the root from environmental stress and functions in gravity perception. To perform its functions, the position and size of the root cap remains stable throughout root growth. This occurs due to constant root cap cell turnover, in which the last layer of the root cap is released, and new root cap cells are produced. Cells in the last root cap layer are known as border cells or border-like cells, and have important functions in root protection against bacterial and fungal pathogens. Despite the importance of root cap cell release to root health and plant growth, the mechanisms regulating this phenomenon are not well understood. Recent work identified several factors including transcription factors, auxin, and small peptides with roles in the production and release of root cap cells. Here, we review the involvement of the known players in root cap cell release, compare the release of border-like cells and border cells, and discuss the importance of root cap cell release to root health and survival.

The evolutionary trajectory of root stem cells

Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.

Developmental Responses to Water and Salinity in Root Systems

Roots provide the primary mechanism that plants use to absorb water and nutrients from their environment. These functions are dependent on developmental mechanisms that direct root growth and branching into regions of soil where these resources are relatively abundant. Water is the most limiting factor for plant growth, and its availability is determined by the weather, soil structure, and salinity. In this review, we define the developmental pathways that regulate the direction of growth and branching pattern of the root system, which together determine the expanse of soil from which a plant can access water. The ability of plants to regulate development in response to the spatial distribution of water is a focus of many recent studies and provides a model for understanding how biological systems utilize positional cues to affect signaling and morphogenesis. A better understanding of these processes will inform approaches to improve crop water use efficiency to more sustainably feed a growing population.

TiO2 nanoparticles may alleviate cadmium toxicity in co-treatment experiments on the model hydrophyte Azolla filiculoides

The hydrophyte Azolla filiculoides can be a useful model to assess if TiO₂ NPs may in some way alleviate the Cd injuries and improve the ability of the plant to cope with this metal. With this mechanistic hypothesis, after a pre-treatment with TiO₂ NPs, A. filiculoides plants were transferred to cadmium-contaminated water with or without TiO₂ nanoparticles. After 5 days of treatment, cadmium uptake, morpho-anatomical, and physiological aspects were studied in plants. The continuous presence of TiO₂ nanoparticles, though not increasing the uptake of cadmium in comparison with a priming treatment, induced a higher translocation of this heavy metal to the aerial portion. Despite the translocation factor was always well below 1, cadmium contents in the fronds, generally greater than 100 ppm, ranked A. filiculoides as a good cadmium accumulator. Higher cadmium contents in leaves did not induce damages to the photosynthetic machinery, probably thanks to a compartmentalization strategy aimed at confining most of this pollutant to less metabolically active peripheral cells. The permanence of NPs in growth medium ensured a better efficiency of the antioxidant apparatus (proline and glutathione peroxidase and catalase activities) and induced a decrease in H₂O₂ content, but did not suppress TBARS level.

Rhynie chert fossils demonstrate the independent origin and gradual evolution of lycophyte roots

Mapping fossil traits onto the land plant phylogenetic framework indicates that there were at least two independent origins of roots among extant vascular plants - once in lycophytes and independently in euphyllophytes. At least two rooting structural types are found among extinct species preserved in the Rhynie chert. First, species that lacked roots and developed horizontal axes that developed rhizoids. Second, the rooting axes of Asteroxylon mackiei resembled the roots of extant lycopsids but lacked root hairs and root caps. These two rooting structures preceded the evolution of the roots of extant lycophytes comprising axes on which root hairs and root caps developed. These data demonstrate the defining root characters evolved gradually in the lycophyte lineage.