Control of leaf development in the water fern Ceratopteris richardii by the auxin efflux transporter CrPINMa in the CRISPR/Cas9 analysis.

BACKGROUND: PIN-FORMED genes (PINs) are crucial in plant development as they determine the directionality of auxin flow. They are present in almost all land plants and even in green algae. However, their role in fern development has not yet been determined. This study aims to investigate the function of CrPINMa in the quasi-model water fern Ceratopteris richardii. RESULTS: CrPINMa possessed a long central hydrophilic loop and characteristic motifs within it, which indicated that it belonged to the canonical rather than the non-canonical PINs. CrPINMa was positioned in the lineage leading to Arabidopsis PIN6 but not that to its PIN1, and it had undergone numerous gene duplications. CRISPR/Cas9 genome editing had been performed in ferns for the first time, producing diverse mutations including local frameshifts for CrPINMa. Plants possessing disrupted CrPINMa exhibited retarded leaf emergence and reduced leaf size though they could survive and reproduce at the same time. CrPINMa transcripts were distributed in the shoot apical meristem, leaf primordia and their vasculature. Finally, CrPINMa proteins were localized to the plasma membrane rather than other cell parts. CONCLUSIONS: CRISPR/Cas9 genome editing is feasible in ferns, and that PINs can play a role in fern leaf development.

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.

An ontogenetic framework for functional studies in the model fern Ceratopteris richardii.

As the sister group to seed plants, ferns are a phylogenetically informative lineage. Functional studies in representatives of the fern lineage are helping bridge the knowledge gap in developmental mechanisms between angiosperms and non-vascular plants. The fern life cycle has the advantage of combining a sizable free-living haploid gametophyte, more amenable for developmental studies than the reduced seed plant gametophyte, with an indeterminate and complex diploid sporophyte. Ceratopteris richardii has long been proposed as a model fern and has recently become tractable due to stable transgenesis and increasing genomic resources, allowing researchers to test explicit questions about gene function in a fern for the first time. As with any model system, a detailed understanding of wild-type morphology and a staged ontogeny are indispensable for the characterization of mutant phenotypes resulting from genetic manipulations. Therefore, the goal of this study is to provide a unified reference ontogeny for this emerging model fern as a tool for comparative evolutionary and developmental studies. It complements earlier research by filling gaps in major stages of development of the haploid gametophyte and diploid sporophyte generations, and provides additional descriptions of the shoot apical meristem and early leaf development. This resource is meant to facilitate not only studies of candidate genes within C. richardii, but also broader ontogenetic comparisons to other model plants.

Meristem development and activity in gametophytes of the model fern, Ceratopteris richardii.

Ceratopteris richardii is a model fern species widely used to analyze various developmental processes and their regulation in gametophytes. The form of mature C. richardii gametophytes depends on the activity of the marginal meristem, but knowledge on meristem formation and structure is limited. Therefore, we analyzed cellular events accompanying the development of gametophytes using cell lineage and proliferation analyses to explain the establishment and functioning of the marginal meristem. We show that: i) gametophytes are devoid of the apical initial cell or the apical cell-based meristem in the early developmental stages; ii) the cells that are predestined to form the marginal meristem divide according to a stable pattern; iii) only one transient initial cell is present in the marginal meristem, and the selection of a new functioning initial cell is related to a stable sequence of its divisions. Our results contribute to a better understanding of the developmental events underlying gametophyte growth and marginal meristem functioning in Ceratopteris. The principles, which were established in this study and enabled the identification of functioning initial cells, can be applied to analyze genetic and/or physiological mechanism(s) governing meristem maintenance in vascular plants, both in developmental and evolutionary contexts.

LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii.

During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged.

Plasma membrane-anchored chloroplasts are necessary for the gravisensing system of Ceratopteris richardii prothalli.

The prothalli of the fern Ceratopteris richardii exhibit negative gravitropism when grown in darkness. However, no sedimentable organelles or substances have been detected in the prothallial cells, suggesting that a non-sedimentable gravisensor exists. We investigated whether chloroplasts are involved in the gravisensing system of C. richardii prothalli. We used a clumped-chloroplast mutant, clumped chloroplast 1 (cp1), in which the chloroplasts are detached from the plasma membrane and clustered around the nucleus likely because of a partial deletion in the KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 gene. The cp1 mutation resulted in prothalli that had a significantly diminished gravitropic response, while the phototropic response occurred normally. These results suggest that plasma membrane-anchored chloroplasts in prothallial cells function as one of the gravisensors in C. richardii prothalli.

Studying molecular changes during gravity perception and response in a single cell.

Early studies revealed a highly predictable pattern of gravity-directed growth and development in Ceratopteris richardii spores. This makes the spores a valuable model system for the study of how a single cell senses and responds to the force of gravity. Gravity regulates both the direction and magnitude of a trans-cell calcium current in germinating spores, and the orientation of this current predicts the polarization of spore development. Molecular techniques have been developed to evaluate the transcriptomic and proteomic profiles of spores before and after gravity establishes the polarity of their development. Here we describe these techniques, along with protocols for sterilizing the spores, sowing them in a solid or liquid growth media, and evaluating germination.

A preliminary study on the phytoremediation of antibiotic contaminated sediment.

In Vietnam's coastal wetlands, fluoroquinolones, a widely used class of antibiotics in shrimp farming, are frequently detected in sediments of former shrimp farms. This phenomenon could lead to negative impacts on the aquatic ecosystem, since the antibiotic residues could induce changes in the microorganism communities of the water body. The potential of native wetland plants (Acrostichum aureum L. and Rhizophora apiculata Blume Fl. Javae) for phytoremediation of fluoroquinolones (ciprofloxacin and norfloxacin) was investigated. The half-life for each antibiotic was estimated at approximately 10 days in the planted sediment. With respect to the accumulation of ciprofloxacin and norfloxacin in plants, these antibiotics were found mainly in roots. Antibiotic translocation from root to stem and leaves occurred at a low rate. The results showed that A. aureum and R. apiculata can be valuable for the phytoremediation of antibiotic-contaminated sediments. Additionally, the initialfindings of the presence of resistant bacteria indicated that bacteria could play a role in facilitating the phytodegradation.

Changes in gravity rapidly alter the magnitude and direction of a cellular calcium current.

In single-celled spores of the fern Ceratopteris richardii, gravity directs polarity of development and induces a directional, trans-cellular calcium (Ca(2+)) current. To clarify how gravity polarizes this electrophysiological process, we measured the kinetics of the cellular response to changes in the gravity vector, which we initially estimated using the self-referencing calcium microsensor. In order to generate more precise and detailed data, we developed a silicon microfabricated sensor array which facilitated a lab-on-a-chip approach to simultaneously measure calcium currents from multiple cells in real time. These experiments revealed that the direction of the gravity-dependent polar calcium current is reversed in less than 25 s when the cells are inverted, and that changes in the magnitude of the calcium current parallel rapidly changing g-forces during parabolic flight on the NASA C-9 aircraft. The data also revealed a hysteresis in the response of cells in the transition from 2g to micro-g in comparison to cells in the micro-g to 2-g transition, a result consistent with a role for mechanosensitive ion channels in the gravity response. The calcium current is suppressed by either nifedipine (calcium-channel blocker) or eosin yellow (plasma membrane calcium pump inhibitor). Nifedipine disrupts gravity-directed cell polarity, but not spore germination. These results indicate that gravity perception in single plant cells may be mediated by mechanosensitive calcium channels, an idea consistent with some previously proposed models of plant gravity perception.

Asanoa hainanensis sp. nov., isolated from rhizosphere soil of Acrostichum speciosum in a mangrove, and emended description of the genus Asanoa.

A Gram-reaction-positive, non-motile actinobacterium, designated strain 210121(T), was isolated from rhizosphere soil of the mangrove fern Acrostichum speciosum. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Asanoa. DNA-DNA relatedness values between strain 210121(T) and the type strains of the three recognized species of the genus Asanoa were below the 70 % threshold recommended for distinguishing bacterial genomic species. The novel isolate contained glutamic acid, glycine, alanine and meso-A(2)pm as cell-wall amino acids, indicating peptidoglycan type A1γ. The characteristic whole-cell sugars were xylose, ribose, glucose and mannose. The predominant menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)). The major fatty acids were iso-C(16 : 0) (30.9 %), C(17 : 0) (23.0 %), anteiso-C(15 : 0) (14.9 %) and iso-C(15 : 0) (12.3 %). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The G+C content of the DNA was 70.3 mol%. On the basis of the phenotypic and genotypic data, strain 210121(T) ( = CGMCC 4.5593(T)  = DSM 45427(T)) represents a novel species of the genus Asanoa, for which the name Asanoa hainanensis sp. nov., is proposed. An emended description of the genus Asanoa is also proposed.

Mycothallic/mycorrhizal symbiosis of chlorophyllous gametophytes and sporophytes of a fern, Pellaea viridis (Forsk.) Prantl (Pellaeaceae, Pteridales).

Gametophytes of Pellaea viridis that appeared spontaneously on the surface of substratum originating from an ultramafic area were found to form mycothallic symbiosis with arbuscular mycorrhizal fungi (AMF) under laboratory conditions. In gametophytes and sporophytes grown with Glomus tenue, abundant arbuscule formation was observed at both stages. In gametophytes, the fungus was found in the region where the rhizoids are initiated. If G. intraradices was added to the soil, the gametophytes were colonised mostly by G. tenue, and roots of sporophytes were colonised by G. intraradices. The presence of AM fungi in both gametophytes and sporophytes of P. viridis resulted in the development of larger leaf area and root length of the sporophyte. The analysis of gametophytes from the Botanical Garden in Krakow (Poland) showed that cordate gametophytes of Pteridales, namely Pellaea viridis (Pellaeaceae), Adiantum raddianum and A. formosum (Adiantaceae), were also mycothallic.

A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes.

BACKGROUND: Ceratopteris richardii is a useful experimental system for studying gametophyte development and sexual reproduction in plants. However, few tools for cloning mutant genes or disrupting gene function exist for this species. The feasibility of systemic gene silencing as a reverse genetics tool was examined in this study. RESULTS: Several DNA constructs targeting a Ceratopteris protoporphyrin IX magnesium chelatase (CrChlI) gene that is required for chlorophyll biosynthesis were each introduced into young gametophytes by biolistic delivery. Their transient expression in individual cells resulted in a colorless cell phenotype that affected most cells of the mature gametophyte, including the meristem and gametangia. The colorless phenotype was associated with a 7-fold decrease in the abundance of the endogenous transcript. While a construct designed to promote the transient expression of a CrChlI double stranded, potentially hairpin-forming RNA was found to be the most efficient in systemically silencing the endogenous gene, a plasmid containing the CrChlI cDNA insert alone was sufficient to induce silencing. Bombarded, colorless hermaphroditic gametophytes produced colorless embryos following self-fertilization, demonstrating that the silencing signal could be transmitted through gametogenesis and fertilization. Bombardment of young gametophytes with constructs targeting the Ceratopteris filamentous temperature sensitive (CrFtsZ) and uroporphyrin dehydrogenase (CrUrod) genes also produced the expected mutant phenotypes. CONCLUSION: A method that induces the systemic silencing of target genes in the Ceratopteris gametophyte is described. It provides a simple, inexpensive and rapid means to test the functions of genes involved in gametophyte development, especially those involved in cellular processes common to all plants.

Developmental anatomy and auxin response of lateral root formation in Ceratopteris richardii.

The homosporous fern Ceratopteris richardii exhibits a homorhizic root system where roots originate from the shoot system. These shoot-borne roots form lateral roots (LRs) that arise from the endodermis adjacent to the xylem poles, which is in contrast to flowering plants where LR formation arises from cell division in the pericycle. A detailed study of the fifth shoot-borne root showed that one lateral root mother cell (LRMC) develops in each two out of three successive merophytes. As a result, LRs emerge alternately in two ranks from opposite positions on a parent root. From LRMC initiation to LR emergence, three developmental stages were identified based on anatomical criteria. The addition of auxins (either indole-3-acetic acid or indole-3-butyric acid) to the growth media did not induce additional LR formation, but exogenous applications of both auxins inhibited parent root growth rate. Application of the polar auxin-transport inhibitor N-(1-naphthyl)phthalamic acid (NPA) also inhibited parent root growth without changing the LR initiation pattern. The results suggest that LR formation does not depend on root growth rate per se. The result that exogenous auxins do not promote LR formation in C. richardii is similar to reports for certain species of flowering plants, in which there is an acropetal LR population and the formation of the LRs is insensitive to the application of auxins. It also may indicate that different mechanisms control LR development in non-seed vascular plants compared with angiosperms, taking into consideration the long and independent evolutionary history of the two groups.