Utricularia Gibba Research Articles

Preliminary study on the man-made habitat of Utricularia gibba L. in the tropical peatland environment

Utricularia gibba L. is a free-floating aquatic carnivorous plant found in some parts of the world, including Asian tropical regions. However, data on water’s physical and chemical properties for the ecology of this species in Asian tropical peatland environments are underrepresented in the literature. Here, we reported water physical and chemical properties for the habitat of U. gibba occurring in the tropical peatland of Kalimantan Barat, Indonesia. The study site is on the man-made water canal in Jalan Parit Haji Muksin II, Kubu Raya Regency, Kalimantan Barat. We measured temperature, electrical conductivity (EC), Total Dissolved Solid (TDS), pH, Dissolved Oxygen (DO), total nitrogen, total phosphorus, nitrates, and nitrite of the waters at three points along the water canal where the bladderworts occur. The results showed that U. gibba inhabits waters with low conductivity (< 66 µS cm-1), low TDS (< 32 ppm), acidic (< pH 6), low DO (< 8 mg L-1), but higher total nitrogen (7.02 – 19.4 mg L-1), total phosphorus (0.86 – 1.71 mg L-1), nitrates (3.01 – 4.06 mg L-1) and nitrite (3.53 – 5.18 mg L-1). These findings demonstrate that U. gibba in tropical peatland environments reportedly occurs in acidic (pH 5.03 – 5.29) but relatively high nutrient habitats compared to its counterpart and other species found elsewhere.

Mining the Utricularia gibba genome for insulator-like elements for genetic engineering.

Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.

Brassinosteroid coordinates cell layer interactions in plants via cell wall and tissue mechanics.

Growth coordination between cell layers is essential for development of most multicellular organisms. Coordination may be mediated by molecular signaling and/or mechanical connectivity between cells, but how genes modify mechanical interactions between layers is unknown. Here we show that genes driving brassinosteroid synthesis promote growth of internal tissue, at least in part, by reducing mechanical epidermal constraint. We identified a brassinosteroid-deficient dwarf mutant in the aquatic plant Utricularia gibba with twisted internal tissue, likely caused by mechanical constraint from a slow-growing epidermis. We tested this hypothesis by showing that a brassinosteroid mutant in Arabidopsis enhances epidermal crack formation, indicative of increased tissue stress. We propose that by remodeling cell walls, brassinosteroids reduce epidermal constraint, showing how genes can control growth coordination between layers by means of mechanics.

Climate change may exacerbate the risk of invasiveness of non-native aquatic plants: the case of the Pannonian and Mediterranean regions of Croatia

Non-native aquatic plants are amongst the major threats to freshwater biodiversity and climate change is expected to facilitate their further spread and invasiveness. To date, in Croatia, no complete list of non-native extant and horizon aquatic plants has been compiled nor has a risk screening been performed. To address this knowledge gap, 10 extant and 14 horizon aquatic plant species were screened for their risk of invasiveness in the Pannonian and Mediterranean regions of Croatia under current and predicted (future) climate conditions. Overall, 90% and 60% of the extant species were classified as high risk for the Pannonian and Mediterranean regions, respectively, under both climate scenarios. Of the horizon species, 42% were classified as high risk under current conditions and, under climate change, this proportion increased to 78%. The ‘top invasive’ species (i.e. scored as very high risk) under both climate conditions and for both regions were extant Elodea nuttallii and horizon Lemna aequinoctialis. The horizon Hygrophila polysperma was very high risk for the Mediterranean Region under current climate conditions and for both regions under projected climate conditions. Azolla filiculoides, Elodea canadensis, Egeria densa and Utricularia gibba were also classified as high risk under current climate conditions and, after accounting for climate change, they became of very high risk in both regions. Further, Gymnocoronis spilanthoides and Lemna minuta were found to pose a very high risk under climate change only for the Pannonian Region. It is anticipated that the outcomes of this study will contribute to knowledge of the invasiveness of aquatic plants in different climatic regions and enable prioritisation measures for their control/eradication.

Genome-Wide Analysis of the Growth-Regulating Factor (GRF) Family in Aquatic Plants and Their Roles in the ABA-Induced Turion Formation of Spirodela polyrhiza.

Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.

The annotation and analysis of complex 3D plant organs using 3DCoordX.

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

Genetic Basis of Carnivorous Leaf Development.

Plant carnivory is often manifested as dramatic changes in the structure and morphology of the leaf. These changes appear to begin early in leaf development. For example, the development of the Sarracenia purpurea leaf primordium is associated with the formation of an adaxial ridge, whose growth along with that of the leaf margin resulted in a hollow structure that later developed into a pitcher. In Nepenthes khasiana, pitcher formation occurs during the initial stages of leaf development, although this has not been shown at the primordial stage. The formation of the Utricularia gibba trap resulted from the growth of the dome-shaped primordium in both the longitudinal and transverse directions. Recent research has begun to unfold the genetic basis of the development of the carnivorous leaf. We review these findings and discuss them in relation to the flat-shaped leaves of the model plant Arabidopsis.

Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.

On the Origin of Carnivory: Molecular Physiology and Evolution of Plants on an Animal Diet.

Charles Darwin recognized that carnivorous plants thrive in nutrient-poor soil by capturing animals. Although the concept of botanical carnivory has been known for nearly 150 years, its molecular mechanisms and evolutionary origins have not been well understood until recently. In the last decade, technical advances have fueled the genome and transcriptome sequencings of active and passive hunters, leading to a better understanding of the traits associated with the carnivorous syndrome, from trap leaf development and prey digestion to nutrient absorption, exemplified, for example, by the Venus flytrap (Dionaea muscipula), pitcher plant (Cephalotus follicularis), and bladderwort (Utricularia gibba). The repurposing of defense-related genes is an important trend in the evolution of plant carnivory. In this review, using the Venus flytrap as a representative of the carnivorous plants, we summarize the molecular mechanisms underlying their ability to attract, trap, and digest prey and discuss the origins of plant carnivory in relation to their genomic evolution.

Bladderworts, the smallest known suction feeders, generate inertia-dominated flows to capture prey.

Aquatic bladderworts (Utriculariagibba and U.australis) capture zooplankton in mechanically triggered underwater traps. With characteristic dimensions less than 1mm, the trapping structures are among the smallest known to capture prey by suction, a mechanism that is not effective in the creeping-flow regime where viscous forces prevent the generation of fast and energy-efficient suction flows. To understand what makes suction feeding possible on the small scale of bladderwort traps, we characterised their suction flows experimentally (using particle image velocimetry) and mathematically (using computational fluid dynamics and analytical mathematical models). We show that bladderwort traps avoid the adverse effects of creeping flow by generating strong, fast-onset suction pressures. Our findings suggest that traps use three morphological adaptations: the trap walls' fast release of elastic energy ensures strong and constant suction pressure; the trap door's fast opening ensures effectively instantaneous onset of suction; the short channel leading into the trap ensures undeveloped flow, which maintains a wide effective channel diameter. Bladderwort traps generate much stronger suction flows than larval fish with similar gape sizes because of the traps' considerably stronger suction pressures. However, bladderworts' ability to generate strong suction flows comes at considerable energetic expense.

Agrobacterium tumefaciens mediated transformation of the aquatic carnivorous plant Utricularia gibba

BackgroundThe genus Utricularia belongs to Lentibulariaceae, the largest family of carnivorous plants, which includes terrestrial, epiphytic and aquatic species. The development of specialized structures that evolved for carnivory is a feature of this genus that has been of great interest to biologists since Darwin‘s early studies. Utricularia gibba is itself an aquatic plant with sophisticated bladder traps having one of the most complex suction mechanisms for trapping prey. However, the molecular characterization of the mechanisms that regulate trap development and the biophysical processes involved in prey trapping are still largely unknown due to the lack of a simple and reproducible gene transfer system.ResultsHere, we report the establishment of a simple, fast and reproducible protocol for genetic transformation of U. gibba based on the T-DNA of Agrobacterium tumefaciens. An in vitro selection system using Phosphinotricin as a selective agent was established for U. gibba. Plant transformation was confirmed by histochemical GUS assays and PCR and qRT-PCR analyses. We report on the expression pattern of the 35S promoter and of the promoter of a trap-specific ribonuclease gene in transgenic U. gibba plants.ConclusionsThe genetic transformation protocol reported here is an effective method for studying developmental biology and functional genomics of this genus of carnivorous plants and advances the utility of U. gibba as a model system to study developmental processes involved in trap formation.

Production and Characterization of Crude Protease from RS1 Isolate from silage of Floating Bladderwort (Utricularia gibba)

The purpose of this research was to produce and characterizing crude protease from RS1 isolate of swamp plant silage. The optimum production time of RS1 isolate was 40 h. The optimum pH and temperature of protease from RS1 isolate were 10 and 45℃, respectively. Ion Mg3+ increased RS1 protease whereas ion of Na+, K+, Fe2+, and Zn2+ inhibited protease from RS1 isolate. Study on the effect of metals ion indicated that protease from RS1 isolate was metaloenzyme. Based analysis on SDS-PAGE, the molecular weight of RS1 protease had 12 bands with molecular weights ranging from 34.75 kDa to 263.53 kDa.

Form Follows Function: How to Build a Deadly Trap

The carnivorous plant Utricularia gibba forms cup-shaped leaflets to capture prey. Whitewoods etal. (2020) use computational modeling to simulate the formation of the trap's 3D geometry. Directional expansion of the young leaflet is proposed to be a crucial morphogenetic driver, pointing at a fundamental principle of plant development.

Utricularia.

Whitewoods introduces the plant genus Utricularia.

Subtle origin for complex shapes

Plant Science The cup-shaped leaves of carnivorous plants have evolved multiple times from ancestors with flat leaves. Studying development of the carnivorous trap in the humped bladderwort, Utricularia gibba , Whitewoods et al. identified genes similar to those expressed in surfaces of flat leaves (see the Perspective by Moulton and Goriely). Ectopic expression and computational modeling reveals how slight shifts in gene expression domains make the difference between a flat leaf and a convoluted trap structure. Flexibility in growth rates in orthogonal polarity fields allows for diversity in shapes formed through development. Science , this issue p. [91][1]; see also p. [24][2] [1]: /lookup/doi/10.1126/science.aay5433 [2]: /lookup/doi/10.1126/science.aba3797

Expansin gene loss is a common occurrence during adaptation to an aquatic environment.

Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.

Evolution of carnivorous traps from planar leaves through simple shifts in gene expression.

Leaves vary from planar sheets and needle-like structures to elaborate cup-shaped traps. Here, we show that in the carnivorous plant Utricularia gibba, the upper leaf (adaxial) domain is restricted to a small region of the primordium that gives rise to the trap's inner layer. This restriction is necessary for trap formation, because ectopic adaxial activity at early stages gives radialized leaves and no traps. We present a model that accounts for the formation of both planar and nonplanar leaves through adaxial-abaxial domains of gene activity establishing a polarity field that orients growth. In combination with an orthogonal proximodistal polarity field, this system can generate diverse leaf forms and account for the multiple evolutionary origins of cup-shaped leaves through simple shifts in gene expression.

Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism.

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies.

Hydrodynamics of the bladderwort feeding strike.

The aquatic bladderwort Utricularia gibba captures zooplankton in mechanically triggered underwater traps. With characteristic dimensions <1 mm, the trapping structures are among the smallest known that work by suction-a mechanism that would not be effective in the creeping-flow regime. To understand the adaptations that make suction feeding possible on this small scale, we have measured internal flow speeds during artificially triggered feeding strikes in the absence of prey. These data are compared with complementary analytical models of the suction event: an inviscid model of the jet development in time and a steady-state model incorporating friction. The initial dynamics are well described by a time-dependent Bernoulli equation in which the action of the trap door is represented by a step increase in driving pressure. According to this model, the observed maximum flow speed (5.2 m/s) depends only on the pressure difference, whereas the initial acceleration (3 × 104 m/s2 ) is determined by pressure difference and channel length. Because the terminal speed is achieved quickly (~0.2 ms) and the channel is short, the remainder of the suction event (~2.0 ms) is effectively an undeveloped viscous steady state. The steady-state model predicts that only 17% of power is lost to friction. The energy efficiency and steady-state fluid speed decrease rapidly with decreasing channel diameter, setting a lower limit on practical bladderwort size.

The Evolution Force of Genome Reduction in Carnivorous Plants

The introns are widely present in the genome of eukaryotes and the distribution of intron varies greatly among different organisms or different genes. Generally, introns loss is an important way for uneven distribution of intron during genome evolution. In this study, two closely related carnivorous plants (Genlisea aurea and Utricularia gibba) were chosen, their genome were relatively integrity and high quality, especially, the large difference in genome size between them. We detected intron loss events, then investigated the relationship between the genome size, intron density, intron loss and the mutation rate in the carnivorous plants. Finally, a total of 752 and 124 intron loss positions were identified in G. aurea and U. gibba, respectively. In carnivorous plants, we found that the region around lost site had high mutation rate, the genes of intron loss had high mutation rate. Besides, for the species with more intron losses, the genome size was smaller and the mutation rate was higher. Thus, we propose that the mutation rate was positively correlated with intron losses, but negatively correlated with intron number and genome size. These could be explained by the selection to minimize mutational hazards.