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Self‐inhibition of growth has been observed in different organisms, but an underlying common mechanism has not been proposed so far. Recently, extracellular DNA (exDNA) has been reported as species‐specific growth inhibitor in plants and proposed as an explanation of negative plant–soil feedback. In this work the effect of exDNA was tested on different species to assess the occurrence of such inhibition in organisms other than plants. Bioassays were performed on six species of different taxonomic groups, including bacteria, fungi, algae, plants, protozoa and insects. Treatments consisted in the addition to the growth substrate of conspecific and heterologous DNA at different concentration levels. Results showed that treatments with conspecific DNA always produced a concentration dependent growth inhibition, which instead was not observed in the case of heterologous DNA. Reported evidence suggests the generality of the observed phenomenon which opens new perspectives in the context of self‐inhibition processes. Moreover, the existence of a general species‐specific biological effect of exDNA raises interesting questions on its possible involvement in self‐recognition mechanisms. Further investigation at molecular level will be required to unravel the specific functioning of the observed inhibitory effects.

In extratropical ecosystems, the growth of trees is cyclic, producing tree rings composed of large-lumen and thin-walled cells (earlywood) alternating with narrow-lumen and thick-walled cells (latewood). So far, the physiology behind wood formation processes and the associated kinetics has rarely been considered to explain this pattern. We developed a process-based mechanistic model that simulates the development of conifer tracheids, explicitly considering the processes of cell enlargement and the deposition and lignification of cell walls. The model assumes that (1) wall deposition gradually slows down cell enlargement and (2) the deposition of cellulose and lignin is regulated by the availability of soluble sugars. The model reliably reproduces the anatomical traits and kinetics of the tracheids of four conifer species. At the beginning of the growing season, low sugar availability in the cambium results in slow wall deposition that allows for a longer enlargement time; thus, large cells with thin walls (i.e., earlywood) are produced. In late summer and early autumn, high sugar availability produces narrower cells having thick cell walls (i.e., latewood). This modeling framework provides a mechanistic link between plant ecophysiology and wood phenology and significantly contributes to understanding the role of sugar availability during xylogenesis.

Spatial patterns and self-organization of plants has been a subject of fascination because the underlying mechanisms have been hard to determine, raising different explanatory hypotheses. Plant–soil negative feedback (PSNF) – defined as the induction of negative conditions for conspecific establishment – has been widely studied in both field and laboratory conditions, and conceptually demonstrated by some modelling works. We present a mechanistic model, integrating individual plants inside an agent-based framework, to explore the effects of PSNF on the spatial and temporal dynamics of virtual populations and communities of plants of diverse growth forms. This endeavour led to the reproduction of well-known vegetation patterns observed at various scales, demonstrating for the first time a unified mechanism behind the spatial patterns of Janzen–Connell seedlings’ distribution, ring formation, and the high species mobility in species-rich grasslands. These results support the ecological relevance of PSNF in the regulation of spatial organization and biodiversity dynamics in plant communities. More specifically, PSNF due to autoxicity seems most coherent with the spatio-temporal scale of dynamics displayed here.

Plant–soil negative feedback (NF) is recognized as an important factor affecting plant communities. The objectives of this work were to assess the effects of litter phytotoxicity and autotoxicity on root proliferation, and to test the hypothesis that DNA is a driver of litter autotoxicity and plant–soil NF. The inhibitory effect of decomposed litter was studied in different bioassays. Litter biochemical changes were evaluated with nuclear magnetic resonance (NMR) spectroscopy. DNA accumulation in litter and soil was measured and DNA toxicity was assessed in laboratory experiments. Undecomposed litter caused nonspecific inhibition of root growth, while autotoxicity was produced by aged litter. The addition of activated carbon (AC) removed phytotoxicity, but was ineffective against autotoxicity. Phytotoxicity was related to known labile allelopathic compounds. Restricted¹³C NMR signals related to nucleic acids were the only ones negatively correlated with root growth on conspecific substrates. DNA accumulation was observed in both litter decomposition and soil history experiments. Extracted total DNA showed evident species‐specific toxicity. Results indicate a general occurrence of litter autotoxicity related to the exposure to fragmented self‐DNA. The evidence also suggests the involvement of accumulated extracellular DNA in plant–soil NF. Further studies are needed to further investigate this unexpected function of extracellular DNA at the ecosystem level and related cellular and molecular mechanisms.

Many mushroom-forming fungi can develop circular colonies affecting the vegetation in a phenomenon named fairy rings. Since the nineteenth century, several hypotheses have been proposed to explain how fairy ring fungi form ring-like shapes instead of disks and why they produce negative or positive effects on the surrounding vegetation. In this context, we present a novel process-based mathematical model aimed at reproducing the mycelial spatial configuration of fairy rings and test different literature-supported hypotheses explaining the suppressive and stimulating effects of fungi on plants. Simulations successfully reproduced the shape of fairy rings through the accumulation of fungal self-inhibitory compounds. Moreover, regarding the negative effects of fungi on vegetation, results suggest that fungal-induced soil hydrophobicity is sufficient to reproduce all observed types of fairy rings, while the potential production of phytotoxins is not. In relation to the positive effects of fungi on plants, results show that the release of phytostimulants is needed to reproduce the vegetation patterns associated to some fairy ring types. Model outputs can guide future experiments and field work to corroborate the considered hypotheses and provide more information for further model improvements.

Plant-soil negative feedback (NF) is a well-established phenomenon that, by preventing the dominance of a single species, allows species coexistence and promotes the maintenance of biodiversity. At community scale, localized NF may cause the formation of exclusion zones under adult conspecifics leading to Janzen-Connell (JC) distribution. In this study, we explore the connection between adult density, either conspecifics or heterospecifics, on the probability of occurrence of JC distributions. Using an individual-based modelling approach, we simulated the formation of exclusion zones due to the build-up of NF in proximity of conspecific adult plants and assessed the frequency of JC distribution in relation to conspecifics and heterospecifics density ranging from isolated trees to closed forest stands. We found that JC recruitment distribution is very common in the case of an isolated tree when NF was strong and capable to form an exclusion zone under the parent tree. At very low NF intensity, a prevalence of the decreasing pattern was observed because, under such conditions, the inhibitory effect due to the presence of the mother tree was unable to overcome the clustering effect of the seed dispersal kernel. However, if NF is strong the JC frequency suddenly decreases in stands with a continuous conspecific cover likely as a result of progressive expansion of the exclusion zone surrounding all trees in closed forest stands. Finally, our simulations showed that JC distribution should not be frequent in the case of rare species immersed in a matrix of heterospecific adults. Overall, the model shows that a plant suffering from strong NF in monospecific stands can rarely exhibit a recruitment pattern fitting the JC model. Such counterintuitive results would provide the means to reconcile the well-established NF framework with part the forest ecologists’ community that is still skeptical towards the JC model.

Computer-Generated Imagery (CGI) has received increasing interest in both research and the entertainment industry. Recent advancements in computer graphics allowed researchers and companies to create large-scale virtual environments with growing resolution and complexity. Among the different applications, the generation of biological assets is a relevant task that implies challenges due to the extreme complexity associated with natural structures. An example is represented by trees, whose composition made by thousands of leaves, branches, branchlets, and stems with oriented directions is hard to be modeled. Realistic 3D models of trees can be exploited for a wide range of applications including decision-making support, visualization of ecosystem changes over time, and for simple visualization purposes. In this review, we give an overview of the most common approaches used to generate 3D tree models, discussing both methodologies and available commercial software. We focus on strategies for modeling and rendering of plants, highlighting their accordance or not with botanical knowledge and biological models. We also present a proof of concept to link biological models and 3D rendering engines through Ordinary Differential Equations.

Background: Previous evidence demonstrated DNA methylation changes in response to stress in plants, showing rapid changes within a limited time frame. Exposure to self-DNA inhibits seedling root elongation, and it was shown that it causes changes in CG DNA methylation in Lactuca sativa. We assessed cytosine methylation changes and associated gene expression patterns in roots of Arabidopsis thaliana Col-0 seedlings exposed to self-DNA for 6 and 24 h. Methods: We used whole genome bisulfite sequencing (WGBS) and RNA-seq analyses to assess genomic cytosine methylation and corresponding gene expression, respectively, on DNA and RNA extracted with commercial kits from roots exposed to self-DNA by an original setup. Fifteen hundred roots replicates, including the control in distilled water, were collected after exposure. Sequencing was performed on a NovaSeq 6000 platform and Ultralow Methyl-Seq System for RNA and DNA WGBS, respectively. Results: Gene expression in roots exposed to self-DNA differed from that of untreated controls, with a total of 305 genes differentially expressed and 87 ontologies enriched in at least one treatment vs. control comparison, and particularly after 24 h of exposure. DNA methylation, particularly in CHG and CHH contexts, was also different, with hyper- and hypomethylation prevailing in treatments vs. controls at 6 h and 24 h, respectively. Differentially expressed genes (DEGs) analysis, Gene Ontology (GO) enrichment analysis, and differentially methylated regions (DMRs) analysis, provided an integrated understanding of the changes associated with self-DNA exposure. Our results suggest differential gene expression associated with DNA methylation in response to self-DNA exposure in A. thaliana roots, enhanced after prolonged exposure. Conclusions: Main functional indications of association between DNA methylation and gene expression involved hypomethylation and downregulation of genes related to nucleotide/nucleoside metabolism (ATP synthase subunit) and cell wall structure (XyG synthase), consistent with previous observations from metabolomics and physiological studies. Further confirmation of these findings will contribute to improving our understanding of the plant molecular response to self-DNA and its implications in stress responses.

Biological–mathematical models of trees can be exploited for a wide range of agronomic applications including crop management, visualization of ecosystem changes over time, in-field phenotyping, crop load effects, testing of plant functions, biomechanics, and many others. Some models propose a 3D output of tree that, in addition to having functionality to visualize the result, offers an additional tool for the evaluation of some parameters of the model itself (interception and amount of light, temperature, obstacles, physical competition between multiple trees). The present study introduces a biological–mathematical model of tree growth with a 3D output of its structure in a realtime 3D rendering environment (Unity©). Thanks to the virtual environment created in Unity©, it was possible to obtain variable environmental parameters (amount of light, temperature) used as inputs to the mathematical simulation of growth. The model is based on ordinary differential equations (ODEs) that compute the growth of each single internode in length (primary growth) and width (secondary growth) and the accumulation of growth inhibitors regulating the seasonal cyclicity of the tree. Virtual experiments were conducted varying environmental conditions (amount of light and temperature), and the species-specific characteristics of the simulated tree (number of buds, branching angle). The results have been analyzed showing also how the model can be adapted for the creation of different tree species and discussing the potential agronomic applications of model.

The Mediterranean Basin’s diverse climates and ecosystems have shaped a rich botanical heritage through centuries of selective cultivation, resulting in a wide array of horticultural plants with valuable therapeutic properties. The use of horticultural food plants as herbal remedies has become an integral part of traditional medicine in this geographical context. The present review aims to highlight the use of horticultural food plants (HFPs) in the context of traditional herbal medicine in the countries of the Mediterranean Basin and explore their traditional uses and therapeutic properties. A comprehensive ethnobotanical literature search was conducted on the food plants used as herbal medicine in the Mediterranean region using existing online scientific databases. Based on the literature review, 64 taxa used as medicinal plants by traditional users in the Mediterranean Basin were documented. Overall, horticultural plants are used in Mediterranean countries to treat a total of 573 ailments. Italy has the highest number of use reports (998), followed by Morocco (281) and Spain (193). Apiaceae (11 taxa), Cucurbitaceae (9 taxa), and Brassicaceae (8 taxa) are the most frequently cited families. The genus Allium is the most abundant in species (5).