Testing the effect of semi-transparent spectrally selective thin film photovoltaics for agrivoltaic application: A multi-experimental and multi-specific approach.

The integration of photovoltaic technologies within the agricultural framework, known as agrivoltaics, emerges as a promising and sustainable solution to meet the growing global demands for energy and food production. This innovative technology enables the simultaneous utilization of sunlight for both photovoltaics (PV) and photosynthesis. A key challenge in agrivoltaic research involves identifying technologies applicable to a wide range of plant species and diverse geographic regions. To address this challenge, we adopt a multi-experimental and multi-species approach to assess the viability of semi-transparent, spectrally selective thin-film silicon PV technology. Our findings demonstrate compatibility with crop production in controlled environments for both plants and algae. Notably, selective thin-film PV exhibits the potential to enhance crop yields and serves as a photo-protectant. We observe that plant and algal growth increases beneath the selective PV film when supplemented with appropriate diffuse light in the growth environment. Conversely, in situations where light intensity exceeds optimal levels for plant growth, the selective PV film provides a photo-protective effect. These results suggest potential supplementary benefits of employing this technology in regions characterized by excessive light irradiation, where it can contribute to healthy plant growth.

Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation.

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.

Process based modelling of plants-fungus interactions explains fairy ring types and dynamics.

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.

Adult conspecific density affects Janzen-Connell patterns by modulating the recruitment exclusion zones.

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. Synthesis: Our model highlights the complex interconnection between NF intensity, stand density, and recruitment patterns explaining where and why the JC distribution occurs. Moreover, predicting the occurrence of JC in relation to stand density we clarify the relevance of this ecological phenomenon for future integration in plant community frameworks.

PhenoCaB: a new phenological model based on carbon balance in boreal conifers.

Traditional phenological models use chilling and thermal forcing (temperature sum or degree-days) to predict budbreak. Because of the heightening impact of climate and other related biotic or abiotic stressors, a model with greater biological support is needed to better predict budbreak. Here, we present an original mechanistic model based on the physiological processes taking place before and during budbreak of conifers. As a general principle, we assume that phenology is driven by the carbon status of the plant, which is closely related to environmental variables and the annual cycle of dormancy-activity. The carbon balance of a branch was modelled from autumn to winter with cold acclimation and dormancy and from winter to spring when deacclimation and growth resumption occur. After being calibrated in a field experiment, the model was validated across a large area (> 34 000 km2 ), covering multiple conifers stands in Québec (Canada) and across heated plots for the SPRUCE experiment in Minnesota (USA). The model accurately predicted the observed dates of budbreak in both Québec (±3.98 d) and Minnesota (±7.98 d). The site-independent calibration provides interesting insights on the physiological mechanisms underlying the dynamics of dormancy break and the resumption of vegetative growth in spring.

Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas.

Metabolic flux analysis (MFA) quantitatively describes cellular fluxes to understand metabolic phenotypes and functional behaviour after environmental and/or genetic perturbations. In the last decade, the application of stable isotopes became extremely important to determine and integrate in vivo measurements of metabolic reactions in systems biology. 13C-MFA is one of the most informative methods used to study central metabolism of biological systems. This review aims to outline the current experimental procedure adopted in 13C-MFA, starting from the preparation of cell cultures and labelled tracers to the quenching and extraction of metabolites and their subsequent analysis performed with very powerful software. Here, the limitations and advantages of nuclear magnetic resonance spectroscopy and mass spectrometry techniques used in carbon labelled experiments are elucidated by reviewing the most recent published papers. Furthermore, we summarise the most successful approaches used for computational modelling in flux analysis and the main application areas with a particular focus in metabolic engineering.

Self-DNA Exposure Induces Developmental Defects and Germline DNA Damage Response in Caenorhabditis elegans.

All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes to respond to and recognise not only infections, i.e., pathogen-associated molecular patterns (PAMPs), but also to sense injury and tissue dysfunctions, i.e., damage-associated molecular patterns (DAMPs). Mis-localized self-DNA can be sensed as DAMP by specific DNA-sensing pathways, and self-DNA chronic exposure can be detrimental to the organisms. Here, we investigate the effects of dietary delivered self-DNA in the nematode Caenorhabditis elegans. The hermaphrodite worms were fed on Escherichia coli genomic libraries: a C. elegans library (self) and a legume (Medicago truncatula) library (non-self). We show that the self-library diet affects embryogenesis, larval development and gametogenesis. DNA damage and activation of p53/CEP-1-dependent apoptosis occur in gonadal germ cells. Studies of self-DNA exposure in this model organism were not pursued up to now. The genetic tractability of C. elegans will help to identify the basic molecular pathways involved in such mechanisms. The specificity of the adverse effects associated with a self-DNA enriched diet suggests applications in biological pest control approaches.

Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure.

The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis.

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

A System Dynamics Approach to Model Photosynthesis at Leaf Level Under Fluctuating Light.

Photosynthesis has been mainly studied under steady-state conditions even though this assumption results inadequate for assessing the biochemical responses to rapid variations occurring in natural environments. The combination of mathematical models with available data may enhance the understanding of the dynamic responses of plants to fluctuating environments and can be used to make predictions on how photosynthesis would respond to non-steady-state conditions. In this study, we present a leaf level System Dynamics photosynthesis model based and validated on an experiment performed on two soybean varieties, namely, the wild type Eiko and the chlorophyll-deficient mutant MinnGold, grown in constant and fluctuating light conditions. This mutant is known to have similar steady-state photosynthesis compared to the green wild type, but it is found to have less biomass at harvest. It has been hypothesized that this might be due to an unoptimized response to non-steady-state conditions; therefore, this mutant seems appropriate to investigate dynamic photosynthesis. The model explained well the photosynthetic responses of these two varieties to fluctuating and constant light conditions and allowed to make relevant conclusions on the different dynamic responses of the two varieties. Deviations between data and model simulations are mostly evident in the non-photochemical quenching (NPQ) dynamics due to the oversimplified combination of PsbS- and zeaxanthin-dependent kinetics, failing in finely capturing the NPQ responses at different timescales. Nevertheless, due to its simplicity, the model can provide the basis of an upscaled dynamic model at a plant level.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures.

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Phenological shifts in conifer species stressed by spruce budworm defoliation.

Synchrony between host budburst and insect emergence greatly influences the time window for insect development and survival. A few alterations of bud phenology have been reported under defoliation without clear consensus regarding the direction of effects, i.e., advance or delay. Here, we compared budburst phenology between conifers in defoliation and control treatments, and measured carbon allocation as a potential mechanistic explanation of changes in phenology. In a 2-year greenhouse experiment, saplings of balsam fir, black spruce and white spruce of two different provenances (north and south) were subjected to either control (no larvae) or natural defoliation treatment (larvae added) by spruce budworm. Bud and instar phenology, primary and secondary growth, defoliation and non-structural carbohydrates were studied during the growing season. No differences were observed in bud phenology during the first year of defoliation. After 1 year of defoliation, bud phenology advanced by 6-7 days in black spruce and balsam fir and by 3.5 days in white spruce compared with the control. Because of this earlier bud break, apical and shoot growth exceeded 50% of its final length before mature instar defoliation occurred, which decreased the overall level of damage. A sugar-mediated response, via earlier starch breakdown, and higher sugar availability to buds explains the advanced budburst in defoliated saplings. The advanced phenological response to defoliation was consistent across the conifer species and provenances except for one species × provenance combination. Allocation of carbon to buds and shoots growth at the expense of wood growth in the stem and reserve accumulation represents a shift in the physiological resources priorities to ensure tree survival. This advancement in bud phenology could be considered as a physiological response to defoliation based on carbohydrate needs for primary growth, rather than a resistance trait to spruce budworm.

The Physiological Mechanisms Behind the Earlywood-To-Latewood Transition: A Process-Based Modeling Approach.

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.

Faster N Release, but Not C Loss, From Leaf Litter of Invasives Compared to Native Species in Mediterranean Ecosystems.

Plant invasions can have relevant impacts on biogeochemical cycles, whose extent, in Mediterranean ecosystems, have not yet been systematically assessed comparing litter carbon (C) and nitrogen (N) dynamics between invasive plants and native communities. We carried out a 1-year litterbag experiment in 4 different plant communities (grassland, sand dune, riparian and mixed forests) on 8 invasives and 24 autochthonous plant species, used as control. Plant litter was characterized for mass loss, N release, proximate lignin and litter chemistry by 13C CPMAS NMR. Native and invasive species showed significant differences in litter chemical traits, with invaders generally showing higher N concentration and lower lignin/N ratio. Mass loss data revealed no consistent differences between native and invasive species, although some woody and vine invaders showed exceptionally high decomposition rate. In contrast, N release rate from litter was faster for invasive plants compared to native species. N concentration, lignin content and relative abundance of methoxyl and N-alkyl C region from 13C CPMAS NMR spectra were the parameters that better explained mass loss and N mineralization rates. Our findings demonstrate that during litter decomposition invasive species litter has no different decomposition rates but greater N release rate compared to natives. Accordingly, invasives are expected to affect N cycle in Mediterranean plant communities, possibly promoting a shift of plant assemblages.

Revisiting the Crabtree/Warburg effect in a dynamic perspective: a fitness advantage against sugar-induced cell death.

The mechanisms behind the Warburg effect in mammalian cells, as well as for the similar Crabtree effect in the yeast Saccharomyces cerevisiae, are still a matter of debate: why do cells shift from the energy-efficient respiration to the energy-inefficient fermentation at high sugar concentration? This review reports on the strong similarities of these phenomena in both cell types, discusses the current ideas, and provides a novel interpretation of their common functional mechanism in a dynamic perspective. This is achieved by analysing another phenomenon, the sugar-induced-cell-death (SICD) occurring in yeast at high sugar concentration, to highlight the link between ATP depletion and cell death. The integration between SICD and the dynamic functioning of the glycolytic process, suggests that the Crabtree/Warburg effect may be interpreted as the avoidance of ATP depletion in those conditions where glucose uptake is higher than the downstream processing capability of the second phase of glycolysis. It follows that the down-regulation of respiration is strategic for cell survival allowing the allocation of more resources to the fermentation pathway, thus maintaining the cell energetic homeostasis.

Effects of Hydraulic Soil Properties on Vegetation Pattern Formation in Sloping Landscapes.

Current models of vegetation pattern formation rely on a system of weakly nonlinear reaction-diffusion equations that are coupled by their source terms. While these equations, which are used to describe a spatiotemporal planar evolution of biomass and soil water, qualitatively capture the emergence of various types of vegetation patterns in arid environments, they are phenomenological and have a limited predictive power. We ameliorate these limitations by deriving the vertically averaged Richards' equation to describe flow (as opposed to "diffusion") of water in partially saturated soils. This establishes conditions under which this nonlinear equation reduces to its weakly nonlinear reaction-diffusion counterpart used in the previous models, thus relating their unphysical parameters (e.g., diffusion coefficient) to the measurable soil properties (e.g., hydraulic conductivity) used to parameterize the Richards equation. Our model is valid for both flat and sloping landscapes and can handle arbitrary topography and boundary conditions. The result is a model that relates the environmental conditions (e.g., precipitation rate, runoff and soil properties) to formation of multiple patterns observed in nature (such as stripes, labyrinth and spots).

Spatial Self-Organization of Vegetation Subject to Climatic Stress-Insights from a System Dynamics-Individual-Based Hybrid Model.

In simulation models of populations or communities, individual plants have often been obfuscated in favor of aggregated vegetation. This simplification comes with a loss of biological detail and a smoothing out of the demographic noise engendered by stochastic individual-scale processes and heterogeneities, which is significant among others when studying the viability of small populations facing challenging fluctuating environmental conditions. This consideration has motivated the development of precise plant-centered models. The accuracy gained in the representation of plant biology has then, however, often been balanced by the disappearance in models of important plant-soil interactions (esp. water dynamics) due to the inability of most individual-based frameworks to simulate complex continuous processes. In this study, we used a hybrid modeling approach, namely integrated System Dynamics (SD)-Individual-based (IB), to illustrate the importance of individual plant dynamics to explain spatial self-organization of vegetation in arid environments. We analyzed the behavior of this model under different parameter sets either related to individual plant properties (such as seed dispersal distance and reproductive age) or the environment (such as intensity and yearly distribution of precipitation events). While the results of this work confirmed the prevailing theory on vegetation patterning, they also revealed the importance therein of plant-level processes that cannot be rendered by reaction-diffusion models. Initial spatial distribution of plants, reproductive age, and average seed dispersal distance, by impacting patch size and vegetation aggregation, affected pattern formation and population survival under climatic variations. Besides, changes in precipitation regime altered the demographic structure and spatial organization of vegetation patches by affecting plants differentially depending on their age and biomass. Water availability influenced non-linearly total biomass density. Remarkably, lower precipitation resulted in lower mean plant age yet higher mean individual biomass. Moreover, seasonal variations in rainfall greater than a threshold (here, ±0.45 mm from the 1.3 mm baseline) decreased mean total biomass and generated limit cycles, which, in the case of large variations, were preceded by chaotic demographic and spatial behavior. In some cases, peculiar spatial patterns (e.g., rings) were also engendered. On a technical note, the shortcomings of the present model and the benefit of hybrid modeling for virtual investigations in plant science are discussed.

Self-DNA inhibitory effects: Underlying mechanisms and ecological implications.

DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.

A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures.

BACKGROUND: Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. RESULTS: A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. CONCLUSIONS: The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.

Inhibitory effects of extracellular self-DNA: a general biological process?

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.