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Practical guide toward discovery of biomolecules with biostimulant activity
Abstract
The growing demand for sustainable solutions in agriculture, critical for crop productivity and food quality in the face of climate change and reduced agrochemical usage, has brought biostimulants into the spotlight as valuable tools for regenerative agriculture. Due to their diverse biological activities, biostimulants contribute to crop growth, nutrient use efficiency, abiotic resilience, and soil health restoration. Biomolecules, including but not limited to humic substances, protein lysates, phenolics and carbohydrates have undergone thorough investigation because of their demonstrated biostimulant activities. Here, we review the process of discovery and development of extract-based biostimulants and propose a practical step-by-step pipeline starting with biomolecule investigation, followed by extraction and isolation, bioactivity determination, identification of active compound(s), mechanistic elucidation, formulation, and effectiveness assessment. The different steps generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to pilot-scale production in practical scenarios aligned with the regulatory framework.
... This unsustainable approach has underlined the need for more sustainable agricultural practices promoting biodiversity, which will be critical for food production and quality in the future, especially in the climate change context [5,6]. As one of the more promising farming models, the RA model practice has been introduced alongside other sustainable initiatives [7]. ...
... Recycling agricultural processes such as composting, green manuring, Cover crops and mulching are used to restore degraded soils. It enhances ecosystem services such as water quality, vegetation, and land productivity through elevated biological processes [7][8][9]. Recently, the focus has been on RA being an appropriate response to climate change. It is an environmentally friendly agricultural practice that aims to improve soils, sequester carbon in soil, and enhance the soil carbon stock while reducing greenhouse gases emitted from agricultural soils [10,11]. ...
Regenerative Agriculture (RA) represents a significant approach toward sustainable and eco-friendly practices, provides environmental, economic, and social benefits. The objective of the review is to evaluate research trends and gaps, conduct a SWOT analysis, and explore the potential of regenerative agriculture in areas like energy conservation, food security, ecosystem services, soil health, circular agriculture, and climate-smart, resilient farming practices. This review emphasizes the holistic approach of Regenerative Agriculture, SWOT analysis reveals that RA offers significant benefits of environmental sustainability and several opportunities like carbon market and food security. Despite multiple benefits, bibliometric analysis showed that research on RA is limited, with a notable increase in publications only emerging in recent years. RA contributes to better sustainable practices compared to other agricultural systems. RA efforts to mitigate climate change by reducing the carbon footprint, enhancing climate adaptability, improving soil health, and providing ecosystem services. It also addresses challenges such as biodiversity loss, food waste, and food security. Furthermore, integrating RA presents economic and ecological opportunities, such as carbon credits and a circular economy. This approach increases resource efficiency, minimizes agricultural waste, and promotes nature-based solutions with potential for energy conservation and healthier ecosystems. Based on our findings, we recommend that research should focus on developing carbon credit schemes from RA, enhancing farmer’s awareness of RA's economic and environmental benefits, and modifying RA to improve on circular economy principles for sustainability.
... The growing need for sustainable agricultural practices has highlighted biostimulants as essential assets for regenerative farming [80,81]. With their diverse biological functions, biostimulants significantly contribute to boosting crop growth, enhancing nutrient utilization, increasing resilience to environmental stressors, and revitalizing soil health [81]. ...
... The growing need for sustainable agricultural practices has highlighted biostimulants as essential assets for regenerative farming [80,81]. With their diverse biological functions, biostimulants significantly contribute to boosting crop growth, enhancing nutrient utilization, increasing resilience to environmental stressors, and revitalizing soil health [81]. Biostimulants like salicylic acid [82][83][84][85][86] and melatonin [87][88][89][90] have been shown to exert several positive functions in plant biotic and abiotic stress tolerance and to induce a hormetic stimulation of the PSII function by modulating the chlorophyll content and optimizing the antenna size, which resulted in enhanced effective quantum yield of PSII photochemistry (Φ PSII ) [91][92][93]. ...
In recent years, inorganic nanoparticles, including calcium hydroxide nanoparticles [Ca Ca(OH) 2 NPs], have attracted significant interest for their ability to impact plant photosynthesis and boost agricultural productivity. In this study, the effects of 15 and 30 mg L −1 oleylamine-coated calcium hydroxide nanoparticles [Ca(OH) 2 @OAm NPs] on photosystem II (PSII) photochemistry were investigated on tomato plants at their growth irradiance (GI) (580 µmol photons m −2 s −1) and at high irradiance (HI) (1000 µmol photons m −2 s −1). Ca(OH) 2 @OAm NPs synthesized via a microwave-assisted method revealed a crystallite size of 25 nm with 34% w/w of oleylamine coater, a hydrodynamic size of 145 nm, and a ζ-potential of 4 mV. Compared with the control plants (sprayed with distilled water), PSII efficiency in tomato plants sprayed with Ca(OH) 2 @OAm NPs declined as soon as 90 min after the spray, accompanied by a higher excess excitation energy at PSII. Nevertheless, after 72 h, the effective quantum yield of PSII electron transport (Φ PSII) in tomato plants sprayed with Ca(OH) 2 @OAm NPs enhanced due to both an increase in the fraction of open PSII reaction centers (qp) and to the enhancement in the excitation capture efficiency (Fv'/Fm') of these centers. However, the decrease at the same time in non-photochemical quenching (NPQ) resulted in an increased generation of reactive oxygen species (ROS). It can be concluded that Ca(OH) 2 @OAm NPs, by effectively regulating the non-photochemical quenching (NPQ) mechanism, enhanced the electron transport rate (ETR) and decreased the excess excitation energy in tomato leaves. The delay in the enhancement of PSII photochemistry by the calcium hydroxide NPs was less at the GI than at the HI. The enhancement of PSII function by calcium hydroxide NPs is suggested to be triggered by the NPQ mechanism that intensifies ROS generation, which is considered to be beneficial. Calcium hydroxide nanoparticles, in less than 72 h, activated a ROS regulatory network of light energy partitioning signaling that enhanced PSII function. Therefore, synthesized Ca(OH) 2 @OAm NPs could potentially be used as photosynthetic biostimulants to enhance crop yields, pending further testing on other plant species.
... To overcome these hurdles, advancements in techniques such as agronomics, metabolomics, and phenomics are necessary. These methods will help clarify how biostimulants work and guide the optimization of their dosages [174]. ...
Climate change significantly impacts agriculture by increasing the frequency and intensity of environmental stresses, which can severely reduce agricultural yields. Adopting sustainable practices is crucial to mitigating these risks and enhancing crop resilience. Applying natural compounds and microorganisms as biostimulants has gained popularity as an eco-friendly approach to alleviating abiotic stress in agricultural plants. This study reviews the current research on applying biostimulants in horticulturally significant crops to boost their resistance to abiotic stressors such as salinity, drought, and high temperatures. It explores the mechanisms through which these stimulants offer protection, focusing on the roles of key bioactive substances in regulating physiological and molecular processes for stress adaptation. The study addresses biostimulant formulation, regulation, and application challenges. Future research directions are suggested to harness biostimulants’ potential fully, aiming to develop climate-resilient horticultural systems that follow sustainability principles. This comprehensive review underscores the use of biostimulants as a sustainable strategy to increase crop yields in the face of climate change, reducing reliance on synthetic agrochemicals.
... Specifically, biostimulants have been classified into five main groups: algae and plant extracts, humic substances, protein hydrolysates, microorganisms, and inorganic compounds with biostimulant action [11]. Relative to the major non-microbial biostimulants (protein hydrolysates, plant, and algal extracts), the biostimulatory action is related primarily to the presence of specific signal molecules that trigger gene regulatory mechanisms that can result in phenotypic responses that culminate in improved productivity [12]. In any case, it should be emphasized that the chemodiversity of these molecules is strongly influenced by the type of biostimulant. ...
Citation: Ciriello, M.; Pannico, A.; Rouphael, Y.; Basile, B. Enhancing Yield, Physiological, and Quality Traits of Strawberry Cultivated Under Organic Management by Applying Different Non-Microbial Biostimulants. Plants 2025, 14, 712. Abstract: Organic farming is an environmentally friendly management practice that excludes the use of synthetic inputs, but at the same time is associated with lower yields than conventional production. In an attempt to compensate for yield reduction, resulting from foregoing the use of synthetic fertilizers, we hypothesized that the use of biostimulant products could provide much-desired food security. In light of this, a greenhouse experiment was conducted to compare and evaluate the effects of the foliar application of three different non-microbial biostimulants (a seaweed extract, a plant protein hydrolysate, and a plant extract) on the yield, mineral profile, and physiological response of strawberry (Fragaria × ananassa Duch.) grown in an organic farming context. Regardless of the type of biostimulant, treated plants showed significant improvement in photosynthetic performance. Specifically, the application of plant-derived protein hydrolysate increased ACO 2 by 34.5% compared with control. Despite this, only the application of plant-derived protein hydrolysate significantly increased fruit yield per unit area (+13.5%). The improved performance of plants treated with plant-derived protein hydrolysate was associated with an overall improvement in mineral profile (compared to control +49.4 and 33.0% in NO 3 − and Mg 2+ concentration, respectively). In contrast, application of the seaweed biostimulant increased (+17.4%) fruit antioxidant activity (DPPH) compared with control plants. These results underscore how the diverse origins of non-microbial biostimulants are responsible for specific responses in crops that can be exploited by organic growers to increase productivity.
... Different authors have pointed out the key role of these bio-compounds in enhancing nutrient use efficiency [90]. Moreover, formulations based on protein hydrolysates are widely used due to their ability to enhance nutrient uptake, promote plant growth, and improve stress tolerance [91] (Figure 2). ...
The escalating impact of abiotic stress on crop productivity requires innovative strategies to ensure sustainable agriculture. This review examines the promising role of biostimulants in mitigating the adverse effects of abiotic stress on crops. Biostimulants, ranging from simple organic compounds to complex living microorganisms, have demonstrated significant potential in enhancing plant resilience, stress tolerance, and overall performance. The mechanisms underlying biostimulant action—such as enhancing antioxidant defenses, regulating hormonal pathways, and inducing metabolic adjustments—are reviewed. Furthermore, we incorporate the latest research findings, methodologies, and advancements in biostimulant applications for addressing abiotic stressors, including drought, salinity, high temperatures, and nutrient deficiencies. This review also highlights current challenges and future opportunities for optimizing biostimulant use in sustainable crop production. This revision aims to guide researchers and agronomists in applying biostimulants to improve crop resilience in the context of climate change.
... Over the last decade, the agricultural industry has used bio-stimulants as a key approach to stimulate plant growth and enhance crop production under both non-stress and stress conditions [49][50][51][52][53]. The increasing demand for ecological agricultural solutions has positioned bio-stimulants as valuable tools for reinventing farming and sustaining resilience to environmental stressors [54,55]. Applying bio-stimulants mitigates the harmful effects of abiotic stresses, enhancing growth performance and plant tolerance [56]. ...
Melatonin (MT) is considered as an antistress molecule that plays a constructive role in the acclimation of plants to both biotic and abiotic stress conditions. In the present study, we assessed the impact of 10 and 100 μM MT foliar spray, on chlorophyll content, and photosystem II (PSII) function, under moderate drought stress, on oregano (Origanum vulgare L.) plants. Our aim was to elucidate the molecular mechanism of MT action on the photosynthetic electron transport process. Foliar spray with 100 μM MT was more effective in mitigating the negative impact of moderate drought stress on PSII function, compared to 10 μM MT. MT foliar spray significantly improved the reduced efficiency of the oxygen-evolving complex (OEC), and PSII photoinhibition (Fv/Fm), which were caused by drought stress. Under moderate drought stress, foliar spray with 100 μM MT, compared with the water sprayed (WA) leaves, increased the non-photochemical quenching (NPQ) by 31%, at the growth irradiance (GI, 205 μmol photons m-2 s-1), and by 13% at a high irradiance (HI, 1000 μmol photons m-2 s-1). However, the lower NPQ increase at HI was demonstrated to be more effective in decreasing the singlet-excited oxygen (1O2) production at HI (-38%), in drought-stressed oregano plants sprayed with 100 μM MT, than the corresponding decrease in 1O2 production at the GI (-20%), both compared with the respective WA-sprayed leaves under moderate drought. The reduced 1O2 production resulted in a significant increase in the quantum yield of PSII photochemistry (ΦPSII), and the electron transport rate (ETR), in moderate drought-stressed plants sprayed with 100 μM MT, compared with WA-sprayed plants, but only at the HI (+27%). Our results suggest that the enhancement of PSII functionality, with 100 μM MT under moderate drought stress, was initiated by the NPQ mechanism, which decreased the 1O2 production and increased the fraction of open PSII reaction centers (qp), resulting in an increased ETR.
... Water deficit is the major stress factor magnified by climate change that causes the most reductions in productivity when compared to other stress factors [3][4][5][6][7][8]. The increasing demand for sustainable agricultural solutions has brought biostimulants to the forefront as valuable tools for regenerative farming [9,10]. Biostimulants, with their varied biological activities, play a significant signaling pathways in different plants [22]. ...
Water deficit is the major stress factor magnified by climate change that causes the most reductions in plant productivity. Knowledge of photosystem II (PSII) response mechanisms underlying crop vulnerability to drought is critical to better understanding the consequences of climate change on crop plants. Salicylic acid (SA) application under drought stress may stimulate PSII function, although the exact mechanism remains essentially unclear. To reveal the PSII response mechanism of celery plants sprayed with water (WA) or SA, we employed chlorophyll fluorescence imaging analysis at 48 h, 96 h, and 192 h after watering. The results showed that up to 96 h after watering, the stroma lamellae of SA-sprayed leaves appeared dilated, and the efficiency of PSII declined, compared to WA-sprayed plants, which displayed a better PSII function. However, 192 h after watering, the stroma lamellae of SA-sprayed leaves was restored, while SA boosted chlorophyll synthesis, and by ameliorating the osmotic potential of celery plants, it resulted in higher relative leaf water content compared to WA-sprayed plants. SA, by acting as an antioxidant under drought stress, suppressed phototoxicity, thereby offering PSII photoprotection, together with enhanced effective quantum yield of PSII photochemistry (ΦPSII) and decreased quantity of singlet oxygen (1O2) generation compared to WA-sprayed plants. The PSII photoprotection mechanism induced by SA under drought stress was triggered by non-photochemical quenching (NPQ), which is a strategy to protect the chloroplast from photo-oxidative damage by dissipating the excess light energy as heat. This photoprotective mechanism, triggered by NPQ under drought stress, was adequate in keeping, especially in high-light conditions, an equal fraction of open PSII reaction centers (qp) as of non-stress conditions. Thus, under water deficit stress, SA activates a regulatory network of stress and light energy partitioning signaling that can mitigate, to an extent, the water deficit stress on PSII functioning.
Even though plant proteins are more plentiful and affordable than animal proteins in comparison, direct usage of plant-based proteins (PBPs) is still limited because PBPs are fed to animals as feed to produce animal-based proteins. Thus, this work has comprehensively reviewed the effects of various factors such as pH, temperature, pressure, and ionic strength on PBP properties, as well as describes the protein interactions, and extraction methods to know the optimal conditions for preparing PBP-based products with high functional properties and health benefits. According to the cited studies in the current work, the environmental factors, particularly pH and ionic strength significantly affected on physicochemical and functional properties of PBPs, especially solubility was 76.0% to 83.9% at pH = 2, while at pH = 5.0 reduced from 5.3% to 9.6%, emulsifying ability was the lowest at pH = 5.8 and the highest at pH 8.0, and foaming capacity was lowest at pH 5.0 and the highest at pH = 7.0. Electrostatic interactions are the main way for protein interactions, which can be used to create protein/polysaccharide complexes for food industrial purposes. The extraction yield of proteins can be reached up to 86–95% with high functional properties using sustainable and efficient routes, including enzymatic, ultrasound-, microwave-, pulsed electric field-, and high-pressure-assisted extraction. Nondairy alternative products, especially yogurt, 3D food printing and meat analogs, synthesis of nanoparticles, and bioplastics and packaging films are the best available PBPs-based products. Moreover, PBPs particularly those that contain pigments and their products showed good bioactivities, especially antioxidants, antidiabetic, and antimicrobial.
Horticultural crops are an essential part of food and nutritional security. Moreover, these form an integral part of the agricultural economy and have enormous economic potential. They are a rich source of nutrients that are beneficial to human health. Plant breeding of horticultural crops has focussed primarily on increasing the productivity and related traits of these crops. However, fruit and vegetable quality is paramount to their perishability, marketability, and consumer acceptance. The improved nutritional value is beneficial to underprivileged and undernourished communities. Due to a declining genetic base, conventional plant breeding does not contribute much to quality improvement as the existing natural allelic variations and crossing barriers between cultivated and wild species limit it. Over the past two decades, 'omics' and modern biotechnological approaches have made it possible to decode the complex genomes of crop plants, assign functions to the otherwise many unknown genes, and develop genome-wide DNA markers. Genetic engineering has enabled the validation of these genes and the introduction of crucial agronomic traits influencing various quality parameters directly or indirectly. This review discusses the significant advances in the quality improvement of horticultural crops, including shelf life, aroma, browning, nutritional value, colour, and many other related traits.
Many studies have shown the capacity of soil humic substances (HS) to improve plant growth in natural ecosystems. This effect involves the activation of different processes within the plant at different coordinated molecular, biochemical, and physiological levels. However, the first event triggered by plant root-HS interaction remains unclear. Some studies suggest the hypothesis that the interaction of HS with root exudates involves relevant modification of the molecular conformation of humic self-assembled aggregates, including disaggregation, which might be directly involved in the activation of root responses. To investigate this hypothesis, we have prepared two humic acids. A natural humic acid (HA) and a transformed humic acid obtained from the treatment of HA with fungal laccase (HA enz). We have tested the capacity of the two humic acids to affect plant growth (cucumber and Arabidopsis) and complex Cu. Laccase-treatment did not change the molecular size but increased hydrophobicity, molecular compactness and stability, and rigidity of HA enz. Laccase-treatment avoided the ability of HA to promote shoot- and root-growth in cucumber and Arabidopsis. However, it does not modify Cu complexation features. There is no molecular disaggregation upon the interaction of HA and HA enz with plant roots. The results indicate that the interaction with plant roots induced in both HA and laccase-treated HA (HA enz), changes in their structural features that showed higher compactness and rigidity. These events might result from the interaction of HA and HA enz with specific root exudates that can promote intermolecular crosslinking. In summary, the results indicate that the weakly bond stabilized aggregated conformation (supramolecular-like) of HA plays a crucial role in its ability to promote root and shoot growth. The results also indicate the presence of two main types of HS in the rhizosphere corresponding to those non-interacting with plant roots (forming aggregated molecular assemblies) and those produced after interacting with plant root exudates (forming stable macromolecules).
Bioethanol is recognized as a valuable substitute for renewable energy sources to meet the fuel and energy demand of the nation, considered an environmentally friendly resource obtained from agricultural residues such as sugarcane bagasse, rice straw, husk, wheat straw and corn stover. The energy demand is sustained using lignocellulosic biomass to produce bioethanol. Lignocellulosic biomass (LCBs) is the point of attention in replacing the dependence on fossil fuels. The recalcitrant structure of the lignocellulosic biomass is disrupted using effective pretreatment techniques that separate complex interlinked structures among cellulose, hemicellulose, and lignin. Pretreatment of biomass involves various physical, chemical, biological, and physiochemical protocols which are of importance, dependent upon their individual or combined dissolution effect. Physical pretreatment involves a reduction in the size of the
biomass using mechanical, extrusion, irradiation, and sonification methods while chemical pretreatment involves the breaking of various bonds present in the LCB structure. This can be obtained by using an acidic, alkaline, ionic liquid, and organosolvent methods. Biological pretreatment is considered an environment-friendly and safe process involving various bacterial and fungal microorganisms. Distinct pretreatment methods, when combined and utilized in synchronization lead to more effective disruption of LCB, making biomass more accessible for further processing. These could be utilized in terms of their effectiveness for a particular type of cellulosic fiber and are namely steam explosion,
liquid hot water, ammonia fibre explosion, CO2 explosion, and wet air oxidation methods. The present review encircles various distinct and integrated pretreatment processes developed till now and their advancement according to the current trend and future aspects to make lignocellulosic biomass available for further hydrolysis and fermentation.
Humic substances (HS) are originated from naturally decaying biomass. The main products of HS are humic acids, fulvic acids, and humins. HS are extracted from natural origins (e.g., coals, lignite, forest, and river sediments). However, the production of HS from these resources is not environmentally friendly, potentially impacting ecological systems. Earlier theories claimed that the HS might be transformed from lignin by enzymatic or aerobic oxidation. On the other hand, lignin is a by-product of pulp and paper production processes and is available commercially. However, it is still under-utilized. To address the challenges of producing environmentally friendly HS and accommodating lignin in valorized processes, the production of lignin-derived HS has attracted attention. Currently, several chemical modification pathways can be followed to convert lignin into HS-like materials, such as alkaline aerobic oxidation, alkaline oxidative digestion, and oxidative ammonolysis of lignin. This review paper discusses the fundamental aspects of lignin transformation to HS comprehensively. The applications of natural HS and lignin-derived HS in various fields, such as soil enrichment, fertilizers, wastewater treatment, water decontamination, and medicines, were comprehensively discussed. Furthermore, the current challenges associated with the production and use of HS from lignin were described.
Motivation:
Annotation of the mass signals is still the biggest bottleneck for the untargeted mass spectrometry analysis of complex mixtures. Molecular networks are being increasingly adopted by the mass spectrometry community as a tool to annotate large scale experiments. We have previously shown that the process of propagating annotations from spectral library matches on molecular networks can be automated using Network Annotation Propagation (NAP). One of the limitations of NAP is that the information for the spectral matches is only propagated locally, to the first neighbor of a spectral match. Here we show that annotation propagation can be expanded to nodes not directly connected to spectral matches using random walks on graphs, introducing the ChemWalker python library.
Results:
Similarly to NAP, ChemWalker relies on combinatorial in silico fragmentation results, performed by MetFrag, searching biologically relevant databases. Departing from the combination of a spectral network and the structural similarity among candidate structures, we have used MetFusion Scoring function to create a weight function, producing a weighted graph. This graph was subsequently used by the random walk to calculate the probability of 'walking' through a set of candidates, departing from seed nodes (represented by spectral library matches). This approach allowed the information propagation to nodes not directly connected to the spectral library match. Compared to NAP, ChemWalker has a series of improvements, on running time, scalability and maintainability and is available as a stand alone python package.
Availability:
ChemWalker is freely available at https://github.com/computational-chemical-biology/ChemWalker.
Supplementary information:
Supplementary data are available at Bioinformatics online.
Spectral matching of MS ² fragmentation spectra has become a popular method for characterizing natural products libraries but identification remains challenging due to differences in MS ² fragmentation properties between instruments and the low coverage of current spectral reference libraries. To address this bottleneck we present Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) which matches chemical similarity grouping in the Natural Products Atlas to grouping of mass spectrometry features from molecular networking. This approach assigns compound families to molecular networking subnetworks without the need for experimental or calculated reference spectra. We demonstrate SNAP-MS can accurately annotate subnetworks built from both reference spectra and an in-house microbial extract library, and correctly predict compound families from published molecular networks acquired on a range of MS instrumentation. Compound family annotations for the microbial extract library are validated by co-injection of standards or isolation and spectroscopic analysis. SNAP-MS is freely available at www.npatlas.org/discover/snapms .
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of changes were made to PubChem. Data from more than 120 data sources was added to PubChem. Some major highlights include: the integration of Google Patents data into PubChem, which greatly expanded the coverage of the PubChem Patent data collection; the creation of the Cell Line and Taxonomy data collections, which provide quick and easy access to chemical information for a given cell line and taxon, respectively; and the update of the bioassay data model. In addition, new functionalities were added to the PubChem programmatic access protocols, PUG-REST and PUG-View, including support for target-centric data download for a given protein, gene, pathway, cell line, and taxon and the addition of the 'standardize' option to PUG-REST, which returns the standardized form of an input chemical structure. A significant update was also made to PubChemRDF. The present paper provides an overview of these changes.
Coloring compounds are widely applied to manufacturing foods and beverages. The worldwide food market is replacing artificial colorants with natural alternatives, given the increased consumer demand for natural products. However, these substitutes are still an issue due to their high production cost and low chemical and physical stability. Furthermore, natural pigments are highly sensitive to processes applied in conventional extraction techniques, such as thermal, mechanical, and chemical stresses. In this regard, pulsed electric field (PEF) technology has emerged as a promising non-thermal alternative for recovering and producing natural colorings from food matrices. Its action mechanism on cell structures through the electroporation effect is a smart alternative to overcoming the challenging issues associated with producing natural colorants. In this scenario, this review provides an overview of the PEF-assisted extraction of natural pigments and colorants, such as anthocyanins (red-blue-purple), betalains (red), carotenoids (yellow-orange-red), and chlorophylls (green) from plant sources. Moreover, the potential and limitations of this emerging technology to integrate the extraction process of natural colorants were discussed.
Commercial interest in biostimulants as a tool of sustainable green economics and agriculture concepts is on the steep increase, being followed by increasing demand to employ efficient scientific ways to develop new products and understand their mechanisms of action. Biostimulants represent a highly diverse group of agents derived from various natural sources. Regardless of their nutrition content and composition, they are classified by their ability to improve crop performance through enhanced nutrient use efficiency, abiotic stress tolerance, and quality of crops. Numerous reports have described modern, non-invasive sensor-based phenotyping methods in plant research. This review focuses on applying phenotyping approaches in biostimulant research and development and maps the evolution of interaction of these two intensively growing domains. How phenotyping served to identify new biostimulants, the description of their biological activity, and the mechanism/mode of action are summarized. Special attention is dedicated to the indoor high-throughput methods using model plants suitable for biostimulant screening and developmental pipelines and high-precision approaches used to determine biostimulant activity. The need for a complex way of testing biostimulants as multi-component products through integrating other –omic approaches followed by advanced statistical/mathematical tools is emphasized.
Humic substances (HSs) occupy 80% of organic matter in soil and have been widely applied for soil remediation agents, potential battery materials, and adsorbents. Since the HS extraction rate is very low by microbial degradation in nature, artificial humification processes such as aerobic composting (AC) and hydrothermal treatment (HT) have attracted a great deal of attention as the most important strategies in HS production. This article aims to provide a state-of-the-art review on the development of conversion of biomass waste into HSs based on AC and HT for the first time in terms of mechanisms, characteristics of HSs’ molecular structure, and influencing factors. In addition, some differences based on the aforementioned information between AC and HT are reviewed and discussed in the conversion of biomass waste into HSs in a pioneering way. For biomass waste conversion, a feasible strategy on effective humification processes by combining AC with HT is proposed.
Plant ascorbate and glutathione metabolism counteracts oxidative stress mediated, for example, by excess light. In this review, we discuss the properties of immunocytochemistry and transmission electron microscopy, redox-sensitive dyes or probes and bright-field microscopy, confocal microscopy or fluorescence microscopy for the visualization and quantification of glutathione at the cellular or subcellular level in plants and the quantification of glutathione from isolated organelles. In previous studies, we showed that subcellular ascorbate and glutathione levels in Arabidopsis are affected by high light stress. The use of light-emitting diodes (LEDs) is gaining increasing importance in growing indoor crops and ornamental plants. A combination of different LED types allows custom-made combinations of wavelengths and prevents damage related to high photon flux rates. In this review we provide an overview on how different light spectra and light intensities affect glutathione metabolism at the cellular and subcellular levels in plants. Findings obtained in our most recent study demonstrate that both light intensity and spectrum significantly affected glutathione metabolism in wheat at the transcriptional level and caused genotype-specific reactions in the investigated Arabidopsis lines.
Microalgae have evolved into a promising sustainable source of a wide range of compounds, including protein, carbohydrates, biomass, vitamins, animal feed, and cosmetic products. The process of extraction of intracellular composites in the microalgae industry is largely determined by the microalgal species, cultivation methods, cell wall disruption techniques, and extraction strategies. Various techniques have been applied to disrupt the cell wall and recover the intracellular molecules from microalgae, including non-mechanical, mechanical, and combined methods. A comprehensive understanding of the cell disruption processes in each method is essential to improve the efficiency of current technologies and further development of new methods in this field. In this review, an overview of microalgal cell disruption techniques and an analysis of their performance and challenges are provided. A number of studies on cell disruption and microalgae extraction are examined in order to highlight the key challenges facing the field of microalgae and their future prospects. In addition, the amount of product recovery for each species of microalgae and the important parameters for each technique are discussed. Finally, pulsed electric field (PEF)-assisted treatments, which are becoming an attractive option due to their simplicity and effectiveness in extracting microalgae compounds, are discussed in detail.
Today's agriculture faces many concerns in maintaining crop yield while adapting to climate change and transitioning to more sustainable cultivation practices. The application of plant biostimulants (PBs) is one of the methods that step forward to address these challenges. The advantages of PBs have been reported numerous times. Yet, there is a general lack of quantitative assessment of the overall impact of PBs on crop production. Here we report a comprehensive meta-analysis on biostimulants (focus on non-microbial PBs) of over one thousand pairs of open-field data in a total of 180 qualified studies worldwide. Yield gains in open-field cultivation upon biostimulant application were compared across different parameters: biostimulant category, application method, crop species, climate condition, and soil property. The overall results showed that (1) the add-on yield benefit among all biostimulant categories is on average 17.9% and reached the highest potential via soil treatment; (2) biostimulant applied in arid climates and vegetable cultivation had the highest impact on crop yield; and (3) biostimulants were more efficient in low soil organic matter content, non-neutral, saline, nutrient-insufficient, and sandy soils. This systematic review provides general biostimulant application guidelines and gives consultants and growers insights into achieving an optimal benefit from biostimulant application.
The agricultural sector is facing corollary challenges of increasing food production to feed the growing global population and enhance the resources use efficacy, with the least impact on the ecosystem, environment, and human health. In the past few decades, several frontier technologies have been advanced to improve the sustainability of agricultural production systems, through a significant reduction of synthetic agrochemicals. Amongst all, potential and environmentally friendly innovation would be the use of natural substances as plant bio-stimulant that upsurge nutrient uptake for better productivity and also ameliorate the tolerance against several abiotic factors. Moreover, nano-technology is a handy tool for the development of an effective plant bio-stimulant for boosting crop production, assuring sustainability and achieving food security. This review highlights the potential of nano-chitosan, alginate oligosaccharides, nano-silicon, plant extracts, microalgae, agricultural and industrial organic wastes in the development of plant bio-stimulant. Challenges pertaining to nano-formulations and their application in agricultural production are also discussed. Nanoparticles derived from organic and natural elements that are not destructive to the environment and boost sustainable crop cultivation have a great perspective to be developed as an innovative and efficient plant bio-stimulant.
Bioeffector (BE) application is emerging as a strategy for achieving sustainable agricultural practices worldwide. However, the effect of BE on crop growth and quality is still controversial and there is still no adequate impact assessment that determines factors on the efficiency of BE application. Therefore, we carried out a network metaanalysis on the effect of BEs using 1,791 global observations from 186 studies to summarize influencing factors and the impact of BEs on crop growth, quality, and nutrient contents. The results show that BEs did not only improve plant growth by around 25% and yield by 30%, but also enhanced crop quality, e.g., protein (55% increase) and soluble solids content (75% increase) as well as aboveground nitrogen (N) and phosphate (P) content by 28 and 40%, respectively. The comparisons among BE types demonstrated that especially non-microbial products, such as extracts and humic/amino acids, have the potential to increase biomass growth by 40–60% and aboveground P content by 54–110%. The soil pH strongly influenced the efficiency of the applied BE with the highest effects in acidic soils. Our results showed that BEs are most suitable for promoting the quality of legumes and increasing the yield of fruits, herbs, and legumes. We illustrate that it is crucial to optimize the application of BEs with respect to the right application time and technique (e.g., placement, foliar). Our results provide an important basis for future research on the mechanisms underlying crop improvement by the application of BEs and on the development of new BE products.
In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.
Main conclusion
The relationship of fructan to plant growth regulators is clearly more complicated than it looks and is likely related to differences between fructan molecules in size and structure as well as localization.
Abstract
Fructans are a complex group of carbohydrates composed mainly of fructose units linked to a sucrose molecule. Fructans are present in plants as heterogeneous mixtures with diverse molecular structures and mass, different polymerization degrees, and linkage types between fructosyl residues. Like sucrose, they are frequently stored in leaves and other organs, acting as carbohydrate reserves. Fructans are synthesized in the cell vacuole by fructosyltransferase enzymes and catabolized by fructan exohydrolase enzymes. Several publications have shown that fructan metabolism varies with the stage of plant development and in response to the environment. Recent studies have shown a correlation between plant growth regulators (PGR), fructan metabolism, and tolerance to drought and cold. PGR are compounds that profoundly influence the growth and differentiation of plant cells, tissues, and organs. They play a fundamental role in regulating plant responses to developmental and environmental signals. In this review, we summarize the most up-to-date knowledge on the metabolism of fructans and their crosstalk with PGR signaling pathways. We identify areas that require more research to complete our understanding of the role of fructans in plants.
Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.
Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data.
This study compared bulk stable isotope analysis and compound‐specific liquid chromatography‐mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U‐¹³C5‐¹⁵N2‐l‐glutamine and axenically grown Arabidopsis thaliana.
After 15–120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the ¹⁵N and ¹³C content increased over time, resulting in very different estimated uptake rates. The ¹³C : ¹⁵N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15% within 120 min.
The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post‐uptake metabolism, compound‐specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post‐uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre‐uptake metabolism by microbes that accounts for the ¹⁵N–¹³C mismatch reported in ecological studies, but also post‐uptake metabolism in the plant.
Flavonoids are specialized metabolites largely widespread in plants where they play numerous roles including defense and signaling under stress conditions. These compounds encompass several chemical subgroups such as flavonols which are one the most represented classes. The most studied flavonols are kaempferol, quercetin and myricetin to which research attributes antioxidative properties and a potential role in UV-defense through UV-screening mechanisms making them critical for plant adaptation to climate change. Despite the great interest in flavonol functions in the last decades, some functional aspects remain under debate. This review summarizes the importance of flavonoids in plant defense against climate stressors and as signal molecules with a focus on flavonols in Mediterranean plant species. The review emphasizes the relationship between flavonol location (at the organ, tissue and cellular scales) and their function as defense metabolites against climate-related stresses. It also provides evidence that biosynthesis of flavonols, or flavonoids as a whole, could be a crucial process allowing plants to adapt to climate change, especially in the Mediterranean area which is considered as one of the most sensitive regions to climate change over the globe.
The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. The uptake of macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), and sulphur (S) from the soil is critical for plant growth and development. Small signaling peptide (SSP) hormones are best known as potent regulators of plant growth and development with a few also known to have specialized roles in macronutrient utilization. Here we describe a high throughput phenotyping platform for testing SSP effects on root uptake of multiple nutrients. The SSP, CEP1 (C-TERMINALLY ENCODED PEPTIDE) enhanced nitrate uptake rate per unit root length in Medicago truncatula plants deprived of N in the high-affinity transport range. Single structural variants of M. truncatula and Arabidopsis thaliana specific CEP1 peptides, MtCEP1D1:hyp4,11 and AtCEP1:hyp4,11, enhanced uptake not only of nitrate, but also phosphate and sulfate in both model plant species. Transcriptome analysis of Medicago roots treated with different MtCEP1 encoded peptide domains revealed that hundreds of genes respond to these peptides, including several nitrate transporters and a sulfate transporter that may mediate the uptake of these macronutrients downstream of CEP1 signaling. Likewise, several putative signaling pathway genes including LEUCINE-RICH REPEAT RECPTOR-LIKE KINASES and Myb domain containing transcription factors, were induced in roots by CEP1 treatment. Thus, a scalable method has been developed for screening synthetic peptides of potential use in agriculture, with CEP1 shown to be one such peptide.
Plant quality and survival prediction tools are useful when applied in the field in different agricultural sectors. The objectives of this study were to conduct a review and bibliometric analysis of the Dickson Quality Index (DQI) as a key plant quality indicator and with respect to its scientific applications. A third objective was to identify the main morphological and physiological parameters used in plant production research. The methodology and findings of 289 scientific articles were analysed based on the morphological, physiological, and mathematical parameters used as plant quality indicators in research on forest, medicinal, horticultural, aromatic, and ornamental species. During the last 10 years, the number of publications that have used the DQI as a plant quality parameter has increased by 150%, and Brazilian researchers stand out as the most frequent users. Forestry is the discipline where quality parameters and their biometric relationships are most often used to facilitate intensive plant production. Use of the DQI increases the certainty of prediction, selection, and productivity in the plant production chain. The DQI is a robust tool with scientific application and great potential for use in the preselection of plants with high quality standards among a wide range of plant species.
Steam Explosion (SE) is one of the most efficient and environmentally friendly processes for the pretreatment of lignocellulosic biomass. It is an important tool for the development of the biorefinery concept to mitigate the recalcitrance of biomass. However, the two distinct steps of SE, steam cracking and explosive decompression, leading to the breakdown of the lignocellulosic matrix have generally been studied in empiric ways and clarification are needed. This mini-review provides new insights and recommendations regarding the properties of subcritical water, process modeling and the importance of the depressurization rate.
Plant growth-promoting bacteria (PGPB) and humic substances (HSs) are promising options for reducing the use of pesticides and mineral fertilizers. Although many studies have shown the effects of PGPB and HSs separately, little information is available on plant responses to the combined application of these biostimulants despite the great potential for the simultaneous action of these biological inputs. Thus, the objective of this review is to present an overview of scientific studies that addressed the application of PGPB and HSs to different crops. First, we discuss the effect of these biostimulants on biological nitrogen fixation, the various effects of the inoculation of beneficial bacteria combined with the application of HSs on promoting the growth of nonleguminous plants and how this combination can increase bacterial colonization of plant hosts. We also address the effect of PGPB and HSs on plant responses to abiotic stresses, in addition to discussing the role of HSs in protecting plants against pathogens. There is a lack of studies that address the role of PGPB + HSs in biocontrol. Understanding the factors involved in the promotion of plant growth through the application of PGPB and HSs can assist in the development of efficient biostimulants for agricultural management. This approach has the potential to accelerate the transition from conventional cultivation to sustainable agrosystems.
Pectin is an abundant cell wall polysaccharide with essential roles in various biological processes. The structural diversity of pectins, along with the numerous combinations of the enzymes responsible for pectin biosynthesis and modification, plays key roles in ensuring the specificity and plasticity of cell wall remodeling in different cell types and under different environmental conditions. This review focuses on recent progress in understanding various aspects of pectin, from its biosynthetic and modification processes to its biological roles in different cell types. In particular, we describe recent findings that cell wall modifications serve not only as final outputs of internally determined pathways, but also as key components of intercellular communication, with pectin as a major contributor to this process. The comprehensive view of the diverse roles of pectin presented here provides an important basis for understanding how cell wall-enclosed plant cells develop, differentiate, and interact.
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome‐scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi‐automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single‐cell transcriptomics data from the Arabidopsis root to infer cell type‐specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide‐ranging utility in integrating metabolism with other areas of plant biology.
Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
As sessile organisms, plants are exposed to constantly changing environments that are often stressful for their growth and development. To cope with these stresses, plants have evolved complex and sophisticated stress-responsive signaling pathways regulating the expression of transcription factors and biosynthesis of osmolytes that confer tolerance to plants. Signaling peptides acting like phytohormones control various aspects of plant growth and development via cell-cell communication networks. These peptides are typically recognized by membrane-embedded receptor-like kinases, inducing activation of cellular signaling to control plant growth and development. Recent studies have revealed that several signaling peptides play important roles in plant responses to abiotic stress. In this mini review, we provide recent findings on the roles and signaling pathways of peptides that are involved in coordinating plant responses to abiotic stresses, such as dehydration, high salinity, reactive oxygen species, and heat. We also discuss recent developments in signaling peptides that play a role in plant adaptation responses to nutrient deficiency stress, focusing on nitrogen and phosphate deficiency responses.
HyPer7 senses minute amounts of H2O2 independent of pH and the glutathione redox potential and enables detection of physiological H2O2 fluxes within the cytosol and between subcellular compartments.
H2O2 is recognized as an important signaling molecule in plants. We sought to establish a genetically encoded, fluorescent H2O2 sensor that allows H2O2 monitoring in all major subcompartments of a Chlamydomonas cell. To this end, we used the Chlamydomonas Modular Cloning toolbox to target the hypersensitive H2O2 sensor roGFP2-Tsa2ΔCR to the cytosol, nucleus, mitochondrial matrix, chloroplast stroma, thylakoid lumen, and endoplasmic reticulum (ER). The sensor was functional in all compartments, except for the ER where it was fully oxidized. Employing our novel sensors, we show that H2O2 produced by photosynthetic linear electron transport (PET) in the stroma leaks into the cytosol but only reaches other subcellular compartments if produced under non-physiological conditions. Furthermore, in heat-stressed cells, we show that cytosolic H2O2 levels closely mirror temperature up- and downshifts and are independent from PET. Heat stress led to similar up- and downshifts of H2O2 levels in the nucleus and, more mildly, in mitochondria but not in the chloroplast. Our results thus suggest the establishment of steep intracellular H2O2 gradients under normal physiological conditions with limited diffusion into other compartments. We anticipate that these sensors will greatly facilitate future investigations of H2O2 biology in plant cells.
Reactive oxygen species (ROS) are produced throughout plant cells as a by-product of electron transfer processes. While highly oxidative and potentially damaging to a range of biomolecules, there exists a suite of ROS-scavenging antioxidant strategies that maintain a redox equilibrium. This balance can be disrupted in the event of cellular stress leading to increased ROS levels, which can act as a useful stress signal but, in excess, can result in cell damage and death. As crop plants become exposed to greater degrees of multiple stresses due to climate change, efforts are ongoing to engineer plants with greater stress tolerance. It is therefore important to understand the pathways underpinning ROS-mediated signalling and damage, both through measuring ROS themselves and other indicators of redox imbalance. The highly reactive and transient nature of ROS makes this challenging to achieve, particularly in a way that is specific to individual ROS species. In this review, we describe the range of chemical and biological tools and techniques currently available for ROS and redox marker measurement in plant cells and tissues. We discuss the limitations inherent in current methodology and opportunities for advancement.
The continuing need to protect food and fiber production to address the demands of an expanding global population requires new pest management tools for crop protection. Natural products (NPs) have been and continue to be a key source of inspiration for new active ingredients (AIs) for crop protection, accounting for 17% of all crop protection AIs. However, potentially 50% of all crop protection compounds have or could have a NP origin if NP synthetic equivalents (NPSEs, synthetic compounds discovered by other approaches but for which a NP model also happens to exist) are also considered. The real and hypothetical NPs have their greatest impact as insight for new classes of crop protection compounds. Among the different product areas, NPs have their largest influence on the discovery of new insecticides, while herbicides have been the least affected by mining NPs for new AIs. While plants have historically been the largest (60% of the total) source of NPs of AIs for crop protection, in the last 30 years, bacterial NPs have become the largest source (42% of the total) of new classes (first in class) of NP-inspired crop protection AIs. Interest in NPs for crop protection continues, an aspect that is highlighted by the notable rise in the numbers of publications and patents on this topic, especially in the last 20 years. The present analysis further illustrates the continuing interest and value in NPs as sources of and inspiration for new classes of crop protection compounds.
Hydrodynamic cavitation is considered to be a promising technology for process intensification, due to its high energy efficiency, cost-effective operation, ability to induce chemical reactions, and scale-up possibilities. In the past decade, advancements have been made in the fundamental understanding of hydrodynamic cavitation and its main variables, which provide a basis for applications of hydrodynamic cavitation in radical-induced chemical reaction processes. Here, we provide an extensive review of these research efforts, including the fundamentals of hydrodynamic cavitation, the design of cavitation reactors, cavitation-induced reaction enhancement, and relevant industrial applications. Two types of hydrodynamic cavitation reactors—namely, stationary and rotational—are compared. The design parameters of a hydrodynamic cavitation reactor and reactor performance at the laboratory and pilot scales are discussed, and recommendations are made regarding optimal operation and geometric conditions. The commercial cavitation reactors that are currently on the market are reviewed here for the first time. The unique features of hydrodynamic cavitation have been widely applied to various chemical reactions, such as oxidization reactions and wastewater treatment, and to physical processes, such as emulsion generation and component extraction. The roles of radicals and gas bubble implosion are also thoroughly discussed.
Nitrate is an essential nutrient and signaling molecule for plant growth. Plants sense intracellular nitrate to adjust their metabolic and growth responses. Here we identify the primary nitrate sensor in plants. We found that mutation of all seven Arabidopsis NIN-like protein (NLP) transcription factors abolished plants’ primary nitrate responses and developmental programs. Analyses of NIN-NLP7 chimeras and nitrate binding revealed that NLP7 is derepressed upon nitrate perception via its amino terminus. A genetically encoded fluorescent split biosensor, mCitrine-NLP7, enabled visualization of single-cell nitrate dynamics in planta. The nitrate sensor domain of NLP7 resembles the bacterial nitrate sensor NreA. Substitutions of conserved residues in the ligand-binding pocket impaired the ability of nitrate-triggered NLP7 to control transcription, transport, metabolism, development, and biomass. We propose that NLP7 represents a nitrate sensor in land plants.
Plants constantly come into contact with a diverse mix of pathogenic and beneficial microbes. The ability to distinguish between them and to respond appropriately is essential for plant health. Here we review recent progress in understanding the role of amino acid sensing, signaling, transport, and metabolism during plant–microbe interactions. Biochemical pathways converting individual amino acids into active compounds have recently been elucidated, and comprehensive large-scale approaches have brought amino acid sensors and transporters into focus. These findings show that plant central amino acid metabolism is closely interwoven with stress signaling and defense responses at various levels. The individual biochemical mechanisms and the interconnections between the different processes are just beginning to emerge and might serve as a foundation for new plant protection strategies.
Achieving detection of the phytohormone abscisic acid (ABA) is of critical importance for understanding plant growth and development. We report a hybrid supramolecular fluorescent probe that uses bovine serum albumin (BSA) as a host. Aggregation-induced emission of fluorescent chromophores (AIEgens) enables luminescence in the presence of BSA. ABA and its aptamer act as a switch to trigger this fluorescent system, the strategy that exhibits high sensitivity to abscisic acid with a detection limit of 0.098 nM. The probe test strip also enables visualization of ABA content from plants by colorimetric observation with the naked eye. In particular, the high biocompatibility and small molecular size of the prepared fluorescent probe allow for effective monitoring of ABA in plant tissues by fluorescence imaging. This strategy provides a new perspective to achieve the detection of endogenous and exogenous ABA in plants and has important implications for plant biology research.
Environmental stress greatly decreases crop yield. The application of noninvasive techniques is one of the most practical and feasible ways of monitoring the health condition of plants under stress. However, it remains largely unsolved. A chemical fluorescent probe can be applied as a typical nondestructive method, but it has not been applied in living plants for stress detection to date. The abscisic acid (ABA) receptor plays a central role in conferring tolerance to environmental stresses and is an excellent target for developing fluorescent probes. Herein, we developed a fluorescence molecular imaging technology to monitor live plant stress by visualizing the protein expression level of the ABA receptor PYR1. A computer-aided designed indicator dye, flubactin, exhibited an 8-fold enhancement in fluorescence intensity upon interaction with PYR1. In vitro and in vivo experiments showed that flubactin is suitable to be used to detect salt stress in plants in real time. Moreover, the low toxicity of flubactin promotes its application in the future. Our work opens a new era for the nondestructive visualization of plant stress in vivo.
Plants require solar energy to grow through oxygenic photosynthesis. However, when light intensity exceeds the optimal range for photosynthesis it causes abiotic stress and physiological damage in plants. In response to high light stress, plants initiate a series of signal transduction from chloroplasts to whole cells and from locally stressed tissues to the rest of the plant body. These signals trigger a variety of physiological and biochemical reactions intended to mitigate the deleterious effects of high light intensity such as photodamage and photoinhibition. Light stress protection mechanisms include chloroplastic Reactive Oxygen Species (ROS) scavenging, chloroplast and stomatal movement, and anthocyanin production. Photosynthetic apparatuses, being the direct targets of photodamage, have also developed various acclimation processes such as thermal energy dissipation through Non-Photochemical Quenching (NPQ), photorepair of Photosystem II (PSII), and transcriptional regulation of photosynthetic proteins. Fluctuating light is another mild but persistent type of light stress in nature, which has unfortunately been poorly investigated. Current studies suggest however that state transitions and cyclic electron transport are the main adaptive mechanisms for mediating fluctuating light stress in plants. Here, we review the current breadth of knowledge regarding physiological and biochemical responses to both high light stress and fluctuating light stress.
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.
Fluorescent 1 : 1, 1 : 2 and 1 : 3 sugar-O-BODIPY conjugates of glucose, xylose and ribose were characterised by ¹ H– ¹¹ B HMBC and ¹¹ B NMR to discriminate between boron bound to 1,2-, 1,3- or 1,4-diol sites and furanose/pyranose sugar forms.
Biological macromolecules are large cellular components abundantly obtained naturally and are responsible for varieties of essential functions for the growth and survival of living organisms. There are four important classes of biological macromolecules, viz., carbohydrates, lipids, proteins, and nucleic acids. These possess some favorable characteristics, such as good biocompatibility, excellent biodegradability, desired mechanical strength, better bioavailability, etc., and these characteristics are directing the uses of these biological macromolecules in the biomedical and related fields. Biological macromolecules can also modulate the pathophysiology of neurodegenerative disorders/diseases. The current chapter deals with a brief discussion about the sources, properties, and valued applications of various biological macromolecules.
Plants use electrical and chemical signals for systemic communication. Herbivory, for instance, appears to trigger local apoplasmic glutamate accumulation, systemic electrical signals and calcium waves that travel to report insect damage to neighboring leaves and initiate defense. To monitor extra‐ and intracellular glutamate concentrations in plants, we generated Arabidopsis lines expressing genetically encoded fluorescent glutamate sensors. In contrast to cytosolically localized sensors, extracellularly displayed variants inhibited plant growth and proper development. Phenotypic analyses of high‐affinity display sensor lines revealed that root meristem development, particularly the quiescent center (QC), number of lateral roots, vegetative growth and floral architecture were impacted. Notably, the severity of the phenotypes was positively correlated with the affinity of the display sensors, intimating that their ability to sequester glutamate at the surface of the plasma membrane was responsible for the defects. Root growth defects were suppressed by supplementing culture media with low levels of glutamate. Together, the data indicate that sequestration of glutamate at the cell surface either disrupts the supply of glutamate to meristematic cells and/or impairs localized glutamatergic signaling important for developmental processes.
Aerobic composting is a typical biochemical process of stabilization and harmlessness of organic wastes during which organic matter degrades, and then aggregates, to produce humic substances (HSs). HSs are a core product of—and a crucial indicator of—the maturation of compost that can be used in soil amendments. The formation of HSs is affected by the characteristics of the raw materials involved, the presence of compost additives, microbial activity, temperature, pH, the C/N ratio, moisture content, oxygen content and particle size, all of which can interact with each other. The formation of HSs is therefore complex. Moreover, it is difficult to identify definitive structures of humic acids (HAs) and fulvic acids (FAs), which are the two major components of HSs. However, HSs represent the same functional groups and structural arrangements, which helps to predict their structures. Functional groups represented by phenol and carboxylic acid groups of HAs and FAs can provide various agronomic functions, such as plant growth enhancement, water and nutrient retention, and disease suppression capacity. Overall, HSs can act as a soil amendment, fertilizer, and plant growth regulator. These functions of HSs enhance the reuse potential of organic waste compost products; however, this requires scientific control of various composting parameters and appropriate application of final products.
Background
Spices are rich source of naturally occurring bioactives and are used in different food applications. Major spice bioactives include essential oils, oleoresins, polysaccharides, phenolics, alkaloids, vitamins, and carotenoids. Conventional extraction of these bioactives has been associated with a high requirement of time, solvent, and energy which diminishes the application.
Scope and approach
This review discusses and summaries the recent findings on UAE for extraction of bioactives from spices. The concepts, mechanisms, factors affecting the sonication process, and their application in the extraction of spice bioactives are reviewed. The integration of UAE with other emerging technologies, mainly microwave-assisted and supercritical fluid (CO2) assisted extraction methods in the field of spice bioactives extraction are also explored. A comparison of different optimization and modeling methods used for UAE of spices are discussed and enunciate the gaps and possible future trend.
Key findings and conclusion
Acoustic cavitation generated during ultrasound treatment produces shock waves, microjets, shear force, and sonochemical reactions causing plant cell erosion and pore formation. It enhances mass transfer paving way for application of green solvents such as water. Further the Two-site kinetic model and Peleg's model are most versatile in explaining the UAE of bioactives from spices. Maximized recovery of bioactives, could be attained by selecting combination of technologies and process parameters for improved energy efficiency reduced time and energy consumption.
The tools available to carry out in vivo analysis of Ca2+ dynamics in plants are powerful and mature technologies that still require the proper controls.
Biological processes are highly dynamic, and during plant growth, development, and environmental interactions, they occur and influence each other on diverse spatiotemporal scales. Understanding plant physiology on an organismic scale requires analyzing biological processes from various perspectives, down to the cellular and molecular levels. Ideally, such analyses should be conducted on intact and living plant tissues. Fluorescent protein-based in vivo biosensing using genetically encoded fluorescent indicators (GEFIs) is a state-of-the-art methodology for directly monitoring cellular ion, redox, sugar, hormone, ATP and phosphatidic acid dynamics, and protein kinase activities in plants. The steadily growing number of diverse but technically compatible genetically encoded biosensors, the development of dual-reporting indicators, and recent achievements in plate-reader-based analyses now allow for GEFI multiplexing: the simultaneous recording of multiple GEFIs in a single experiment. This in turn enables in vivo multiparameter analyses: the simultaneous recording of various biological processes in living organisms. Here we provide an update on currently established direct fluorescent protein-based biosensors in plants, discuss their functional principles, and highlight important biological findings accomplished by employing various approaches of GEFI-based multiplexing. We also discuss challenges and provide advice for fluorescent protein-based biosensor analyses in plants.
Fluorescence is widely used to detect functional groups and ions, and peptides are used in various fields due to their excellent biological activity. In recent years, research on fluorescent amino acids has intensified, especially with the natural fluorescent amino acids such as tryptophan (Trp), tyrosine (Tyr) and phenylalanine (Phe). They use their respective fluorophores to undergo π-π transition under excitation with light of a particular wavelength, and then release a large number of photons, which produce fluorescence. Thus, they are widely used as building units to enhance the fluorescence properties of other molecules. Peptide-based fluorescence technology has expanded the research in the field of biochemistry. Peptide-based fluorescence involving fluorescent amino acids not only retains the biocompatibility of peptides, but also relies on their fluorescent groups to enhance the fluorescent properties of the peptide itself, breaking the original limitations and connecting different fields to complement each other. This review summarizes the luminescence mechanism and fluorescent properties of the natural fluorescent amino acids and focuses on the fluorescence emission of peptides embedded with these fluorescent amino acids or fluorophores. Finally, we summarize the applications of peptide-based fluorescence in sensing drug release, metal ions and biomolecules, and present new challenges and expectations for the future development in this field. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2021.
The pH parameter of soil plays a key role for plant nutrition as it is affecting the availability of minerals and consequently determines plant growth. Although the mechanisms by which root perceive the external pH is still unknown, the impact of external pH on tissue growth has been widely studied especially in hypocotyl and root. Thanks to technological development of cell imaging and fluorescent sensors, we can now monitor pH in real time with at subcellular definition. In this focus, fluorescent dye-based, as well as genetically-encoded pH indicators are discussed especially with respect to their ability to monitor acidic pH in the context of primary root. The notion of apoplastic subdomains is discussed and suggestions are made to develop fluorescent indicators for pH values below 5.0.