Temporal transcriptome and metabolite analyses provide insights into the biochemical and physiological processes underlying endodormancy release in pistachio (Pistacia vera L.) flower buds.

Pistachio (Pistacia vera L.), an economically and nutritionally important tree crop, relies on winter chill for bud endodormancy break and subsequent blooming and nut production. However, insufficient winter chill poses an increasing challenge in pistachio growing regions. To gain a better understanding of the physiological and biochemical responses of endodormant pistachio buds to chilling accumulation, we investigated the global gene expression changes in flower buds of pistachio cv. Kerman that were cultivated at three different orchard locations and exposed to increasing durations of winter chill. The expression of genes encoding ß-1,3-glucanase and ß-amylase, enzymes responsible for breaking down callose (ß-1,3-glucan) and starch (α-1,4-glucan), respectively, increased during the endodormancy break of pistachio buds. This result suggested that the breakdown of callose obstructing stomata as well as the release of glucose from starch enables symplasmic trafficking and provides energy for bud endodormancy break and growth. Interestingly, as chilling accumulation increased, there was a decrease in the expression of nine-cis-epoxycarotenoid dioxygenase (NCED), encoding an enzyme that uses carotenoids as substrates and catalyzes the rate-limiting step in abscisic acid (ABA) biosynthesis. The decrease in NCED expression suggests ABA biosynthesis is suppressed, thus reducing inhibition of endodormancy break. The higher levels of carotenoid precursors and a decrease in ABA content in buds undergoing endodormancy break supports this suggestion. Collectively, the temporal transcriptome and biochemical analyses revealed that the degradation of structural (callose) and non-structural (starch) carbohydrates, along with the attenuation of ABA biosynthesis, are critical processes driving endodormancy break in pistachio buds.

Estimation of tomato water status with photochemical reflectance index and machine learning: Assessment from proximal sensors and UAV imagery.

Tracking plant water status is a critical step towards the adaptive precision irrigation management of processing tomatoes, one of the most important specialty crops in California. The photochemical reflectance index (PRI) from proximal sensors and the high-resolution unmanned aerial vehicle (UAV) imagery provide an opportunity to monitor the crop water status efficiently. Based on data from an experimental tomato field with intensive aerial and plant-based measurements, we developed random forest machine learning regression models to estimate tomato stem water potential (ψ stem), (using observations from proximal sensors and 12-band UAV imagery, respectively, along with weather data. The proximal sensor-based model estimation agreed well with the plant ψ stem with R 2 of 0.74 and mean absolute error (MAE) of 0.63 bars. The model included PRI, normalized difference vegetation index, vapor pressure deficit, and air temperature and tracked well with the seasonal dynamics of ψ stem across different plots. A separate model, built with multiple vegetation indices (VIs) from UAV imagery and weather variables, had an R 2 of 0.81 and MAE of 0.67 bars. The plant-level ψ stem maps generated from UAV imagery closely represented the water status differences of plots under different irrigation treatments and also tracked well the temporal change among flights. PRI was found to be the most important VI in both the proximal sensor- and the UAV-based models, providing critical information on tomato plant water status. This study demonstrated that machine learning models can accurately estimate the water status by integrating PRI, other VIs, and weather data, and thus facilitate data-driven irrigation management for processing tomatoes.

Tree-level almond yield estimation from high resolution aerial imagery with convolutional neural network.

Introduction: Estimating and understanding the yield variability within an individual field is critical for precision agriculture resource management of high value tree crops. Recent advancements in sensor technologies and machine learning make it possible to monitor orchards at very high spatial resolution and estimate yield at individual tree level. Methods: This study evaluates the potential of utilizing deep learning methods to predict tree-level almond yield with multi-spectral imagery. We focused on an almond orchard with the 'Independence' cultivar in California, where individual tree harvesting and yield monitoring was conducted for ~2,000 trees and summer aerial imagery at 30cm was acquired for four spectral bands in 2021. We developed a Convolutional Neural Network (CNN) model with a spatial attention module to take the multi-spectral reflectance imagery directly for almond fresh weight estimation at the tree level. Results: The deep learning model was shown to predict the tree level yield very well, with a R2 of 0.96 (±0.002) and Normalized Root Mean Square Error (NRMSE) of 6.6% (±0.2%), based on 5-fold cross validation. The CNN estimation captured well the patterns of yield variation between orchard rows, along the transects, and from tree to tree, when compared to the harvest data. The reflectance at the red edge band was found to play the most important role in the CNN yield estimation. Discussion: This study demonstrates the significant improvement of deep learning over traditional linear regression and machine learning methods for accurate and robust tree level yield estimation, highlighting the potential for data-driven site-specific resource management to ensure agriculture sustainability.

Selenium Speciation in Se-Enriched Soybean Grains from Biofortified Plants Grown under Different Methods of Selenium Application.

Since soybean is widely cultivated around the world and has a high protein content, it is a great nutritional vehicle for increasing the dietary uptake of selenium (Se). Several studies have evaluated biofortification with Se through fertilizer application in several crops. However, it is not clear how each method and source affect the total Se content or Se species in soybean grains. This work aimed to assess the total Se content and Se speciation in Se-enriched soybean grains produced under different Se application methods in the field. The treatments consisted of Se application (soil or foliar), using organic or inorganic Se sources at 10 g ha-1 or 80 g ha-1, in two genotypes. The results showed that all treatments with inorganic Se (soil and foliar) increased the Se content in grains compared with the control. More than 80% of the total Se in grains was present as selenomethionine (SeMet), and the speciation was affected by the Se source and the method of application. The treatments using inorganic Se, applied via soil or foliar, produced the highest content of Se as SeMet in soybean grains. Finally, we propose that the preservation of the Se species in products derived from soybean grains be evaluated as the following step.

Neutral-to-positive cadmium effects on germination and seedling vigor, with and without seed priming.

This review gathered and analyzed data about (i) the Cd-induced impacts on seed germination and seedling vigor, and (ii) the use of different priming agents to mitigate Cd-induced impacts on the early plant development. Critical evaluation of the obtained data revealed intriguing results. First, seeds of diverse species can endure exposures to Cd. Such endurance is exhibited as maintenance of or even improvement in the seed germination and vigor (up to 15% and 70%, respectively). Second, the main factors influencing seed tolerance to Cd toxicity are related to temporal variations in anatomical, physiological, and/or biochemical features. Third, Cd can trigger diverse transgenerational effects on plants by shaping seed endophytes, by modulating seed provisioning with resources and regulatory elements, and/or by altering seed (epi)genomics. Fourth, different chemical, biological and physical priming agents can mitigate Cd-induced impacts on seeds, sometimes enhancing their performance over the control (reference) values. Overall, this review shows that the impacts of Cd on seed germination and vigor encompass not only negative outcomes but also neutral and positive ones, depending upon the Cd dose, media properties, plant species and genotypes, plant developmental stage and organ, and management approaches. Increasing our understanding of plant tolerance mechanisms against the growing background Cd pollution is relevant to support breeding programs, agricultural practices, and health-environmental policies.

Foliar Application of an Inositol-Based Plant Biostimulant Boosts Zinc Accumulation in Wheat Grains: A µ-X-Ray Fluorescence Case Study.

There has been much interest in the incorporation of organic molecules or biostimulants into foliar fertilizers with the rationalization that these compounds will enhance the uptake, or subsequent mobility of the applied nutrient. The objective of this research was to investigate the effects of an inositol-based plant stimulant on the mobility and accumulation of foliar-applied zinc (Zn) in wheat plants (Triticum aestivum L.). High-resolution elemental imaging with micro-X-ray fluorescence (µ-XRF) was utilized to examine Zn distribution within the vascular bundle of the leaf and whole grains. The inclusion of myo-inositol with Zinc sulfate, significantly increased Zn concentration in shoots in contrast to untreated controls and Zn sulfate applied alone. Foliar Zn treated plants increased Zn in grains by 5-25% with myo-inositol plus Zn treated plants significantly increasing grain Zn concentration compared to both Zn treated and non-treated controls. XRF imaging revealed Zn enrichment in the bran layer and germ, with a very low Zn concentration present in the endosperm. Plants treated with Zn plus myo-inositol showed an enhanced and uniform distribution of Zn throughout the bran layer and germ with an increased concentration in the endosperm. While our data suggest that foliar application of myo-inositol in combination with Zn may be a promising strategy to increase the absorption and mobility of Zn in the plant tissue and subsequently to enhance Zn accumulation in grains, further research is needed to clarify the mechanisms by which myo-inositol affects plant metabolism and nutrient mobility.

A gift from parent to offspring: transgenerational hormesis.

Hormesis is a biological phenomenon characterized by opposite effects between low and high doses of stresses that can result in stimulatory and adaptive benefits to individuals within a population. While evidence of hormesis is well established, two recent studies (Nogueira et al., Belz and Sinkkonen) suggest that hormesis can also offer transgenerational benefit.

Spatial imaging reveals the pathways of Zn transport and accumulation during reproductive growth stage in almond plants.

The reproductive processes of several deciduous trees are highly sensitive to Zn deficiency. An understanding of the patterns of Zn storage and remobilization during bud development and bud break is critical for the development of fertilization strategies to prevent deficiencies and may be valuable in selection and breeding programs to develop more Zn-resilient cultivars. In this study, we provide insights into the in situ distribution of Zn in almond reproductive organs at tissue, cellular, and subcellular scales using synchrotron-based X-ray fluorescence. The concentrations of Zn in different parts of the vegetative and reproductive tissues were also analysed. Our results show that the small branches subtending the flower and fruit, pollen grain, transmitting tissues of styles, and seed embryo are all important storage sites for Zn. An increase in Zn concentrations in almond reproductive organs mostly occur during the expanding growth phase, such as bud-flush and the mid-fruit enlargement stage; however, Zn transport to floral parts and fruit tissues was restricted at the pedicel and seed coat, suggesting a bottleneck in the export of Zn from the mother plant to filial tissues. Our results provide direct visual evidence for in-situ Zn distribution within the reproductive tissues of a deciduous tree species.

Nutrient Storage in the Perennial Organs of Deciduous Trees and Remobilization in Spring - A Study in Almond (Prunus dulcis) (Mill.) D. A. Webb.

The annual dynamics of whole mature almond tree nutrient remobilization in spring and the accumulation of nutrients in perennial tissues during the year were determined by sequential coring, tissue sampling, nutrient analysis, whole tree excavation and biomass estimation for trees grown under four nitrogen rate treatments 140 kg ha-1 N (N140), 224 kg ha-1 N (N224), 309 kg ha-1 N (N309), and 392 kg ha-1 N (N392) over 2 years. Whole tree perennial organ N content was greatest in dormancy then declined through bud swell, flowering and fruit set, achieving the lowest total whole tree nutrient content of perennial organs by March 12 [12-14 days after full bloom (DAFB)] coincident with 60-70% leaf expansion. During this period no net increment in whole tree N content (annual plus perennial N) was observed indicating that tree demand for N for bud break, flowering, fruit set and leaf out was met by remobilized stored N and that there was no net N uptake from soil. Remobilizable N increased with increasing N application up to N309 and was maximal at 44.4 ± 4 kg ha-1 and 37.5 ± 5.7 kg ha-1 for the optimally fertilized N309 in 2012 and 2013 respectively. Net increases in perennial organ N (stored N) commenced 41 DAFB and continued through full leaf abscission at 249 DAFB. Total annual N increment in perennial organs varied from 25 to 60 kg ha-1 and was strongly influenced by N rate and tree yield. N remobilized from senescing leaves contributed from 11 to 15.5 ± 0.6 kg ha-1 to perennial stored N. Similar patterns of nutrient remobilization and storage were observed for P, K, and S with maximal whole tree perennial storage occurring during dormancy and remobilization of that stored P, K, S to support annual tree demands through to fruit set and 70-100% leaf development. Net annual increment in perennial organ P, K, S commenced 98 DAFB and continued through full leaf abscission at 249 DAFB. Organ specific contribution to remobilizable and stored nutrients changes over the growing season are presented. Details of the pattern of perennial organ nutrient allocation, storage, and remobilization provides a framework for the optimal management of nutrients in almond with relevance for other deciduous tree species.

Advancing Agricultural Production With Machine Learning Analytics: Yield Determinants for California's Almond Orchards.

Agricultural productivity is subject to various stressors, including abiotic and biotic threats, many of which are exacerbated by a changing climate, thereby affecting long-term sustainability. The productivity of tree crops such as almond orchards, is particularly complex. To understand and mitigate these threats requires a collection of multi-layer large data sets, and advanced analytics is also critical to integrate these highly heterogeneous datasets to generate insights about the key constraints on the yields at tree and field scales. Here we used a machine learning approach to investigate the determinants of almond yield variation in California's almond orchards, based on a unique 10-year dataset of field measurements of light interception and almond yield along with meteorological data. We found that overall the maximum almond yield was highly dependent on light interception, e.g., with each one percent increase in light interception resulting in an increase of 57.9 lbs/acre in the potential yield. Light interception was highest for mature sites with higher long term mean spring incoming solar radiation (SRAD), and lowest for younger orchards when March maximum temperature was lower than 19°C. However, at any given level of light interception, actual yield often falls significantly below full yield potential, driven mostly by tree age, temperature profiles in June and winter, summer mean daily maximum vapor pressure deficit (VPDmax), and SRAD. Utilizing a full random forest model, 82% (±1%) of yield variation could be explained when using a sixfold cross validation, with a RMSE of 480 ± 9 lbs/acre. When excluding light interception from the predictors, overall orchard characteristics (such as age, location, and tree density) and inclusive meteorological variables could still explain 78% of yield variation. The model analysis also showed that warmer winter conditions often limited mature orchards from reaching maximum yield potential and summer VPDmax beyond 40 hPa significantly limited the yield. Our findings through the machine learning approach improved our understanding of the complex interaction between climate, canopy light interception, and almond nut production, and demonstrated a relatively robust predictability of almond yield. This will ultimately benefit data-driven climate adaptation and orchard nutrient management approaches.

Complete Genomic Sequences of Three Salmonella enterica subsp. enterica Serovar Muenchen Strains from an Orchard in San Joaquin County, California.

We present here the complete genome sequences of three Salmonella enterica subsp. enterica serovar Muenchen strains, LG24, LG25, and LG26. All three strains were isolated from almond drupes grown in an orchard in San Joaquin County, California, in 2016. These genomic sequences are nonidentical and will contribute to our understanding of S. enterica genomics.

Intensive fertilizer use increases orchard N cycling and lowers net global warming potential.

Nitrogen (N) fertilizer use has simultaneously increased global food production and N losses, resulting in degradation of water quality and climate pollution. A better understanding of N application rates and crop and environmental response is needed to optimize management of agroecosystems. Here we show an orchard agroecosystem with high N use efficiency promoted substantial gains in carbon (C) storage, thereby lowering net global warming potential (GWP). We conducted a 5-year whole-system analysis comparing reduced (224 kg N ha-1 yr-1) and intensive (309 kg N ha-1 yr-1) fertilizer N rates in a California almond orchard. The intensive rate increased net primary productivity (Mg C ha-1) and significantly increased N productivity (kg N ha-1) and net N mineralization (mg N kg-1 soil d-1). Use of 15N tracers demonstrated short and long-term mechanisms of soil N retention. These low organic matter soils (0.3-0.5%) rapidly immobilized fertilizer nitrate within 36 h of N application and 15N in tree biomass recycled back into soil organic matter over five years. Both fertilizer rates resulted in high crop and total N recovery efficiencies of 90% and 98% for the reduced rate, and 72% and 80% for the intensive rate. However, there was no difference in the proportion of N losses to N inputs due to a significant gain in soil total N (TN) in the intensive rate. Higher soil TN significantly increased net N mineralization and a larger gain in soil organic carbon (SOC) from the intensive rate offset nitrous oxide (N2O) emissions, leading to significantly lower net GWP of -1.64 Mg CO2-eq ha-1 yr-1 compared to -1.22 Mg CO2-eq ha-1 yr-1 for the reduced rate. Our study demonstrates increased N cycling and climate mitigation from intensive fertilizer N use in this orchard agroecosystem, implying a fundamentally different result than seen in conventional annual cropping systems.

Efficient phloem remobilization of Zn protects apple trees during the early stages of Zn deficiency.

Apple trees are extensively cultivated worldwide but are often affected by zinc (Zn) deficiency. Limited knowledge regarding Zn remobilization within fruit crops has hampered the development of efficient strategies for providing adequate amounts of Zn. In the present study, Zn distribution and remobilization were compared among apple trees cultivated under different Zn conditions. Without Zn application, plants showed visible symptoms of Zn deficiency at the shoot tips after 1 year but appeared to grow normally during the first 6 months (early stage of Zn deficiency). Compared with apple plants under sufficient Zn treatment, plants suffering from early-stage Zn deficiency showed preferential Zn distribution to young leaves and higher Zn levels in phloem, demonstrating that hidden Zn deficiency triggers a highly efficient remobilization of Zn in this species. The in vivo Zn-nicotianamine complex in phloem tissues, combined with the significant enhanced expression of MdNAS3 and MdYSL6, suggested a positive role for nicotianamine in the phloem remobilization of Zn. These results strongly suggest that a proportion of Zn in the old leaves of apple trees can be efficiently remobilized by phloem transport to the shoot tips, partially in the form of Zn-nicotianamine, thus protecting apple trees against the early stages of Zn deficiency.

Measuring macromolecular size distributions and interactions at high concentrations by sedimentation velocity.

In concentrated macromolecular solutions, weak physical interactions control the solution behavior including particle size distribution, aggregation, liquid-liquid phase separation, or crystallization. This is central to many fields ranging from colloid chemistry to cell biology and pharmaceutical protein engineering. Unfortunately, it is very difficult to determine macromolecular assembly states and polydispersity at high concentrations in solution, since all motion is coupled through long-range hydrodynamic, electrostatic, steric, and other interactions, and scattering techniques report on the solution structure when average interparticle distances are comparable to macromolecular dimensions. Here we present a sedimentation velocity technique that, for the first time, can resolve macromolecular size distributions at high concentrations, by simultaneously accounting for average mutual hydrodynamic and thermodynamic interactions. It offers high resolution and sensitivity of protein solutions up to 50 mg/ml, extending studies of macromolecular solution state closer to the concentration range of therapeutic formulations, serum, or intracellular conditions.

Spatial patterns of tree yield explained by endogenous forces through a correspondence between the Ising model and ecology.

Spatial patterning of periodic dynamics is a dramatic and ubiquitous ecological phenomenon arising in systems ranging from diseases to plants to mammals. The degree to which spatial correlations in cyclic dynamics are the result of endogenous factors related to local dynamics vs. exogenous forcing has been one of the central questions in ecology for nearly a century. With the goal of obtaining a robust explanation for correlations over space and time in dynamics that would apply to many systems, we base our analysis on the Ising model of statistical physics, which provides a fundamental mechanism of spatial patterning. We show, using 5 y of data on over 6,500 trees in a pistachio orchard, that annual nut production, in different years, exhibits both large-scale synchrony and self-similar, power-law decaying correlations consistent with the Ising model near criticality. Our approach demonstrates the possibility that short-range interactions can lead to long-range correlations over space and time of cyclic dynamics even in the presence of large environmental variability. We propose that root grafting could be the common mechanism leading to positive short-range interactions that explains the ubiquity of masting, correlated seed production over space through time, by trees.

Grower Analysis of Organic Matter Amendments in California Orchards.

Organic matter amendments supply crop nutrients and enhance soil health, yet information specific to orchards is lacking. A survey was conducted to analyze use of these materials by California almond [ (Mill.) D.A. Webb] growers. Significant differences were observed for benefits, concerns, and accessibility to manure and green waste sources and between users and nonusers. Use patterns were significantly influenced by heavy and light users, farm size, and geographic region. Enhanced soil biology was the main benefit attributed to organic matter amendments by both users and nonusers. Nonusers showed greater concern for food safety compared to users, and all growers reported greater concern for food safety from manure. The greatest adoption of organic matter amendments occurred on small farms (≤170 ha) located in the north San Joaquin Valley in California. Greater accessibility to manure correlated with presence of dairy farms. Poorer accessibility ratings by nonusers suggest access is a barrier to adoption, as opposed to nonusers having an undesirable view of the practice. Common management included applying organic matter amendments during tree dormancy from manure sources in composted forms with no-till. Heavy users on small farms exhibited the greatest year-to-year consistency and were more flexible with selection of sources and diverse in application methods. Large farms (>170 ha) were less likely to use organic matter amendments every year and less likely to apply them on all their farm area. This study identifies a number of strategies to fill knowledge gaps, increase practice awareness, and overcome barriers to adoption.

Uptake, sequestration and tolerance of cadmium at cellular levels in the hyperaccumulator plant species Sedum alfredii.

Sedum alfredii is one of a few plant species known to hyperaccumulate cadmium (Cd). Uptake, localization, and tolerance of Cd at cellular levels in shoots were compared in hyperaccumulating (HE) and non-hyperaccumulating (NHE) ecotypes of Sedum alfredii. X-ray fluorescence images of Cd in stems and leaves showed only a slight Cd signal restricted within vascular bundles in the NHEs, while enhanced localization of Cd, with significant tissue- and age-dependent variations, was detected in HEs. In contrast to the vascular-enriched Cd in young stems, parenchyma cells in leaf mesophyll, stem pith and cortex tissues served as terminal storage sites for Cd sequestration in HEs. Kinetics of Cd transport into individual leaf protoplasts of the two ecotypes showed little difference in Cd accumulation. However, far more efficient storage of Cd in vacuoles was apparent in HEs. Subsequent analysis of cell viability and hydrogen peroxide levels suggested that HE protoplasts exhibited higher resistance to Cd than those of NHE protoplasts. These results suggest that efficient sequestration into vacuoles, as opposed to rapid transport into parenchyma cells, is a pivotal process in Cd accumulation and homeostasis in shoots of HE S. alfredii. This is in addition to its efficient root-to-shoot translocation of Cd.

Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations.

Recent in vivo studies have established ultrasmall (<3 nm) gold nanoparticles coated with glutathione (AuGSH) as a promising platform for applications in nanomedicine. However, systematic in vitro investigations to gain a more fundamental understanding of the particles' biointeractions are still lacking. Herein we examined the behavior of ultrasmall AuGSH in vitro, focusing on their ability to resist aggregation and adsorption from serum proteins. Despite having net negative charge, AuGSH particles were colloidally stable in biological media and able to resist binding from serum proteins, in agreement with the favorable bioresponses reported for AuGSH in vivo. However, our results revealed disparate behaviors depending on nanoparticle size: particles between 2 and 3 nm in core diameter were found to readily aggregate in biological media, whereas those strictly under 2 nm were exceptionally stable. Molecular dynamics simulations provided microscopic insight into interparticle interactions leading to aggregation and their sensitivity to the solution composition and particle size. These results have important implications, in that seemingly small variations in size can impact the biointeractions of ultrasmall AuGSH, and potentially of other ultrasmall nanoparticles as well.

Biostimulants in Plant Science: A Global Perspective.

This review presents a comprehensive and systematic study of the field of plant biostimulants and considers the fundamental and innovative principles underlying this technology. The elucidation of the biological basis of biostimulant function is a prerequisite for the development of science-based biostimulant industry and sound regulations governing these compounds. The task of defining the biological basis of biostimulants as a class of compounds, however, is made more complex by the diverse sources of biostimulants present in the market, which include bacteria, fungi, seaweeds, higher plants, animals and humate-containing raw materials, and the wide diversity of industrial processes utilized in their preparation. To distinguish biostimulants from the existing legislative product categories we propose the following definition of a biostimulant as "a formulated product of biological origin that improves plant productivity as a consequence of the novel or emergent properties of the complex of constituents, and not as a sole consequence of the presence of known essential plant nutrients, plant growth regulators, or plant protective compounds." The definition provided here is important as it emphasizes the principle that biological function can be positively modulated through application of molecules, or mixtures of molecules, for which an explicit mode of action has not been defined. Given the difficulty in determining a "mode of action" for a biostimulant, and recognizing the need for the market in biostimulants to attain legitimacy, we suggest that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for the determination of a specific mode of action. While there is a clear commercial imperative to rationalize biostimulants as a discrete class of products, there is also a compelling biological case for the science-based development of, and experimentation with biostimulants in the expectation that this may lead to the identification of novel biological molecules and phenomenon, pathways and processes, that would not have been discovered if the category of biostimulants did not exist, or was not considered legitimate.