A growing body of research points to a positive interplay between viruses and plants. Tomato yellow curl virus (TYLCV) is able to protect tomato host plants against extreme drought. To envisage the use of virus protective capacity in agriculture, TYLCV-resistant tomato lines have to be infected first with the virus before planting. Such virus-resistant tomato plants contain virus amounts that do not cause disease symptoms, growth inhibition, or yield loss, but are sufficient to modify the metabolism of the plant, resulting in improved tolerance to drought. This phenomenon is based on the TYLCV-dependent stabilization of amounts of key osmoprotectants induced by drought (soluble sugars, amino acids, and proteins). Although in infected TYLCV-susceptible tomatoes, stress markers also show an enhanced stability, in infected TYLCV-resistant plants, water balance and osmolyte homeostasis reach particularly high levels. These tomato plants survive long periods of time during water withholding. However, after recovery to normal irrigation, they produce fruits which are not exposed to drought, similarly to the control plants. Using these features, it might be possible to cultivate TYLCV-resistant plants during seasons characterized by water scarcity.

Abstract Ecological theory predicts that the soil seed bank stabilizes the composition of annual plant communities in the face of environmental variability. However, long-term data on the community dynamics in the seed bank and the standing vegetation are needed to test this prediction. We tested the hypothesis that the composition of the seed bank undergoes lower temporal variability than the standing vegetation in a 9-year study in Mediterranean, semi-arid and arid ecosystems. The composition of the seed bank was estimated by collecting soil cores from the studied sites on an annual basis. Seedling emergence under optimal watering conditions was measured in each soil core for three consecutive years, to account for seed dormancy. In all sites, the composition of the seed bank differed from the vegetation throughout the years. Small-seeded and dormant-seeded species had a higher frequency in the seed bank than in the standing vegetation. In contrast, functional group membership (grasses vs. forbs) did not explain differences in species frequency between the seed bank and the vegetation after controlling for differences between grasses and forbs in seed mass and seed dormancy. Contrary to predictions, the magnitude of year-to-year variability (the mean compositional dissimilarity between consecutive years) was not lower in the seed bank than in the vegetation in all sites. However, long-term compositional trends in the seed bank were weaker than in the vegetation in the Mediterranean and semi-arid sites. In the arid site where year-to-year variability was highest, no long-term trends were observed. Synthesis. The effect of the seed bank on the temporal variability of the vegetation in annual communities depends on site conditions and time-scale. While the year-to-year variability of the seed bank is similar to the vegetation, the soil seed bank can buffer long-term trends.

AbstractLife-history trade-offs among species are major drivers of community assembly. Most studies investigate how trade-offs promote deterministic coexistence of species. It remains unclear how trade-offs may instead promote historically contingent exclusion of species, where species dominance is affected by initial abundances, causing alternative community states via priority effects. Focusing on the establishment-longevity trade-off, in which high longevity is associated with low competitive ability during establishment, we study the transient dynamics and equilibrium outcomes of competitive interactions in a simulation model of plant community assembly. We show that in this model, the establishment-longevity trade-off is a necessary but not sufficient condition for alternative stable equilibria, which also require low fecundity for both species. An analytical approximation of our simulation model demonstrates that alternative stable equilibria are driven by demographic stochasticity in the number of seeds arriving at each establishment site. This site-scale stochasticity is affected only by fecundity and therefore occurs even in infinitely large communities. In many cases where the establishment-longevity trade-off does not cause alternative stable equilibria, the trade-off still decreases the rate of convergence toward the single equilibrium, resulting in decades of transient dynamics that can appear indistinguishable from alternative stable equilibria in empirical studies.

ABSTRACT Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different selection types on trait distribution, but the effects of selection on species diversity have remained unclear. Here, we propose a framework for inferring the type and strength of selection by studying species diversity and trait distribution together against null expectations. We use a simulation model to confirm our prediction that directional selection should lead to lower species diversity than stabilizing selection despite a similar effect on trait community-weighted variance. We apply the framework to a mesocosm system of annual plants to test whether differences in species diversity between two habitats that vary in productivity are related to differences in selection on seed mass. We show that, in both habitats, species diversity was lower than the null expectation, but that species diversity was lower in the more productive habitat. We attribute this difference to strong directional selection for large-seeded species in the productive habitat as indicated by trait community-weighted-mean being higher and community-weighted variance being lower than the null expectations. In the less productive habitat, we found that community-weighted variance was higher than expected by chance, suggesting that seed mass could be a driver of niche partitioning under such conditions. Altogether, our results suggest that viewing species diversity and trait distribution as interrelated patterns driven by the same process, ecological selection, is helpful in understanding community assembly.

Abstract Lateral ligament tears, also known as high-grade ankle sprains, are common, debilitating, and usually heal slowly. Ten to thirty percent of patients continue to suffer from chronic pain and ankle instability even after 3 to 9 months. Previously, we showed that the recombinant human amelogenin (rHAM+) induced regeneration of fully transected rat medial collateral ligament, a common proof-of-concept model. Our aim was to evaluate whether rHAM+ can regenerate torn ankle calcaneofibular ligament (CFL), an important component of the lateral ankle stabilizers. Right CFLs of Sabra rats were transected and treated with 0, 0.5, or 1?µg/µL rHAM+ dissolved in propylene glycol alginate (PGA). Results were compared with the normal group, without surgery. Healing was evaluated 12 weeks after treatment by mechanical testing (ratio between the right and left, untransected ligaments of the same rat), and histology including immunohistochemical staining of collagen I and S100. The mechanical properties, structure, and composition of transected ligaments treated with 0.5??g/?L rHAM+ (experimental) were similar to untransected ligaments. PGA (control) treated ligaments were much weaker, lax, and unorganized compared with untransected ligaments. Treatment with 1??g/?L rHAM+ was not as efficient as 0.5??g/?L rHAM+. Normal arrangement of collagen I fibers and of proprioceptive nerve endings, parallel to the direction of the force, was detected in ligaments treated with 0.5??g/?L rHAM+, and scattered arrangement, resembling scar tissue, in control ligaments. In conclusion, we showed that rHAM+ induced significant mechanical and structural regeneration of torn rat CFLs, which might be translated into treatment for grades 2 and 3 ankle sprain injuries.

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

Inappropriate use of antibiotics is one of the leading causes of the increasing numbers of resistant bacteria strains, resulting in 700,000 deaths worldwide each year. Reducing unnecessary use of antibiotics and choosing the most effective antibiotics instead of broad-spectrum drugs will slow the arms race between germs and humans. Urinary tract infections (UTIs) are among the most common bacterial infections. Currently, accurate diagnosis of UTI requires approximately 48 h from the time of urine sample collection until antibiotic susceptibility test (AST) results. This work presents a rapid bacterial detection device that integrates a centrifuge, microscope, and incubator. Two disposable microfluidic chips were developed. The first chip was designed for bacteria concentration, detection, and medium exchange. A second multi-channel chip was developed for AST. This chip contains superhydrophobic and hydrophilic coatings to ensure liquid separation between the channels without the need for valves. The designed chips supported the detection of E. coli at a concentration as low as 5 × 103 cells/mL within 5 min and AST in under 2 h. AST was also successfully performed with Klebsiella pneumonia isolated from a human urine sample. In addition, machine-learning-based image recognition was shown to reduce the required time for AST and to provide results within 1 h for E. coli cells. Thus, the BactoSpin device can serve as an efficient and rapid platform for UTI diagnostics and AST.

Wild oat (Avena sterilis) is a very common annual plant species. Successful seed dispersion support its wide distribution in Africa, Asia and Europe. The seed dispersal units are made of two elongated stiff awns that are attached to a pointy compartment containing two seeds. The awns bend and twist with changes in humidity, pushing the seeds along and into the soil. The present work reveals the material structure of the awns, and models their functionality as two-link robotic arms. Based on nano-to-micro structure analyses the bending and twisting hygroscopic movements are explained. The coordinated movements of two sister awns attached to one dispersal unit were followed. Our work shows that sister awns intersect typically twice every wetting-drying cycle. Once the awns cross each other, epidermal silica hairs are suggested to lock subsequent movements, resulting in stress accumulation. Sudden release of the interlocked awns induces jumps of the dispersal unit and changes in its movement direction. Our findings propose a new role to epidermis silica hairs and a new facet of wild oat seed dispersion. Reversible jumping mechanism in multiple-awn seed dispersal units may serve as a blueprint for reversibly jumping robotic systems.Statement of significance The seed dispersal unit of wild oats carries two elongated stiff awns covered by unidirectional silica hairs. The awns bend and twist with changes in humidity, pushing the seed capsule along and into the ground. We studied structures constructing the movement mechanism and modeled the awn as a two-link robotic arm. We show that sister awns, attached to the same seed capsule, intersect twice every drying cycle. Once the awns cross each other, the epidermal silica hairs are suggested to lock any subsequent movements, causing stress accumulation. Sudden release of the interlocked awns may cause the dispersal unit to jump and change its direction. Our findings suggest a new role to silica hairs and a new dispersal mechanism in multiple-awn seed dispersal units.

Abscisic acid (ABA) is a phytohormone that plants utilize to coordinate responses to abiotic stress, modulate seed dormancy, and is central to plant development in several contexts. Chemicals that activate or block ABA signaling are useful as research tools and as potential agrochemical leads. Many successes have been reported for ABA activators (agonists), but existing ABA blockers (antagonists) are limited by modest in vivo activity. Here we report antabactin (ANT), a potent ABA blocker developed using “click chemistry”–based diversification of a known ABA activator. Structural studies reveal, ANT disrupts signaling by stabilizing ABA receptors in an unproductive form. ANT can accelerate seed germination in multiple species, making it a chemical tool for improving germination.Abscisic acid (ABA) is a key plant hormone that mediates both plant biotic and abiotic stress responses and many other developmental processes. ABA receptor antagonists are useful for dissecting and manipulating ABA’s physiological roles in vivo. We set out to design antagonists that block receptor–PP2C interactions by modifying the agonist opabactin (OP), a synthetically accessible, high-affinity scaffold. Click chemistry was used to create an ∼4,000-member library of C4-diversified opabactin derivatives that were screened for receptor antagonism in vitro. This revealed a peptidotriazole motif shared among hits, which we optimized to yield antabactin (ANT), a pan-receptor antagonist. An X-ray crystal structure of an ANT–PYL10 complex (1.86 Å) reveals that ANT’s peptidotriazole headgroup is positioned to sterically block receptor–PP2C interactions in the 4′ tunnel and stabilizes a noncanonical closed-gate receptor conformer that partially opens to accommodate ANT binding. To facilitate binding-affinity studies using fluorescence polarization, we synthesized TAMRA–ANT. Equilibrium dissociation constants for TAMRA–ANT binding to Arabidopsis receptors range from ∼400 to 1,700 pM. ANT displays improved activity in vivo and disrupts ABA-mediated processes in multiple species. ANT is able to accelerate seed germination in Arabidopsis, tomato, and barley, suggesting that it could be useful as a germination stimulant in species where endogenous ABA signaling limits seed germination. Thus, click-based diversification of a synthetic agonist scaffold allowed us to rapidly develop a high-affinity probe of ABA–receptor function for dissecting and manipulating ABA signaling.The atomic coordinates and structure factors reported in this article have been deposited in the Protein Data Bank, https://www.wwpdb.org/ [PDB ID codes 7MLC (45) and 7MLD (46)].

Summary Plants reduce transpiration to avoid dehydration during drought episodes by stomatal closure and inhibition of canopy growth. Previous studies have suggested that low gibberellin (GA) activity promotes these ?drought avoidance? responses. Using genome editing, molecular, physiological and hormone analyses, we examined if drought regulates GA metabolism in tomato (Solanum lycopersicum) guard cells and leaves, and studied how this affects water loss. Water deficiency inhibited the expression of the GA biosynthesis genes GA20 oxidase1 (GA20ox1) and GA20ox2 and induced the GA deactivating gene GA2ox7 in guard cells and leaf tissue, resulting in reduced levels of bioactive GAs. These effects were mediated by abscisic acid-dependent and abscisic acid-independent pathways, and by the transcription factor TINY1. The loss of GA2ox7 attenuated stomatal response to water deficiency and during soil dehydration, ga2ox7 plants closed their stomata later, and wilted faster than wild-type (WT) M82 cv. Mutations in GA20ox1 and GA20ox2, had no effect on stomatal closure, but reduced water loss due to the mutants? smaller canopy areas. The results suggested that drought-induced GA deactivation in guard cells, contributes to stomatal closure at the early stages of soil dehydration, whereas inhibition of GA synthesis in leaves suppresses canopy growth and restricts transpiration area.

Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Silicon (Si) is widely accepted as a beneficial element for plants. Despite the substantial progress made in understanding Si transport mechanisms and modes of action in plants, several questions remain unanswered. In this review, we discuss such outstanding questions and issues commonly encountered by biologists studying the role of Si in plants in relation to Si bioavailability. In recent years, advances in our understanding of the role of Si-solubilizing bacteria and the efficacy of Si-nanoparticles have been made. However, there are many unknown aspects associated with structural and functional features of Si transporters, Si loading into the xylem, and the role of specialized cells like silica cells and compounds preventing Si polymerization in plant tissues. In addition, despite several thousand reports showing the positive effects of Si in high as well as low Si-accumulating plant species, the exact roles of Si at the molecular level are yet to be understood. Some evidence suggests that Si regulates hormonal pathways and nutrient uptake, thereby explaining various observed benefits of Si uptake. However, how Si modulates hormonal pathways or improves nutrient uptake remains to be explained. Finally, we summarize the knowledge gaps that will provide a roadmap for further research on plant silicon biology, leading to an exploration of the benefits of Si uptake to enhance crop production.

SUMMARY The leaf vascular bundle sheath cells (BSCs) that tightly envelop the leaf veins, are a selective and dynamic barrier to xylem sap water and solutes radially entering the mesophyll cells. Under normal conditions, xylem sap pH below 6 is presumably important for driving and regulating the transmembranal solute transport. Having discovered recently a differentially high expression of a BSC proton pump, AHA2, we now test the hypothesis that it regulates the xylem sap pH and leaf radial water fluxes. We monitored the xylem sap pH in the veins of detached leaves of wild-type Arabidopsis, AHA mutants and aha2 mutants complemented with AHA2 gene solely in BSCs. We tested an AHA inhibitor (vanadate) and stimulator (fusicoccin), and different pH buffers. We monitored their impact on the xylem sap pH and the leaf hydraulic conductance (Kleaf), and the effect of pH on the water osmotic permeability (Pf) of isolated BSCs protoplasts. We found that AHA2 is necessary for xylem sap acidification, and in turn, for elevating Kleaf. Conversely, AHA2 knockdown, which alkalinized the xylem sap, or, buffering its pH to 7.5, reduced Kleaf, and elevating external pH to 7.5 decreased the BSCs Pf. All these showed a causative link between AHA2 activity in BSCs and leaf radial hydraulic water conductance.

Shoot branching is an important aspect of plant architecture because it substantially affects plant biology and agricultural performance. Sugars play an important role in the induction of shoot branching in several species, including potato (Solanum tuberosum L.). However, the mechanism by which sugars affect shoot branching remains mostly unknown. In the present study, we addressed this question using sugar-mediated induction of bud outgrowth in potato stems under etiolated conditions. Our results indicate that sucrose feeding to detached stems promotes the accumulation of cytokinin (CK), as well as the expression of vacuolar invertase (VInv), an enzyme that contributes to sugar sink strength. These effects of sucrose were suppressed by CK synthesis and perception inhibitors, while CK supplied to detached stems induced bud outgrowth and VInv activity in the absence of sucrose. CK-induced bud outgrowth was suppressed in vinv mutants, which we generated by genome editing. Altogether, our results identify a branching-promoting module, and suggest that sugar-induced lateral bud outgrowth is in part promoted by the induction of CK-mediated VInv activity.

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.

Plant organs initiate as a group of tiny meristematic cells. After expansion, three basic shapes of organs may be defined: cylindrical, laminar, and spherical (Trinh et al., 2021). The development of a lamina can be followed by various surface and subsurface microscopy methods. However, organs shaped as opaque spheres are most conveniently studied in sections.Antreich et al. (2021) applied 3D reconstructions based on optical and scanning electron microscopy to study the development of cells building the walnut shell. Restricted by cellulose, the growing cells bulge and interdigitate with neighboring cells, leaving gaps at the regions of high curvature. Examining the cell interfaces with Raman microspectroscopy, they show that these gaps are lined with pectin.

The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing for novel functions that are not commonly documented in the organism in its natural environment. Here, the basic concept of genetic code and associated mechanisms for the generation of genetic codon variants, including biased codon usage, codon reassignment, and ambiguous decoding, are extensively discussed. Knowledge of the concept of natural genetic code expansion is also detailed. The generation of recoded organisms and associated mechanisms with basic targeting components, including aminoacyl-tRNA synthetase–tRNA pairs, elongation factor EF-Tu and ribosomes, are highlighted for a comprehensive understanding of this concept. The research associated with the generation of diverse recoded organisms is also discussed. The success of genome recoding in diverse multicellular organisms offers a platform for expanding protein chemistry at the biochemical level with non-canonical amino acids, genetically isolating the synthetic organisms from the natural ones, and fighting viruses, including SARS-CoV2, through the creation of attenuated viruses. In conclusion, genome recoding can offer diverse applications for improving cellular properties in the genome-recoded organisms.

Summary The recent years have witnessed the emergence of high-throughput phenotyping techniques. In particular, these techniques can characterize a comprehensive landscape of physiological traits of plants responding to dynamic changes in the environment. These innovations, along with the next-generation genomic technologies, have brought plant science into the big-data era. However, a general framework that links multifaceted physiological traits to DNA variants is still lacking. Here, we developed a general framework that integrates functional physiological phenotyping (FPP) with functional mapping (FM). This integration, implemented with high-dimensional statistical reasoning, can aid in our understanding of how genotype is translated toward phenotype. As a demonstration of method, we implemented the transpiration and soil-plant-atmosphere measurements of a tomato introgression line population into the FPP-FM framework, facilitating the identification of quantitative trait loci (QTLs) that mediate the spatiotemporal change of transpiration rate and the test of how these QTLs control, through their interaction networks, phenotypic plasticity under drought stress.

Summary Root meristem organization is maintained by an interplay between hormone signaling pathways that both interpret and determine their accumulation and distribution. The interacting hormones Brassinosteroids (BR) and auxin control the number of meristematic cells in the Arabidopsis root. BR was reported both to promote auxin signaling input and to repress auxin signaling output. Whether these contradicting molecular outcomes co-occur and what their significance in meristem function is remain unclear. Here, we established a dual effect of BR on auxin, with BR simultaneously promoting auxin biosynthesis and repressing auxin transcriptional output, which is essential for meristem maintenance. Blocking BR-induced auxin synthesis resulted in rapid BR-mediated meristem loss. Conversely, plants with reduced BR levels were resistant to a critical loss of auxin biosynthesis, maintaining their meristem morphology. In agreement, injured root meristems, which rely solely on local auxin synthesis, regenerated when both auxin and BR synthesis were inhibited. Use of BIN2 as a tool to selectively inhibit BR signaling yielded meristems with distinct phenotypes depending on the perturbed tissue: meristem reminiscent either of BR-deficient mutants or of high BR exposure. This enabled mapping of the BR-auxin interaction that maintains the meristem to the outer epidermis and lateral root cap tissues and demonstrated the essentiality of BR signaling in these tissues for meristem response to BR. BR activity in internal tissues however, proved necessary to control BR levels. Together, we demonstrate a basis for inter-tissue coordination and how a critical ratio between these hormones determines the meristematic state.

The overarching aim of this research was to develop a method for deriving crop maps from a time series of Sentinel-2 images between 2017 and 2018 to address global challenges in agriculture and food security. This study is the first step towards improving crop mapping based on phenological features retrieved from an object-based time series on a national scale. Five main crops in Israel were classified: wheat, barley, cotton, carrot, and chickpea. To optimize the object-based classification process, different characteristics and inputs of the mean shift segmentation algorithm were tested, including vegetation indices, three-band combinations, and high/low emphasis on the spatial and spectral characteristics. Four known vegetation indices (VIs)-based time series were tested. Additionally, we compared two widely used machine learning methods for crop classification, support vector machine (SVM) and random forest (RF), in addition to a newer classifier, extreme gradient boosting (XGBoost). Lastly, we examined two accuracy measures—overall accuracy (OA) and area under the curve (AUC)—in order to optimally estimate the accuracy in the case of imbalanced class representation. Mean shift best performed when emphasizing both the spectral and spatial characteristics while using the green, red, and near-infrared (NIR) bands as input. Both accuracy measures showed that RF and XGBoost classified different types of crops with significantly greater success than achieved by SVM. Nevertheless, AUC was better able to represent the significant differences between the classification algorithms than OA was. None of the VIs showed a significantly higher contribution to the classification. However, normalized difference infrared index (NDII) with XGBoost classifier showed the highest AUC results (88%). This study demonstrates that the short-wave infrared (SWIR) band with XGBoost improves crop type classification results. Furthermore, the study emphasizes the importance of addressing imbalanced classification datasets by using a proper accuracy measure. Since object-based classification and phenological features derived from a VI-based time series are widely used to produce crop maps, the current study is also relevant for operational agricultural management and informatics at large scales.