Diverse Plant Research Articles

Fine-tuning plant valuable secondary metabolite biosynthesis via small RNA manipulation: strategies and potential.

Plants produce secondary metabolites that serve various functions, including defense against biotic and abiotic stimuli. Many of these secondary metabolites possess valuable applications in diverse fields, including medicine, cosmetic, agriculture, and food and beverage industries, exhibiting their importance in both plant biology and various human needs. Small RNAs (sRNA), such as microRNA (miRNA) and small interfering RNA (siRNA), have been shown to play significant roles in regulating the metabolic pathways post-transcriptionally by targeting specific key genes and transcription factors, thus offering a promising tool for enhancing plant secondary metabolite biosynthesis. In this review, we summarize current approaches for manipulating sRNAs to regulate secondary metabolite biosynthesis in plants. We provide an overview of the latest research strategies for sRNA manipulation across diverse plant species, including the identification of potential sRNAs involved in secondary metabolite biosynthesis in non-model plants. We also highlight the potential future research directions, focusing on the manipulation of sRNAs to produce high-value compounds with applications in pharmaceuticals, nutraceuticals, agriculture, cosmetics, and other industries. By exploring these advanced techniques, we aim to unlock new potentials for biotechnological applications, contributing to the production of high-value plant-derived products.

Molecular Dialogue During Host Manipulation by the Vascular Wilt Fungus Fusarium oxysporum.

Vascular wilt fungi are a group of hemibiotrophic phytopathogens that infect diverse crop plants. These pathogens have adapted to thrive in the nutrient-deprived niche of the plant xylem. Identification and functional characterization of effectors and their role in the establishment of compatibility across multiple hosts, suppression of plant defense, host reprogramming, and interaction with surrounding microbes have been studied mainly in model vascular wilt pathogens Fusarium oxysporum and Verticillium dahliae. Comparative analysis of genomes from fungal isolates has accelerated our understanding of genome compartmentalization and its role in effector evolution. Also, advances in recent years have shed light on the cross talk of root-infecting fungi across multiple scales from the cellular to the ecosystem level, covering their interaction with the plant microbiome as well as their interkingdom signaling. This review elaborates on our current understanding of the cross talk between vascular wilt fungi and the host plant, which eventually leads to a specialized lifestyle in the xylem. We particularly focus on recent findings in F. oxysporum, including multihost associations, and how they have contributed to understanding the biology of fungal adaptation to the xylem. In addition, we discuss emerging research areas and highlight open questions and future challenges.

Intercropping Alters Phytochemical Defenses Against Insect Herbivory.

Given the multiple possible mechanisms for interspecific chemical interaction between adjacent heterospecific plants, phytochemical defenses of pest-susceptible crop species could potentially be enhanced or altered by intercropping with phytochemically diverse neighbors. We assessed the influence of intercropping between phytochemically diverse plants on aerial volatile organic compound (VOC) emission profiles by intercropping Melilotus alba and Triticum aestivum with Silphium integrifolium in AMF-inoculated soil. We also assessed the impact of intercropping on induced plant defenses by conducting an in-situ, no-choice bioassay with Spodoptera frugiperda. Of eight compound classes we identified across the three plant species, prenol lipids (terpenoids) were upregulated in silflower plants when monocropped with wheat and when herbivory was induced. Carboxylic acids and organooxygen compounds were reduced in sweetclover when intercropped with silflower, but increased under herbivory. Uninfested wheat plants emitted more organooxygen compounds and fatty acyls than infested plants when intercropped with silflower, but not when monocropped. This study showed that VOC emissions of plants from three diverse taxa are altered by both intercropping and herbivory in ways that may impact their resistance to insect herbivory. Further research into the role of intercropping on pest resistance in agroecological systems could help farmers to design intercropping systems that optimize natural plant herbivory defenses, thus improving agricultural sustainability.

In vitro and ex vivo metabolism of chemically diverse fructans by bovine rumen Bifidobacterium and Lactobacillus species

BackgroundInulin and inulin-derived fructooligosaccharides (FOS) are well-known prebiotics for use in companion animals and livestock. The mechanisms by which FOS contribute to health has not been fully established. Further, the fine chemistry of fructan structures from diverse sources, such as graminan-type fructans found in cereal crops, has not been fully elucidated. New methods to study fructan structure and microbial responses to these complex carbohydrates will be key for evaluating the prebiotic potency of cereal fructans found in cattle feeds. As the rumen microbiome composition is closely associated with their metabolic traits, such as feed utilization and waste production, prebiotics and probiotics represent promising additives to shift the microbial community toward a more productive state.ResultsWithin this study, inulin, levan, and graminan-type fructans from winter wheat, spring wheat, and barley were used to assess the capacity of rumen-derived Bifidobacterium boum, Bifidobacterium merycicum, and Lactobacillus vitulinus to metabolize diverse fructans. Graminan-type fructans were purified and structurally characterized from the stems and kernels of each plant. All three bacterial species grew on FOS, inulin, and cereal crop fructans in pure cultures. L. vitulinus was the only species that could metabolize levan, albeit its growth was delayed. Fluorescently labelled polysaccharides (FLAPS) were used to demonstrate interactions with Gram-positive bacteria and confirm fructan metabolism at the single-cell level; these results were in agreement with the individual growth profiles of each species. The prebiotic potential of inulin was further investigated within naïve rumen microbial communities, where increased relative abundance of Bifidobacterium and Lactobacillus species occurred in a dose-dependent and temporal-related manner. This was supported by in situ analysis of rumen microbiota from cattle fed inulin. FLAPS probe derived from inulin and fluorescent in situ hybridization using taxon-specific probes confirmed that inulin interacts with Bifidobacteria and Lactobacilli at the single-cell level.ConclusionThis research revealed that rumen-derived Bifidobacteria and Lactobacilli vary in their metabolism of structurally diverse fructans, and that inulin has limited prebiotic potential in the rumen. This knowledge establishes new methods for evaluating the prebiotic potential of fructans from diverse plant sources as prebiotic candidates for use in ruminants and other animals.

A hybrid biosynthetic-catabolic pathway for norspermidine production.

The only known pathway for biosynthesis of the polyamine norspermidine starts from aspartate β-semialdehyde to form the diamine 1,3-diaminopropane, which is then converted to norspermidine via a carboxynorspermidine intermediate. This pathway is found primarily in the Vibrionales order of the γ-Proteobacteria. However, norspermidine is also found in other species of bacteria and archaea, and in diverse single-celled eukaryotes, chlorophyte algae and plants that do not encode the known norspermidine biosynthetic pathway. We reasoned that products of polyamine catabolism could be an alternative route to norspermidine production. 1,3-diaminopropane is formed from terminal catabolism of spermine and spermidine, and norspermidine can be formed from catabolism of thermospermine. We found that the single-celled chlorophyte alga Chlamydomonas reinhardtii thermospermine synthase (CrACL5) did not aminopropylate exogenously-derived 1,3-diaminopropane efficiently when expressed in Escherichia coli. In contrast, it completely converted all E. coli native spermidine to thermospermine. Co-expression in E. coli of the polyamine oxidase 5 from lycophyte plant Selaginella lepidophylla (SelPAO5), together with the CrACL5 thermospermine synthase, converted almost all thermospermine to norspermidine. Although CrACL5 was efficient at aminopropylating norspermidine to form tetraamine norspermine, SelPAO5 oxidizes norspermine back to norspermidine, with the balance of flux being inclined fully to norspermine oxidation. The steady-state polyamine content of E. coli co-expressing thermospermine synthase CrACL5 and polyamine oxidase SelPAO5 was an almost total replacement of spermidine by norspermidine. We have recapitulated a potential hybrid biosynthetic-catabolic pathway for norspermidine production in E. coli, which could explain norspermidine accumulation in species that do not encode the known aspartate β-semialdehyde-dependent pathway.

Legacy effects of Phragmites australis and herbicide treatments can reduce survival but do not prevent native plant establishment

Introduced Phragmites australis represents a widespread threat to North American wetlands. Management agencies invest millions of dollars annually to manage the species, mostly by applying herbicides, to mitigate and prevent negative impacts. The often temporary reduction of P. australis rarely increases native diversity, and long‐term legacy effects of P. australis and repeat herbicide treatments are unknown. We used a coordinated management program targeting mostly small P. australis populations in the Adirondack Park in New York State, United States, to assess the potential for such legacy effects. We planted individuals of three native species as sentinels into treated and untreated, uninvaded reference wetlands after unassisted succession had occurred in treatment areas. Sentinel plants survived and grew in treated areas, suggesting legacy of P. australis and its management did not permanently limit establishment of native plants. However, responses were variable among sentinel species, with negative or neutral impacts on survival rates and neutral or positive effects on growth. Species‐specific responses and large variation in survival rates between sites and sentinels indicate that site factors are a dominant influence on survival and growth. Importantly, as treatment frequency increased, survival of one sentinel species decreased significantly, indicating a potential for long‐term negative impacts of repeated herbicide applications. Additional replanting after P. australis treatment and initial unassisted plant succession may enable more diverse plant communities to return, including species not able to recruit from local seed banks or seed sources. However, it remains unclear if active transplanting will enable more long‐term suppression of P. australis.

Native Plant Diversity Generates Microbial Legacies That Either Promote or Suppress Non-Natives, Depending on Drought History.

Diverse native plant communities resist non-native plants more than species-poor communities, in part through resource competition. The role of soil biota in diversity-invasibility relationships is poorly understood, although non-native plants interact with soil biota during invasions. We tested the responses of non-native plants to soil biota generated by different native plant diversities. We applied well-watered and drought treatments in both conditioning and response phases to explore the effects of 'historical' and 'contemporary' environmental stresses. When generated in well-watered soils, the microbial legacies from higher native diversity inhibited non-native growth in well-watered conditions. In contrast, when generated in drought-treated soils, the microbial legacies from higher native diversity facilitated non-native growth in well-watered conditions. Contemporary drought eliminated microbial legacy effects on non-native growth. We provide a new understanding of mechanisms behind diversity-invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota and non-native plants.

Antimicrobial peptides derived from food byproducts: Sources, production, purification, applications, and challenges.

Food wastes can be a valuable reservoir of bioactive substances that can serve as natural preservatives in foods or as functional ingredients with potential health benefits. The antimicrobial properties of protein hydrolysates, especially antimicrobial peptides (AMPs) derived from food byproducts (FBs), have been extensively explored. These protein fragments are defined by their short length, low molecular weight, substantial content of hydrophobic and basic amino acids, and positive net charge. The intricate mechanisms by which these peptides exert their antimicrobial effects on microorganisms and pathogens have been elaborately described. This review also focuses on techniques for producing and purifying AMPs from diverse FBs, including seafood, livestock, poultry, plants, and dairy wastes. According to investigations, incorporating AMPs as additives and alternatives to chemical preservatives in food formulations and packaging materials has been pursued to enhance both consumer health and the shelf life of foods and their products. However, challenges associated with the utilization of AMPs derived from food waste depend on their interaction with the food matrix, acceptability, and commercial viability. Overall, AMPs can serve as alternative safe additives, thereby ensuring the safety and prolonging the storage duration of food products based on specific regulatory approvals as recommended by the respective safety authorities.

Competition for nutrient niches within the apple blossom microbiota antagonizes the initiation of fire blight infection.

Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression. To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full-bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings. Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression. The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression.

An unmanned ground vehicle phenotyping-based method to generate three-dimensional multispectral point clouds for deciphering spatial heterogeneity in plant traits

Fusing three-dimensional (3D) and multispectral (MS) imaging data holds promise for high-throughput and comprehensive plant phenotyping to decipher genome-to-phenome knowledge. Acquiring high-quality 3D MS point clouds (3DMPCs) of plants remains challenging because of poor 3D data quality and limited radiometric calibration methods for plants with a complex canopy structure. Here, we present a novel 3D spatial–spectral data fusion approach to collect high-quality 3DMPCs of plants by integrating the next-best-view planning for adaptive data acquisition and neural reference field (NeREF) for radiometric calibration. This approach was used to acquire 3DMPCs of perilla, tomato, and rapeseed plants with diverse plant architecture and leaf morphological features evaluated by the accuracy of chlorophyll content and equivalent water thickness (EWT) estimation. The results showed that the completeness of plant point clouds collected by this approach was improved by an average of 23.6% compared with the fixed viewpoints alone. The NeREF-based radiometric calibration with the hemispherical reference outperformed the conventional calibration method by reducing the root mean square error (RMSE) of 58.93% for extracted reflectance spectra. The RMSE for chlorophyll content and EWT predictions decreased by 21.25% and 14.13% using partial least squares regression with the generated 3DMPCs. Collectively, our study provides an effective and efficient way to collect high-quality 3DMPCs of plants under natural light conditions, which improves the accuracy and comprehensiveness of phenotyping plant morphological and physiological traits, and thus will facilitate plant biology and genetic studies as well as crop breeding.

Dynamic responses of chlorophyll fluorescence parameters to drought across diverse plant families.

Chlorophyll fluorescence measurement is a quick and efficient tool for plant stress-level detection. The use of Pulse amplitude modulation (PAM), allows the detection of the plant stress level under field conditions. Over the years, several parameters estimating different parts of the chlorophyll and photosystem response were developed to describe the plant stress level. Despite all fluorescence parameters being based on the same measurements, their relationship remains unclear, and their response to drought stress is significantly influenced by the incoming light intensity. In this study, we use six different annual plants from different families, both C3 and C4 photosynthesis types, to describe the plant response to drought through the fluorescence parameters response (NPQ, Y(NPQ), and qN). To describe the dynamic response to drought, we employed light-response curves, adapting and fitting an equation for each curve to compare the drought response for each fluorescence parameter. The results demonstrated that the non-photochemical quenching (NPQ) and the quantum yield of non-photochemical quenching [Y(NPQ)] maximal values decrease when the PSII functionality (Fv/Fm) is lower than ~0.7. The basal fluorescence level ( and remained unaffected by the stress level and stayed stable across the various plants and stress levels. Our results indicate that the response of different stress parameters follows a distinct order under continuous drought. Consequently, monitoring just one parameter during long-term stress assessments may result in biased analysis outcomes. Incorporating multiple chlorophyll fluorescence parameters offers a more accurate reflection of the plant's stress level.

Performance of plant growth regulators in soybean cultivation under differente aplication methods

The utilization of biostimulants has emerged as a promising approach in agriculture, aiming to augment the physiological processes associated with germination and growth across diverse plant species, thereby leading to substantial and sustainable enhancements in agricultural productivity. Grounded in scientific insights, this study endeavored to juxtapose the efficacy of a biostimulant compound against conventional market-available products. The application methodologies encompassed seed treatment and foliar spraying at the V2 growth stage, with a primary focus on productivity augmentation. The investigation transpired at the Agricultural Technological Center of Paraguay (CETAPAR) in Colônia Iguazu, Paraguay, utilizing a randomized complete block design (RCBD) featuring 16 treatments replicated four times. Dosages were administered in adherence to label recommendations. Productivity data underwent rigorous statistical analyses, including the F-test and Dunnett's test, with a significance level set at 10%. Remarkably, foliar applications at the V2 phenological stage and seed treatments outperformed other modalities, yielding notable outputs of 4,431 kg.ha-1 and 4,419 kg.ha-1, respectively. Noteworthy is the observation that the tested biostimulant formulation exhibited equivalent or superior potential when juxtaposed with commercial counterparts. The findings underscore the viability of integrating biostimulants as a compelling strategy to optimize agricultural productivity, thereby furnishing farmers with an efficacious and sustainable alternative.

Biosintesis Nanopartikel ZnO dengan Ekstrak Temu Kunci (Boesenbergia rotunda) Dibantu Gelombang Mikro, Serta Pengujian Aktivitasnya Terhadap Bakteri

Numerous ZnO nanoparticles have been successfully synthesized using diverse plant extracts, yet research utilizing B. rotunda extract as a capping agent with microwave assistance has been lacking. Hence, this study aimed to employ microwave-assisted B. rotunda extract to produce ZnO nanoparticles and test their antibacterial activity. By utilizing 10 mL of 1% (m/v) B. rotunda extract at pH 12.5 and calcinating for 3.8 hours at 200°C, coupled with 20 minutes of microwave treatment, ZnO nanoparticles averaging 78.78 nm in diameter were synthesized. Particle size was determined using the ImageJ software to analyze TEM images. UV-Vis absorption spectroscopy indicated a peak wavelength at 360 nm, while FTIR analysis identified compounds from B. rotunda extract crucial in nanoparticle formation. Antibacterial testing revealed the nanoparticles' ability to create an inhibition zone against E. coli growth.

Unlocking the techno-economic potential of biomass gasification for power generation: Comparative analysis across diverse plant capacities

This research aims to evaluate the techno-economic viability and commercial potential of biomass gasification across different capacities. Sensitivity analysis was conducted based on an established downdraft gasifier model using Aspen Plus. Results underscored the significant impact of gasification temperature and equivalence ratio (ER) on syngas composition, low heating value (LHV), and cold gas efficiency (CGE). Among the feedstocks tested, coconut shell emerged as a feasible feedstock, yielding syngas with an LHV of 8.93 MJ/Nm3 and achieving a CGE of up to 71.12 %. Optimal gasification temperatures ranged between 750 °C to 1,000 °C, with peak ER falling within 0.1 to 0.3. Economic analysis revealed that smaller-scale operations like Plant A resulted in a negative net present value of − US$0.63 million, indicating unfavorable investments. The internal rate of return notably increased from 9.53 % for Plant B compared to −2.56 % for Plant A (20 kW). Plant D, with larger capacity of 20 MW, showed an impressive payback period of less than two years (1.69 years). Medium to large-scale plants such as Plant C (2 MW) and Plant D demonstrated greater economic resilience, with Plant D achieving a significantly lower levelized cost of electricity of US$ 0.19/kWh compared to Plant A at US$ 0.86/kWh. It was noted that the impact of capital costs, operating expenses, and revenue variations is less pronounced at larger scales. The findings from this study shed light on the feasibility of biomass gasification for power generation as a viable option, thereby unlocking the potential for its large-scale commercialization.

Impact of Plant Community Diversity on Greenhouse Gas Emissions in Riparian Zones.

Plant community succession can impact greenhouse gas (GHG) emissions from the soil by altering the soil carbon and nitrogen cycles. However, the effects of community landscape diversity on soil GHG emissions have rarely been fully understood. Therefore, this study investigated how plant landscape diversity, structure type, and species composition, affect soil GHG emissions in a riparian zone. Soil GHG emissions were assessed by measuring the air samples collected from four study sites, which have different plant community structure types and species compositions (natural sites with complex plants, landscaped sites with fruit trees and grasses, untended sites with ruderals, and farmland sites), using the static chamber method. Significant differences were observed in soil carbon dioxide (CO2; p < 0.001), nitrous oxide (N2O; p < 0.001), and methane (CH4; p = 0.005) emissions. The untended site with ruderals exhibited the highest CO2 emissions, while N2O emissions increased as plant community diversity decreased. All sites acted as sinks for CH4 emissions, with decreased CH4 uptake efficiency in more diverse plant communities. The Mantel test and variance partitioning analysis revealed soil microbial biomass as an indirect influencer of GHG emissions. This study could help predict soil GHG emissions and their global warming potential under future changes in the island riparian zones.

Consistent generalization of plant-hummingbird networks despite increasing vegetation cover across a tropical urban landscape

Human activities, particularly urbanization, profoundly impact ecosystems often resulting in biotic homogenization. Whether or not urban landscapes can sustain diverse pollinator and plant communities is an important question to be addressed. Here, we investigated the influence of urbanization on plant-hummingbird interaction networks in a large tropical city, Belo Horizonte, Brazil. We recorded 13198 legitimate interactions between seven hummingbirds and 57 plant species across 12 local networks. Urban landscapes exhibited predominantly generalized networks, maintaining this pattern across varying vegetation cover and floral resource abundance. Although some functionally specialized hummingbirds with long bills were recorded performing more specialized interactions, urban environments did not generally support specialized networks. Nevertheless, network specialization did increase with the proportion of native nectar plants, emphasizing their importance for maintaining some specialized interactions. Furthermore, we observed a positive effect of plant richness, but not of flower abundance, on hummingbird abundance, indicating that it is not only the amount of flowers, but the diversity of floral resources that may be a key factor in maintaining hummingbirds. Therefore, promoting a diverse assemblage of native plants in urban green areas is crucial for sustainable pollinator communities. Our study highlights that while a biodiverse urban landscape will require careful urban vegetation planning considering both floral resource diversity and availability, vegetation cover per se may not be sufficient to mitigate the negative impacts of urbanization. Maintaining a diverse vegetation with different life forms, flowering phenology, and especially of native plants across the urban landscape is needed to create welcoming spaces for pollinators.

Crop Rotation and Diversification in China: Enhancing Sustainable Agriculture and Resilience

Crop rotation and diversification (CRD) are crucial strategies in sustainable agriculture, offering multiple benefits to both farmers and the environment. By alternating crops or introducing diverse plant species, CRD practices improve soil fertility, reduce pest populations, and enhance nutrient availability. For example, legume-based rotations increase soil nitrogen levels through biological nitrogen fixation, reducing the need for synthetic fertilizers. Moreover, these practices promote more efficient water and nutrient use, reducing the reliance on synthetic fertilizers and minimizing the risk of pests and diseases. This review synthesizes findings from recent research on the role of CRD in enhancing sustainable agriculture and resilience, highlighting the potential contributions of these practices towards climate change mitigation and adaptation. Specific crop rotation systems, such as the cereal–legume rotation in temperate regions and the intercropping of maize with beans in tropical environments, are reviewed to provide a comprehensive understanding of their applicability in different agroecological contexts. The review also addresses the challenges related to implementing CRD practices, such as market demand and knowledge transfer, and suggests potential solutions to encourage broader adoption. Lastly, the potential environmental benefits, including carbon sequestration and reduced greenhouse gas emissions, are discussed, highlighting the role of CRD in building resilient agricultural systems. Collectively, this review paper emphasizes the importance of CRD methods as sustainable agricultural practices and provides key insights for researchers and farmers to effectively integrate these practices into farming systems.

Trigonelline prevents high-glucose-induced endothelial-to-mesenchymal transition, oxidative stress, mitochondrial dysfunction, and impaired angiogenic activity in human endothelial EA.hy926 cells

Trigonelline (TRIG) is a natural compound in an alkaloid family found in diverse plants. This compound exerts anti-inflammatory, anti-allergic, anti-oxidative and anti-fibrotic activities in several disease models. However, its beneficial role in endothelial injury, especially induced by diabetes, is unclear. We, therefore, evaluated the effects of TRIG on the cellular proteome of human endothelial (EA.hy926) cells followed by functional validation in high-glucose (HG)-induced endothelial deteriorations. Label-free quantification using nanoLC-ESI-Qq-TOF MS/MS revealed 40 downregulated and 29 upregulated proteins induced by TRIG. Functional enrichment analysis using DAVID and REVIGO tools suggested the involvement of these altered proteins in several biological processes and molecular functions, particularly cell-cell adhesion, ATP metabolic process, cell redox homeostasis, cadherin binding, and ATP hydrolysis activity. Experimental validation showed that HG triggered endothelial-to-mesenchymal transition (EndMT) (as demonstrated by increased spindle index and mesenchymal markers, i.e., fibronectin and vimentin, and decreased endothelial markers, i.e., PECAM-1 and VE-cadherin), increased oxidized proteins, and reduced intracellular ATP, active mitochondria, endothelial tube/mesh formation and VEGF secretion. However, TRIG successfully abolished all these defects induced by HG. These data indicate that TRIG prevents HG-induced EndMT, oxidative stress, mitochondrial dysfunction, and impaired angiogenic activity in human endothelial cells.

Tropospheric ozone pollution increases the sensitivity of plant production to vapor pressure deficit across diverse ecosystems in the Northern Hemisphere

Tropospheric ozone (O3) pollution often accompanies droughts and heatwaves, which could collectively reduce plant productivity. Previous research suggested that O3 pollution can alter plant responses to drought by interfering with stomatal closure while drought can reduce stomatal conductance and provide protection against O3 stress. However, the interactions between O3 pollution and drought stress remain poorly understood at ecosystem scales with diverse plant functional types. To address this research gap, we used 10-year (2012−2021) satellite near-infrared reflectance of vegetation (NIRv) observations, reanalysis data of vapor pressure deficit (VPD), soil moisture (SM), and air temperature (Ta), along with O3 measurements and reanalysis data across the Northern Hemisphere to statistically disentangle the interconnections between NIRv, VPD, SM, and Ta under varying O3 levels. We found that high O3 concentrations significantly exacerbate the sensitivity of NIRv to VPD while have no notable impacts on the sensitivity of NIRv to Ta or SM for all plant functional types, indicating an enhanced combined impact of VPD and O3 on plants. Specifically, the sensitivity of NIRv to VPD increased by >75 % when O3 anomalies increased from the lowest 10 to the highest 10 percentiles across diverse plant functional types. This is likely because long-term exposure to high O3 concentrations can inhibit stomatal closure and photosynthetic enzyme activities, resulting in reduced water use efficiency and photosynthetic efficiency. This study highlights the need to consider O3 in understanding plant responses to climate factors and that O3 can alter plant responses to VPD independently of Ta and SM.

Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.

Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conservation and offer cross-species prediction better than supervised models through fine-tuning limited labeled data. We introduce PlantCaduceus, a plant DNA LM based on the Caduceus and Mamba architectures, pre-trained on a curated dataset of 16 Angiosperm genomes. Fine-tuning PlantCaduceus on limited labeled Arabidopsis data for four tasks, including predicting translation initiation/termination sites and splice donor and acceptor sites, demonstrated high transferability to 160 million year diverged maize, outperforming the best existing DNA LM by 1.45 to 7.23-fold. PlantCaduceus is competitive to state-of-the-art protein LMs in terms of deleterious mutation identification, and is threefold better than PhyloP. Additionally, PlantCaduceus successfully identifies well-known causal variants in both Arabidopsis and maize. Overall, PlantCaduceus is a versatile DNA LM that can accelerate plant genomics and crop breeding applications.