David G. Mendoza-Cozatl

Iron-sulfur (Fe-S) clusters are at the core of photosynthesis, respiration, and redox homeostasis, yet their biogenesis and stability are highly sensitive to fluctuations in iron (Fe) and sulfur (S) availability. Although the molecular players of Fe and S assimilation pathways are well characterized, the mechanisms mediating the crosstalk between these nutrient networks remain largely unknown, particularly within the context of plant–microbiome interactions. Recent work has revealed that plant-associated microbial communities play active roles in shaping Fe-S metabolism through metabolite exchange, hormonal modulation, and redox signalling. Here we discuss recent research demonstrating how root-associated microbes and synthetic microbial communities (SynComs) can influence Fe and S homeostasis, including the reprogramming of plant transcriptional and metabolic networks to preserve photosynthesis under nutrient limitation. We also highlight key microbial strategies, including siderophore-mediated Fe mobilization, S-containing metabolites release, and microbial modulation of hormonal pathways that collectively enhance Fe and S use efficiency. Finally, we discuss future directions for AI-driven trait-based design of SynComs, multi-omics integration, and field-level validation to translate these novel insights into agricultural solutions. Harnessing the power of plant–microbe interactions to improve Fe-S metabolism offers a promising path towards sustainable agriculture and crop productivity under stress and challenging environments.

Annually, chloroplasts fix 258 billion tons of CO2 through photosynthesis. Photosynthesis and other biochemical pathways require specific amounts of metal ions in the organelle. Transport proteins in the plastid inner envelope maintain the organellar ion homeostasis. Despite substantial progress over the last decades, many genes encoding plastid ion channels and ion carriers or their regulators remain unknown. To fill this knowledge gap, detailed information on the elemental composition of chloroplasts ie, a plastid ionome, is needed. This will allow us to compare mutants of transporter candidates with wild-type plants. Here, we provide quantitative descriptions of chloroplast ionomes from Arabidopsis thaliana, the metal hyperaccumulator Arabidopsis halleri, Pisum sativum, and Nicotiana benthamiana and analyze similarities and distinctions. Using A. thaliana, we show that plastid ionomes can be genetically manipulated. Chloroplasts of OLIGOPEPTIDE TRANSPORTER3 (OPT3)-deficient mutants contain 14-fold more iron, likely associated with stromal FERRITIN. The removal of FERRITIN in opt3 mutants leads to a substantial decrease in plastid and leaf iron, pointing to an important role of ferritins in shaping the chloroplast ionome. Our study reveals that chloroplast ferritins can be turned into iron sinks. Since crop biofortification to fight hidden hunger has become a global mission, this research provides groundwork to reach this goal.

Climate change and enhanced pollution levels are subjecting plants and crops to an increased number of different stressors, simultaneously or sequentially, generating conditions of multifactorial stress combination (MFSC). Although MFSC was shown to severely diminish plant growth, yield, and survival, how plants acclimate to increased levels of stress complexity is largely unknown. Here, we reveal that the Arabidopsis thaliana transcriptional regulator basic helix-loop-helix 35 (bHLH35) is required for plant acclimation to a specific set of MFSC conditions that includes a combination of salinity, excess light, and heat, occurring simultaneously (but not to each of these stresses applied individually or in any other combination). Under the three-stress combination, bHLH35 interacts with no apical meristem/transcription activator factor/cup-shaped cotyledon 69 (NAC069), binds the promoter of lateral organ boundaries domain 31 (LBD31) , and regulates the expression of transcripts involved in flavonoid metabolism and ethylene signaling. Our findings uncover a high degree of specificity in plant responses to stress combination, suggesting that different conditions of MFSC could require the function of specific genetic programs for acclimation.

Summary: Guard cells (GCs) regulate gas exchange and water loss in plants and have been extensively studied in Arabidopsis thaliana . However, cross‐species comparisons at single‐cell resolution remain limited. To address this, we aimed to define conserved and divergent transcriptomic signatures of GCs by generating a comparative single‐cell atlas encompassing five species: A. thaliana , soybean ( Glycine max ), tomato ( Solanum lycopersicum ), rice ( Oryza sativa ), and sorghum ( Sorghum bicolor ). We performed single‐nucleus RNA sequencing (sNucRNA‐seq) on leaf tissues from each species, followed by integrative bioinformatic analyses to identify and annotate GC populations. Orthology‐informed transcriptomic comparisons and co‐expression analyses were applied to assess shared and species‐specific regulatory modules. Our analyses revealed a conserved core transcriptome in GCs across species, enriched for genes involved in stomatal movement, abscisic acid signaling, carbon dioxide signaling, reactive oxygen species metabolism, and ion transport. Conserved expression of transcription factors (e.g. MYB60, FAMA orthologs), transporters (e.g. KAT1, SLAC1), and stress‐responsive genes was observed, despite considerable evolutionary divergence. These findings provide a reference framework for cross‐species GC biology, reveal conserved regulatory features, and nominate candidate genes for functional validation. This work contributes molecular insights toward improving drought resilience and stomatal efficiency in crop species through targeted gene engineering.

Premise: The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy.Methods: Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium.Results: Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance.Conclusions: These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

SUMMARY: Global warming, climate change, and industrial pollution are altering our environment subjecting plants, microbiomes, and ecosystems to an increasing number and complexity of abiotic stress conditions, concurrently or sequentially. These conditions, termed, “multifactorial stress combination” (MFSC), can cause a significant decline in plant growth and survival. However, the impacts of MFSC on reproductive tissues and yield of major crop plants are largely unknown. We subjected soybean (Glycine max) plants to a MFSC of up to five different stresses (water deficit, salinity, low phosphate, acidity, and cadmium), in an increasing level of complexity, and conducted integrative transcriptomic‐phenotypic analysis of their reproductive and vegetative tissues. We reveal that MFSC has a negative cumulative effect on soybean yield, that each set of MFSC condition elicits a unique transcriptomic response (that is different between flowers and leaves), and that selected genes expressed in leaves or flowers of soybean are linked to the effects of MFSC on different vegetative, physiological, and/or reproductive parameters. Our study identified networks and pathways associated with reactive oxygen species, ascorbic acid and aldarate, and iron/copper signaling/metabolism as promising targets for future biotechnological efforts to augment the resilience of reproductive tissues of major crop plants to MFSC. In addition, we provide unique phenotypic and transcriptomic datasets for dissecting the mechanistic effects of MFSC on the vegetative, physiological, and reproductive processes of a crop plant.

SUMMARY: The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High‐throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open‐source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf‐specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high‐throughput screens to identify and characterize previously unidentified phenotypes in a leaf‐specific time‐dependent manner. Moreover, the modular and open‐source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs.

Global warming, climate change, and industrial pollution are altering our environment subjecting crops to an increasing number and complexity of abiotic stress conditions, concurrently or sequentially. Recent studies revealed that a combination of 3 or more stresses simultaneously impacting a plant (termed ‘multifactorial stress combination’; MFSC) can cause a drastic decline in plant growth and survival, even if the level of each stress involved in the MFSC has a negligible effect on plants. However, the impacts of MFSC on crops are largely unknown. We subjected soybean plants to a MFSC of up to five different stresses (water deficit, salinity, low phosphate, acidity, and cadmium), in an increasing level of complexity, and conducted integrative transcriptomic-phenotypic analysis of reproductive and vegetative tissues. We reveal that MFSC has a negative cumulative effect on soybean yield, that each set of MFSC condition elicits a unique transcriptomic response (that is different between flowers and leaves), and that selected genes expressed in leaves or flowers are linked to the effects of MFSC on different vegetative, physiological, and/or reproductive parameters. We further reveal that the transcriptomic response of soybean and Arabidopsis to MFSC shares common features associated with reactive oxygen and iron/copper signaling/metabolism. Our study provides unique phenotypic and transcriptomic datasets for dissecting the mechanistic effects of MFSC on the vegetative, physiological, and reproductive processes of a crop plant.

Waterlogging stress (WLS) negatively impacts the growth and yield of crops resulting in heavy losses to agricultural production. Previous studies have revealed that WLS induces a systemic response in shoots that is partially dependent on the plant hormones ethylene and abscisic acid. However, the role of rapid cell-to-cell signaling pathways, such as the reactive oxygen species (ROS) and calcium waves, in systemic responses of plants to WLS is unknown at present. Here we reveal that an abrupt WLS treatment of Arabidopsis (Arabidopsis thaliana) plants growing in peat moss triggers systemic ROS and calcium wave responses and that the WLS-triggered ROS wave response of Arabidopsis is dependent on the ROS-generating RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD), calcium-permeable channels GLUTAMATE-LIKE RECEPTOR 3.3 and 3.6 (GLR3.3 and GLR3.6), and aquaporin PLASMA MEMBRANE INTRINSIC PROTEIN 2; 1 (PIP2; 1) proteins. We further show that WLS is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation, includes many hypoxia-response transcripts, and is partially dependent on RBOHD. Interestingly, the abrupt WLS of Arabidopsis resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. In addition, it induced in plants a heightened state of tolerance to a subsequent submergence stress. Taken together, our findings reveal that the initiation of WLS in plants is accompanied by rapid systemic physiological and transcriptomic responses that involve the ROS, calcium, and hydraulic waves, as well as the induction of hypoxia acclimation mechanisms in systemic tissues.