Plant, Cell & Environment

O_LIVolatile organic compounds (VOCs) facilitate aboveground plant communication, but belowground signaling remains less understood. C_LIO_LIThis study explored root-root interactions between Picea abies and Fagus sylvatica saplings in monospecific (Fagus-Fagus) and heterospecific (Picea-Fagus) pairs (n=6), excluding shoot-level VOC communication. Sender plants were treated with jasmonic acid to simulate herbivory and labeled with 13CO2 and 15NH4NO3 to trace nutrient transfer in a split-root design. VOC emissions and gas exchange were measured over ten days using PTR-TOF-MS and 13CO2-spectroscopy and 13C and 15N were analyzed in roots and shoots via EA-IRMS. C_LIO_LIOur findings reveal, that (i) JA treatment induced strong de novo terpenoid emissions from P. abies and enhanced emissions of oxygenated VOCs and benzenoids from F. sylvatica, (ii) F. sylvatica receiver plants responded similarly to JA-treated neighbors, indicating belowground signaling, and (iii) responses of receiver plants were more pronounced in the heterospecific treatment. Furthermore, formic acid emissions from soils increased following JA treatment, suggesting altered soil microbial activity. Isotopic analysis revealed C exudation into the rhizosphere and N transfer to receiver plants. C_LIO_LIThese results suggest that belowground signaling enables early priming of herbivore-induced defenses in neighboring plants, and that the response intensity is modulated by species identity. C_LI

Studies of plant responses to temperature often focus on rates photosynthesis and respiration. However, within-plant utilisation and allocation of carbon are also strongly affected. It is unclear how much each of these processes contribute to determining the overall temperature response of growth. We applied a data assimilation framework to a glasshouse experiment with detailed physiological and growth measurements to investigate the relative contribution of different physiological processes to the overall temperature response of tree seedling growth. We found that both short-term effects of temperature and acclimatory responses of photosynthesis and respiration had a significant impact on the temperature response of growth. However, the effect of temperature on biomass allocation patterns to different tissues, non-structural carbohydrate utilisation and C losses to other unmeasured losses were also substantial in determining the temperature response of growth, particularly at sub-optimal temperatures. Our work demonstrates that the growth response to warming cannot be predicted using only the direct effect of temperature on photosynthesis and respiration and emphasizes the importance of temperature acclimation of photosynthesis, respiration and other C balance processes. Our results provide new guidance for process-based models to correctly describe the temperature effects on tree growth.

A sudden cold exposure (4{degrees}C, 24 h) primes resistance of Arabidopsis thaliana against the virulent biotrophic pathogen Pseudomonas syringae pv. tomato DC3000 (Pst) for several days. This effect is mediated by chloroplast cold sensing and the activity of stromal and thylakoid-bound ascorbate peroxidases (sAPX/tAPX). In this study, we investigated the impact of such cold exposure on plant defence against the necrotrophic fungus Botrytis cinerea. Plant resistance was transiently enhanced if the B. cinerea infection occurred immediately after the cold exposure, but this cold-enhanced B. cinerea resistance was absent when the cold treatment and the infection were separated by 5 days at normal growth conditions. Plastid ascorbate peroxidases partially contributed to the transient cold-enhanced resistance against the necrotrophic fungus. In response to B. cinerea, the levels of reactive oxygen species (ROS) were significantly higher in cold-pretreated Arabidopsis leaves. Pathogen-triggered ROS levels varied in the absence of sAPX, highlighting the strong capacity for sAPX-dependent ROS regulation in the chloroplast stroma. The cold-enhanced resistance against B. cinerea was associated with cold-induced plant cell wall modifications, including sAPX-dependent callose formation and significant lignification in cold-treated Arabidopsis leaves. FundingThis work was supported by the German Research Foundation (CRC973/C4) and the FU Berlin.

O_LIVolatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and with plant roots. While their potential as plant-growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remains poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress. C_LIO_LIArabidopsis thaliana plants were exposed to VOCs emitted by Pseudomonas strains under both control and osmotic-stress conditions. VOC exposure generally enhanced plant growth, and this effect was even more pronounced under both drought and salt stress. Transcriptomic analysis revealed that VOC exposure modulates key stress-responsive pathways, including those related to abscisic acid biosynthesis and signalling, sugar transport, iron uptake, aliphatic glucosinolate biosynthesis, and plant defences. Using Arabidopsis mutants, we identified abscisic acid and aliphatic glucosinolates as important components in mediating the plant response to VOCs. SWEET11/12 sugar transporters and ABA signaling genes were downregulated by VOCs exposure, in order to allow for a positive regulation of lateral root numbers (in case of SWEET genes) and plant growth in general under drought stress. In summary, using metabolomics, transcriptomics and functional analysis, we showed a negative cross-talk between the effects of VOCs on plant growth and glucosinolate production, whereas a positive interaction was observed between the biosynthesis of coumarins and VOCs. C_LIO_LINotably, VOCs also improved drought tolerance in soil-grown Brassica oleracea plants. We showed that VOC treatment altered the root-associated microbiome under drought, leading to a community composition more similar to that of well-watered plants. C_LIO_LIOur results show that Pseudomonas emitted VOCs can promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation. C_LI

Leaf gas exchange is the key driver of forest carbon uptake and directly determines forest carbon sink activity. Additionally, plants release a variety of biogenic volatile organic compounds (VOCs) acting as stress signals of trees. However, continuous hourly resolved measurements of leaf gas exchange and VOC emissions in tall tree canopies are challenging and remain scarce. To this end, we developed a sophisticated in-situ leaf gas exchange measurement system with 24 cuvettes deployed on mature Fagus sylvatica (n=3) and Pseudotsuga menziesii (n=3) individuals in a mixed temperate forest. We additionally measured sap flux density (Js), radial growth and tree water deficit (TWD) to gain a holistic picture of seasonal leaf and stem water and carbon flux dynamics during the summer of 2024. During midsummer, we found a gradual reduction of stomatal conductance (gs) and VOC emissions of sun, but not shade branchlets of P. menziesii in response to moderate atmospheric and edaphic drying. Decreased gs led to a downregulation of transpiration (E), Js, and carbon isotope discrimination accompanied by an increase in TWD and intrinsic water used efficiency. Leaf gas exchange of shade branchlets remained unaffected due to microclimatic buffering effects. Contrarily, sun leaves of F. sylvatica, profited from sunny midsummer conditions and increased leaf gas exchange, whereas shade leaves benefitted from more diffuse light during early summer exhibiting similar carbon assimilation, transpiration and VOC emissions as sun leaves. For both species we found a clear time lag of four to five hours between maximum leaf and stem water fluxes and a delay of up to 20 hours for the recovery of TWD, highlighting the role of stem water reserves. Pronounced seasonal and diurnal differences of leaf gas exchange, stem water fluxes and VOC emissions showed, that continuous data are essential to better understand variability of ecosystem flux dynamics.

The rotation of Earth creates a cycle of day and night, leading to predictable changes in environmental conditions. The circadian clock synchronizes an organism with these environmental changes and alters their physiology in anticipation. Prediction of the probable timing of pathogen infection enables plants to prime their immune system without wasting resources or sacrificing growth. Here, we explore the relationship between the immune hormone salicylic acid (SA), and the circadian clock in Arabidopsis. We found that SA altered circadian rhythmicity through the SA receptor and master transcriptional coactivator, NPR1. Reciprocally, the circadian clock gates SA-induced expression of NPR1-dependent immune genes. Furthermore, the clock gene CCA1 is essential for SA-induced immunity to the major bacterial plant pathogen Pseudomonas syringae. These results reveal new interactions between the circadian clock and SA signaling which produce an effective immune response. Understanding how and why the immune response in plants is linked to the circadian clock is crucial in working towards improved crop productivity.

Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Heat acclimation empowers plants to survive under extreme temperature conditions but the potential of beneficial microbes to make plants thermotolerant has not been considered so far. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces heat tolerance in Arabidopsis thaliana by reprogramming the plant transcriptome to a similar extent as acclimation. Acclimation induces priming of heat stress memory genes such as APX2 and HSP18.2 via the transcription factors HSFA1A, B, D, and E and the downstream master regulator HSFA2. hsfa1a,b,d,e and hsfa2 mutants compromised both acclimation and bacterial priming through the same pathway of HSF transcription factors. However, while acclimation transiently modifies H3K4me3 levels at heat stress memory gene loci, SA187 induces the constitutive priming of these loci. In summary, we demonstrate the molecular mechanism by which SA187 imparts thermotolerance in A. thaliana, suggesting that beneficial microbes might be a promising way to enhance crop production under global warming conditions.

O_LIRoots adapt to temperature ranges that restrict growth but are not lethal. Although lethal heat shock and moderately high temperatures have been studied in detail, the effects of non-lethal high temperatures on root development remain largely unknown. We defined 31{degrees}C as a non-lethal thermal stress in Arabidopsis thaliana and examined its impact on root growth using phenotypic analyses and developmental-zone-specific transcriptomics. C_LIO_LICompared to growth at 22{degrees}C, at 31{degrees}C, primary root growth, meristem size, and superoxide (O2-) accumulation were reduced, and the distribution of the meristem master regulator PLETHORA2 (PLT2) became restricted. Transcriptome analysis revealed a strong downregulation of RGFs, RGFRs, and PLT2, rather than activation of heat shock-inducible genes. C_LIO_LIThese gene mutants were more sensitive to non-lethal thermal stress. In contrast, RGF treatment recovered heat-stress-induced defects. Beyond alleviating the stress in the primary root meristem, RGF treatments promoted lateral root elongation under prolonged non-lethal thermal stress, resulting in a more complex root system. C_LIO_LIThese results indicate that the RGF-RGF receptor-PLT2 pathway plays a central role in root adaptation to non-lethal heat stress rather than the canonical heat shock response pathway and suggest that manipulating RGF signaling could enhance root thermotolerance and crop resilience under elevated temperatures. C_LI

Beech (Fagus sylvatica) is one of the most important forest tree species in Europe, both in terms of land coverage and ecosystem services. Although it is projected to be strongly affected by climate change, insights into its functional genomic responses to realistic future scenarios are still lacking. We conducted a fully controlled ecotron experiment to examine the transcriptomic responses of 125 young, naturally regenerated beech trees exposed to regionalized dynamic climate series representing a reference period (1987-2016) and two future climate scenarios (Representative Concentration Pathways, RCP2.6 and RCP8.5, for 2071-2100) in Germany. RCPs describe alternative greenhouse gas trajectories established by the IPCC, ranging from strong mitigation (RCP2.6) to high, unmitigated emissions (RCP8.5), the latter representing a worst-case future scenario. Although both scenarios produced substantial transcriptional changes relative to the reference period, RCP8.5 elicited markedly stronger responses than RCP2.6, with nearly twice as many differentially expressed genes and unique transcriptional programs across functional categories that were not predictable from the RCP2.6 transcriptomes. Our study reveals emergent functional responses in European beech under projected late 21st-century climate conditions in Germany and highlights potential biomarkers for monitoring ecosystem responses to climate change.

In agricultural crops, forests and grasslands, water deficit often occurs in the presence of cues from neighbouring vegetation. However, most studies have addressed separately the mechanisms of plant growth responses to these two aspects of the environment. Here we show that transferring Arabidopsis thaliana seedlings to agar containing polyethylene glycol (PEG) to restrict water availability reduces hypocotyl growth responses to shade without simultaneous affecting cotyledon expansion or its response to shade. Water restriction diminished the activity of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4), PIF5, PIF3 and PIF3-LIKE 1 gene promoters, particularly in seedlings exposed to simulated shade. The response of PIF4 expression to PEG required the presence of its positive morning regulators CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), which also reduced their expression in response to PEG. Water restriction diminished the nuclear abundance of PIF4 in hypocotyl cells only in the seedlings exposed to shade. In addition to the changes in PIF4 levels, post-transcriptional processes also contributed to the response to PEG. Hypocotyl growth showed significant triple interaction among water availability, shade and the presence of PIF4, PIF5 and PIF3. Collectively, these results unveil PIFs as a hub that interlinks shade and drought information to control growth.

Cold acclimation in plants is a complex phenomenon involving numerous stress-responsive transcriptional and metabolic pathways. Existing gene expression studies have primarily addressed short-term cold acclimation responses in herbaceous plants, while few have focused on perennial evergreens, such as conifers, that survive extremely low temperatures during winter. To characterize the transcriptome changes during cold acclimation in Picea abies (L.) H. Karst (Norway spruce), we performed RNA-Sequencing analysis of needles and roots subjected to a chilling progression (5 {degrees}C) followed by 10 days at freezing temperature (-5 {degrees}C). Comparing gene expression responses of needles against Arabidopsis thaliana L. (Arabidopsis) leaves, our results showed that early transient inductions were observed in both species but the transcriptional response of Norway spruce was delayed. Our results indicate that, similar to herbaceous species, Norway spruce principally utilizes early response transcription factors (TFs) that belong to the APETALA 2/ethylene-responsive element binding factor (AP2/ERF) superfamily and NACs. However, unique to the Norway spruce response was a large group of TFs that mounted a late transcriptional response to low temperature. A predicted regulatory network analysis identified key conserved TFs, including a root-specific bHLH101 homolog and other members of the same family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3 and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. One sentence summaryNorway spruce shares elements of the cold regulon described in herbaceous species but has undescribed components that contribute to the cold tolerance of this evergreen coniferous species.

Global warming will lead to significantly increased temperatures on earth. Plants respond to high ambient temperature with altered developmental and growth programs, termed thermomorphogenesis. Here we show that thermomorphogenesis is conserved in Arabidopsis, soybean, and rice and that it is linked to a decrease in the levels of the two macronutrients nitrogen and phosphorus. We also find that low external levels of these nutrients abolish root growth responses to high ambient temperature. We show that in Arabidopsis, this is due to the function of the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and its transcriptional regulation of the transceptor NITRATE TRANSPORTER 1.1 (NRT1.1). Soybean and Rice homologs of these genes are expressed consistently with a conserved role in regulating temperature responses in a nitrogen and phosphorus level dependent manner. Overall, our data show that root thermomorphogenesis is a conserved feature in species of the two major groups of angiosperms, monocots and dicots, that it leads to a reduction of nutrient levels in the plant, and that it is dependent on sufficient environmental nutrient supply, a regulatory process mediated by the HY5-NRT1.1 module.

RAPID ALKALINIZATION FACTOR (RALF) peptides are important players in regulating cell expansion. In Arabidopsis, volatile compounds (VCs) emitted by the fungal phytopathogen Penicillium aurantiogriseum promote root hair (RH) proliferation and hyper-elongation through ethylene and enhanced photosynthesis signalling actions. A striking alteration in the proteome of fungal VC-treated roots involves up-regulation of RALF22. To test the possible involvement of RALF22 in the fungal VC-promoted RH changes, we characterized RH density and number responses to fungal VCs in ralf22 and fer-4 plants impaired in RALF22 and its receptor FERONIA, respectively. Unlike WT plants, ralf22 and fer-4 RHs responded weakly to fungal VCs, strongly indicating that the RALF22-FERONIA module is a key determinant of the RH response to fungal VCs. To investigate the regulatory mechanisms behind this response, we analysed the RALF22 transcript levels in roots of etr1-3 and eir1 ethylene signalling mutants and those of ethylene-responsive, RH-related RSL4, RHD2, PRX1 and PRX44 transcripts in ralf22 and fer-4 roots. Moreover, we characterized the RH and RALF22 transcript level responses to fungal VCs of the cfbp1 mutant defective in photosynthetic responsiveness to VCs. Unlike in WT roots, fungal VCs weakly enhanced RALF22 expression in etr1-3, eir1 and cfbp1 roots, and RSL4, RHD2, PRX1 and PRX44 expression in ralf22 and fer-4 roots. In addition, fungal VCs weakly promoted RH changes in cfbp1 roots. Collectively, our findings showed that the ethylene and enhanced photosynthesis signalling-mediated RH response to fungal VCs involves RALF22-FERONIA.

O_LIRising atmospheric CO2 levels are predicted to influence forest health directly and indirectly, yet the long-term effects of elevated CO2 (eCO2) on mature trees in natural ecosystems remain poorly understood. Understanding how eCO2 affects susceptibility to biotic stress and alters leaf metabolism is critical for predicting forest responses to climate change. C_LIO_LIWe examined the effects of eCO2 (+150 ppm) on 180-year-old Quercus robur at the Birmingham Institute of Forest Research (BIFoR) Free Air CO2 Enrichment (FACE) facility. From 2016 (pre-treatment) to 2024 (year 8 of enrichment), we monitored natural powdery mildew infection and insect herbivory, alongside targeted and untargeted metabolomic profiling of leaf material collected across the growing season. C_LIO_LIWhile seasonal patterns and an overall decline in PM and herbivory were observed, no consistent differences in biotic stress incidence emerged due to eCO2. Metabolomic data revealed subtle but widespread shifts, especially in amino acid, CoenzymeA, and redox pathways. C_LIO_LIThese results suggest that although eCO2 drives extensive metabolic changes, it does not alter biotic stress resistance in mature oaks. Instead, eCO2 appears to promote physiological plasticity that may shape future responses to combined environmental stressors. These insights offer a valuable reference point for interpreting long-term ecosystem dynamics. C_LI

The carbon (C) balance of plants is the sum of all source and sink processes. However, due to methodological limitations, most studies focus predominantly on measurements of leaf-level assimilation and respiration, with less attention given to these processes in heterotrophic organs or the whole-plant level. As a result, knowledge of the whole-plant net C balance is scarce, limiting our understanding of the dynamics between C source and sink activities. Therefore, we developed an easily reproducible chamber system for continuous measurements of whole-plant net CO2 fluxes. We present the obtained dynamics of net CO2 fluxes of several C3 and CAM species, including germinating Quercus robur, over several days, as well as the whole-plant net CO2 flux temperature response of Q. robur seedlings, identifying the temperature thresholds at which they shift from a net CO2 sink to source. We show distinct diel patterns of net CO2 fluxes in C3 plants, likely driven by a dynamic diurnal up- and downregulation of sink activities in woody C3 plants. These patterns appear temperature-driven, suggesting a dynamic response of plants sink and source activity to environmental drivers. Our results highlight the importance of whole-plant C balance measurements for understanding plant responses to environmental conditions.

The baseline for thermal dissipation probes is a reference for simultaneous cessation of both nighttime transpiration and refilling of trees internal water stores. Finding this moment is challenging as the baseline is dynamically changing, and the complete sap flux cessation may not even occur. We proposed a novel framework using VPD and dendrometer measurements to partition transpiration and refilling from nighttime sap flux density, and introduced a night-by-night baselining scheme that does not rely on identifying the zero-flow moment. One conventional baselining method using the maximum probe voltage (or temperature) difference substantially underestimated sap flux density by 204.56% for nighttime, 28.30% for daytime, and 45.20% for full-day flux in P. sylvestris, and by 344.77%, 45.68%, and 54.76%, respectively, in A. glutinosa. Baseline calibrations using commonly available variables are thus provided. Evaluation through gas exchange and evapotranspiration data confirmed the accuracy of partitioning between nighttime transpiration and refilling, demonstrating that nighttime transpiration can drive measurable nighttime evapotranspiration responses. Nightly variations in water allocation within stem tissue add complexity to stem swelling. Seasonally, sap flux density showed an initial increase in both transpiration and refilling, followed by a decline, with transpiration dominating until mid-summer before refilling gradually took precedence. HighlightsO_LIPartitioned nighttime transpiration & stem refilling using VPD & dendrometers. C_LIO_LITracked seasonal shifts in transpiration & refilling ratios to nighttime sap flux. C_LIO_LIIndependently evaluated model with eddy covariance & leaf gas exchange measurements. C_LIO_LIProposed a new high-frequency baselining strategy for thermal dissipation probes. C_LIO_LIRevealed & corrected errors in sap flux density baselining methods. C_LI

The extent to which plants thermoregulate to maintain relatively stable metabolic function in response to gradual and rapid temperature changes that jeopardize crop production is unclear. Maize thermoregulation was investigated based on leaf temperature (TL) measurements and its relationship with photochemistry and stomatal conductance (gs) under dry and wet soil scenarios. Seasonal climatology was simulated in a growth chamber according to Beijings climatology with extreme "hot days" based on historical maxima. Maize behaved as a limited homeotherm, an adaptive strategy to maintain photosynthesis around optimum temperatures (Topt). Plants on drier soil had lower thermoregulatory capacity, with reduced gs, photosynthesis and transpiration, which impacted final yields, despite acclimation with a higher Topt to sustained stress. On hot days thermoregulation was affected by heat stress and water availability, suggesting that strong and frequent heatwaves will reduce crop activity although increased temperatures could bring photosynthesis closer to Topt in the region. We propose a novel mechanism to explain thermoregulation from the contribution of heat dissipation via non-photochemical quenching (NPQ) to TL, supporting our hypothesis that NPQ acts as a negative feedback mechanism from photosynthesis by increasing TL in suboptimal conditions. These results could help to design adaptation strategies based on deficit irrigation. HighlightMaize was able to maintain leaf temperatures in narrower ranges than air temperatures by dissipating sunlight not used in photosynthesis as heat energy with a key role of transpiration cooling to sustain optimum photosynthesis temperature.

Host plant-derived strigolactones trigger hyphal branching in arbuscular mycorrhizal (AM) fungi, initiating a symbiotic interaction between land plants and AM fungi. However, our previous studies revealed that gibberellin-treated Eustoma grandiflorum (Gentianaceae) activates rhizospheric hyphal branching in AM fungi using unidentified molecules other than strigolactones. In this study, we analyzed independent transcriptomic data of E. grandiflorum and found that the gentiopicroside (GPS) and swertiamarin (SWM), which are characteristic monoterpene glucosides in Gentianaceae, were highly biosynthesized in gibberellin-treated E. grandiflorum roots. Moreover, these metabolites considerably promoted hyphal branching in the Glomeraceae AM fungi Rhizophagus irregularis and R. clarus. GPS treatment also enhanced R. irregularis colonization of the monocotyledonous crop Allium schoenoprasum. Interestingly, these metabolites did not provoke the germination of the root parasitic plant Orobanche minor. Altogether, our study unveiled the crucial role of GPS and SWM in activating the symbiotic relationship between AM fungi and E. grandiflorum.

O_LICadmium (Cd) is a major environmental pollutant with high toxicity potential. Even though a reduction of growth, including the primary root, is a clear consequence of Cd exposure, a profound understanding of the impact of Cd on the root apical meristem (RAM) and the elongation/differentiation zone (EDZ) is still lacking. C_LIO_LIIn this study, Arabidopsis thaliana roots were subjected to Cd and divided into root tips (RT) and remaining roots (RR) to separately assess the effect of Cd using transcriptomics, ionomics and metabolomics. C_LIO_LIElemental profiling revealed lower Cd accumulation in RT and differences in mineral contents between RT and RR. Transcriptomic analysis demonstrated distinct gene expression patterns in RT and RR, with Cd having less impact in RT. Functional enrichment analysis revealed genes associated with iron and sulfur homeostasis as well as the response to light in both RR and RT. RT-specific responses to Cd included several genes regulated by the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and notably, the hy5 mutant showed increased Cd sensitivity and accumulation compared to the wild type. C_LIO_LIThis study provides comprehensive insights into the inhibitory effects of Cd on primary root growth, elucidating molecular mechanisms involved, particularly highlighting the role of HY5 in Cd accumulation. C_LI

Climate change is causing increases in global average temperatures with detrimental consequences to food security, in part because most plants are sensitive to increases of even 1-2 degrees Celsius. Our molecular understanding of how plants perceive and acclimatise to mild increases in temperature (aka thermomorphogenesis) have largely been built upon transcriptomic analyses of whole seedling using the plant model Arabidopsis thaliana. In this work, we demonstrate that this widely used approach has significant limitations that may have skewed our understanding of gene regulation in thermomorphogenesis.We found a surprisingly poor consensus among published whole seedling transcriptomic datasets. On average, nearly 60% of reported differentially expressed genes (DEGs) are unique to a single study. To investigate the source of this variability, we performed a controlled comparison of RNA sequencing data from whole seedlings versus dissected organs (root, hypocotyl, and cotyledon), which revealed strong organ-specific transcriptional responses to warmth. Critically, we found that ~70% of DEGs identified in whole seedlings were not differentially expressed in any of the individual organs, suggesting that whole seedling data is confounded by the pooling of distinct, and sometimes opposing, organ-level responses. These findings are further supported by proteomic analysis. Our work provides a word of caution and clear guidance for the field to advance when producing and interpreting RNA sequencing data for plant response to warm temperatures.