Search

Author(s): Dewhirst, RA; Handakumbura, P; Clendinen, CS; Arm, E; Tate, K; Wang, W; Washton, NM; Young, RP; Mortimer, JC; McDowell, NG; Jardine, KJ | Abstract: High temperatures alter the thermal sensitivities of numerous physiological and biochemical processes that impact tree growth and productivity. Foliar and root applications of methanol have been implicated in plant acclimation to high temperature via the C1 pathway. Here, we characterized temperature acclimation at 35 °C of leaf gas exchange, chlorophyll fluorescence, and extractable metabolites of potted Populus trichocarpa saplings and examined potential influences of mM concentrations of methanol added during soil watering over a two-month period. Relative to plants grown under the low growth temperature (LGT), high growth temperature (HGT) plants showed a suppression of leaf water use and carbon cycling including transpiration (E), net photosynthesis (Pn), an estimate of photorespiration (Rp), and dark respiration (Rd), attributed to reductions in stomatal conductance and direct negative effects on gas exchange and photosynthetic machinery. In contrast, HGT plants showed an upregulation of nonphotochemical quenching (NPQt), the optimum temperature for ETR, and leaf isoprene emissions at 40 °C. A large number of metabolites (867) were induced under HGT, many implicated in flavonoid biosynthesis highlighting a potentially protective role for these compounds. Methanol application did not significantly alter leaf gas exchange but slightly reduced the suppression of Rd and Rp by the high growth temperature while slightly impairing ETR, Fv′/Fm′, and qp. However, we were unable to determine if soil methanol was sufficiently taken up by the plant to have a direct effect on foliar processes. A small number of extracted leaf tissue metabolites (55 out of 10 015) showed significantly altered abundances under LGT and methanol treatments relative to water controls, and this increased in compound number (222) at the HGT. The results demonstrate the large physiological and biochemical impacts of high growth temperature on poplar seedlings and highlight the enhancement of the optimum temperature of ETR as a rapid thermal acclimation mechanism. Although no large effect on leaf physiology was observed, the results are consistent with methanol both impairing photochemistry of the light reactions via formaldehyde toxicity and stimulating photosynthesis and dark respiration through formate oxidation to CO2.

The rhizosphere is arguably the most complex microbial habitat on Earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome). Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate the effects of climate change by designing ecosystems for long-term soil carbon storage. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) were used for the first time for the correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only a few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that the attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by the formation of extracellular polymeric substances (EPS).

Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget. Exploring and understanding the molecular mechanisms governing ecosystem responses via rhizosphere interactions allow the rational and sustainable design of future ecosystems. However, visualizing the plant root system architecture with spatially resolved root exudate and microbiome profiles along the root in its native state remains an ambitious grand challenge in rhizosphere biology. To address this challenge, we developed a three-dimensional (3D) root cartography platform to accurately visualize molecular and microbial constituents and their interactions in the root-rhizosphere zone.

Plant growth is mediated by the integration of internal and external cues, perceived by cells and transduced into a developmental program that gives rise to cell division, elongation, and wall thickening. Extra-, inter-, and intra- physical cellular forces contribute to this regulation. Across the plant kingdom thigmomorphogenesis is widely observed to alter plant morphology by reducing stem height and increasing stem diameter. The transcriptome is highly responsive to touch, including components of calcium signaling pathways and cell wall modification. One aspect of this cascade involves gibberellins (GA) and bZIP family transcription factors. Here, we present data connecting thigmomorphogenesis with secondary cell wall synthesis by GA inactivation and bZIP translocation into the nucleus. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus in response to mechanical stimulation. This translocation was mitigated by supplementing with exogenous bioactive GA, and induced by chemical inhibition of GA synthesis. Misregulation of SWIZ expression resulted in plants with reduced stem and root elongation, and following mechanical stimulation, increased secondary wall thickness. Classical touch responsive genes were upregulated in B. distachyon following touch, and we observe significant induction of the glycoside hydrolase 17 family, which may be indicative of a facet of grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. Thus, SWIZ is a transcriptional regulatory component of thigmomorphogenesis, which includes the thickening of secondary cell walls.

Agricultural cropping systems and pasture comprise one third of the world’s arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., National Science Foundation 1916797 David W Ehrhardt, Kenneth D Birnbaum, Seung Yon Rhee; National Science Foundation 2052590 Seung Yon Rhee

The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of Arabidopsis thaliana using Ca2+-imaging identified mevalonate kinase (MVK) as a critical component of plant purinergic signaling. MVK interacts directly with the plant extracellular ATP (eATP) receptor P2K1 and is phosphorylated by P2K1 in response to eATP. Mutation of P2K1-mediated phosphorylation sites in MVK eliminates the ATP-induced cytoplasmic calcium response, MVK enzymatic activity, and suppresses pathogen defense. The data demonstrate that the plasma membrane associated P2K1 directly impacts plant cellular metabolism by phosphorylation of MVK, a key enzyme in the mevalonate pathway. The results underline the importance of purinergic signaling in plants and the ability of eATP to influence the activity of a key metabolite pathway with global effects on plant metabolism., Products of the mevalonate pathway support plant development. Here the authors show that the extracellular ATP receptor P2K1 phosphorylates mevalonate kinase and this affects the mevalonate pathway.

Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS box protein function remains unknown. To assess the impact of changing MADS box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS box proteins vary. We tested the functional consequences of this evolutionary variability using maize (Zea mays) as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS box interactions. Our results highlight complexity in the evolution of developmental gene networks: changing protein-protein interactions could affect not only the composition of transcription factor complexes but also their degradation and persistence in developing flowers. Our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.

Coastal landscapes and their terrestrial-aquatic interface (TAI) will be increasingly exposed to short-term tidal inundation due to sea level rise and extreme weather events. These events can generate hot moments of biogeochemical activity and also alter ecosystem structure if occuring frequently. However, such responses of these vulnerable ecosystems to environmental perturbations are poorly understood, limiting our ability to evaluate the contribution of local processes on global scale carbon and nutrient budgets. Here, we evaluated whether and to what degree seawater inundation impacts biogeochemical responses in soils collected along a naturally variable salinity gradient in a first order tidal stream floodplain in the Pacific Northwest. A laboratory incubation experiment simulating episodic inundation was performed to detect the impacts on soil carbon chemistry. We characterized carbon before and after inundation using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), metabolite signatures via Liquid Chromatography-Mass Spectrometry (LC-MS), and high-frequency carbon dioxide (CO2) and methane (CH4) gas fluxes from intact soil cores. Following three inundation events, we observed significant decreases in the thermodynamic favorability of the remaining organic compounds in soils with high natural salinity as compared to low salinity soils. Low salinity soils showed higher average flux compared to high salinity soils following periodic inundation events. Seawater inundation led to distinct metabolite features in low salinity soils, with surficial soil preferentially getting enriched in phenolic compounds. Biogeochemical transformations inferred from FTICR-MS data showed an increase in total transformations with increasing salinity for soil cores from naturally low salinity exposure sites, likely suggesting higher microbial activity. In conclusion, ecosystem responses in a tidal landscape frequently experiencing seawater inundation preferentially influences terrestrial soils to behave as a carbon source. This response is likely a function of historical salinity gradient-driven molecular-level organic carbon characteristics.

Shifting interactions between MADS-box transcription factors may have been critical in the emergence of the flower, and in floral diversification. However, how evolutionary variation in MADS-box interactions affects the development and evolution of floral form remains unknown. Interactions between B-class MADS-box proteins are variable across the grass family. Here, we test the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to protein complex composition and downstream gene expression. Differential dimerization also affected B-class complex abundance, independent of RNA levels. Thus, differential dimerization may affect protein stability. This reveals an important consequence for evolutionary variability in MADS-box interactions, adding complexity to the evolution of developmental gene networks. Our results show that floral development is robust to molecular change, even coding change in a master regulator of development. This robustness may contribute to the evolvability of floral form.

The rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a diverse microbial consortium of bacteria, archaea, viruses, and microeukaryotes. Understanding, predicting and controlling the structure and function of the rhizosphere will allow us to harness plant-microbe interactions and other rhizosphere activities as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage. Here, we review critical knowledge gaps in rhizosphere science, and how mechanistic understanding of rhizosphere interactions can be leveraged in rhizosphere engineering efforts with the goal of maintaining sustainable plant ecosystem services for food and bioenergy production in an ever changing global climate.

Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today’s biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.

Coastal landscapes are increasingly exposed to seawater due to sea level rise and extreme weather events. The biogeochemical responses of these vulnerable ecosystems are poorly understood, limiting our ability to predict how their role in local and global biogeochemical cycles will shift under future conditions. Here we evaluate how antecedent conditions influence the biogeochemical response of soil to seawater inundation events based on a 42-day laboratory incubation experiment with soils collected from a natural salinity gradient across a coastal floodplain. We quantified influences of seawater inundation on intact soil cores through high-frequency carbon dioxide (CO2) and methane (CH4) gas fluxes measurements as well as ultrahigh resolution characterization of organic matter chemistry and metabolites. Mean CO2 and CH4 fluxes were higher after inundation compared to control cores for soils that had low in situ electrical conductivity (EC). Soils with low in situ EC also exhibited significant shifts in organic matter profiles after inundation, with surficial soils (0–7.5 cm) becoming more enriched in phenolic compounds, compared to deeper soils (7.5–15 cm). The number of biochemical transformations inferred from mass spectrometry increased significantly after inundation for soils with low in situ EC. Our results suggest that seawater inundation of low-salinity terrestrial environments can lead to increased microbial activity and increasing likelihood of soil carbon release, with sites experiencing infrequent or new seawater exposure likely to be more sensitive to saltwater exposure relative to sites with more frequent exposure. We conclude that the biogeochemical impacts of future seawater exposure will be modulated by antecedent conditions associated with landscape position within coastal watersheds.

Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. We identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Background Cellulose is an integral component of the plant cell wall and accounts for approximately forty percent of total plant biomass but understanding its mechanism of synthesis remains elusive. CELLULOSE SYNTHASE A (CESA) proteins function as catalytic subunits of a rosette-shaped complex that synthesizes cellulose at the plasma membrane. Arabidopsis thaliana and rice (Oryza sativa) secondary wall CESA loss-of-function mutants have weak stems and irregular or thin cell walls. Results Here, we identify candidates for secondary wall CESAs in Brachypodium distachyon as having similar amino acid sequence and expression to those characterized in A. thaliana, namely CESA4/7/8. To functionally characterize BdCESA4 and BdCESA7, we generated loss-of-function mutants using artificial microRNA constructs, specifically targeting each gene driven by a maize (Zea mays) ubiquitin promoter. Presence of the transgenes reduced BdCESA4 and BdCESA7 transcript abundance, as well as stem area, cell wall thickness of xylem and fibers, and the amount of crystalline cellulose in the cell wall. Conclusion These results suggest BdCESA4 and BdCESA7 play a key role in B. distachyon secondary cell wall biosynthesis.