New Phytologist最新文献

Sustainable crop production demands solutions to reduce the overuse of synthetic nitrogen (N) fertilizers, and plant-growth-promoting bacteria offer a promising strategy by enhancing nutrient acquisition. This study investigated the ability of a nondiazotrophic bacterium, Enterobacter sp. SA187 (SA187), in enhancing Arabidopsis growth under low-nitrate conditions and the underlying mechanisms. Arabidopsis seedlings were grown under different nitrate concentrations with or without SA187 inoculation. Growth traits were quantified alongside shoot and root nitrate and total N contents, and C : N ratios. Transcriptomic profiling (RNA-seq) and qRT-PCR were used to assess modified gene expression. Functional validation was conducted using ethylene-insensitive (ein2-1) and high-affinity nitrate transporter (HATS) mutants (nrt2.5, nrt2.6). SA187 significantly enhanced fresh weight, primary root length, and lateral root density under low nitrate, with benefits increasing as nitrate availability decreased. SA187 improved nitrate accumulation and shoot N allocation, reducing shoot C : N ratios. SA187 regulated expression of HATS and hormone-responsive genes. The growth-promoting effects were abolished in ein2-1, nrt2.5, and nrt2.6 mutants, and SA187-induced regulation of NRT2.5 occurred downstream of ethylene signaling, while NRT2.6 was partly ethylene independent. SA187 promotes growth under low nitrate possibly through ethylene-mediated and HATS-dependent reprogramming of nitrate accumulation and N allocation, supporting its use as a microbial solution for low-input agriculture.

Betty Chung, University of Cambridge (UK). Image credit: Pari Naderi (https://www.parinaderi.com/info).

Temperature influences the distribution and performance of both plants and insect herbivores. Consequently, plant-herbivore interactions are likely to vary across thermal gradients, which could affect the evolution of plant defense. Furthermore, temperature fluctuations may elicit immediate changes in defense. To study the evolutionary and ecological aspects of plant antiherbivore defense depending on temperature, we conducted a transplant experiment on a mountain slope involving 30 Brassicaceae species varying in elevational distribution. Additionally, we carried out a climate-chamber experiment on a subset of 12 species to assess the temperature dependence of constitutive and induced defenses. The transplant experiment revealed that species from higher elevations experienced less herbivory than those from lower elevations. The climate-chamber experiment demonstrated that high-elevation species mounted stronger induced defenses in physical properties of leaves and in phytochemical diversity. Plant responses to low temperature, compared to control temperature, were lower constitutive defense and increased defense induction limited to leaf toughness. By contrast, high temperature increased constitutive chemical defense and defense-induced leaf toughness. Results suggest higher herbivory resistance in high-elevation Brassicaceae species by the induced remodeling of chemical defense. Such defense indication may have been shaped by rare but hard-to-tolerate herbivory in the evolutionary past.

In plants, multiple cell types contribute to immunity, but what division of labor exists among cell types when immunity is activated? We compared, at single-cell resolution, the response of Arabidopsis thaliana leaf cells during pattern-triggered and effector-triggered immunity (PTI/ETI), sampled at 3 and 5 h after infection with Pseudomonas syringae DC3000. Core defense modules were broadly shared across cell clusters, but their activation varied in timing and intensity, with key immune receptors also showing cell type-specific expression dynamics. Mesophyll cell populations could be distinguished based on their resilience patterns: after the initial response, some populations continue to express defense genes at high levels during both PTI and ETI, while others quickly reinitiate growth-related gene expression programs but only during PTI. Gene regulatory network inference revealed WRKY-regulated modules enriched in cells sensing effectors, while salicylic acid biosynthesis regulators were activated in complementary clusters. Analysis of cue1 mutants demonstrated that core immune responses are robust to altered leaf architecture. In addition, we uncovered cryptic defense pathways, including sucrose-responsive modules, in this mutant. By capturing early immune responses at high resolution, our study reveals cell type-specific coordination of plant immunity and provides a framework for decoding immune signaling networks.

Droughts pose a major threat to the Amazon rainforest, yet the mechanisms enabling trees to maintain growth under prolonged drought remain poorly understood, particularly in the understory layer. We leveraged a 22-yr Throughfall Exclusion (TFE) in a 1-ha plot in eastern Amazonia, paired with a Control plot, to test whether small understory trees (1-10 cm diameter) grow faster under long-term drought due to acquisitive resource-use strategies and competition release, given that the TFE plot experienced large-tree mortality and canopy gap formation over time. Despite a 51% reduction in density, small trees grew 2.2 times faster in the TFE than in the Control. At the species scale, growth rates increased with acquisitive traits, such as high foliar nutrient concentrations, greater hydraulic conductivity, and higher leaf-to-wood area ratio, but only in the TFE. These shifts towards acquisitive resource-use strategies were observed within species, indicating plastic responses to drought. At the community scale, growth rates were negatively associated with neighbour density in the TFE, suggesting that competition release facilitates growth under drought. Our findings reveal that plastic and competitive processes stabilise the growth of surviving small understory trees after drought-induced self-thinning, highlighting key mechanisms that can enhance forest resilience to future climate extremes.

In Poaceae, the rho whole-genome duplication (ρ-WGD) event gave rise to three Paleo-duplicated chromosome pairs (PdCPs) that are enriched in resistance genes (nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes) but show low transcriptional levels. Despite their evolutionary importance, systematic family-wide studies of PdCPs have been lacking. We analyzed 37 Poaceae genomes using karyotyping and evolutionary analyses, mapped NBS-LRR genes distributions, and examined transcriptomic and epigenomic patterns across representative species to characterize the evolution and regulation of PdCPs. Our findings show that PdCPs have persisted throughout the evolutionary history of Poaceae, exhibiting distinct patterns of rearrangements among different subfamilies. Notably, one PdCPs is consistently enriched in disease resistance genes across multiple subfamilies and displays conserved low transcriptional activity. This PdCPs also exhibits conserved CHH hypomethylation around transcription start site regions. Further analyses suggest that this PdCPs maintains a more closed chromatin state, associated with repressive histone modifications that suppress gene expression. These results imply that the low transcriptional levels of genes on this PdCPs may be regulated by multiple epigenetic mechanisms. This study advances our understanding of the formation, diversification, and epigenetic regulation of PdCPs following the ρ-WGD in Poaceae.

The mechanisms controlling lateral root emergence in monocots, particularly the role of the exodermis, are poorly understood. We investigated how natural variation in the Brachypodium distachyon stress response shapes root system architecture by modulating cell wall dynamics. We used root tip excision to synchronize lateral root development across natural accessions. The resulting phenotypes were analysed using comparative transcriptomics, biochemical lignin quantification, confocal Raman spectroscopy, and chemical inhibition of lignin biosynthesis. Two distinct root system architectures, 'pine tree' and 'fishbone', were identified. The 'fishbone' phenotype results from an altered lateral emergence caused by a differential lignification intensity of the exodermis. This phenotype was accompanied by the transcriptional upregulation of lignin biosynthesis genes and was partially rescued by treatment with a lignin inhibitor. Stress-induced exodermal lignification acts as a mechanical 'brake' on lateral root emergence. This positions the exodermis as a key regulatory hub that integrates environmental cues with lateral root development to control Root System Architecture plasticity in grasses.

Phylogenies of long-lived plants often exhibit short molecular branch lengths and high levels of gene-tree conflict. However, the biological mechanisms underlying these patterns remain unclear. We examine this with simulations and through empirical examination of several large seed plant clades. We used an agent-based simulation model varying lifespan, degree of overlapping generations, and somatic mutation. We also compared simulated outcomes to phylogenomic patterns in several datasets of seed plants that include life-history shifts. Lifespan and overlapping generations together can generate both short branches and elevated gene-tree conflict. Somatic mutation can amplify these effects, although available evidence suggests mutation rates are often too low to drive major phylogenetic consequences. Variation across simulation parameterizations can mirror the diversity of phylogenomic patterns observed among lineages with differing life histories. Lifespan and generation overlap are potentially major contributors to characteristic phylogenetic signatures in long-lived plants. Consequently, life history should be considered when interpreting evolutionary patterns, substitution rates, and among-lineage heterogeneity in long-lived plant lineages.

Plasmids contribute to the efficient adaptation of bacteria to specific niches in nature. The gram-positive bacterium Clavibacter michiganensis carries two plasmid-borne important virulence genes, celA and pat-1, necessary for wilting in tomato. The 88 C. michiganensis field isolates collected between 2011 and 2020 were examined for phenotypic variation, including virulence in host plants. Four isolates lacking plasmids with celA, pat-1, or both failed to cause wilting, and nine isolates, including these four, failed to cause wilting in Nicotiana benthamiana. Whole genome analyses revealed 11 distinct plasmid types, including 9 newly identified, and 10 bacterial groups with different plasmid compositions, despite having almost identical chromosomes. Comparative genomic analyses revealed significant genetic diversity among the plasmids, while three plasmids containing the genomic island (GI) α with celA or GIβ with pat-1 and three newly identified plasmids carrying both islands shared large blocks of synteny. In addition, GIα is closely associated with mobile genetic elements, suggesting the genetic rearrangement or transfer at this locus. These results suggest that C. michiganensis harbors a wide variety of virulence and nonvirulence plasmids, and that there is genetic rearrangement among plasmids in GI regions, determining bacterial virulence in plants.