Institute of Botany, Chinese Academy of Sciences

Freeze–thaw‐induced N2O pulses could account for nearly half of annual N2O fluxes in cold climates, but their episodic nature, sensitivity to snow cover dynamics, and the challenges of cold‐season monitoring complicate their accurate estimation and representation in global models. To address these challenges, we combined in situ automated high‐frequency flux measurements with cross‐ecoregion soil core incubations to investigate the mechanisms driving freeze–thaw‐induced N2O emissions. We found that deepened snow significantly amplified freeze–thaw N2O pulses, with these ~50‐day episodes contributing over 50% of annual fluxes. Additionally, freeze–thaw‐induced N2O pulses exhibited significant spatial heterogeneity, ranging from 3.4 to 1184.1 μg N m⁻² h⁻¹ depending on site conditions. Despite significant spatiotemporal variation, our results indicated that 68%–86% of this variation can be explained by shifts in controlling factors: from water‐filled pore space (WFPS), which drove anaerobic conditions, to microbial constraints as snow depth increases. Below 43% WFPS, soil moisture was the overwhelmingly dominant driver of emissions; between 43% and 66% WFPS, moisture and microbial attributes (including denitrifying gene abundance, nitrogen enzyme kinetics, and microbial biomass) jointly triggered N2O emissions pulses; above 66% WFPS, microbial attributes, particularly nitrogen enzyme kinetics, prevailed. These findings suggested that maintaining higher soil moisture served as a trigger for activating microbial activity, particularly enhancing nitrogen cycling. Furthermore, we showed that hotspots of freeze–thaw‐induced N2O emissions were linked to high root production and microbial activity in cold and humid grasslands. Overall, our study highlighted the hierarchical control of WFPS and microbial processes in driving freeze–thaw‐induced N2O emission pulses. The easily measurable WFPS and microbial attributes predictable from plant and soil properties could forecast the magnitude and spatial distribution of N2O emission “hot moments” under changing climate. Integrating these hot moments, particularly the dynamics of WFPS, into process‐based models could refine N2O emission modeling and enhance the accuracy of global N2O budget prediction.

It remains uncertain whether native plant diversity increases resistance to plant invasions at meaningful scales in nature due to contradictions between observational and experimental studies. In a field survey of 253 sites spanning 15 latitudinal degrees in China, we found that the relative abundance of the invader Alternanthera philoxeroides decreased with increasing native plant richness. Results from a 3‐year field experiment and a 2‐year mesocosm experiment further demonstrated that native diversity can suppress A. philoxeroides population growth (but not dominance) when natives precede the invader, or limit its population size when natives arrive after the invader. Insect herbivores and the soil biota were unlikely to influence diversity‐based resistance in the field experiment, as their effects on both A. philoxeroides and native species did not change with native richness. Our results provide solid evidence that native plant diversity can provide resistance against plant invasion in natural ecosystems.

Allocation of leaf phosphorus (P) among different functional fractions represents a crucial adaptive strategy for optimizing P use. However, it remains challenging to monitor the variability in leaf P fractions and, ultimately, to understand P‐use strategies across diverse plant communities. We explored relationships between five leaf P fractions (orthophosphate P, Pi; lipid P, PL; nucleic acid P, PN; metabolite P, PM; and residual P, PR) and 11 leaf economic traits of 58 woody species from three biomes in China, including temperate, subtropical and tropical forests. Then, we developed trait‐based models and spectral models for leaf P fractions and compared their predictive abilities. We found that plants exhibiting conservative strategies increased the proportions of PN and PM, but decreased the proportions of Pi and PL, thus enhancing photosynthetic P‐use efficiency, especially under P limitation. Spectral models outperformed trait‐based models in predicting cross‐site leaf P fractions, regardless of concentrations (R² = 0.50–0.88 vs 0.34–0.74) or proportions (R² = 0.43–0.70 vs 0.06–0.45). These findings enhance our understanding of leaf P‐allocation strategies and highlight reflectance spectroscopy as a promising alternative for characterizing large‐scale leaf P fractions and plant P‐use strategies, which could ultimately improve the physiological representation of the plant P cycle in land surface models.

Soil nematode communities are increasingly subjected to pressures from multiple global change drivers, such as nitrogen (N) enrichment and land management practices. Although the critical role of N inputs in regulating soil nematode communities has been well studied, the contrasting responses of soil nematode diversity to N enrichment in natural versus managed ecosystems remain poorly understood. To address this knowledge gap, we conduct a global meta‐analysis using 3323 paired observations from 173 publications to quantify the impacts of mineral N inputs on the richness and abundance of soil nematode diversity across natural ecosystems (e.g. unmanaged grasslands and forests) and managed ecosystems (e.g. croplands). N enrichment significantly reduced the richness and abundance of soil nematode communities in natural ecosystems, primarily driven by the prohibiting effects of N enrichment‐induced soil ammonium toxicity and soil acidification on the abundances of plant‐feeding, fungal‐feeding and omnivorous‐carnivorous nematodes. In contrast, while N enrichment reduced the taxon richness of soil nematodes in managed ecosystems, it did not diminish their total abundance. This discrepancy may be explained by the increased soil microbial biomass under N enrichment, which favoured the dominance of bacterial‐feeding nematodes. These nematodes thrived at the expense of other trophic guilds with low resource competitiveness and high N sensitivities, leading to a loss of species diversity but maintaining overall community abundance. Furthermore, the responses of soil nematode richness and abundance to N enrichment in managed ecosystems were not regulated by N addition regimes and climate factors. This suggests that management practices may override the constraints imposed by climate change on nematode diversity. Synthesis and application. Our findings demonstrate that N enrichment exerts a greater negative impact on soil nematode diversity in natural ecosystems compared with managed cropping systems, which arises from the distinct responses of different soil nematode trophic guilds to management practices and environmental changes. Understanding the mechanisms underlying the contrasting effects of N enrichment on soil nematode diversity in natural versus managed ecosystems is critical for enhancing the ecological resilience of soil food webs and sustaining soil biodiversity in the face of global change.

Precipitation fluctuations strongly influence biomass production and its stability of terrestrial ecosystems. However, our understanding of the extent to which plant communities adjust their water‐use strategies in response to non‐growing season precipitation variations remains limited. Our 5‐year snow manipulation experiment in a semi‐arid grassland, complemented with paired stable isotope measurements of δ¹⁸O and δ¹³C for all species within the community, demonstrated that the impact of snowmelt on plant physiological activities extended into the peak growing season. Deepened snow enhanced ecosystem water use efficiency (WUE), biomass production, and its temporal stability. We further examined whether the observed increase in biomass stability was associated with the functional diversity of plant water‐use strategies. Plant cellulose Δ¹⁸Ocell analysis revealed that both community‐weighted mean and functional dispersion of stomatal conductance were positively associated with biomass production and its stability. The δ¹³C results further indicated that even with increased stomatal conductance, grasses were able to maintain their high intrinsic WUE by increasing photosynthesis more than transpiration. This resulted in higher biomass and greater dominance of high‐WUE functional groups under deepened snow. In addition, we also found that deepened snow increased root biomass, particularly in the 0‐ to 5‐cm and 20‐ to 40‐cm soil layers. This increase in root biomass enhanced the uptake of snowmelt from both surface and deep soil layers, further contributing to community stability. Overall, our study demonstrates that plant communities can optimize water acquisition and utilization, thereby enhancing the stability of biomass production through coordinated changes in plant physiology, species reordering, and root distribution under altered snow regimes.

Global climate changes and intensified land use have made desertification one of the most pressing threats to vegetation integrity and associated ecosystem services worldwide. Wind‐eroded desertified patches (WEDP) in sandland vegetation communities threaten semiarid sandland ecosystems. Although the soil seed bank can be replenished by surrounding vegetation, the self‐renewal of vegetation within WEDP remains severely constrained by low soil nutrient availability, high maximum daytime soil surface temperatures, frequent eolian sand dynamics activity, and fast soil desiccation. We hypothesized that a positive feedback of environmental harshness inside such patches leads to growing patch size with impoverished current regeneration by seedlings and future potential regeneration from the seed bank. To test this hypothesis, we chose WEDPs of different sizes as representatives of different retrogressive succession stages in sandlands in northern China, and investigated the effects of environmental changes among these successive stages on the densities and composition of soil seed banks and seedling regeneration. We found that WEDPs had unique internal environmental conditions, different from their surrounding area, which caused the failed establishment of seedlings even where a substantial soil seed bank existed. Seed bank and seedling densities and composition in WEDPs were strongly influenced by patch size, surrounding vegetation, and the prevailing strong wind. Because of the positive feedback between patch size and environmental degradation with retrogressive succession, human intervention is needed to promote future vegetation regeneration in WEDPs. Based on our findings, we propose a combination of the following interventions: (1) building sand barriers or planting native, drought‐tolerant shrubs, (2) adding seeds of key local species to enrich the soil seed bank and increase the possibility of successful vegetation regeneration, and (3) improving soil stabilization, moisture retention, and fertility by covering the soil with local plant litter.

The goal of the EcoVeg approach is to fully describe and classify the diversity of the Earth's terrestrial ecosystems based on vegetation and ecological processes. The EcoVeg approach was used to develop the International Vegetation Classification (IVC) and various national classifications, which integrate patterns of vegetation growth form, structure, and floristics with ecological and biogeographic drivers at multiple spatial scales, from global formations to local plant communities. The approach remains unique among terrestrial ecological classifications in providing types at these scales. However, as a terrestrial typology, lack of context with respect to freshwater, marine and subterranean realms limited its clarity. Further, growth forms and structure were limited to readily observable features, which excluded important functional traits. The release by the International Union for Conservation of Nature (IUCN) of the Global Ecosystem Typology (GET) presented an opportunity to revisit the EcoVeg approach because GET has a conceptually robust, scalable, and spatially explicit functional approach for all of earth's ecosystems (terrestrial, freshwater, marine, subterranean). Here, we briefly introduce the EcoVeg approach and the GET, and then outline a biome‐based revision to EcoVeg and the IVC that builds on the strengths of GET for global terrestrial types and the IVC for continental to local terrestrial types. The outcome is a revised IVC that we rename the ecosystem‐based International Vegetation Classification (eIVC). As with GET, the eIVC has a conceptual foundation based on realms and transitional realms, but it focuses on the terrestrial and transitional terrestrial (wetland) realms. It then fully implements terrestrial biome concepts across all the upper levels based on the integration of vegetation with global ecosystem processes and properties. Interoperable compatibility with GET is reflected in the fact that 84% of the global ecosystem types are largely equivalent, which facilitates the linkage of GET with the continental to local ecosystem types of the eIVC. The revisions that now form the eIVC will enhance collaborative development of ecosystem types across the globe and provide more robust opportunities for co‐application of the eIVC and GET in the terrestrial realm for management, conservation, and restoration.

Based on observations of living plants of Hydrocotyle calcicola in the field, together with examination of herbarium specimens and descriptions of both H. calcicola and H. chiangdaoensis (including type material), we demonstrated that H. calcicola is a synonym of H. chiangdaoensis. The species was previously compared with H. sibthorpioides; our phylogenetic analysis revealed that H. chiangdaoensis and H. sibthorpioides belong to different lineages, the former being closely related to the larger-leaved clade.

Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass worldwide. However, bermudagrass often faces the challenges from drought stress in practical application. Selection and breeding of drought-tolerant cultivars of bermudagrass is crucial for thriving in arid environments. In this study, we employed two different drought-tolerant bermudagrass cultivars ‘Yangjiang’ and ‘Guanzhong’ to assess the morphology, physiology and transcriptome under various drought stress conditions. The outcomes unveiled that drought-tolerant ‘Guanzhong’ exhibited superiority in morphology, light utilization efficiency, relative water content, antioxidant and osmotic regulation capabilities compared to drought-susceptible ‘Yangjiang’. In addition, transcriptome sequencing showed that photosynthesis, amino acid metabolism, peroxisome and plant hormone signal transduction pathways were the key metabolic pathways of bermudagrass in response to drought stress. Compared to the drought-sensitive cultivar ‘Yangjiang’, the drought-tolerant ‘Guanzhong’ exhibited lower expression of AUX/IAA genes (negative regulators of auxin signaling), which reduces their inhibitory effect on auxin response factors (ARF), thereby enhancing auxin signaling efficiency to coordinate adaptive growth. Additionally, compared with ‘Yangjiang’, the down-regulated protein phosphatases (PP2C) in ‘Guanzhong’ weaken their suppression of SnRK2, resulting in heightened ABA signaling sensitivity. In comparison to ‘Yangjiang’, ‘Guanzhong’ displayed a higher IAA concentration and a lower ABA concentration under stress conditions, thus ensuring a more efficient utilization of water by minimizing stomatal aperture and reducing water evaporation. The results suggested that regulation of morphology, physiological metabolism and genes expression could contribute to drought tolerance in bermudagrass. Graphical Abstract

With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.

Land plants evolved mechanisms to cope with terrestrial challenges. The methylerythritol phosphate (MEP) pathway intermediate 2‐ C‐ methyl‐D‐erythritol 2,4‐cyclodiphosphate (MEcPP) plays a central role in chloroplast retrograde signalling (CRS) and stress responses in Arabidopsis. However, its regulation in nonvascular plants remains underexplored. This study characterizes the 1‐hydroxy‐2‐methyl‐2‐( E )‐butenyl‐4‐diphosphate synthase (HDS) gene family in Physcomitrium patens , uncovering unique evolutionary patterns with multiple HDS copies compared to the single‐copy HDS in most angiosperms. We demonstrate that HDS catalyses a key step in MEP and interacts with heat shock transcription factor A1 (HSFA1) to modulate thermotolerance. CRISPR/LbCas12a‐edited hds mutants exhibited enhanced thermotolerance and elevated MEcPP levels, with exogenous MEcPP mimicking this effect. Transcriptomic analysis identified upregulated stress‐responsive genes, including small heat shock proteins, which prepare the plant for heat stress. This priming effect depends on HSFA1, which regulates MEP pathway genes, including HDS , thereby influencing MEcPP accumulation and thermotolerance. Furthermore, HDS and HSFA1 synergistically regulate growth in P. patens , with hds2 hds3 hsfa1 triple mutant displaying reduced size, lower IAA levels, and altered non‐photochemical quenching. These findings highlight a novel HDS‐HSFA1 regulatory module, expanding CRS paradigms and offering new insights into the evolution of stress adaptation in bryophytes, bridging gaps in understanding HDS function across species.

The mechanisms underlying leaf variegation in the ornamental Ilex × ‘Solar Flare’ remain poorly understood. To investigate this phenomenon, we conducted a comprehensive characterization of its variegated leaves. Compared to green sectors, yellow sectors exhibited severe chloroplast structural abnormalities, including swollen chloroplasts, damaged thylakoid membranes, and reduced chloroplast numbers. These yellow sectors also showed significantly lower chlorophyll and carotenoid levels, along with a depletion of key chlorophyll precursors—protoporphyrin IX (Proto IX), magnesium protoporphyrin IX (Mg-Proto IX), and protochlorophyllide (Pchlide). Photosynthetic efficiency was significantly impaired. Comparative transcriptome analysis identified 3510 differentially expressed genes (DEGs) between yellow and green sectors. Key disruptions in chlorophyll biosynthesis included upregulated CHLD expression and downregulated CHLH and CHLG expression, leading to impaired chlorophyll synthesis. Additionally, chlorophyll degradation was accelerated by PAO upregulation. Defective chloroplast development in yellow sectors was associated with the downregulation of GLK1, GLK2, and thylakoid membrane-related genes (PsbC, PsbO, PsbR, PsaD, and PsaH). These molecular alterations likely drive the variegated phenotype of I. × ‘Solar Flare’. These observations advance our understanding of the genetic and physiological mechanisms regulating leaf variegation in this cultivar.

While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe–metabolite relationship. These results provide novel insight into how the environment–microbiome–plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision‐making in vineyard microbial management.

Three major hypotheses aim to explain latitudinal trends of leaf phosphorus (P) concentration: the Temperature-Plant Physiological Hypothesis (TPH), Soil-Nutrient Hypothesis (SNH) and Evergreen-Deciduous Hypothesis (EDH). However, these hypotheses only address leaf total P, preventing a deeper insight into the underlying physiological mechanisms. We extended these hypotheses to include variations in leaf P fractions with different physiological functions (extended TPH, SNH and EDH, respectively). We analysed latitudinal variation in leaf P fractions and their correlations with mean annual temperature (MAT), soil total P concentration (soil TP), and leaf habit. Leaf total P and P-fraction concentrations increased with increasing latitude in the Northern Hemisphere, with metabolic P increasing most. The concentrations of all leaf P fractions, higher in deciduous than in evergreen plants, increased with decreasing MAT and increasing soil TP. The proportion of metabolic P was higher at low MAT and in deciduous plants, while that of residual P increased with increasing soil TP. MAT had a much stronger influence than other factors on leaf P fractions, especially for their allocation proportions. Our results predominantly supported the extended TPH, but also generally supported the other two hypotheses, highlighting eco-physiological mechanisms underpinning the macroecology of plant P-use strategy.

The formation of boundaries, or inhibition zones, between neighboring colonies is a prevalent phenomenon in nature, occurring not only between different species but also within the same species or even within a single colony. The first paper in this series presents extracellular Fenton chemistry as an alternative mechanism for cellular energy production. Specifically, PKS‐derived polycyclic aromatic metabolites initiate and amplify robust extracellular Fenton reactions, whereas NRPS‐derived siderophores or iron chelators recycle iron and protect the host from the potentially harmful effects of these reactions. Our findings further demonstrate that extracellular Fenton reactions are pivotal in the formation of boundaries, both within and between strains and species. PKS‐derived aromatic metabolites promote the establishment of self‐inhibition boundaries, while NRPS‐derived siderophores primarily alleviate these boundaries. Notably, the development of these boundaries can be modulated by adjusting media components, such as proteins and starch, thereby influencing metabolic pathways. Consequently, experimental methodologies should be redesigned not merely to assess the antibiotic properties of compounds or metabolites, but to investigate their involvement in extracellular Fenton reactions and self‐protection mechanisms, which are fundamental to understanding their natural biological roles.

Salix brachista, commonly known as the Cushion willow, is a plant species that is indigenous to the alpine ice edge zones. This remarkable plant is predominantly found in the Hengduan Mountains. As a quintessential example of an alpine plant, the development of a genetic transformation system for Salix brachista is of paramount importance for unraveling the origins and the intricate mechanisms that underpin the diversity of alpine plant species. In the course of our research, we initially focused on creating a robust regeneration system for this species, utilizing stem segments of Salix brachista. Through meticulous optimization of various factors, we achieved a commendable average regeneration rate of 52%. Building upon this foundational work, we then established a straightforward and highly effective genetic transformation protocol, employing the Agrobacterium-mediated method. The successful establishment of this genetic transformation method not only represents a significant advancement in itself but also opens up new avenues for further gene editing and functional research endeavors in Salix brachista.

Trichomes and cuticles are critical epidermal adaptations that serve protective roles in plants. The cuticle functions as a barrier, allowing for controlled interactions between the plant and its environment. Cutin synthesis is crucial for plants to withstand various external stresses. In this study, we report on the Arabidopsis mutant gpat1 gpat2 , which exhibits a highly permeable cuticle and defects in trichome development. Mutation of GPAT1 and GPAT2 resulted in a reduction of cutin monomer. In gpat1 gpat2 , the structure of the cuticular layer of the cell wall is notably altered. Additionally, GPAT1 and GPAT2 are found to negatively regulate the synthesis of lignin and cellulose, which are related to secondary cell wall (SCW) formation. The dysfunction of GPAT1 and GPAT2 disrupted the water balance of the plant. Our findings reveal a network where mitochondrial GPAT1 and GPAT2 play roles in maintaining water balance by participating in both Arabidopsis cutin synthesis and SCW formation.