Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Effects of Simulated Nitrogen and Phosphorus Deposition on Dioecious Populus cathayana Growth and Defense Traits

Human activities have increased the imbalance in atmospheric N and P deposition, which changes soil nutrient availability and subsequently affects the structure and function of terrestrial ecosystems. Dioecious plants are important parts of terrestrial ecosystems and are characterized by sex-related differences in their response to the external environment and always exhibit a skewed sex ratio, which makes them more vulnerable to climate change and increases their risk of extinction. However, little attention has been paid to the effects of unbalanced N and P deposition on these plants, especially on their defense traits. In this study, we used dioecious Populus cathayana to investigate the influence of gradient N and P deposition on the correlation between growth and defense traits. The results showed that although the different rates of N and P deposition enhanced biomass accumulation in both sexes to varying degrees, the most substantial biomass increment was noted under a lower-nitrogen and higher-phosphorus (LNHP) treatment regimen, with females showing an approximately 112% increase and males a 47% increase in total biomass. In response to varying levels of simulated N and P deposition, males and females adopt distinct strategies for biomass allocation. Although declines in root biomass were observed in both sexes as nutrient availability increased, the decrement was more marked in males; under the LNHP treatment, it dropped by about 11%, while under a high-nitrogen and high-phosphorus (HNHP) treatment, the decrease was about 35%. Conversely, females demonstrated a heightened propensity to allocate biomass towards leaf development. Furthermore, with increasing N and P deposition, there was a general reduction in the concentrations of physical and chemical defense substances within the leaves of both sexes. Nonetheless, the correlations between defense substances, nutrient element content, non-structural carbohydrate (NSC) content, and dry biomass were more pronounced in males, suggesting a greater sensitivity to defense substance responses in males than in females. Overall, these results indicate that there is sexual dimorphism in the accumulation of chemical substances in male and female P. cathayana under unbalanced N and P deposition and they provide a technical and theoretical basis for predicting the population dynamics of dioecious plants, maintaining the stability of poplar populations, and constructing high-productivity poplar plantations globally in the future.

Simulated nitrogen deposition enhances resistance of female poplars over males to Pestalotiopsis microspora infection through the recruitment of antagonistic microbes in phyllosphere

Atmospheric nitrogen deposition has globally increased due to human activities and has strongly interfered with plant growth and resistance to biotic stressors. Dioecious plant species have shown secondary dimorphism in growth and development between male and female individuals in response to increased nitrogen deposition. However, the extent to whether these sexual differences influence variations in phyllosphere microbial communities and the associated pathogen resistance between male and female conspecifics remains unclear. To address this knowledge gap, female and male full-sibs of a poplar species were exposed to simulated nitrogen deposition and then artificially infected with a leaf pathogenic fungus, Pestalotiopsis microspora. The findings revealed that simulated nitrogen deposition promoted the growth of both sexes, with male plants exhibiting superior growth. Following P. microspora infection, female control plants displayed a greater leaf lesion area compared to males, but simulated nitrogen deposition reversed this difference. Further phyllosphere microbiome analysis and toxicity test indicated that the sexual differences in pathogen resistance between male and female conspecifics were likely attributable to alterations in the composition and structure of epiphytic microbes as the phyllosphere of female plants harbored a higher abundance of ecologically beneficial microbes with potential biological control capabilities, whereas males exhibited an increase abundance in the phytopathogens genera in response to simulated nitrogen deposition. Confirmatively, two bacterial strains were successfully isolated from the epiphytic phyllosphere of female plants that exhibited strong antagonistic effect against the pathogenic fungus P. microspora in both in vitro and in vivo conditions. The findings have significant implications for the selection of suitable poplar sexes for landscaping and reforestation efforts in areas experienced severe atmospheric nitrogen deposition.

Flavones enrich rhizosphere Pseudomonas to enhance nitrogen utilization and secondary root growth in Populus

Plant growth behavior is a function of genetic network architecture. The importance of root microbiome variation driving plant functional traits is increasingly recognized, but the genetic mechanisms governing this variation are less studied. Here, we collect roots and rhizosphere soils from nine Populus species belonging to four sections (Leuce, Aigeiros, Tacamahaca, and Turanga), generate metabolite and transcription data for roots and microbiota data for rhizospheres, and conduct comprehensive multi-omics analyses. We demonstrate that the roots of vigorous Leuce poplar enrich more Pseudomonas, compared with the poorly performing poplar. Moreover, we confirm that Pseudomonas is strongly associated with tricin and apigenin biosynthesis and identify that gene GLABRA3 (GL3) is critical for tricin secretion. The elevated tricin secretion via constitutive transcription of PopGL3 and Chalcone synthase (PopCHS4) can drive Pseudomonas colonization in the rhizosphere and further enhance poplar growth, nitrogen acquisition, and secondary root development in nitrogen-poor soil. This study reveals that plant-metabolite-microbe regulation patterns contribute to the poplar fitness and thoroughly decodes the key regulatory mechanisms of tricin, and provides insights into the interactions of the plant's key metabolites with its transcriptome and rhizosphere microbes.

Comparative analysis of community composition and network structure between phyllosphere endophytic and epiphytic fungal communities of Mussaenda pubescens

The phyllosphere constitutes a critical habitat for microorganisms, exerting profound influences on host vitality, developmental dynamics, reproductive functions, and stress resilience. However, the diversity and network structure of endophytic and epiphytic fungal communities within this microecosystem have not been thoroughly explored. In this investigation, high-throughput sequencing technologies were employed to assess the diversity, community composition, and network structure of endophytic and epiphytic fungal communities associated with Mussaenda pubescens across six geographically distinct locations in Southeast China. The results revealed significant differences in community composition and diversity between endophytic and epiphytic fungi, with pronounced geographical variation observed within these phyllosphere fungal communities. Network analysis indicated that epiphytic fungal networks possess enhanced complexity compared with their endophytic counterparts, although the latter exhibit greater network stability. Moreover, stochastic processes were identified as pivotal in shaping the composition of these fungal communities. This research substantially enriches our comprehension of the diversity and organizational mechanisms of phyllosphere fungal communities, providing novel insights into the modalities of species coexistence and the stability of community equilibrium within ecosystems.IMPORTANCEThis study employs high-throughput sequencing technologies to explore the fungal communities within the phyllosphere of Mussaenda pubescens across Southeast China, offering significant insights into plant mycobiome. It demonstrates geographical variations in these fungal communities, with epiphytic fungi exhibiting more complex interaction networks compared with the endophytic fungi. Crucially, the research indicates that stochastic processes play a substantial role in the composition of fungal communities. These findings enhance our comprehension of plant-associated microecosystems and underscore the intricate interplay of randomness in maintaining ecosystem stability and diversity.

Functional redundancy enables a simplified consortium to match the lignocellulose degradation capacity of the original consortium

The relationship between structure and function in microbial communities is intriguing and complex. In this study, we used single-carbon source domestication to derive consortium YL from the straw-degrading consortium Y. Y and YL exhibited similar straw degradation capabilities, yet YL harbored only half the species diversity of Y, with distinct dominant species. The most enriched microorganisms in Y were Ureibacillus, Acetanaerobacterium, and Hungateiclostridiaceae, whereas Bacillaceae, Bacillus, and Peptostreptococcales-Tissierellales were most enriched in YL. In-depth analysis revealed that Y and YL had comparable abundances of core lignocellulose-degrading genes, as validated by lignocellulolytic enzyme activity assays. However, the number of species harboring these key lignocellulose-degrading genes (K01179, K01181, K00432) in YL was reduced by over 50%, suggesting that functional redundancy enabled YL to maintain similar degradation capabilities to Y despite reduced diversity. Further analyses of key degradative species and co-occurrence networks highlighted the critical functional roles of dominant degradative species within these communities. An analysis of the overall functional pathways in the two microbial consortia revealed distinct metabolic characteristics between them. Pathways such as polycyclic aromatic hydrocarbon degradation and fluorobenzoate degradation were down-regulated in YL compared to Y, a finding corroborated by the metabolomic data. These results suggest a coupling between community structure and functional capacities within these microbial consortia. Overall, our findings deepen our understanding of the structure-function relationship in microbial communities and provide valuable insights for the design of lignocellulose-degrading consortia.

Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.

Sex-specific responses of Taxus mairei to UV-B radiation involved altering the interactions between the microbiota assembly and host secondary metabolism

BACKGROUND

To adapt to constantly changing environments, ancient gymnosperms have coevolved with diverse endophytic fungi that are essential for the fitness and adaptability of the plant host. However, the effect of sex on plant-endophyte interactions in response to environmental stressors remains unknown. RNA-seq integrated with ITS analysis was applied to reveal the potential mechanisms underlying the sex-specific responses of Taxus mairei to ultraviolet (UV)-B radiation.

RESULTS

Enrichment analysis suggested that sex influenced the expression of several genes related to the oxidation-reduction system, which might play potential roles in sex-mediated responses to UV-B radiations. ITS-seq analysis clarified the effects of UV-B radiation and sex on the composition of endophytic fungal communities. Sex influenced various secondary metabolic pathways, thereby providing chemicals for T. mairei host to produce attractants and/or inhibitors to filter microbial taxa. Analysis of fungal biomarkers suggested that UV-B radiation reduced the effect of sex on fungal communities. Moreover, Guignardia isolate #1 was purified to investigate the role of endophytic fungi in sex-mediated responses to UV-B radiation. Inoculation with spores produced by isolate #1 significantly altered various oxidation-reduction systems of the host by regulating the expression of APX2, GST7 NCED1, ZE1, CS1, and CM1.

CONCLUSION

These results revealed the roles of endophytic fungi in sex-mediated responses to UV-B radiation and provided novel insights into the sex-specific responses of Taxus trees to environmental stressors. Video Abstract.

Amaranth Plants with Various Color Phenotypes Recruit Different Soil Microorganisms in the Rhizosphere

To explore and utilize the abundant soil microorganisms and their beneficial functions, high-throughput sequencing technology was used to analyze soil microbial compositions in the rhizosphere of red and green amaranth varieties. The results showed that significant differences in soil microbial composition could be found in the rhizosphere of amaranth plants with different color phenotypes. Firstly, soil bacterial compositions in the rhizosphere were significantly different between red and green amaranths. Among them, Streptomyces, Pseudonocardia, Pseudolabrys, Acidibacter, norank_ f_ Micropepsaceae, Bradyrhizobium, and Nocardioides were the unique dominant soil bacterial genera in the rhizosphere of red amaranth. In contrast, Conexibacter, norank_f_norank_o_norank_c_TK10, and norank_f_ norank_o_ norank_ c_AD3 were the special dominant soil bacterial genera in the rhizosphere of green amaranth. Additionally, even though the soil fungal compositions in the rhizosphere were not significantly different between red and green amaranths, the abundance of the dominant soil fungal genera in the rhizosphere showed significant differences between red and green amaranths. For example, unclassified_k__Fungi, Fusarium, Cladophialophora, unclassified_c__Sordariomycetes and unclassified_p__Chytridiomycota significantly enriched as the dominant soil fungal genera in the rhizosphere of the red amaranth. In contrast, Aspergillues only significantly enriched as the dominant soil fungal genus in the rhizosphere of green amaranth. All of the above results indicated that amaranth with various color phenotypes exactly recruited different microorganisms in rhizosphere, and the enrichments of soil microorganisms in the rhizosphere could be speculated in contributing to amaranth color formations.

Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens?

Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.

Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential

The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology.

How does plant sex alter microbiota assembly in dioecious plants?

Plant microbiota can greatly impact plant growth, defense, and health in different environments. Thus, it might be evolutionarily beneficial for plants to be able to control processes related to microbiota assembly. Dioecious plant species display sexual dimorphism in morphology, physiology, and immunity. These differences imply that male and female individuals might differently regulate their microbiota, but the role of sex in microbiota assembly has been largely neglected so far. Here, we introduce the mechanism of how sex controls microbiota in plants analogically to the sex regulation of gut microbiota in animals, in particular in humans. We argue that plant sex imposes selective pressure on filtering and constructing microbiota in the rhizosphere, phyllosphere, and endosphere along the soil-plant continuum. Since male plants are more resistant than female plants to environmental stresses, we suggest that a male host forms more stable and resistant plant microbiota that cooperate more effectively with the host to resist stresses. Male and female plants can distinguish whether a plant is of the same or different sex, and males can alleviate stress-caused damage in females. The impact of a male host on microbiota would protect female plants from unfavorable environments.

Drought stress-mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars

Phyllosphere-associated microbes play a crucial role in plant-pathogen interactions while their composition and diversity are strongly influenced by drought stress. As dioecious plant species exhibited secondary dimorphism between the two sexes in response to drought stress, whether such difference will lead to sex-specific differences in phyllosphere microbiome and associated pathogen resistance between male and female conspecifics is still unknown. In this study, we subjected female and male full siblings of a dioecious poplar species to a short period of drought treatment followed by artificial infection of a leaf pathogenic fungus. Our results showed that male plants grew better than females with or without drought stress. Female control plants had more leaf lesion area than males after pathogen infection, whereas drought stress reversed such a difference. Further correlation and in vitro toxicity tests suggested that drought-mediated sexual differences in pathogen resistance between the two plant sexes could be attributed to the shifts in structure and function of phyllosphere-associated microbiome rather than the amount of leaf main defensive chemicals contained in plant leaves. Supportively, the microbiome analysis through high-throughput sequencing indicated that female phyllosphere enriched a higher abundance of ecologically beneficial microbes that serve as biological plant protectants, while males harbored abundant phytopathogens under drought-stressed conditions. The results could provide potential implications for the selection of suitable poplar sex to plants in drought or semi-drought habitats.

Nutrient resorption responses of female and male Populus cathayana to drought and shade stress

Nutrient resorption can increase nutrient use and play important roles in terrestrial plant nutrient cycles. Although several studies have reported individual responses of plant nutrient resorption to drought or shade stress, the interaction of drought and shade remains unclear, especially for dioecious plants. This study explored whether nutrient resorption is correlated to growth characteristics (such as biomass and root/shoot ratio [R/S ratio]) and leaf economics (such as leaf thickness, leaf mass per area [LMA] and leaf vein density [LVD]) in female and male Populus cathayana across different conditions. We found that drought stress significantly increased nitrogen (N) resorption efficiency (NRE) in both sexes, but shade and interactive stress decreased NRE in P. cathayana females. Under drought stress, nutrient resorption was sexually dimorphic such that P. cathayana males have higher NRE than females. Furthermore, NRE and phosphorous (P) resorption efficiency (PRE) were positively related to R/S ratio, leaf thickness, LMA, and LVD in both sexes across different treatments. Our study is the first to present how nutrient resorption is related to biomass accumulation and allocation, and leaf economics, suggesting that nutrient uptake may be modulated by R/S ratio and leaf economics, which is important for understanding the conservation mechanism of plant nutrients.

Selenium species transforming along soil-plant continuum and their beneficial roles for horticultural crops

Selenium (Se) acquirement from daily diet can help reduce the risk of many diseases. The edible parts of crop plants are the main source of dietary Se, while the Se content in crops is determined by Se bioavailability in soil. We summarize recent research on the biogeochemical cycle of Se driven by specific microorganisms and emphasize the oxidizing process in the Se cycle. Moreover, we discuss how plant root exudates and rhizosphere microorganisms affect soil Se availability. Finally, we cover beneficial microorganisms, including endophytes, that promote crop quality and improve crop tolerance to environmental stresses. Se availability to plants depends on the balance between adsorption and desorption, reduction, methylation and oxidation, which are determined by interactions among soil properties, microbial communities and plants. Reduction and methylation processes governed by bacteria or fungi lead to declined Se availability, while Se oxidation regulated by Se-oxidizing microorganisms increases Se availability to plants. Despite a much lower rate of Se oxidization compared to reduction and methylation, the potential roles of microbial communities in increasing Se bioavailability are probably largely underestimated. Enhancing Se oxidation and Se desorption are crucial for the promotion of Se bioavailability and uptake, particularly in Se-deficient soils. Beneficial roles of Se are reported in terms of improved crop growth and quality, and enhanced protection against fungal diseases and abiotic stress through improved photosynthetic traits, increased sugar and amino acid contents, and promoted defense systems. Understanding Se transformation along the plant-soil continuum is crucial for agricultural production and even for human health.

Rapid biodegradation of atrazine by a novel Paenarthrobacter ureafaciens ZY and its effects on soil native microbial community dynamic

An atrazine-utilizing bacterium, designated as ZY, was isolated from agricultural soil and identified as Paenarthrobacter ureafaciens. The P. ureafaciens ZY demonstrated a significant degradation capacity of atrazine, with the degradation efficiency of 12.5 mg L^-1 h^-1 in liquid media (at pH 7, 30°C, and the atrazine level of 100 mg L^-1). The P. ureafaciens ZY contained three atrazine-degrading genes (i.e., trzN, atzB, and atzC) could metabolize atrazine to form cyanuric acid, which showed lower biotoxicity than the parent atrazine as predicted by Ecological Structure Activity Relationships model. A laboratory-scale pot experiment was performed to examine the degradation of atrazine by P. ureafaciens ZY inoculation and investigate its effects on the native microbial communities. The results exhibited that the P. ureafaciens ZY was conductive to the degradation of atrazine, increased the total soil phospholipid fatty acids at the atrazine level of 50, 70, and 100 mg kg^-1. By using high-throughput sequencing analysis, Frateuria, Dyella, Burkholderia-Caballeronia-Paraburkholderia were considered as the most important indigenous atrazine-degrading microorganisms due to their relative abundances were positively correlated with the atrazine degradation rate. In addition, P. ureafaciens ZY also increased the abundance of atrazine-degrading genus Streptomyces and Bacillus, indicating that there may be a synergic relationship between them in the process of atrazine degradation. Our work provides a new insight between inoculums and native microorganisms on the degradation of atrazine.