Microbe-dependent and independent nitrogen and phosphate acquisition and regulation in plants

Optimizing plant phosphate uptake: Advances in the core regulatory mechanisms of phosphate starvation response proteins and their macromolecular partners: A review

Phosphorus (P), essential for plant survival, is primarily absorbed as inorganic phosphate (Pi), yet soil Pi scarcity severely limits plant growth and agricultural productivity. This review synthesizes current research on plant adaptations to Pi scarcity, with a focus on the root system as the primary site of Pi absorption and the role of MYB transcription factors, particularly PHOSPHATE STARVATION RESPONSE 1 (PHR1), a core regulatory biological macromolecule. PHR1 orchestrates a wide array of genetic responses that modify root architecture to enhance Pi acquisition under nutrient-poor conditions. This review delves into the biological activities, molecular associations, chemical and biological modifications, and functional properties of PHR1 and related MYB transcription factors, examining how these regulatory macromolecular proteins interact with other molecular components to form complexes that coordinate adaptive root development. By integrating findings from diverse plant species, the review highlights the potential of leveraging molecular breeding techniques to develop cultivars with enhanced phosphate uptake efficiency by targeting these regulatory macromolecular proteins. Such advancements promise to mitigate the impacts of Pi deficiency, supporting sustainable agricultural and forestry practices. The insights provided aim to inform and guide future research in plant nutrient management, focusing on the intricate interplay of biological and molecular factors that regulate phosphate uptake.

Micronutrients: Minor yet crucial for symbiotic nitrogen fixation

Nodulation represents a crucial but energy-intensive strategy for legumes to survive in nutrient-poor soils. A recent study by Ren et al. (2025) highlights the significance of micronutrients, particularly iron (Fe), in regulating symbiotic nitrogen fixation, which ensures that nodulation occurs only under favorable environmental conditions.

Genome-wide identification of WRKY transcription factor genes in Euphorbia lathyris reveals ElWRKY48 as a negative regulator of phosphate uptake and ingenol biosynthesis

WRKY transcription factors (TFs) play pivotal roles in regulating plant nutrient uptake, particularly phosphate (Pi) acquisition, and biosynthesis of secondary metabolites. Euphorbia lathyris, a significant medicinal plant with diverse pharmacological activities, lacks a systematic analysis of WRKY members and their functional roles. In this study, 58 ElWRKY genes were identified in the E. lathyris genome, classified into seven subgroups through comparative genomics analysis, and distributed on 10 chromosomes. Phylogenetic and expression pattern analyses identified ElWRKY48 as a candidate gene involved in Pi uptake regulation. The transgenic validation assay demonstrated that ElWRKY48 overexpression negatively regulated Pi uptake and led to phosphorus-deficient phenotypes in the hairy roots of E. lathyris. Furthermore, the transcriptome analysis revealed an opposite expression pattern between the Pi transporter gene ElPHT1 (Elat0034050.1) and ElWRKY48 in the transgenic lines overexpressing ElWRKY48. The negative regulation of ElPHT1 expression by ElWRKY48 was validated through qRT-PCR, Y1H, EMSA, gene knockout (CRISPR/Cas9), and LUC assays. Additionally, the overexpression of ElWRKY48 reduced diterpenoid ingenol biosynthesis by suppressing the expression of its biosynthesis-related genes. These findings provide valuable insights into the role of WRKY in Pi uptake and offer potential avenues for genetic improvement in the yield and quality of E. lathyris.

Natural variation in the GmVPE1 promoter contributes to phosphorus re-translocation to seeds and improves soybean yield

Phosphorus (P) is an essential yet frequently deficient plant nutrient. Optimizing P distribution and recycling between tissues is vital for improving P utilization efficiency (PUE). Yet, the mechanisms underlying the transport and re-translocation of P within plants remain unclear. Here, wide-ranging natural diversity in seed P allocation and positive correlations among yield traits were found using 190 soybean accessions in field trials. Among them, the P-efficient genotype BX10 outperformed BD2 in assessments of PUE that were largely explained through differences in P redistribution from pods to seeds under low P stress. Pods of BX10 were therefore subjected to transcriptome analysis, and GmVPE1 was identified as a vacuolar Pi transporter to investigate further. Importantly, significant DNA polymorphism in GmVPE1 promoter regions was remarkably associated with seed weight among soybean accessions grown on P-deficient soils. Further analyses suggested that mRNA abundance of GmVPE1 in haplotype 2 (Hap) is significantly higher than that GmVPE1Hap1. GmVPE1 was highly upregulated by P deficiency and preferentially expressed in pods, seeds, and seed coats, which was consistent with GUS staining using transgenic soybean plants carrying pGmVPE1Hap2::GUS. Near-isogenic lines carrying the GmVPE1Hap2 allele, along with stable transgenic soybeans overexpressing GmVPE1 in a GmVPE1Hap1 background, had increases in PUE, more seed setting, and greater yields in both greenhouse and field trials than control plants. In summary, natural variation among GmVPE1 alleles determines genetic expression and subsequent P re-translocation phenotypes, which impacts PUE and yield, and thereby makes this an important genetic resource for soybean molecular breeding.

Molecular Insights into the Positive Role of Soybean Nodulation by GmWRKY17

Soybean is an important economic oilseed crop, being rich in protein and plant oil, it is widely cultivated around the world. Soybeans have been shown to establish a symbiotic nitrogen fixation (SNF) with their compatible rhizobia, resulting in the formation of nodules. Previous studies have demonstrated the critical roles of phytohormones, such as abscisic acid and cytokinin, in the process of legume nodulation. The present study investigated the role of GmWRKY17, a homolog of Rosa hybrida (Rh)WRKY13 in regulating plant immunity through cytokinin content and abscisic acid signaling in soybean nodulation. Utilizing real-time PCR and histochemical staining, we demonstrated that GmWRKY17 is predominantly expressed in soybean root nodules. Subsequently, we analyzed the function of GmWRKY17-overexpression, RNA interference (RNAi), and the CRISPR/Cas9 system. Overexpression of GmWRKY17 significantly increases soybean nodule number, while RNAi or CRISPR/Cas9-mediated knockout of GmWRKY17 resulted in a dramatic repression of nodule formation in soybeans. These results highlight that GmWRKY17 functions as a positive regulator involved in soybean nodulation. Furthermore, manipulation of GmWRKY17 expression impacts the expression of genes associated with the nod factor (NF) signaling pathway, thereby influencing soybean nodulation. This study demonstrated that WRKY-type transcription factors are involved in the regulation of legume nodulation, offering new light on the molecular basis of the symbiotic interaction between legumes and rhizobia.

The Rhizophagus irregularis permease RiFTR1 functions without a ferroxidase partner for reductive iron transport

The contribution of arbuscular mycorrhizal fungi (AM fungi) to plant iron (Fe) acquisition has been demonstrated in several studies. A previous investigation revealed that the AM fungus Rhizophagus irregularis utilizes a high-affinity reductive pathway for Fe uptake, mediated by the Fe transporter RiFTR1. In this study, we used a genome-wide approach in R. irregularis to find genes encoding ferroxidases of the multicopper oxidase (MCO) gene family in an attempt to identify the ferroxidase partner of RiFTR1. Nine genes putatively encoding MCOs (RiMCO1-9) were identified. Yeast complementation assays demonstrated that RiMCO1 and RiMCO3 can function as ferroxidases, suggesting their involvement in the reductive Fe uptake pathway. Surprisingly, RiFTR1 was capable of transporting Fe in yeast without a ferroxidase partner, resembling the Fe transport mechanism of plant IRT1-like systems. RiFTR1 exhibited increase expression in arbuscules. Overexpression of RiFTR1 in Medicago truncatula roots led to enhanced mycorrhizal colonization and arbuscule abundance, highlighting the significance of Fe for AM symbiosis.

Microplastic effects on soil nitrogen cycling enzymes: A global meta-analysis of environmental and edaphic factors

Microplastic accumulation in soil ecosystems poses significant environmental concerns, potentially impacting nitrogen cycling processes and ecosystem health. This meta-analysis of 147 studies (1138 data points) assessed the impact of microplastics (MPs) on soil nitrogen-acquisition enzymes. We found that MPs exposure significantly increased soil urease (UE) and leucine aminopeptidase activities by 7.6 % and 8.0 %, respectively, while N-acetyl-β-D-glucosaminidase activity was not significantly affected. Biodegradable MPs showed more pronounced effects compared to conventional MPs. Enzyme activities were influenced by MPs properties (e.g., polymer type, size, concentration), experimental conditions (e.g., field or laboratory setting, temperature, nitrogen fertilization), and soil properties (e.g., clay content, pH, organic carbon, total nitrogen). For instance, acidic soils enhanced UE activity, while neutral soils reduced it. These findings emphasize the complex interactions between MPs and soil ecosystems, highlighting the need for context-specific environmental management strategies and policy-making approaches to mitigate the impacts of MPs pollution on soil health.

Labile Carbon Input Mitigates the Negative Legacy Effects of Nitrogen Addition on Arbuscular Mycorrhizal Symbiosis in a Temperate Grassland

Nitrogen (N) deposition and carbon (C) addition significantly influence the dynamics of plant-microbe interactions, particularly altering the symbiotic relationship between plants and arbuscular mycorrhizal fungi (AMF). However, the effects and underlying mechanisms of labile C input on the relationship between AMF and various plant species in a nitrogen-enriched environment remain a knowledge gap. A seven-year field experiment was conducted to examine how six levels of N and three levels of labile C addition impact AMF colonization in four key plant species: Leymus chinensis (Trin. ex Bunge) Tzvelev, Stipa baicalensis Roshev., Thermopsis lanceolata R. Br. and Potentilla bifurca Linn. Our results showed that N and C additions exert significantly different effects on the relationship between AMF and various plant species. Labile C addition mitigated historical N negative effects, particularly for S. baicalensis, enhancing AMF infection and promoting nutrient exchange under high-N and low-C conditions. The relationship between AMF and both L. chinensis and T. lanceolata changed to weak mutualism under low-N and high-C conditions, with significant decreases in vesicular and arbuscular abundance. Plant root stoichiometry plays a critical role in modulating AMF symbiosis, particularly under high-N and -C conditions, as reflected in the increased AMF infection observed in T. lanceolata and P. bifurca. Our findings emphasize the species-specific and nutrient-dependent AMF symbiosis, revealing that targeted C input can mitigate the legacy effects of N enrichment. Effective nutrient management is of crucial importance for ecological restoration efforts in temperate grasslands affected by long-term N enrichment.

MicroRNA399s and strigolactones mediate systemic phosphate signaling between dodder-connected host plants and control association of host plants with rhizosphere microbes

A dodder (Cuscuta) often simultaneously parasitizes two or more adjacent hosts. Phosphate (Pi) deficiency is a common stress for plants, and plants often interact with soil microbes, including arbuscular mycorrhizal fungi (AMF), to cope with Pi stress. Little is known about whether dodder transmits Pi deficiency-induced systemic signals between different hosts. In this study, dodder-connected plant clusters, each composed of two tobacco (Nicotiana tabacum) plants connected by a dodder, were established, and in each cluster, one of the two tobacco plants was treated with Pi starvation. AMF colonization efficiency, rhizosphere bacterial community, and transcriptome were analyzed in the other dodder-connected Pi-replete tobacco plant to study the functions of interplant Pi signals. We found that dodder transfers Pi starvation-induced systemic signals between host plants, resulting in enhanced AMF colonization, changes of rhizosphere bacterial communities, and alteration of transcriptomes in the roots of Pi-replete plants. Importantly, genetic analyses indicated that microRNA399s (miR399s) and strigolactones suppress the systemic Pi signals and negatively affect AMF colonization in the Pi-replete plants. These findings provide new insight into the ecological role of dodder in mediating host-host and host-microbe interactions and highlight the importance of strigolactone and miR399 pathways in systemic Pi signaling.

Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases

Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.

Recent advances in research on phosphate starvation signaling in plants

Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.

Modulation of plant immunity and biotic interactions under phosphate deficiency

Phosphorus (P) is an essential macronutrient for plant life and growth. P is primarily acquired in the form of inorganic phosphate (Pi) from soil. To cope with Pi deficiency, plants have evolved an elaborate system to improve Pi acquisition and utilization through an array of developmental and physiological changes, termed Pi starvation response (PSR). Plants also assemble and manage mutualistic microbes to enhance Pi uptake, through integrating PSR and immunity signaling. A trade-off between plant growth and defense favors the notion that plants lower a cellular state of immunity to accommodate host-beneficial microbes for nutrition and growth at the cost of infection risk. However, the existing data indicate that plants selectively activate defense responses against pathogens, but do not or less against non-pathogens, even under nutrient deficiency. In this review, we highlight recent advances in the principles and mechanisms with which plants balance immunity and growth-related processes to optimize their adaptation to Pi deficiency.

Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions

Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.

Effects of rainfall patterns in dry and rainy seasons on the biomass, ecostoichiometric characteristics, and NSC content of Fraxinus malacophylla seedlings

With global climate change and rising temperatures, rainfall will change. The impact of global rainfall changes on ecosystems has prompted people to delve deeper into how changes in rainfall affect plant growth; Plant biomass, nutrient element content, and non-structural carbohydrate content are very sensitive to changes in precipitation. Therefore, understanding the impact of rainfall changes on seedlings is crucial. However, it is currently unclear how the seedlings of Fraxinus malacophylla Hemsl in rocky desertification areas respond to changes in rainfall. In this study, the response of biomass, nutrient accumulation, and NSC content of Fraxinus malacophylla Hemsl seedlings to different rainfall intervals and rainfall during the dry and rainy seasons was studied. Use natural rainfall duration of 5 days (T) and extended rainfall duration of 10 days(T+) as rainfall intervals; average monthly rainfall was used as the control (W), with a corresponding 40% increase in rainfall (W+) and a 40% decrease in rainfall (W-) as rainfall treatments. The research results indicate that the biomass of roots, stems, and leaves, as well as the accumulation of C, N, and P in Fraxinus malacophylla Hemsl seedlings increase with the increase of rainfall, while the soluble sugar and starch content show a pattern of first increasing and then decreasing. The biomass and nutrient accumulation of each organ showed root>leaf>stem. Except for the beginning of the dry season, prolonging the duration of rainfall in other periods inhibits the biomass accumulation of Fraxinus malacophylla Hemsl seedlings, and promotes the accumulation of C, N, and P nutrients and an increase in soluble sugar and starch content. There was a significant positive correlation (P<0.05) between the nutrient contents of C, N, and P in various organs, as well as between soluble sugar and starch content; And N: P>16, plant growth is limited by P element. These results indicate that changes in rainfall can affect the growth and development of Fraxinus malacophylla Hemsl seedlings, increasing rainfall can promote biomass and nutrient accumulation of Fraxinus malacophylla Hemsl seedlings, and prolonging rainfall intervals and reducing rainfall have inhibitory effects on them. The exploration of the adaptation of Fraxinus malacophylla Hemsl seedlings to rainfall patterns has promoted a basic understanding of the impact of rainfall changes on the growth of Fraxinus malacophylla Hemsl. This provides a theoretical basis for understanding how Fraxinus malacophylla Hemsl can grow better under rainfall changes and for future management of Fraxinus malacophylla Hemsl artificial forests in rocky desertification areas.

Climate Factors Influence Above- and Belowground Biomass Allocations in Alpine Meadows and Desert Steppes through Alterations in Soil Nutrient Availability

Biomass is a direct reflection of community productivity, and the allocation of aboveground and belowground biomass is a survival strategy formed by the long-term adaptation of plants to environmental changes. However, under global changes, the patterns of aboveground-belowground biomass allocations and their controlling factors in different types of grasslands are still unclear. Based on the biomass data of 182 grasslands, including 17 alpine meadows (AMs) and 21 desert steppes (DSs), this study investigates the spatial distribution of the belowground biomass allocation proportion (BGBP) in different types of grasslands and their main controlling factors. The research results show that the BGBP of AMs is significantly higher than that of DSs (p < 0.05). The BGBP of AMs significantly decreases with increasing mean annual temperature (MAT) and mean annual precipitation (MAP) (p < 0.05), while it significantly increases with increasing soil nitrogen content (N), soil phosphorus content (P), and soil pH (p < 0.05). The BGBP of DSs significantly decreases with increasing MAP (p < 0.05), while it significantly increases with increasing soil phosphorus content (P) and soil pH (p < 0.05). The random forest model indicates that soil pH is the most important factor affecting the BGBP of both AMs and DSs. Climate-related factors were identified as key drivers shaping the spatial distribution patterns of BGBP by exerting an influence on soil nutrient availability. Climate and soil factors exert influences not only on grassland biomass allocation directly, but also indirectly by impacting the availability of soil nutrients.

How are microbes helping end hunger?

This article explores the potential of microbiology to positively impact all aspects of the food supply chain, improving the quantity, quality, safety, and nutritional value of food products by providing innovative ways of growing, processing, and preserving food and thus contributing to Zero Hunger, one of the Sustainable Development Goals (SDGs) of the United Nations.