Heavy metal-associated isoprenylated plant proteins (HIPPs) are a class of vascular plant specific metallochaperones, characterized by the presence of one or two N-terminal heavy metal-associated (HMA) domains and a C-terminal isoprenylation motif (CaaX). The HMA domain contains a conserved CysXXCys motif that is responsible for binding transition metals such as Cd2+, Cu2+, Zn2+ and Pb2+. The CaaX motif modulates post-translational prenylation that anchors HIPPs to membranes and facilitates protein-protein interactions. This review systematically summarizes the structural features and multifaceted functions of HIPPs in plants. Beyond their well known function in heavy metal detoxification, HIPPs are more recently recognized as key regulators of abiotic stress responses, including drought, cold, and salinity, and biotic stress resistance via interactions with pathogen effectors. Moreover, HIPPs also participate in plant growth and development and in hormone signaling, including the cytokinin and abscisic acid (ABA) pathways. Translating this knowledge holds great promise for developing stress-tolerant crop varieties, breeding low-cadmium crops, and advancing phytoremediation technologies.

High pH precipitates Fe as insoluble ferric oxides in alkaline/calcareous soils, limiting its availability. Plasma membrane (PM) H⁺-ATPase facilitates nutrient uptake via rhizosphere acidification. Enhanced PM H⁺-ATPase activity in roots has been often observed in plants under phosphorus deprivation. Fe deficiency is generally a weak inducer of root PM H⁺-ATPase activity compared with P deprivation, particularly in graminaceous species such as rice, likely because Fe acquisition mainly relies on Strategy II-related phytosiderophore secretion rather than Strategy I-related H⁺ secretion. Nevertheless, the mechanisms by which P deprivation induced PM H⁺-ATPase activity for Fe utilization in rice under alkaline conditions remains to elusive. Here, we stimulated rice root PM H⁺-ATPase via P deprivation and assessed Fe uptake at pH 7.5 or pH 5.5. P deprivation alleviated chlorosis at pH 7.5, increasing leaf chlorophyll and soluble Fe, while upregulating Fe-homeostasis genes (OsIRT1/2, OsYSL2/15, OsIRO2). Proton efflux and PM H⁺-ATPase gene expression (OSA1, OSA8) were enhanced by P deprivation, alongside increased protein abundance and penultimate threonine (Thr) residue phosphorylation level, indicating improved enzymatic activity under alkaline conditions. Further, OSA1-overexpressing lines showed reduced chlorosis under alkaline conditions. Conversely, the Fe homeostasis and transport-related gene mutants (osirt1, osirt2, osysl15, osiro2) exhibited chlorosis with lower chlorophyll and Fe contents in leaves under alkaline conditions. We conclude that PM H⁺-ATPase-mediated Strategy I responses significantly contribute to rice Fe uptake under alkaline conditions, whereas Strategy II alone is probably insufficient to sustain efficient Fe acquisition. This cooperative mechanism may play a vital role in Fe mobilization by rice plants in alkaline, mainly calcareous soils.

Organic phosphorus (P), which accounts for c. 50% of total soil P, is not directly available for plant uptake and must be first mineralized. Plasma membrane (PM) H+-ATPase facilitates the mobilization of insoluble inorganic P by energizing the release of organic anions from roots. However, its role in modulating the rhizosphere microbiome to facilitate soil organic P mineralization remains unclear. To address the gap, we investigated the role of PM H+-ATPase in recruiting microbiota for soil organic P mineralization through high-throughput sequencing and metabolite analysis. Under low P (LP) conditions in nonsterilized soil, wild-type (WT) rice seedlings exhibited 59%, 73%, and 66% greater shoot P concentration than three PM H+-ATPase gene OsA1 mutants, that is, osa1-1, osa1-2, and osa1-3, respectively. Such growth advantage reduced to 33%, 47%, and 39% in sterilized soil, suggesting a microbial contribution. Under LP conditions, organic P mineralization efficiency in the WT rhizosphere was four times greater than under normal P (NP) conditions, whereas no significant difference was observed in the osa1-1 mutant. The abundance of Bacillus was significantly higher in the WT rhizosphere than in osa1-1 under LP. Compared with the osa1-1 rice, WT exhibits significantly higher malate concentration, which could stimulate the growth of Bacillus cereus. Inoculation with B. cereus significantly increased P uptake in both WT and OsA1 mutants compared with the uninoculated control under LP. Together, these findings suggest that OsA1 promoted soil organic P mineralization by recruiting Bacillus through malate exudation. This highlights a cooperative interaction between PM H+-ATPase and the rhizosphere microbiome, with important implications for enhancing soil organic P mineralization and P-use efficiency in rice production.

Plasma membrane (PM) H+-ATPase is important for plant phosphorus (P) uptake. The endophytic fungus Serendipita indica (S. indica) can increase plant P acquisition under P deficiency conditions, but it is unclear whether PM H+-ATPase OsA1 is involved in S. indica-modulated P uptake in rice. Under low-P conditions, rice seedlings inoculated with S. indica showed a 90% increase in shoot P concentration and a 164% increase in root P concentration compared with the non-inoculated rice, largely due to significantly elongated root hairs. The relative expression of OsA1 in S. indica-inoculated plants was 73.2% higher than in non-inoculated S. indica plants under low-P conditions. Under low-P conditions, S. indica inoculation also enhanced root H+ efflux by 34% and PM H+-ATPase activity by 27% in wild-type rice compared with non-inoculated plants, whereas no such significant difference was observed in the osa1-1 or osa1-2 mutants. Taken together, our results suggest that S. indica promotes root hair growth under low-P conditions by modulating plasma membrane H+-ATPase OsA1. This cooperative interaction reveals a key mechanism through which S. indica enhances P acquisition, providing valuable insights for improving P-use efficiency in rice production.

Microbes drive global nitrogen cycling, yet the extent to which taxonomic identity is associated with functional potential across bacterial diversity remains poorly quantified. Using 73 472 representative bacterial genomes, we develop a quantitative framework integrating Information Gain analysis, functional classification, and molecular evolutionary analysis across six nitrogen cycling pathways and five taxonomic ranks. Association strength increases monotonically from phylum to genus level across all six pathways, with genus-level associations ranging from 39.5

Phosphorus (P) limitation is a major selective pressure in plant evolution and a persistent constraint on modern crop production. However, how domestication has reshaped P adaptation strategies remains poorly understood. Here, we compared wild (Solanum pimpinellifolium) and cultivated (Solanum lycopersicum) tomatoes under contrasting P conditions using integrated physiological, ionomic, and transcriptomic analyses. Our findings reveal distinct P strategies between the examined genotypes. Cultivated tomatoes achieved higher biomass under sufficient P supply but were highly sensitive to P deficiency, responding through acquisition-driven phenotypic plasticity characterized by extensive root remodeling and enhanced external P mobilization. In contrast, wild accessions maintained growth and higher P use efficiency under low P by relying on an optimized internal P management strategy, including efficient P uptake, preferential allocation to photosynthetically active tissues, and effective remobilization from older leaves. Consistently, ionomic profiling revealed that wild tomatoes preserved coordinated macro- and micronutrient homeostasis under P stress. Tissue-specific transcriptomic analyses further uncovered pronounced divergence in P-responsive regulation, with cultivated tomatoes showing predominantly root-centered responses, whereas wild accessions exhibited strong activation in old source leaves. This tissue-specific specialization was accompanied by a putative regulatory divergence, with HD-ZIP transcription factors enriched in cultivated tomatoes and G2-like and bHLH factors central in wild accessions. Together, our results indicate that modern cultivars exhibit a stronger reliance on external P acquisition and greater growth sensitivity under sustained P limitation compared to wild accessions, which showed relatively more stable internal P allocation patterns, highlighting wild germplasm as a resource for improving crop P efficiency.

Phosphorus is a key driver of eutrophication in aquatic ecosystems, and microalgae play a central role in regulating environmental phosphate availability through uptake and retention processes. Although intracellular polyphosphate accumulation has been intensively studied, the contribution of cell surface-adsorbed phosphorus (SAP) to environmental P capture remains poorly understood. Here, using Chlamydomonas reinhardtii as a model, we show that under standard growth conditions, cell wall-intact strains accumulated significantly more SAP (similar to 2-fold) than wall-deficient strains, with SAP levels increasing linearly with external Pi. Although SAP accounted for less than 15% of total cellular P, overall P content was up to similar to 1.8-fold higher in cell wall-intact strains under Pi-replete conditions. Genetic manipulation of the Pi starvation regulator PSR1 further reshaped P partitioning. PSR1 overexpression increased intracellular P accumulation by similar to 66%, whereas PSR1 disruption elevated SAP (>67%) but reduced total P (similar to 28%), accompanied by diminished Pi removal from the medium. In addition, carbon limitation markedly reduced genotypic differences in SAP accumulation, indicating that surface retention is metabolically constrained rather than solely determined by structural features. Together, these findings indicate that SAP formation arises from PSR1-dependent P partitioning dynamics and represents a transient, regulated interfacial pool rather than an independently controlled adsorption process. While intracellular storage remains the dominant P sink, SAP functions as a dynamic and exchangeable buffer at the cell-water interface, facilitating P retention prior to internalization. This work provides a mechanistic framework linking cell surface processes with intracellular accumulation, advancing our understanding of how microalgae buffer fluctuating P availability and regulate P uptake dynamics in aquatic environments.

How to determine the optimal dosage of phosphorus (P) fertilizer input for an agricultural field is important to maintain soil quality and crop production while minimizing environmental impact. In this study, we set up a 5-year rice-wheat rotation with contrasting P fertilization treatments (0, 25, 50, 75, 100, and 150 kg P2O5 ha(-1), hereafter, P-0, P-25, P-50, P-75, P-100, and P-150, respectively) per season to explore the relationship between the amount of P input and crop yield, P use efficiency (PUE), balance of P accumulation and loss, ecosystem multifunctionality (EMF), and soil quality. Our results indicate that increased P amounts significantly boosted rice and wheat production of both straw and grain, but the tendency slowed down when the input was over 75 kg P2O5 ha(-1). The PUE declined with increased P input and soil P balance of 50 kg P2O5 ha(-1) for wheat and 100 kg P2O5 ha(-1) for rice. Runoff emerges as the main pathway for soil P loss and escalates with higher P application rates. We emphasize increasing ridge height and controlling water input for basal fertilizer to minimize P loss. The application of P fertilizer increased the soil P pool, with labile P (L-P) and moderately labile P (M-P) increasing by 13-114 % and 23-111 %, respectively, compared to P0. The transformation of M-P to L-P in paddy soil is associated with an increased abundance of Actinobacteria. Low P applications (P-25 and P-50) increased EMF by 3.27 and 3.58 times, while high P applications (P-75, P-100, and P-150) decreased EMF. Furthermore, P application significantly improved the soil quality index (SQI) compared to P-0. The impact of abiotic factors on yield and P loss is more significant than that of biotic elements, with the SQI serving as a dependable indicator for predicting yield. Central to minimizing P loss while maximizing yield is the reduction of Resin-P content and the maintenance of NaOH-P-i levels, suggesting that organic materials may be a good alternative strategy. These findings provide valuable data and theoretical support for optimizing P application in rice-wheat cropping systems, promoting a mutually beneficial scenario for agricultural production and ecological protection.

Soil pH is critical for the bioavailability of nutrients and their consequent uptake by plant roots. This is specifically true for N and P, two key macronutrients that are essential for all aspects of plant growth and development. Importantly, availability of one nutrient can affect acquisition and translocation of another, although the mechanistic basis of this process remains unexplored. In this work, we combined a physiological (growth; ionomics), molecular (RNAseq and qPCR), biochemical (enzymatic assays) and genetic (using gain-of-function mutants) approaches to investigate the effect of interplay between P availability, two forms of N supply (NO3- vs NH4+) and rhizosphere pH (3.0 vs 6.5) on rice plants. In general, rice plants grown in the presence of NH4+ performed better than those treated with NO3- and better at pH 6.5 than at pH 3. P deprivation significantly reduced N accumulation in leaves but increased N in roots under both NH4+ and NO3- treatments. Transcriptome analysis revealed 8749 differently expressed genes (DEGs) in leaves and 6519 DEGs in roots under P deprivation at pH 6.5, related to membrane function, cellular response, metabolism, and cell signaling. Among the DEGs, the plasma membrane H+-ATPase genes were significantly induced by both P deprivation under NO3- and NH4+ treatments, indicating a possible role of H+-ATPase in plant adaptive responses to P nutrition. The latter was confirmed in direct experiments combining 33P radiotracers. Overexpression of OSA1 encoding a H+-ATPase improved nutrient uptake and rice growth. Overall, these results suggest that PM H+-ATPase plays a crucial role in the regulation of N and P uptake and provide a new approach to develop crop varieties that are more efficient at absorbing and utilizing nutrients and, hence, capable to achieve optimal yields.

Phosphorus (P) is an essential macronutrient required for plant growth, development, and resilience to environmental stresses. Its availability in soil and homeostasis within plants are strongly influenced by environmental conditions, with unfavorable environments and soil factors disrupting phosphate availability, absorption, transport, and utilization. Optimizing phosphate supply can alleviate the detrimental impacts of abiotic stresses, thereby supporting growth and improving stress tolerance. Recent studies reveal that abiotic stresses modulate phosphate signaling pathways and alter the expression of phosphate-responsive genes, often affecting key regulators of P homeostasis. Strategic manipulation of phosphate transporters and their regulatory pathways offers a promising approach to enhance plant adaptation to challenging environments. This review highlights current advances in understanding the molecular mechanisms that coordinate P-responsive gene expression and homeostasis pathways under fluctuating P availability and stress conditions. It emphasizes the critical role of P nutrition in enhancing plant stress tolerance through antioxidant activation, osmolyte accumulation, membrane stabilization, and metal-phosphate complex formation. An in-depth mechanistic understanding of P-stress interactions will inform the development of P-efficient and stress-resistant crop varieties and guide more sustainable P fertilizer management in agriculture.

Using phosphorus (P) fertilizers has historically increased agricultural productivity, yet the highly dissipative nature of phosphate rock and the low efficiency due to soil fixation and runoff raise sustainability concerns. Algae fertilizers have emerged as a promising eco-friendly alternative. However, the potential of algae fertilizers for providing sustained P availability and their impacts on plant growth, soil microbes, and nutrient cycling remains to be explored. In this study, we developed a polyphosphate-enriched algae fertilizer (PEA) and conducted comparative experiments with chemical P fertilizers (CP) through soil and solution cultures, as well as crop growth trials. Soil cultivation experiments showed that PEA released twice as much labile P as initially available in the soil, and it functioned as a slow-release P source. In contrast, soils treated with CP initially exhibited high levels of labile P, which was gradually converted to stable forms, but it dropped to 30% of the labile P level in PEA after three months. Further tests revealed that the slow release of P from PEA was linked to increased microbial activity, and the microbial biomass P (MBP) content was about eight times higher than in soils treated with CP after three months, resulting in a 75% decline in the microbial biomass carbon (MBC) to MBP ratio. Microbial diversity analysis showed that algae fertilizers could recruit more beneficial microbes than CP, like phosphorus-solubilizing bacteria, plant growth-promoting bacteria, and stress-resistant bacteria. Crop pot experiments, along with amplicon and metagenomic analysis of tomato root-associated microbes, revealed that algae fertilizers including PEA promoted plant growth comparable to CP, and enhanced soil P cycling and overall nutrient dynamics. These data showed that algae fertilizers, especially PEA, can stabilize soil P fertility and stimulate plant growth through their slow P release and the recruitment of beneficial microbes. Our study highlights the potential of PEA to foster sustainable agriculture by mitigating the P scarcity and soil P loss associated with chemical fertilizers and improving plant growth and soil health.

Rhizosheath formation is facilitated by root hair length, root exudates, the soil microbes, which collectively enhance plant resistance to drought. This process partly results from the complex interaction between root exudates and microbes, a relationship that remains poorly understood. The roles of root exudates and microbes in rhizosheath formation in rice under soil drying (SD) conditions are investigated. In tetraploid rice, rhizosheath formation under SD is approximately 70% greater than in diploid rice. Inoculation of diploid rice with the rhizosheath soil microbiota from tetraploid rice significantly enhanced rhizosheath formation under SD. The bacterial genus Pseudomonas is identified as the key taxon promoting rhizosheath formation in tetraploid rice under SD. Tetraploid rice exhibits significantly higher root flavonoid concentration than diploid rice under SD. Overexpression of the chalcone synthase gene (OsCHS1), a key gene involved in flavonoid biosynthesis, led to a significant increase in the abundance of Pseudomonadaceae in diploid rice. Pseudomonas nitroreducens, isolated from the rhizosheath of tetraploid rice, demonstrates chemotactic attraction to flavonoids, but this behavior is not observed in histidine kinase mutant ΔcheA. Diploid and tetraploid rice inoculated with P. nitroreducens and IAA biosynthesis complemented strain ΔiaaM-c formed larger rhizosheath under SD than those inoculated with its IAA biosynthesis mutant ΔiaaM. These results suggest that auxin-producing Pseudomonas, recruited by root flavonoids, enhances rice rhizosheath formation through the bacterial histidine kinase under SD. This finding may facilitate the improvement of environmental adaptation in polyploidy crops by regulating their interactions with beneficial soil microorganisms.

Microbes are essential for global nitrogen cycling, yet the extent to which taxonomic identity constrains functional potential remains poorly quantified. Using 73,472 representative bacterial genomes, we establish a multi-scale quantitative framework revealing systematic, hierarchical relationships between taxonomic identity and nitrogen cycling functional potential. Hierarchical variance decomposition reveals that taxonomy explains 20–46% of functional variation across six nitrogen pathways, with the strongest constraints for dissimilatory nitrite reduction to ammonium (46.1%) and nitrogen fixation (44.2%), both negatively correlated with functional prevalence. K-means clustering identifies four class-level functional archetypes (Functionally Inactive, Diversified, Integrated, and Specialized) among 77 bacterial classes. 1,281 genera resolve into five ecological strategies differentiated by their nitrogen retention versus loss capabilities, exhibiting strong phylogenetic signals. Cross-scale validation demonstrates 78.7% genus-level conformity to class-level archetypes, confirming hierarchical functional organization. Molecular evolutionary analysis of 13 genes reveals sequence conservation as a dimension partially independent of pathway-level functional constraints. Paradoxically, the functionally most constrained pathway exhibits only moderate sequence conservation ( nrfA : 9th/13 genes), while a moderately constrained pathway shows exceptional conservation ( napA ). Four constraint-conservation patterns demonstrate that gene-specific structural and ecological factors generate evolutionary rate variation independently of taxonomic associations. Our results establish a hierarchical framework in which taxonomic constraints set baseline functional potential, ecological trade-offs shape strategy diversification, and molecular evolution modulates gene-level conservation patterns across biological scales. This framework establishes quantitative baselines that enable probabilistic inference of nitrogen cycling capabilities from taxonomic composition, with potential applications in amplicon-based community analysis, targeted cultivation, and biogeochemical modeling. Importance A fundamental challenge in microbial ecology is inferring functional potential from taxonomic data—a relationship widely assumed but never rigorously quantified. Resolving this is critical because while amplicon sequencing provides cost-effective taxonomic profiling, functional characterization requires expensive metagenomics, limiting large-scale biogeochemical studies. We provide the first systematic quantification demonstrating that taxonomic identity explains 20-46% of nitrogen cycling functional variation, operating hierarchically from class to genus level. Crucially, we reveal that taxonomic constraints operate at both functional distribution and molecular evolution levels as partially independent dimensions, indicating distinct evolutionary mechanisms. This work establishes quantitative foundations for taxonomy-based functional prediction, enabling researchers to extract functional insights from readily available taxonomic surveys. As reference databases expand, this framework will enhance predictive capabilities for nitrogen cycling and broader biogeochemical processes.

Plasma membrane H+-ATPases (PMAs) pump H+ out of the cytoplasm by consuming ATP to generate a membrane potential and proton motive force for the transmembrane transport of nutrients into and out of plant cells. PMAs are involved in nutrient acquisition by regulating root growth, nutrient uptake, and translocation, as well as the establishment of symbiosis with arbuscular mycorrhizas. Under nutrient stresses, PMAs are activated to pump more H+ and promote organic anion excretion, thus improving nutrient availability in the rhizosphere. Herein we review recent progress in the physiological functions and the underlying molecular mechanisms of PMAs in the efficient acquisition and utilization of various nutrients in plants. We also discuss perspectives for the application of PMAs in improving crop production and quality.

Utilization of nitrogen by crops is essential for sustainable agriculture. The transport of nitrate (NO3-) across the plasma membrane is a critical gateway for N uptake and subsequent utilization. This process requires proton (H+) coupled cotransport, which is driven by proton motive force, provided by plasma membrane (PM) H+-ATPase. In this report, two indica rice varieties [Meixiangzhan 2 (MXZ) and Jifengyou 1002 (JFY)] in South China were selected and cultivated in hydroponic solution with 0.5 mM or 2.0 mM NO3- as the N source. The JFY exhibited stronger growth with higher biomass than MXZ under both 0.5 mM and 2.0 mM NO3-. PM H+-ATPase activity of JFY roots was significantly higher than that of MXZ. The higher PM H+-ATPase activity in JFY was consistent with a higher abundance of PM H+-ATPase protein and higher transcription levels of OSAs, such as OSA2, OSA7 and OSA8 in roots, OSA3, OSA7 and OSA8 in leaves. The expression of nitrate transporters (OsNRT1;1b, OsNRT2.1, OsNRT2.2, and OsNAR2.1) were also higher in roots or shoots of JFY than those in MXZ. Under 0.5 mM and 2.0 mM NO3-, the NO3- absorption and translocation rate, nitrate content, as well as nitrate reductase (NR) activity were all significantly higher in JFY, as compared to those in MXZ. Taken together, in JFY and MXZ, a higher level of PM H+-ATPase protein and higher activity coupled with greater efficiency in nitrate uptake, translocation and assimilation, suggesting the existence of a close correlation between PM H+-ATPase and nitrate utilization in indica rice. PM H+-ATPase may one of the elite genes that can contribute to nitrate use efficiency in rice.

Stoichiometry plays a crucial role in biogeochemical cycles and can modulate soil nutrient availability and functions. In agricultural ecosystems, phosphorus (P) fertilizers (organic or chemical) are often applied to achieve high crop yields. However, P is readily fixed by soil particles, leading to low P use efficiency. Therefore, understanding the role of carbon:nitrogen:P stoichiometries of soil and microorganisms in soil P transformation is of great significance for P management in agriculture. This paper provides a comprehensive review of the recent research on stoichiometry effect on soil P transformation in agricultural ecosystems. Soil microorganisms play an important role in the transformation of soil non-labile inorganic P to microbial biomass P by regulating microbial biomass stoichiometry. They also mobilize soil unavailable organic P into available P by changing ecoenzyme stoichiometry. Organic materials, such as manure and straw, play an important role in promoting the transformation of insoluble P into available P as well. Additionally, periphytic biofilms can reduce P loss from rice field ecosystems. Agricultural stoichiometries are different from those of natural ecosystems and thereby should receive more attention due to the influences of anthropogenic factors. Therefore, it is necessary to conduct further stoichiometry research on the soil biochemical mechanisms underlying P transformation in agricultural ecosystems. In conclusion, understanding stoichiometry impact on soil P transformation is crucial for P management in agricultural ecosystems.

Phosphorus nutrition has been known for a long time to influence floral transition in plants, but the underlying mechanism is unclear. Arabidopsis phosphate transporter PHOSPHATE1 (PHO1) plays a critical role in phosphate translocation from roots to shoots, but whether and how it regulates floral transition is unknown. Here, we show that knockout mutation of PHO1 delays flowering under both long- and short-day conditions. The late flowering of pho1 mutants can be partially rescued by Pi supplementation in rosettes or shoot apices. Grafting assay indicates that the late flowering of pho1 mutants is a result of impaired phosphate translocation from roots to shoots. Knockout mutation of SPX1 and SPX2, two negative regulators of the phosphate starvation response, partially rescues the late flowering of pho1 mutants. PHO1 is epistatic to PHO2, a negative regulator of PHO1, in flowering time regulation. Loss of PHO1 represses the expression of some floral activators, including FT encoding florigen, and induces the expression of some floral repressors in shoots. Genetic analyses indicate that at least jasmonic acid signaling is partially responsible for the late flowering of pho1 mutants. In addition, we find that rice PHO1;2, the homolog of PHO1, plays a similar role in floral transition. These results suggest that PHO1 integrates phosphorus nutrition and flowering time, and could be used as a potential target in modulating phosphorus nutrition-mediated flowering time in plants.

Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.