The impact of the flooding-draining process on soil ecosystems is complex and dynamic. However, the specific effects of different drainage durations on soil microorganisms and metabolites remain unclear. This study adopted a multi-omics research method. After nontargeted metabolomics analysis of lipids as the main metabolite, microbial diversity analysis and lipidomics analysis were conducted to determine the main influencing factors. Subsequently, correlation analysis was performed with physiological and biochemical data to logically explore the changes in soil microorganisms and metabolites during the drainage process (Day 1 after drainage, R1; Day 2, R2; Day 3, R3; Day 4, R4; and Day 5, R5). The results revealed that S-PPO, S-POD, and S-CAT decreased with prolonged drainage time, whereas the soil redox potential (Eh-mV) and POD increased. Among the various postdrainage comparison groups, lipids and lipid-like molecules were the predominant metabolites. Among lipids, the TG subclass of glycerolipids (GLs) and the Cer subclass of sphingolipids (SPs) were the most abundant. The TG subclass was consistently present in the lipid correlation networks across all comparison groups, with TG (15:0/18:1/18:1) exhibiting significant differences between the R4 and R1 groups. Redox reactions involving lipids were associated mainly with triglycerides, with the most pronounced reduction observed on the second day postdrainage. The most pronounced lipid reduction reaction was observed on the second day after drainage. Notable differences in bacterial abundance were detected between the R4 and R5 groups. At the phylum level, the dominant bacterial communities primarily comprised Actinobacteriota and Chloroflexi, with the bacterial community structure being significantly influenced by drainage. The predominant fungal communities were composed of mainly Ascomycota and Rozellomycota. Actinobacteriota and triglyceride (TG) lipids were the major components affected during the drainage period. Correlations were identified among environmental factors, lipids, and microbial communities, indicating their cooperative interactions. The results of this study indicate that with the increase in water intake time, the redox reactions in soil lipids and the richness of bacterial communities in rice soil significantly increase. At the same time, rapid remodeling can have an impact on soil ecosystems, which helps to better understand the adaptation strategies of rice soil ecosystems under adversity.

Exploring the growth and physiological response mechanisms of rice under continuous drought stress circumstances can provide a significant scientific foundation and technological assistance for meeting drought difficulties, improving drought resistance and rice (Oryza sativa L.) output, and ensuring food security. In this study, a rice field experiment was conducted under a rain shelter with five different treatments set up: P1 (drought stress from tillering stage), P2 (drought stress from jointing–booting stage), P3 (drought stress from heading–flowering stage), P4 (drought stress from grain filling stage), and CK (adequate water management throughout the growth stage). Continuous drought stress from different growth stages with four levels (mild, medium, moderate, and severe). The results showed that the effects of different drought stress treatments on rice growth varied significantly. Compared with the CK treatment, plant height was reduced by 12.10%, 8.14%, 3.83%, and 1.06% in the P1, P2, P3, and P4 treatments, respectively, and the number of tillers was reduced by 23.83%, 18.91%, 13.47%, and 8.68%, respectively. With the increase in drought stress levels, SPAD values and Rubisco activity of rice leaf continued to decrease; SOD activity showed a decreasing trend, but the decreasing trend of POD and CAT activities was not significant, while MDA content showed an increasing trend. For yield components, continuous drought stress significantly reduced spike length of rice by an average of 3.5%, effective number of spikes by 18.9%, thousand grain weight by 3.7%, grain number per spike by 11.6%, and fruiting rate by 1.8%, respectively, compared to CK treatments during the growth period. In general, continuous drought stress during the early growth period affected the effective spike number and the grain number per spike. Continuous drought stress after the grain filling stage had the least effect on yield (17.62% of yield reduction), and water use efficiency (1.76 kg m⁻³) was much higher than other treatments. These researchers’ findings provide insight into how rice physiology and growth react to continuous drought stress, which is significant for agricultural operations.

In recent years, there has been a notable increase in the frequency and intensity of floods and heavy rains, which has resulted in the frequent inundation of rice-growing areas. Flooding during the heading–flowering stages of early rice can result in significant yield losses. To elucidate the response of rice to sediment content, flooding, and drainage processes and their underlying mechanisms, a pot experiment was conducted to investigate the effects of sediment contents (S₁: 0, S₂: 0.10 kg m⁻³, and S₃: 0.25 kg m⁻³), flooding time (F₁: 3 days and F₂: 6 days), and drainage time (D₁: 3 days and D₂: 6 days) during the heading–flowering stage on the oxidation resistance and grain yield of early rice in the Poyang Lake Region. At the same time, an experimental control group (CK) was set up with no sediment, no flooding, or no drainage treatment. The results showed that the flag leaf area of S₁F₁D₂ treatment was diminished by flooding. The relative chlorophyll content (SPAD) reached its lowest value prior to drainage. The treatment of S₂F₂D₁ showed the greatest decrease in SPAD value of 41.57%, which was only 53.88% of that of the control treatment. The activity of superoxide dismutase (SOD), peroxidase (POD), and the content of malondialdehyde (MDA) were observed to increase during the flooding period in comparison to the control treatment. The maximum values for these parameters were recorded at 5.68, 3.09, and 1.9 times higher than those of the control treatment, respectively. However, a decrease was observed after drainage. Furthermore, the occurrence of flooding during the early rice heading–flowering stage resulted in a notable reduction in the grain number per spike and the fruiting rate, consequently leading to a considerable decline in grain yields, with a decrease ranging from 31.81% to 69.96%. The findings indicate that flooding during the heading–flowering stage resulted in a reduction in early rice grain yield yet enhanced the antioxidant capacity of the leaves. Regression analyses indicated that a prediction model for the actual yield after flooding stress at the heading–flowering stage of early rice could be constructed using SFW as the independent variable. The findings of this study provide a theoretical basis for the formulation of a scientific and reasonable drainage scheme with the objective of reducing yield loss following rice flooding in the southern rice-growing region of China.

Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.

Exploring the growth and physiological response mechanisms of rice under continuous drought stress circumstances can provide a significant scientific foundation and technological assistance for meeting drought difficulties, improving drought resistance and rice (Oryza sativa L.) output, and ensuring food security. In this study, a rice field experiment was conducted under a rain shelter with five different treatments set up: P1 (drought stress from tillering stage), P2 (drought stress from jointing-booting stage), P3 (drought stress from heading-flowering stage), P4 (drought stress from grain filling stage), and CK (adequate water management throughout the growth stage). Continuous drought stress from different growth stages with four levels (mild, medium, serious, and extreme). The results showed that the effects of different drought stress treatments on rice growth varied significantly. Compared with the CK treatment, plant height was reduced by 12.10%, 8.14%, 3.83%, and 1.06% in the P1, P2, P3, and P4 treatments, respectively; and the number of tillers was reduced by 23.83%, 18.91%, 13.47%, and 8.68%, respectively. With the increase in drought stress levels, SPAD values and Rubisco activity of rice leaf continued to decrease; SOD activity showed a decreasing trend, but the decreasing trend of POD and CAT activities was not significant, while MDA content showed an increasing trend. For yield components, continuous drought stress significantly reduced spike length, effective number of spikes, thousand grain weight, grain number per spike, and fruiting rate of rice compared to CK treatments during the growth period. In general, continuous drought stress during the early growth period affected the effective spike number and the grain number per spike. Continuous drought stress after the grain filling stage had the least effect on yield and water use efficiency was much higher than other treatments. The results of these studies reveal the response of rice growth and physiology to continuous drought stress, which is important for agricultural practices.

Nitrogen (N) management and planting density critically influence rice (Oryza sativa L.) N use efficiency (NUE) and yield stability, though excessive inputs risk ecological and productivity constraints. This study investigated molecular adaptations in japonica rice Hongyang 5 under three N density regimens: high N/low density (HNLD), medium N/medium density (MNMD), and low N/high density (LNHD). Our previous studies found that the N absorption efficiency, antioxidant enzyme activity, and energy metabolism-related phenotypes of rice roots showed significant differences under different treatments. In this study, we found that root morphology, such as root length, root surface area, root volume, and average root diameter, also showed significant differences among different treatments. Based on this, we further integrated transcriptome and co-expression network analysis, revealing 40,218 expressed genes with differential expression patterns across treatments. Weighted gene co-expression network analysis (WGCNA) identified 13 modules, with the Turquoise and Blue modules notably demonstrating strong associations with N assimilation, antioxidant activity, and ATP metabolism. Ten hub genes emerged through intramodular connectivity analysis, including LOC_Os02g53130 (N metabolism), LOC_Os06g48240 (peroxidase activity), and LOC_Os01g48420 (energy transduction), with RT-qPCR validation confirming transcriptome-derived expression profiles. Functional characterization revealed synergistic coordination between Turquoise module N metabolic pathways and Blue module redox homeostasis, suggesting an integrated regulatory mechanism for root adaptation to N density interactions. These findings establish a gene-network framework that reveals the molecular regulatory network of crop responses to N nutrition and planting density and provides important theoretical support for N fertilizer management, population quality optimization, and variety breeding in precision agriculture.