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Endophytic bacteria in different tissue compartments of African wild rice (Oryza longistaminata) promote perennial rice growth

Rui Tang, Qinglin Tian, Shuang Liu, Yurui Gong, Qingmao Li, Rui Chen, Linglin Wang, Fengyi Hu, Liyu Huang, Shiwen Qin

2025, 24 (3): 1001-1016. DOI: 10.1016/j.jia.2023.11.031

Abstract （139） PDF in ScienceDirect

Oryza longistaminata is an African wild rice species with valuable agronomic traits and the donor parent of perennial rice. Endophytic bacteria play an important role in host health, adaptive evolution and stress tolerance. However, endophytic bacterial communities in O. longistaminata and their plant growth-promoting (PGP) effects on the perennial rice of O. longistaminata offspring are poorly understood. In this study, the endophytic bacterial diversity, composition and network structures in the root, stem, and leaf tissues of O. longistaminata were characterized using Illumina sequencing of the 16S rRNA gene. The results suggested that O. longistaminata contains a multitude of niches for different endophytic bacteria, among which the root endosphere is more complex and functionally diverse than the stem and leaf endospheres. Tissue-specific biomarkers were identified, including Paludibaculum, Pseudactinotalea and Roseimarinus and others, for roots, Blautia for stems and Lachnospiraceae NK4A136 for leaves. The endophytic bacterial network of O. longistaminata was reassembled for various functions, including degradation/utilization/assimilation, detoxification, generation of precursor metabolites and energy, glycan pathways, macromolecule modification and metabolism. A total of 163 endophytic bacterial strains with PGP traits of potassium release, phosphate solubilization, nitrogen fixation, siderophore activity, indole-3-acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity were isolated from O. longistaminata. Eleven strains identified as Enterobacter cloacae, Enterobacter ludwigii, Stenotrophomonas maltophilia, Serratia fonticola, and Bacillus velezensis showed stable colonization abilities and PGP effects on perennial rice seedlings. Inoculated plants generally exhibited an enhanced root system and greater photosynthesis, biomass accumulation and nutrient uptake. Interestingly, two strains of E. cloacae have host genotype-dependent effects on perennial rice growth. The results of this study provide insights into the endophytic bacterial ecosystems of O. longistaminata, which can potentially be used as biofertilizers for sustainable perennial rice productivity.

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The synergistic regulatory effect of PTP1B and PTK inhibitors on the development of Oedaleus decorus asiaticus Bei-Bienko

Shuang Li, Sibo Liu, Chaomin Xu, Shiqian Feng, Xiongbing Tu, Zehua Zhang

2024, 23 (8): 2752-2763. DOI: 10.1016/j.jia.2023.12.020

Abstract （76） PDF in ScienceDirect

Tyrosine phosphorylation is crucial for controlling normal cell growth, survival, intercellular communication, gene transcription, immune responses, and other processes. protein tyrosine phosphatase (PTP) and protein tyrosine kinases (PTK) can achieve this goal by regulating multiple signaling pathways. Oedaleus decorus asiaticus is an important pest that infests the Mongolian Plateau grassland. We aimed to evaluate the survival rate, growth rate, overall performance, and ovarian developmental morphology of the 4th instar nymphs of O. decorus asiaticus while inhibiting the activity of protein tyrosine phosphatase-1B (PTP1B) and PTK. In addition, the expression and protein phosphorylation levels of key genes in the MAPK signaling pathway and antioxidant enzyme activity were assessed. The results showed no significant differences in survival rate, growth rate, or overall performance between PTP1B inhibitor treatment and control. However, after PTK inhibitor treatment, these indexes were significantly lower than those in the control. The ovarian size of female larvae after 15 days of treatment with PTK inhibitors showed significantly slower development, while female larvae treated with PTP1B exhibited faster ovarian growth than the control group. In comparison to controls and nymphs treated with PTK inhibitors, the expression and phosphorylation levels of key genes in the MAPK signaling pathway under PTP1B inhibitor treatments were significantly higher in 4th instar nymphs. However, reactiveoxygen (ROS) species levels and the activities of NADPH oxidase and other antioxidant enzymes were considerably reduced, although they were significantly greater in the PTK inhibitor treatment. The results suggest that PTP1B and PTK feedback inhibition in the mitogen-activated-protein kinases (MAPK) signal transfer can regulate the physiological metabolism of the insect as well as its developmental rate. These findings can facilitate future uses of PTP1B and PTK inhibitors in controlling insect development to help control pest populations.

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Genome-wide association study of grain micronutrient concentrations in bread wheat

Yongchao Hao, Fanmei Kong, Lili Wang, Yu Zhao, Mengyao Li, Naixiu Che, Shuang Li, Min Wang, Ming Hao, Xiaocun Zhang, Yan Zhao

2024, 23 (5): 1468-1480. DOI: 10.1016/j.jia.2023.06.030

Abstract （251） PDF in ScienceDirect

Bread wheat (Triticum aestivum) is a staple food crop worldwide. The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world’s growing population. Here, 45,298 single-nucleotide polymorphisms (SNPs) from 55K chip arrays were used to genotype a panel of 768 wheat cultivars, and a total of 154 quantitative trait loci (QTLs) were detected for eight traits under three environments by genome-wide association study (GWAS). Three QTLs (qMn-3B.1, qFe-3B.4, and qSe-3B.1/qFe-3B.6) detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs. Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1, three haplotypes for qFe-3B.4, and three haplotypes for qSe-3B.1/qFe-3B.6. Phenotypic analysis revealed significant differences among haplotypes. These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat. Based on the QTL regions, we identified 15 high-confidence genes, eight of which were stably expressed in different tissues and/or developmental stages. TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology (GO) analysis. TraesCS3B02G199000, which belongs to qSe-3B.1/qFe-3B.6, was determined to be a member of the WRKY gene family. Overall, this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain, and this information will facilitate the breeding of wheat cultivars with improved grain properties.

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Effects of water and nitrogen rate on grain-filling characteristics under high-low seedbed cultivation in winter wheat

Junming Liu, Zhuanyun Si, Shuang Li, Lifeng Wu, Yingying Zhang, Xiaolei Wu, Hui Cao, Yang Gao, Aiwang Duan

2024, 23 (12): 4018-4031. DOI: 10.1016/j.jia.2023.12.002

Abstract （223） PDF in ScienceDirect

A high-efficiency mode of high-low seedbed cultivation (HLSC) has been listed as the main agricultural technology to increase land utilization ratio and grain yield in Shandong Province, China. However, limited information is available on the optimized water and nitrogen management for yield formation, especially the grain-filling process, under HLSC mode. A three-year field experiment with four nitrogen rates and three irrigation rates of HLSC was conducted to reveal the response of grain-filling parameters, grain weight percentage of spike weight (GPS), spike moisture content (SMC), and winter wheat yield to water and nitrogen rates. The four nitrogen rates were N1 (360 kg ha^–1 pure N), N2 (300 kg ha^–1 pure N), N3 (240 kg ha^–1 pure N), and N4 (180 kg ha^–1 pure N), respectively, and the three irrigation quotas were W1 (120 mm), W2 (90 mm), and W3 (60 mm), respectively. Results showed that the determinate growth function generally performed well in simulating the temporal dynamics of grain weight (0.989<R²<0.999, where R²is the determination coefficient). The occurrence time of maximum filling rate (T_max) and active grain-filling period (AGP) increased with the increase in the water or nitrogen rate, whereas the average grain-filling rate (G_mean) had a decreasing trend. The final 1,000-grain weight (FTGW) increased and then decreased with the increase in the nitrogen rates and increased with the increase in the irrigation rates. The GPS and SMC had a highly significant quadratic polynomial relationship with grain weight and days after anthesis. Nitrogen, irrigation, and year significantly affected the T_max, AGP, G_mean, and FTGW. Particularly, the AGP and FTGW were insignificantly different between high seedbed (HLSC-H) and low seedbed (HLSC-L) across the water and nitrogen levels. Moreover, the moderate water and nitrogen supply was more beneficial for grain yield, as well as for spike number and grain number per hectare. The principal component analysis indicated that combining 240–300 kg N ha^–1 and 90–120 mm irrigation quota could improve grain-filling efficiency and yield for the HLSC-cultivated winter wheat.

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Enrichment, domestication, degradation, adaptive mechanism, and nicosulfuron bioremediation of bacteria consortium YM2

Yufeng Xiao, Meiqi Dong, Xian Wu, Shuang Liang, Ranhong Li, Hongyu Pan, Hao Zhang

DOI: 10.1016/j.jia.2024.03.004 Online: 21 March 2024

Abstract （29） PDF in ScienceDirect

Nicosulfuron (NSR), a sulfonylurea herbicide, can easily enter water bodies, affecting aquatic life and human safety. Here, bacteria consortium YM2 was enriched and domesticated from the active sludge of a pesticide plant for the bioremediation of NSR wastewater. The response surface methodology data revealed that under optimal incubation conditions: 9.41 g L^–¹ maltodextrin, 21.37 g L^–¹ yeast extract, and 12.45 g L^–¹NaCl, YM2 bacteria consortium degraded 97.49% of NSR within 4 d. The optimal degradation conditions were temperature 30°C, pH 6.0, inoculum 1%, and initial NSR concentration 20 mg L^–¹), The degradation system was tolerant to heavy metal ions such as Cd²⁺, Pb²⁺, Ni²⁺, and Zn²⁺ and mainly occurred through the bacterial extracellular enzymes (92.17%). Mechanistically, during the degradation process, reactive oxygen species, oxidative stress, cell membrane permeability, cell surface hydrophobicity, and apoptosis rate first increased and then decreased. Also, the expression of biofilm formation-related genes luxS, waaE, spo0A, and wza varied with time and concentration. NSR wastewater and soil were degraded to 1.92 mg L^–¹ and 2.72 mg L^–¹, respectively. In a simulated wastewater treatment unit (hydraulic retention time 12 h), YM2 degraded 84.55% of NSR after 10 d. This study provides a theoretical basis for the microbial remediation of NSR.

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