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Liu HB, Sun HX, Du LQ, Jiang LL, Zhang LA, Qi YY, Cai J, Yu F. Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice. THE ISME JOURNAL 2024; 18:wrae006. [PMID: 38366198 PMCID: PMC10900889 DOI: 10.1093/ismejo/wrae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 01/20/2024] [Indexed: 02/18/2024]
Abstract
Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth-defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux, and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.
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Affiliation(s)
- Hong-Bin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha 410082, P.R. China
- Interdisciplinary and Intelligent Seed Industry Equipment Research Department, Yuelushan Laboratory, Changsha 410082, P.R. China
| | - Hong-Xia Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Li-Qiong Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ling-Li Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Lin-An Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Yin-Yao Qi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
- Interdisciplinary and Intelligent Seed Industry Equipment Research Department, Yuelushan Laboratory, Changsha 410082, P.R. China
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Sun Y, Gao L, Meng X, Huang J, Guo J, Zhou X, Fu G, Xu Y, Firbank LG, Wang M, Ling N, Feng X, Shen Q, Guo S. Large-scale exploration of nitrogen utilization efficiency in Asia region for rice crop: Variation patterns and determinants. GLOBAL CHANGE BIOLOGY 2023; 29:5367-5378. [PMID: 37431724 DOI: 10.1111/gcb.16873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/05/2023] [Indexed: 07/12/2023]
Abstract
Improving rice nitrogen utilization efficiency (NUtE) is imperative to maximizing future food productivity while minimizing environmental threats, yet knowledge of its variation and the underlying regulatory factors is still lacking. Here, we integrated a dataset with 21,571 data compiled by available data from peer-reviewed literature and a large-scale field survey to address this knowledge gap. The overall results revealed great variations in rice NUtE, which were mainly associated with human activities, climate conditions, and rice variety. Specifically, N supply rate, temperature, and precipitation were the foremost determinants of rice NUtE, and NUtE responses to climatic change differed among rice varieties. Further prediction highlighted the improved rice NUtE with the increasing latitude or longitude. The indica and hybrid rice exhibited higher NUtE in low latitude regions compared to japonica and inbred rice, respectively. Collectively, our results evaluated the primary drivers of rice NUtE variations and predicted the geographic responses of NUtE in different varieties. Linking the global variations in rice NUtE with environmental factors and geographic adaptability provides valuable agronomic and ecological insights into the regulation of rice NUtE.
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Affiliation(s)
- Yuming Sun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Limin Gao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, Nanjing, China
| | - Xusheng Meng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Jian Huang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xuan Zhou
- National Agro-Tech Extension and Service Center, Beijing, China
| | - Guohai Fu
- National Agro-Tech Extension and Service Center, Beijing, China
| | - Yang Xu
- National Agro-Tech Extension and Service Center, Beijing, China
| | | | - Min Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xumeng Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
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Pan J, Dong Q, Wen H, Liu Y, Wang X, Liu Y, Zhang X, Shi C, Zhao D, Lu X. Composition and Diversity of Endophytic Rhizosphere Microbiota in Apple Tree with Different Ages. Mol Biotechnol 2023:10.1007/s12033-023-00794-z. [PMID: 37523021 DOI: 10.1007/s12033-023-00794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/14/2023] [Indexed: 08/01/2023]
Abstract
In order to determine the underlying mechanism of the senescence occurring in older apple trees, the effects of tree age on the community structure and dominant genus of endophytic rhizosphere bacteria in apple were investigated. The diversity and structure of the bacterial communities and corresponding changes in the dominant genera of endophytic rhizosphere bacteria of apple at different ages (2, 8, 16, 22 years) were compared based on 16S rRNA high-throughput sequencing technology. The results revealed that the longer the tree age, the less the number of ASV in the endophytic bacteria. Moreover, the number of ASV in the endophytic bacteria gradually decreased as the tree age increased, however no significant changes were observed in the alpha diversity. At the phyla level, the relative abundance of Actinobacteria increased, while that of Proteobateria decreased. At the genus level, the relative abundance of Mycobacterium, Chujaibacter, and other genera increased, while the relative abundance of Aquabacterium, Ralstonia, Streptomyces, Asticcacaulis, Hyphomicrobium, Pseudomonas, and Sphingomonas decreased. The reduced relative abundance of endophytic rhizosphere bacteria associated with plant growth and disease resistance may thus be the cause of tree senescence. This work acts as a reference to increases the understanding of plant-microbe interactions.
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Affiliation(s)
- Jiyuan Pan
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China
| | - Qinglong Dong
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Haibin Wen
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiaojie Wang
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China
| | - Yanan Liu
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China
| | - Xuemei Zhang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Walnut Technical Engineering Research Center, Lincheng, 054300, Hebei, China
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China
| | - Dan Zhao
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China.
| | - Xiujun Lu
- College of Plant Protection, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, Hebei, China.
- Hebei Walnut Technical Engineering Research Center, Lincheng, 054300, Hebei, China.
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Zuo YL, Hu QN, Qin L, Liu JQ, He XL. Species identity and combinations differ in their overall benefits to Astragalus adsurgens plants inoculated with single or multiple endophytic fungi under drought conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:933738. [PMID: 36160950 PMCID: PMC9490189 DOI: 10.3389/fpls.2022.933738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (Alternaria chlamydospora, Sarocladium kiliense, and Monosporascus sp.). For that, we compared the effects of single fungus vs. combined fungi inoculation, on plant morphology and rhizospheric soil microhabitat of desert plant Astragalus adsurgens grown under drought and non-sterile soil conditions. The results indicated that fungal inoculation mainly influenced root biomass of A. adsurgens, but did not affect the shoot biomass. Both single fungus and combined inoculation decreased plant height (7-17%), but increased stem branching numbers (13-34%). However, fungal inoculation influenced the root length and surface area depending on their species and combinations, with the greatest benefits occurring on S. kiliense inoculation alone and its co-inoculation with Monosporascus sp. (109% and 61%; 54% and 42%). Although A. chlamydospora and co-inoculations with S. kiliense and Monosporascus sp. also appeared to promote root growth, these inoculations resulted in obvious soil acidification. Despite no observed root growth promotion, Monosporascus sp. associated with its combined inoculations maximally facilitated soil organic carbon accumulation. However, noticeably, combined inoculation of the three species had no significant effects on root length, surface area, and biomass, but promoted rhizospheric fungal diversity and abundance most, with Sordariomycetes being the dominant fungal group. This indicates the response of plant growth to fungal inoculation may be different from that of the rhizospheric fungal community. Structural equation modeling also demonstrated that fungal inoculation significantly influenced the interactions among the growth of A. adsurgens, soil factors, and rhizospheric fungal groups. Our findings suggest that, based on species-specific and combinatorial effects, endophytic fungi enhanced the plant root growth, altered soil nutrients, and facilitated rhizospheric fungal community, possibly contributing to desert plant performance and ecological adaptability. These results will provide the basis for evaluating the potential application of fungal inoculants for developing sustainable management for desert ecosystems.
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Affiliation(s)
- Yi-Ling Zuo
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Qian-Nan Hu
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Qin
- School of Life Sciences, Hebei University, Baoding, China
| | - Jia-Qiang Liu
- School of Life Sciences, Hebei University, Baoding, China
| | - Xue-Li He
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
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