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Li J, Wu L, Zhou Y, Xie Y, Lu F, Chang F, Yang X, Han X, Cheng M. Kobresia humilis via root-released flavonoids recruit Bacillus for promoted growth. Microbiol Res 2024; 287:127866. [PMID: 39111018 DOI: 10.1016/j.micres.2024.127866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
Alpine meadows, which are critical for biodiversity and ecosystem services, are increasingly degrading, necessitating effective restoration strategies. This study explored the mechanism by which Kobresia humilis, an alpine meadow-constructive species, modulates the rhizosphere microbiome via root exudates to enhance growth. Field investigations revealed that the plant height of K. humilis in a severely degraded (SD) alpine meadow was significantly higher than that in other K. humilis populations. Consequently, we analysed the differences between this plot and other K. humilis samples with different degrees of degradation to explore the reasons underlying the phenotypic differences in K. humilis. 16 S rRNA amplicon sequencing results showed that the SD plots were significantly enriched with more Bacillus, altering the composition of the rhizosphere microbial community of K. humilis. The collection and analysis of root exudates from various K. humilis locations revealed distinct differences. Procrustes analysis indicated a strong correlation between the root exudates and the rhizosphere microbiome composition of K. humilis. Model-based integration of metabolite observations, species abundance 2 (MIMOSA2), and Spearman's rank correlation coefficient analysis were used to identify the root exudates potentially related to the enrichment and recruitment of Bacillus. Bacillus from SD samples was isolated and screened, and the representative strain D334 was found to be differentially enriched compared to other samples. A series of in vitro experiments with the screened root exudates and strain D334 demonstrated that K. humilis could recruit Bacillus and promote its colonisation by releasing flavonoids, particularly baicalin. Additionally, K. humilis can release sucrose and riboflavin, which promote strain growth. Finally, soil microbiome transplantation experiments confirmed that different K. humilis phenotypes were closely related to the functions of the rhizosphere microbiome, especially in root morphological shaping. Moreover, the effects of Bacillus inoculation and the microbiome on the plant phenotypes were consistent. In summary, this study revealed a new mechanism by which K. humilis recruits rhizosphere growth-promoting bacteria and enhances soil nutrient utilisation, thereby promoting plant growth. These findings provide a theoretical basis for ecological restoration using soil microbial communities and clarify the relationship between plant metabolites and microbial community assembly.
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Affiliation(s)
- Junxi Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lingling Wu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Yizhi Zhou
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Yongli Xie
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Xining 810016, China; Key Laboratory of Use of Forage Germplasm Resources on Tibetan Plateau of Qinghai Province, Xining 810016, China.
| | - Fuwei Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Feifei Chang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xue Yang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Xining 810016, China
| | - Xianzhong Han
- Menyuan County Grassland Station, Menyuan 810399, China
| | - Mingxuan Cheng
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
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Wu XH, Ma CY, Jiang HJ, Zhang XY, Wang HM, Li HR, Zhao ZH, Sun K, Zhang W, Dai CC. Root Endophyte-Manipulated Alteration in Rhizodeposits Stimulates Claroideoglomus in the Rhizosphere to Enhance Drought Resistance in Peanut. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:20211-20223. [PMID: 39197047 DOI: 10.1021/acs.jafc.4c05009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Drought dramatically affects plant growth and yield. A previous study indicated that endophytic fungus Phomopsis liquidambaris can improve the drought resistance of peanuts, which is related with the root arbuscular mycorrhizal fungi (AMF) community; however, how root endophytes mediate AMF assembly to affect plant drought resistance remains unclear. Here, we explored the mechanism by which endophytic fungus recruits AMF symbiotic partners via rhizodeposits to improve host drought resistance. The results showed that Ph. liquidambaris enhanced peanut drought resistance by enriching the AMF genus Claroideoglomus of the rhizosphere. Furthermore, metabolomic analysis indicated that Ph. liquidambaris significantly promoted isoformononetin and salicylic acid (SA) synthesis in rhizodeposits, which were correlated with the increase in Claroideoglomus abundance following Ph. liquidambaris inoculation. Coinoculation experiments confirmed that isoformononetin and SA could enrich Claroideoglomus etunicatum in the rhizosphere, thereby improving the drought resistance. This study highlights the crucial role of fungal consortia in plant stress resistance.
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Affiliation(s)
- Xiao-Han Wu
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Xiang-Yu Zhang
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Hao-Ming Wang
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Hao-Ran Li
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Zi-Han Zhao
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
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3
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Nakagami S, Wang Z, Han X, Tsuda K. Regulation of Bacterial Growth and Behavior by Host Plant. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:69-96. [PMID: 38857544 DOI: 10.1146/annurev-phyto-010824-023359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Plants are associated with diverse bacteria in nature. Some bacteria are pathogens that decrease plant fitness, and others are beneficial bacteria that promote plant growth and stress resistance. Emerging evidence also suggests that plant-associated commensal bacteria collectively contribute to plant health and are essential for plant survival in nature. Bacteria with different characteristics simultaneously colonize plant tissues. Thus, plants need to accommodate bacteria that provide service to the host plants, but they need to defend against pathogens at the same time. How do plants achieve this? In this review, we summarize how plants use physical barriers, control common goods such as water and nutrients, and produce antibacterial molecules to regulate bacterial growth and behavior. Furthermore, we highlight that plants use specialized metabolites that support or inhibit specific bacteria, thereby selectively recruiting plant-associated bacterial communities and regulating their function. We also raise important questions that need to be addressed to improve our understanding of plant-bacteria interactions.
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Affiliation(s)
- Satoru Nakagami
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Zhe Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Xiaowei Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Kenichi Tsuda
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
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Mukherjee A, Singh BN, Kaur S, Sharma M, Ferreira de Araújo AS, Pereira APDA, Morya R, Puopolo G, Melo VMM, Verma JP. Unearthing the power of microbes as plant microbiome for sustainable agriculture. Microbiol Res 2024; 286:127780. [PMID: 38970905 DOI: 10.1016/j.micres.2024.127780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.
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Affiliation(s)
- Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Bansh Narayan Singh
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; Crop Research Centre, Oak Park, Carlow, Ireland
| | - Minaxi Sharma
- CARAH ASBL, Rue Pal Pastur 11, Ath 7800, Belgium; China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China, Ningbo 315000, China
| | | | | | - Raj Morya
- Department of Civil and Environmental engineering, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, San Michele all'Adige 38098, Italy; Research and Innovation center, Fondazione Edmund Mach, Via E. Mach 1, San Michelle all'Adige 38098, Italy
| | - Vânia Maria Maciel Melo
- Department of Biological Sciences, Faculty of Science, Federal University of Ceará, Pici, Fortaleza, Ceará 60020-181, Brazil
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Liu J, Xu W, Zhang Q, Liao W, Li L, Chen S, Yang J, Wang Z, Xu F. OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake. PLANT COMMUNICATIONS 2024; 5:100930. [PMID: 38685708 PMCID: PMC11369732 DOI: 10.1016/j.xplc.2024.100930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.
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Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wencheng Liao
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liang Li
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shu Chen
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinyong Yang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengrui Wang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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6
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Kozaeva E, Eida AA, Gunady EF, Dangl JL, Conway JM, Brophy JA. Roots of synthetic ecology: microbes that foster plant resilience in the changing climate. Curr Opin Biotechnol 2024; 88:103172. [PMID: 39029405 DOI: 10.1016/j.copbio.2024.103172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024]
Abstract
Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.
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Affiliation(s)
- Ekaterina Kozaeva
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Abdul Aziz Eida
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ella F Gunady
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan M Conway
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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Zhang J, Jia F, Song K, Wang F, Li J, Huang L, Qu T. Enterobacter ludwigii b3 in the rhizosphere of wild rice assists cultivated rice in mitigating drought stress by direct and indirect methods. Biochem Biophys Res Commun 2024; 735:150489. [PMID: 39096883 DOI: 10.1016/j.bbrc.2024.150489] [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: 04/26/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Drought is the primary factor limiting rice production in ecosystems. Wild rice rhizosphere bacteria possess the potential to assist in the stress resistance of cultivated rice. This study examines the impact of wild rice rhizosphere bacteria on cultivated rice under drought conditions. From the rhizosphere soil of wild rice, 20 potential drought-resistant strains were isolated. Subsequent to the screening, the most effective strain b3, was identified as Enterobacter ludwigii. Pot experiments were conducted on the cultivated Changbai 9 rice. It was found that inoculation with the E. ludwigii b3 strain improved the drought resistance of the rice, promotion of rice growth (shoot height increased by 13.47 %), increased chlorophyll content (chlorophyll a, chlorophyll b and carotenoid increased by 168.74 %, 130.68 % and 87.89 %), improved antioxidant system (content of glutathione was increased by 60.35 %), and accumulation of osmotic regulation substances (soluble sugar and soluble protein increased by 70.36 % and 142.03 %). Furthermore, E. ludwigii b3 had a transformative effect on the rhizosphere bacterial community of cultivated rice, increasing its abundance and diversity while simultaneously recruiting beneficial rhizosphere bacteria, resulting in a more complex community. Additionally, E. ludwigii b3 acted directly and indirectly on cultivated rice through its metabolites (organic acids, amino acids, flavonoids and other substances), which helped alleviate drought stress. In conclusion, the E. ludwigii b3 shows promise as a drought-resistant strain and has the potential to improve the growth and productivity of cultivated rice in arid agricultural ecosystems. This study represents the first investigation of E. ludwigii in the rhizosphere of wild rice under drought conditions on cultivated rice.
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Affiliation(s)
- Jianfeng Zhang
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Fang Jia
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Keji Song
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Fudong Wang
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Junchen Li
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Leye Huang
- College of Life Science, Key Laboratory of Straw Comprehensive Utlisation and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Tongbao Qu
- College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, 130118, China.
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Tang Y, Zhou Y, Wang P, Ge L, Lou W, Yan X, Li S, Wang X, Hu C, Zhao X. Selenium-Mediated Shaping of Citrus Rhizobiome for Promotion in Root Growth and Soil Phosphorus Activation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39018060 DOI: 10.1021/acs.jafc.4c02761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Selenium (Se) has been widely reported to affect plant growth, nutrient cycling, and the rhizobiome. However, how Se shapes the rhizobiome and interacts with plants remains largely elusive. Pot and hydroponic experiments were employed to elucidate the regulatory mechanism of Se in the citrus rhizobiome. Compared to the control, soil Se application significantly increased the root biomass (34.7%) and markedly reduced rhizosphere HCl-P, H2O-P, NaHCO3-IP, and residual-P of citrus, which were related to the variation of citrus rhizobiome. Se primarily enriched Proteobacteria and Actinobacteria as well as the phosphorus (P) functional genes phod and pqqc. Further study revealed that Se altered the metabolite profile of root exudate, particularly enhancing the abundance of l-cyclopentylglycine, cycloleucine, l-proline, l-pipecolic acid, and inositol, which played a key role in reshaping the citrus rhizobiome. These metabolites could serve as both nutrient sources and signaling molecules, thus supporting the growth or chemotaxis of the functional microbes. These bacterial taxa have the potential to solubilize P or stimulate plant growth. These findings provide a novel mechanistic understanding of the intriguing interactions between Se, root exudate, and rhizosphere microbiomes, and demonstrate the potential for utilizing Se to regulate rhizobiome function and enhance soil P utilization in citrus cultivation.
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Affiliation(s)
- Yanni Tang
- College of Resources and Environment/National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Zhou
- College of Resources and Environment/National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengwei Wang
- College of Resources and Environment/National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Liqiang Ge
- National Research Center for Geoanalysis/Key Laboratory of Eco-geochemistry, Ministry of Natural Resources, Beijing 100037, China
| | - Wei Lou
- Ganzhou Citrus Research Institute, Gannan Academy of Sciences, Ganzhou 341000, China
| | - Xiang Yan
- Ganzhou Citrus Research Institute, Gannan Academy of Sciences, Ganzhou 341000, China
| | - Shiqian Li
- Fujian Universities and Colleges Engineering Research Center of Modern Facility Agriculture, Fuqing 350300, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chengxiao Hu
- College of Resources and Environment/National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohu Zhao
- College of Resources and Environment/National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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10
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Wu F, Chen Z, Xu X, Xue X, Zhang Y, Sui N. Halotolerant Bacillus sp. strain RA coordinates myo-inositol metabolism to confer salt tolerance to tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38967265 DOI: 10.1111/jipb.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
Soil salinity is a worldwide problem threatening crop yields. Some plant growth-promoting rhizobacteria (PGPR) could survive in high salt environment and assist plant adaptation to stress. Nevertheless, the genomic and metabolic features, as well as the regulatory mechanisms promoting salt tolerance in plants by these bacteria remain largely unknown. In the current work, a novel halotolerant PGPR strain, namely, Bacillus sp. strain RA can enhance tomato tolerance to salt stress. Comparative genomic analysis of strain RA with its closely related species indicated a high level of evolutionary plasticity exhibited by strain-specific genes and evolutionary constraints driven by purifying selection, which facilitated its genomic adaptation to salt-affected soils. The transcriptome further showed that strain RA could tolerate salt stress by balancing energy metabolism via the reprogramming of biosynthetic pathways. Plants exude a plethora of metabolites that can strongly influence plant fitness. The accumulation of myo-inositol in leaves under salt stress was observed, leading to the promotion of plant growth triggered by Bacillus sp. strain RA. Importantly, myo-inositol serves as a selective force in the assembly of the phyllosphere microbiome and the recruitment of plant-beneficial species. It promotes destabilizing properties in phyllosphere bacterial co-occurrence networks, but not in fungal networks. Furthermore, interdomain interactions between bacteria and fungi were strengthened by myo-inositol in response to salt stress. This work highlights the genetic adaptation of RA to salt-affected soils and its ability to impact phyllosphere microorganisms through the adjustment of myo-inositol metabolites, thereby imparting enduring resistance against salt stress in tomato.
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Affiliation(s)
- Fenghui Wu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zengting Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
| | - Xiaotong Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
| | - Xin Xue
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Yanling Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
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11
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Yang Y, Zhao Y, Pan M, Yu Y, Guo Y, Ge Q, Hao W. Physiology and transcriptome analysis of Artemisia argyi adaptation and accumulation to soil cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116397. [PMID: 38714088 DOI: 10.1016/j.ecoenv.2024.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
The soil pollution caused by cadmium (Cd) poses a significant threat to the environment. Therefore, identifying plants that can effectively remediate Cd-contaminated soils is urgently needed. In this study, physiological, cytological, and transcriptome analyses were performed to comprehensively understand the changes in Artemisia argyi under Cd stress. Physiological and cytological analyses indicated that A. argyi maintained normal growth with intact cell structure under Cd stress levels up to 10 mg/kg. Cytological analysis showed that Cd precipitation in leaf cells occurred in the cytoplasm and intercellular spaces. As the levels of Cd stress increased, proline accumulation in leaves increased, whereas soluble protein and soluble sugar initially increased, followed by a subsequent decline. The translocation factor was above 1 under 0.6 mg/kg Cd stress but decreased when it exceeded this concentration. Transcriptome analyses revealed several crucial Cd-influenced pathways, including amino acid, terpenoid, flavonoid, and sugar metabolisms. This study not only proved that A. argyi could enrich Cd in soil but also revealed the response of A. argyi to Cd and its resistance mechanisms, which provided insight into the cleaner production of A. argyi and the remediation of Cd-contaminated soil.
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Affiliation(s)
- Yingbin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yinghui Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meiqi Pan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaxin Yu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Guo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qing Ge
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Wenfang Hao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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12
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Wu Y, Wang Y, Liu X, Zhang C. Unveiling key mechanisms: Transcriptomic meta-analysis of diverse nanomaterial applications addressing biotic and abiotic stresses in Arabidopsis Thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172476. [PMID: 38621536 DOI: 10.1016/j.scitotenv.2024.172476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/27/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The potential applications of nanomaterials in agriculture for alleviating diverse biotic and abiotic stresses have garnered significant attention. The reported mechanisms encompass promoting plant growth and development, alleviating oxidative stress, inducing defense responses, modulating plant-microbe interactions, and more. However, individual studies may not fully uncover the common pathways or distinguish the effects of different nanostructures. We examined Arabidopsis thaliana transcriptomes exposed to biotic, abiotic, and metal or carbon-based nanomaterials, utilizing 24 microarray chipsets and 17 RNA-seq sets. The results showed that: 1) from the perspective of different nanostructures, all metal nanomaterials relieved biotic/abiotic stresses via boosting metal homeostasis, particularly zinc and iron. Carbon nanomaterials induce hormone-related immune responses in the presence of both biotic and abiotic stressors. 2) Considering the distinct features of various nanostructures, metal nanomaterials displayed unique characteristics in seed priming for combating abiotic stresses. In contrast, carbon nanomaterials exhibited attractive features in alleviating water deprivation and acting as signaling amplifiers during biotic stress. 3) For shared pathway analysis, response to hypoxia emerges as the predominant and widely shared regulatory mechanism governing diverse stress responses, including those induced by nanomaterials. By deciphering shared and specific pathways and responses, this research opens new avenues for precision nano-agriculture, offering innovative strategies to optimize plant resilience, improve stress management, and advance sustainable crop production practices.
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Affiliation(s)
- Yining Wu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yvjie Wang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xian Liu
- Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China.
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13
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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14
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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15
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Zheng Y, Cao X, Zhou Y, Ma S, Wang Y, Li Z, Zhao D, Yang Y, Zhang H, Meng C, Xie Z, Sui X, Xu K, Li Y, Zhang CS. Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress. Nat Commun 2024; 15:3520. [PMID: 38664402 PMCID: PMC11045775 DOI: 10.1038/s41467-024-47773-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.
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Affiliation(s)
- Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xuwen Cao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266200, China
| | - Yanan Zhou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, 271018, China
| | - Siqi Ma
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Youqiang Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhe Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Donglin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yanzhe Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Han Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chen Meng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, 271018, China
| | - Xiaona Sui
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Kangwen Xu
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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16
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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17
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Olanrewaju OS, Glick BR, Babalola OO. Metabolomics-guided utilization of beneficial microbes for climate-resilient crops. Curr Opin Chem Biol 2024; 79:102427. [PMID: 38290195 DOI: 10.1016/j.cbpa.2024.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Unit for Environmental Sciences and Management, Potchefstroom Campus, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa.
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Cao YH, Zhao XW, Nie G, Wang ZY, Song X, Zhang MX, Hu JP, Zhao Q, Jiang Y, Zhang JL. The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170205. [PMID: 38272075 DOI: 10.1016/j.scitotenv.2024.170205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/14/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.
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Affiliation(s)
- Yan-Hua Cao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Xiong-Wei Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, PR China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Zhi-Yong Wang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China
| | - Xin Song
- College of Life Science and Resources and Environment, Yichun University, Yichun 336000, PR China
| | - Ming-Xu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Jin-Peng Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Qi Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China; Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China.
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Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [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: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
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Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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Wu X, Yang Y, Wang M, Shao C, Morillas JIV, Yuan F, Liu J, Zhang H. Improving coriander yield and quality with a beneficial bacterium. MOLECULAR HORTICULTURE 2024; 4:8. [PMID: 38419111 PMCID: PMC10903023 DOI: 10.1186/s43897-024-00087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Miao Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuyang Shao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Juan I V Morillas
- Instituto de Tecnologia Química e Biológica (ITQB), Oeiras, Lisbon, Portugal
| | - Fengtong Yuan
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang, 330224, China
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang, 330200, China
| | - Jie Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang, 330224, China.
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang, 330200, China.
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Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
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Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Chen L, Liu Y. The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria. BIOLOGY 2024; 13:95. [PMID: 38392313 PMCID: PMC10886372 DOI: 10.3390/biology13020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.
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Affiliation(s)
- Lin Chen
- National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain, Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
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Ahmad W, Coffman L, Weerasooriya AD, Crawford K, Khan AL. The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L. FRONTIERS IN PLANT SCIENCE 2024; 14:1280251. [PMID: 38269137 PMCID: PMC10805835 DOI: 10.3389/fpls.2023.1280251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
Introduction With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered. Methods The soybean plants were exposed to cold stress (8-10°C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated. Results and discussion We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.
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Affiliation(s)
- Waqar Ahmad
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Lauryn Coffman
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Aruna D Weerasooriya
- Cooperative Agricultural Research Center, College of Agriculture & Human Sciences, Prairie View A&M University, Prairie View, TX, United States
| | - Kerri Crawford
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Abdul Latif Khan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
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Kumar GA, Kumar S, Bhardwaj R, Swapnil P, Meena M, Seth CS, Yadav A. Recent advancements in multifaceted roles of flavonoids in plant-rhizomicrobiome interactions. FRONTIERS IN PLANT SCIENCE 2024; 14:1297706. [PMID: 38250451 PMCID: PMC10796613 DOI: 10.3389/fpls.2023.1297706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
The rhizosphere consists of a plethora of microbes, interacting with each other as well as with the plants present in proximity. The root exudates consist of a variety of secondary metabolites such as strigolactones and other phenolic compounds such as coumarin that helps in facilitating communication and forming associations with beneficial microbes in the rhizosphere. Among different secondary metabolites flavonoids (natural polyphenolic compounds) continuously increasing attention in scientific fields for showing several slews of biological activities. Flavonoids possess a benzo-γ-pyrone skeleton and several classes of flavonoids have been reported on the basis of their basic structure such as flavanones, flavonols, anthocyanins, etc. The mutualistic association between plant growth-promoting rhizobacteria (PGPR) and plants have been reported to help the host plants in surviving various biotic and abiotic stresses such as low nitrogen and phosphorus, drought and salinity stress, pathogen attack, and herbivory. This review sheds light upon one such component of root exudate known as flavonoids, which is well known for nodulation in legume plants. Apart from the well-known role in inducing nodulation in legumes, this group of compounds has anti-microbial and antifungal properties helping in establishing defensive mechanisms and playing a major role in forming mycorrhizal associations for the enhanced acquisition of nutrients such as iron and phosphorus. Further, this review highlights the role of flavonoids in plants for recruiting non-mutualistic microbes under stress and other important aspects regarding recent findings on the functions of this secondary metabolite in guiding the plant-microbe interaction and how organic matter affects its functionality in soil.
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Affiliation(s)
- Gokul Anil Kumar
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | - Rupesh Bhardwaj
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Prashant Swapnil
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | | | - Ankush Yadav
- School of Basic Science, Department of Botany, Central University of Punjab, Bhatinda, Punjab, India
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Fan W, Xiao Y, Dong J, Xing J, Tang F, Shi F. Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1324333. [PMID: 38179479 PMCID: PMC10766110 DOI: 10.3389/fpls.2023.1324333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Soil salinization is a global environmental issue and a significant abiotic stress that threatens crop production. Root-associated rhizosphere microbiota play a pivotal role in enhancing plant tolerance to abiotic stresses. However, limited information is available concerning the specific variations in rhizosphere microbiota driven by different plant genotypes (varieties) in response to varying levels of salinity stress. In this study, we compared the growth performance of three alfalfa varieties with varying salt tolerance levels in soils with different degrees of salinization. High-throughput 16S rRNA and ITS sequencing were employed to analyze the rhizosphere microbial communities. Undoubtedly, the increasing salinity significantly inhibited alfalfa growth and reduced rhizosphere microbial diversity. However, intriguingly, salt-tolerant varieties exhibited relatively lower susceptibility to salinity, maintaining more stable rhizosphere bacterial community structure, whereas the reverse was observed for salt-sensitive varieties. Bacillus emerged as the dominant species in alfalfa's adaptation to salinity stress, constituting 21.20% of the shared bacterial genera among the three varieties. The higher abundance of Bacillus, Ensifer, and Pseudomonas in the rhizosphere of salt-tolerant alfalfa varieties is crucial in determining their elevated salt tolerance. As salinity levels increased, salt-sensitive varieties gradually accumulated a substantial population of pathogenic fungi, such as Fusarium and Rhizoctonia. Furthermore, rhizosphere bacteria of salt-tolerant varieties exhibited increased activity in various metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and biosynthesis of amino acids. It is suggested that salt-tolerant alfalfa varieties can provide more carbon sources to the rhizosphere, enriching more effective plant growth-promoting bacteria (PGPB) such as Pseudomonas to mitigate salinity stress. In conclusion, our results highlight the variety-mediated enrichment of rhizosphere microbiota in response to salinity stress, confirming that the high-abundance enrichment of specific dominant rhizosphere microbes and their vital roles play a significant role in conferring high salt adaptability to these varieties.
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Affiliation(s)
- Wenqiang Fan
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanzi Xiao
- College of Agriculture and Forestry, Hulunbuir University, Hulunber, China
| | - Jiaqi Dong
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Xing
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fang Tang
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengling Shi
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Su Y, Wang J, Gao W, Wang R, Yang W, Zhang H, Huang L, Guo L. Dynamic metabolites: A bridge between plants and microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165612. [PMID: 37478935 DOI: 10.1016/j.scitotenv.2023.165612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/23/2023]
Abstract
Plant metabolites have a great influence on soil microbiomes. Although few studies provided insights into plant-microbe interactions, we still know very little about how plants recruit their microbiome. Here, we discuss the dynamic progress that typical metabolites shape microbes by a variety of factors, such as physiographic factors, cultivar factors, phylogeny factors, and environmental stress. Several kinds of metabolites have been reviewed, including plant primary metabolites (PPMs), phytohormones, and plant secondary metabolites (PSMs). The microbes assembled by plant metabolites in return exert beneficial effects on plants, which have been widely applied in agriculture. What's more, we point out existing problems and future research directions, such as unclear mechanisms, few species, simple parts, and ignorance of absolute abundance. This review may inspire readers to study plant-metabolite-microbe interactions in the future.
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Affiliation(s)
- Yaowu Su
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Rubing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; State Key Laboratory of Dao-di Herbs, Beijing, 100700, China.
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Nakayasu M, Takamatsu K, Kanai K, Masuda S, Yamazaki S, Aoki Y, Shibata A, Suda W, Shirasu K, Yazaki K, Sugiyama A. Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids. mBio 2023; 14:e0059923. [PMID: 37772873 PMCID: PMC10653915 DOI: 10.1128/mbio.00599-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Saponins are a group of plant specialized metabolites with various bioactive properties, both for human health and soil microorganisms. Our previous works demonstrated that Sphingobium is enriched in both soils treated with a steroid-type saponin, such as tomatine, and in the tomato rhizosphere. Despite the importance of saponins in plant-microbe interactions in the rhizosphere, the genes involved in the catabolism of saponins and their aglycones (sapogenins) remain largely unknown. Here we identified several enzymes that catalyzed the degradation of steroid-type saponins in a Sphingobium isolate from tomato roots, RC1. A comparative genomic analysis of Sphingobium revealed the limited distribution of genes for saponin degradation in our saponin-degrading isolates and several other isolates, suggesting the possible involvement of the saponin degradation pathway in the root colonization of Sphingobium spp. The genes that participate in the catabolism of sapogenins could be applied to the development of new industrially valuable sapogenin molecules.
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Affiliation(s)
- Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Kyoko Takamatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Keiko Kanai
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Shinichi Yamazaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
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Kumar M, Saggu SK, Pratibha P, Singh SK, Kumar S. Exploring the role of microbes for the management of persistent organic pollutants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118492. [PMID: 37384989 DOI: 10.1016/j.jenvman.2023.118492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.
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Affiliation(s)
- Manoj Kumar
- School of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, 144401, India
| | - Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, 144004, India
| | - Pritu Pratibha
- Center for Excellence in Molecular Plant Science, Plant Stress Center, CAS, Shanghai, 201602, China
| | - Sunil Kumar Singh
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, 211002, India.
| | - Shiv Kumar
- Department of Microbiology, Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab, 151203, India.
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Jang S, Choi SK, Zhang H, Zhang S, Ryu CM, Kloepper JW. History of a model plant growth-promoting rhizobacterium, Bacillus velezensis GB03: from isolation to commercialization. FRONTIERS IN PLANT SCIENCE 2023; 14:1279896. [PMID: 37885658 PMCID: PMC10598611 DOI: 10.3389/fpls.2023.1279896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
Bacillus velezensis strain GB03 is a Gram-positive rhizosphere bacterium known for its ability to promote plant growth and immunity. This review provides a comprehensive overview of the research on GB03 from its initial discovery in Australian wheat fields in 1971 to its current applications. Recognized as a model plant growth-promoting rhizobacterium (PGPR), GB03 has exhibited outstanding performance in enhancing the growth and protection of many crop plants including cucumber, pepper, wheat, barley, soybean, and cotton. Notably, GB03 has been reported to elicit plant immune response, referred to as induced systemic resistance (ISR), against above-ground pathogens and insect pests. Moreover, a pivotal finding in GB03 was the first-ever identification of its bacterial volatile compounds, which are known to boost plant growth and activate ISR. Research conducted over the past five decades has clearly demonstrated the potential of GB03 as an eco-friendly substitute for conventional pesticides and fertilizers. Validating its safety, the U.S. Environmental Protection Agency endorsed GB03 for commercial use as Kodiak® in 1998. Subsequently, other compounds, such as BioYield™, were released as a biological control agent against soil-borne pathogens and as a biofertilizer, utilizing a durable spore formulation. More recently, GB03 has been utilized as a keystone modulator for engineering the rhizosphere microbiome and for eliciting microbe-induced plant volatiles. These extensive studies on GB03 underscore its significant role in sustainable agriculture, positioning it as a safe and environmentally-friendly solution for crop protection.
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Affiliation(s)
- Seonghan Jang
- Infectious Disease Research Center, Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, Republic of Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shouan Zhang
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida-IFAS, Homestead, FL, United States
| | - Choong-Min Ryu
- Infectious Disease Research Center, Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Joseph W. Kloepper
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
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Lewis JA, Zhang B, Harza R, Palmer N, Sarath G, Sattler SE, Twigg P, Vermerris W, Kang C. Structural Similarities and Overlapping Activities among Dihydroflavonol 4-Reductase, Flavanone 4-Reductase, and Anthocyanidin Reductase Offer Metabolic Flexibility in the Flavonoid Pathway. Int J Mol Sci 2023; 24:13901. [PMID: 37762209 PMCID: PMC10531346 DOI: 10.3390/ijms241813901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Flavonoids are potent antioxidants that play a role in defense against pathogens, UV-radiation, and the detoxification of reactive oxygen species. Dihydroflavonol 4-reductase (DFR) and flavanone 4-reductase (FNR) reduce dihydroflavonols and flavanones, respectively, using NAD(P)H to produce flavan-(3)-4-(di)ols in flavonoid biosynthesis. Anthocyanidin reductase (ANR) reduces anthocyanidins to flavan-3-ols. In addition to their sequences, the 3D structures of recombinant DFR, FNR and ANR from sorghum and switchgrass showed a high level of similarity. The catalytic mechanism, substrate-specificity and key residues of three reductases were deduced from crystal structures, site-directed mutagenesis, molecular docking, kinetics, and thermodynamic ana-lyses. Although DFR displayed its highest activity against dihydroflavonols, it also showed activity against flavanones and anthocyanidins. It was inhibited by the flavonol quercetin and high concentrations of dihydroflavonols/flavonones. SbFNR1 and SbFNR2 did not show any activity against dihydroflavonols. However, SbFNR1 displayed activity against flavanones and ANR activity against two anthocyanidins, cyanidin and pelargonidin. Therefore, SbFNR1 and SbFNR2 could be specific ANR isozymes without delphinidin activity. Sorghum has high concentrations of 3-deoxyanthocyanidins in vivo, supporting the observed high activity of SbDFR against flavonols. Mining of expression data indicated substantial induction of these three reductase genes in both switchgrass and sorghum in response to biotic stress. Key signature sequences for proper DFR/ANR classification are proposed and could form the basis for future metabolic engineering of flavonoid metabolism.
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Affiliation(s)
- Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Rishi Harza
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Nathan Palmer
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Gautam Sarath
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Scott E. Sattler
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA;
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA;
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
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Khan AL. The phytomicrobiome: solving plant stress tolerance under climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1219366. [PMID: 37746004 PMCID: PMC10513501 DOI: 10.3389/fpls.2023.1219366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.
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Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, United States
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34
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Li Y, Chen Y, Chen J, Shen C. Flavonoid metabolites in tea plant (Camellia sinensis) stress response: Insights from bibliometric analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107934. [PMID: 37572493 DOI: 10.1016/j.plaphy.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/21/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In the context of global climate change, tea plants are at risk from elevating environmental stress factors. Coping with this problem relies upon the understanding of tea plant stress response and its underlying mechanisms. Over the past two decades, research in this field has prospered with the contributions of scientists worldwide. Aiming in providing a comprehensive perspective of the research field related to tea plant stress response, we present a bibliometric analysis of the this area. Our results demonstrate the most studied stresses, global contribution, authorship and collaboration, and trending research topics. We highlight the importance of flavonoid metabolites in tea plant stress response, particularly their role in maintaining redox homeostasis, yield, and adjusting tea quality under stress conditions. Further research on the flavonoid response under various stress conditions can promote the development of cultivation measures, thereby improving stress resistance and tea quality.
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Affiliation(s)
- YunFei Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, 410128, China; National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, 410128, China
| | - YiQin Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, 410128, China; National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, 410128, China
| | - JiaHao Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, 410128, China; National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, 410128, China
| | - ChengWen Shen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, 410128, China; National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, 410128, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, 410128, China.
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35
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Xue X, Chen R, Xu C, Zhang C, Dong L, Zhao X, Wang X. Apple-marigold intercropping improves soil properties by changing soil metabolomics and bacterial community structures. Front Microbiol 2023; 14:1195985. [PMID: 37455738 PMCID: PMC10343436 DOI: 10.3389/fmicb.2023.1195985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Marigold can protect crops against soil-borne diseases. However, the effects of intercropping with marigold on apple rhizosphere soils are not known. In this study, we investigated the metabolite profiles and bacterial community structures in rhizosphere soils of the apple-marigold intercropping system by high-throughput sequencing and soil metabolomics. The results show that intercropping marigold could significantly enhance soil moisture, nitrogen, and enzyme activities compared with clean tillage. The soil metabolite profiles and the soil bacterial community structures in the rhizosphere soils were different between the inter-and mono-cropping systems. Among nine metabolites, carbohydrates were more increased in the intercropping system than in the monocropping system. Pathway enrichment analysis revealed that the greatest differential, in terms of metabolic pathway, was starch and sucrose metabolism. Moreover, intercropping marigold significantly increased the relative abundance of plant growth promoting bacteria in rhizosphere soils, such as Rhizobiales, Pseudomonadales, and Bacillales. These results indicate that marigold intercropping positively affected the apple orchard's soil quality and may provide a new intercropping technique to improve soil fertility in orchards and promote plant growth.
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Affiliation(s)
- Xiaomin Xue
- Shandong Institute of Pomology, Tai’an, China
| | - Ru Chen
- Shandong Institute of Pomology, Tai’an, China
| | - Chao Xu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | | | - Lijuan Dong
- Taishan Forestry Research Institute, Tai’an, China
| | - Xianyan Zhao
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Xiaohan Wang
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
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Wang L, Zhang W, Shen W, Li M, Fu Y, Li Z, Li J, Liu H, Su X, Zhang B, Zhao J. Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV). FRONTIERS IN PLANT SCIENCE 2023; 14:1163232. [PMID: 37396641 PMCID: PMC10308444 DOI: 10.3389/fpls.2023.1163232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT-qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA-target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA-target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wanna Shen
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Min Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Yuchen Fu
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Zheng Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Jinxin Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jiaping Zhao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
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Wang F, Yang J, Hua Y, Wang K, Guo Y, Lu Y, Zhu S, Zhang P, Hu G. Transcriptome and Metabolome Analysis of Selenium Treated Alfalfa Reveals Influence on Phenylpropanoid Biosynthesis to Enhance Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:2038. [PMID: 37653955 PMCID: PMC10224443 DOI: 10.3390/plants12102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Selenium (Se) plays an important role in the growth of plants. Alfalfa (Medicago sativa L.) is a perennial legume forage crop with high nutritional value and Se-rich functions. Many studies have shown that selenium can promote alfalfa growth, but few have explored the molecular biology mechanisms behind this effect. In this study, alfalfa was divided into two groups. One group was sprayed with sodium selenite (Na2SeO3) and the other group was sprayed with distilled water as a control. This study determined the growth, reproductive traits, physiological changes, transcriptome and metabolome of both groups of alfalfa. We found that foliar spraying of 100 mg/L Na2SeO3 could significantly increase the growth rate, dry weight, total Se content, amount of pollen per flower, pollen viability, pod spirals, and seed number per pod of alfalfa plants. The level of chlorophyll, soluble protein, proline, and glutathione also increased dramatically in Na2SeO3-sprayed alfalfa seedlings. After transcriptome and metabolome analysis, a total of 614 differentially expressed genes (DEGs) and 1500 differentially expressed metabolites (DEMs), including 26 secondary differentially metabolites were identified. The DEGs were mainly enriched in MAPK signaling pathway, phenylpropanoid biosynthesis, isoflavonoid biosynthesis, cutin, suberine, and wax biosynthesis, and glycerolipid metabolism. The DEMs were mainly enriched in flavone and flavonol biosynthesis, carbon metabolism, glyoxylate and dicarboxylate metabolism, nitrogen metabolism, and phenylpropanoid biosynthesis. Integrative analysis of transcriptome and metabolome showed that the foliar spraying of Na2SeO3 mainly affects phenylpropanoid biosynthesis to promote alfalfa growth.
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Affiliation(s)
| | | | | | | | | | | | | | - Pan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Guofu Hu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
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38
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Lai J, Li C, Zhang Y, Wu Z, Li W, Zhang Z, Ye W, Guo H, Wang C, Long T, Wang S, Yang J. Integrated Transcriptomic and Metabolomic Analyses Reveal the Molecular and Metabolic Basis of Flavonoids in Areca catechu L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4851-4862. [PMID: 36940468 DOI: 10.1021/acs.jafc.2c08864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Areca catechu L., of the Arecaceae family, is widely distributed in tropical Asia. In A. catechu, the extracts and compounds, including flavonoids, have various pharmacological activities. Although there are many studies of flavonoids, the molecular mechanism of their biosynthesis and regulation remains unclear in A. catechu. In this study, 331 metabolites were identified from the root, stem, and leaf of A. catechu using untargeted metabolomics, including 107 flavonoids, 71 lipids, 44 amino acids and derivatives, and 33 alkaloids. The transcriptome analysis identified 6119 differentially expressed genes, and some were enriched in the flavonoid pathway. To analyze the biosynthetic mechanism of the metabolic differences in A. catechu tissues, 36 genes were identified through combined transcriptomic and metabolomic analysis, in which glycosyltransferase genes Acat_15g017010 and Acat_16g013670 were annotated as being involved in the glycosylation of kaempferol and chrysin by their expression and in vitro activities. Flavonoid biosynthesis could be regulated by the transcription factors, AcMYB5 and AcMYB194. This study laid a foundation for further research on the flavonoid biosynthetic pathway of A. catechu.
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Affiliation(s)
- Jun Lai
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Chun Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Yueran Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Zeyong Wu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Weiguan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Zhonghui Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Weizhen Ye
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Hao Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Chao Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Tuan Long
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Jun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 572208, China
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Poppeliers SW, Sánchez-Gil JJ, de Jonge R. Microbes to support plant health: understanding bioinoculant success in complex conditions. Curr Opin Microbiol 2023; 73:102286. [PMID: 36878082 DOI: 10.1016/j.mib.2023.102286] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.
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Affiliation(s)
- Sanne Wm Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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Morcillo RJL, Baroja-Fernández E, López-Serrano L, Leal-López J, Muñoz FJ, Bahaji A, Férez-Gómez A, Pozueta-Romero J. Cell-free microbial culture filtrates as candidate biostimulants to enhance plant growth and yield and activate soil- and plant-associated beneficial microbiota. FRONTIERS IN PLANT SCIENCE 2022; 13:1040515. [PMID: 36618653 PMCID: PMC9816334 DOI: 10.3389/fpls.2022.1040515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/05/2022] [Indexed: 06/12/2023]
Abstract
In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.
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Affiliation(s)
- Rafael Jorge León Morcillo
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Málaga, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Nafarroa, Spain
| | - Lidia López-Serrano
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Málaga, Spain
| | - Jesús Leal-López
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Málaga, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Nafarroa, Spain
| | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Nafarroa, Spain
| | - Alberto Férez-Gómez
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Málaga, Spain
| | - Javier Pozueta-Romero
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Málaga, Spain
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Wang L, Chen M, Lam PY, Dini-Andreote F, Dai L, Wei Z. Multifaceted roles of flavonoids mediating plant-microbe interactions. MICROBIOME 2022; 10:233. [PMID: 36527160 PMCID: PMC9756786 DOI: 10.1186/s40168-022-01420-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/09/2022] [Indexed: 05/07/2023]
Abstract
Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are-to a large extent-mediated by specialized host-derived secondary metabolites. Flavonoids are one of the most studied classes of such metabolites, regulating both plant development and the interaction with commensal microbes. Here, we provide a comprehensive review of the multiple roles of flavonoids in mediating plant-microbe interactions. First, we briefly summarize the general aspects of flavonoid synthesis, transport, and exudation in plants. Then, we review the importance of flavonoids regulating plant-microbe interactions and dynamically influencing the overall community assembly of plant-root microbiomes. Last, we highlight potential knowledge gaps in our understanding of how flavonoids determine the interactions between plants and commensal microbes. Collectively, we advocate the importance of advancing research in this area toward innovative strategies to effectively manipulate plant-microbiome composition, in this case, via flavonoid production and exudation in plant roots. Video Abstract.
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Affiliation(s)
- Lanxiang Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Pui-Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Tegata Gakuen-machi 1-1, Akita City, Akita, 010-8502, Japan
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.
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43
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Ghitti E, Rolli E, Crotti E, Borin S. Flavonoids Are Intra- and Inter-Kingdom Modulator Signals. Microorganisms 2022; 10:microorganisms10122479. [PMID: 36557733 PMCID: PMC9781135 DOI: 10.3390/microorganisms10122479] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Flavonoids are a broad class of secondary metabolites with multifaceted functionalities for plant homeostasis and are involved in facing both biotic and abiotic stresses to sustain plant growth and health. Furthermore, they were discovered as mediators of plant networking with the surrounding environment, showing a surprising ability to perform as signaling compounds for a multitrophic inter-kingdom level of communication that influences the plant host at the phytobiome scale. Flavonoids orchestrate plant-neighboring plant allelopathic interactions, recruit beneficial bacteria and mycorrhizal fungi, counteract pathogen outbreak, influence soil microbiome and affect plant physiology to improve its resilience to fluctuating environmental conditions. This review focuses on the diversified spectrum of flavonoid functions in plants under a variety of stresses in the modulation of plant morphogenesis in response to environmental clues, as well as their role as inter-kingdom signaling molecules with micro- and macroorganisms. Regarding the latter, the review addresses flavonoids as key phytochemicals in the human diet, considering their abundance in fruits and edible plants. Recent evidence highlights their role as nutraceuticals, probiotics and as promising new drugs for the treatment of several pathologies.
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Rodrigues-dos Santos AS, Rebelo-Romão I, Zhang H, Vílchez JI. Discerning Transcriptomic and Biochemical Responses of Arabidopsis thaliana Treated with the Biofertilizer Strain Priestia megaterium YC4-R4: Boosting Plant Central and Secondary Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 11:3039. [PMID: 36432768 PMCID: PMC9697256 DOI: 10.3390/plants11223039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
As a response to the current challenges in agriculture, the application of alternatives to a more sustainable management is required. Thus, biofertilizers begin to emerge as a reliable alternative to improve crop development and resistance to stresses. Among other effects on the plant, the use of beneficial strains may cause changes in their metabolic regulation, as in cell wall biogenesis and in nutrient/ion transportation, improving their growth process. Previous works showed that inoculation with the strain Priestia megaterium YC4-R4 effectively promoted vegetative growth of Arabidopsis thaliana Col-0 plants. Hence, the present work recorded a strain-mediated induction of several pathways of the central and secondary metabolism of the plant, as the induction of lipid, cellulose, phenol, and flavonoid biosynthesis, by using transcriptomic and biochemical analyses.
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Affiliation(s)
| | - Inês Rebelo-Romão
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA Lisboa, 2780-157 Oeiras, Portugal
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Juan Ignacio Vílchez
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA Lisboa, 2780-157 Oeiras, Portugal
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
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Dai L, Singh SK, Gong H, Tang Y, Peng Z, Zhang J, Wu D, Zhang H, He D. Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system. Front Microbiol 2022; 13:981615. [PMID: 36386686 PMCID: PMC9645529 DOI: 10.3389/fmicb.2022.981615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/05/2022] [Indexed: 08/13/2023] Open
Abstract
Tiger lily (Lilium lancifolium Thunb.) is a cash crop with a long history of cultivation in China. Its roots have long been used as a valuable component of Chinese medicine. Continuous cropping, the conventional planting approach for tiger lily, often leads to severe root rot disease, but it is not yet clear how this planting method leads to root rot. In this study, we analyzed the rhizosphere microbiome and predicted microbial protein function in tiger lily planted with the continuous cropping method in three different geological types of soil. In order to explore the specific rhizosphere microbiota triggering root rot disease, tiger lily was compared to maize grown in a similar system, which showed no disease development. An analysis of the chemical elements in the soil revealed that the Pseudomonas and Streptomyces genera, with pathogenic functions, were dominant in the tiger lily rhizosphere. The lower soil pH of tiger lily compared to maize supports the accumulation of pathogenic bacteria in the tiger lily rhizosphere. Meanwhile, we discovered that bacteria of the Flavobacterium genus, with their predicted phosphate transport function, specifically accumulated in the maize rhizosphere. Our findings suggest that Pseudomonas and Streptomyces bacteria may result in continuous cropping-induced root rot disease in tiger lily and that Flavobacterium could serve to protect maize from pathogenic bacteria.
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Affiliation(s)
- Liangliang Dai
- Changsha General Survey of Natural Resources Center, Changsha, China
| | - Sunil K. Singh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao Gong
- Changsha General Survey of Natural Resources Center, Changsha, China
| | - Yuanyuan Tang
- Changsha General Survey of Natural Resources Center, Changsha, China
| | - Zhigang Peng
- Changsha General Survey of Natural Resources Center, Changsha, China
| | - Jun Zhang
- Changsha General Survey of Natural Resources Center, Changsha, China
| | - Dousheng Wu
- College of Biology, Hunan University, Changsha, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Danxia He
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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46
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Hofer U. Root bacterium protects plants from drought. Nat Rev Microbiol 2022; 20:575. [PMID: 35882918 DOI: 10.1038/s41579-022-00782-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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