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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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Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [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: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Monteagudo-Cascales E, Gavira JA, Xing J, Velando F, Matilla MA, Zhulin IB, Krell T. Bacterial sensor evolved by decreasing complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594639. [PMID: 38798610 PMCID: PMC11118575 DOI: 10.1101/2024.05.17.594639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels and motility. Receptors are typically activated by signal binding to ligand binding domains (LBD). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans. They form the predominant family of extracytosolic bacterial LBDs and were identified in all major receptor types. Cache domains are composed of either a single (sCache) or a double (dCache) structural module. The functional relevance of bimodular LBDs remains poorly understood. Here, we identify the PacF chemoreceptor in the phytopathogen Pectobacterium atrosepticum that recognizes formate at the membrane distal module of its dCache domain, triggering chemoattraction. We further demonstrate that a family of formate-specific sCache domains has evolved from a dCache domain, exemplified by PacF, by losing the membrane proximal module. By solving high-resolution structures of two family members in complex with formate, we show that the molecular basis for formate binding at sCache and dCache domains is highly similar, despite their low sequence identity. The apparent loss of the membrane proximal module may be related to the observation that dCache domains bind ligands typically at the membrane distal module, whereas the membrane proximal module is not involved in signal sensing. This work advances our understanding of signal sensing in bacterial receptors and suggests that evolution by reducing complexity may be a common trend shaping their diversity. Significance Many bacterial receptors contain multi-modular sensing domains indicative of complex sensory processes. The presence of more than one sensing module likely permits the integration of multiple signals, although, the molecular detail and functional relevance for these complex sensors remain poorly understood. Bimodular sensory domains are likely to have arisen from the fusion or duplication of monomodular domains. Evolution by increasing complexity is generally believed to be a dominant force. Here we reveal the opposite - how a monomodular sensing domain has evolved from a bimodular one. Our findings will thus motivate research to establish whether evolution by decreasing complexity is typical of other sensory domains.
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Zhao Q, Yao F, Li W, Liu S, Bi S. Identification of a dCache-type chemoreceptor in Campylobacter jejuni that specifically mediates chemotaxis towards methyl pyruvate. Front Microbiol 2024; 15:1400284. [PMID: 38784811 PMCID: PMC11111895 DOI: 10.3389/fmicb.2024.1400284] [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: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
The foodborne pathogenic bacterium Campylobacter jejuni utilizes chemotaxis to assist in the colonization of host niches. A key to revealing the relationship among chemotaxis and pathogenicity is the discovery of signaling molecules perceived by the chemoreceptors. The C. jejuni chemoreceptor Tlp11 is encoded by the highly infective C. jejuni strains. In the present study, we report that the dCache-type ligand-binding domain (LBD) of C. jejuni ATCC 33560 Tlp11 binds directly to novel ligands methyl pyruvate, toluene, and quinoline using the same pocket. Methyl pyruvate elicits a strong chemoattractant response, while toluene and quinoline function as the antagonists without triggering chemotaxis. The sensory LBD was used to control heterologous proteins by constructing chimeras, indicating that the signal induced by methyl pyruvate is transmitted across the membrane. In addition, bioinformatics and experiments revealed that the dCache domains with methyl pyruvate-binding sites and ability are widely distributed in the order Campylobacterales. This is the first report to identify the class of dCache chemoreceptors that bind to attractant methyl pyruvate and antagonists toluene and quinoline. Our research provides a foundation for understanding the chemotaxis and virulence of C. jejuni and lays a basis for the control of this foodborne pathogen.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fulian Yao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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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: 0] [Impact Index Per Article: 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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7
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Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol 2023; 75:102358. [PMID: 37459734 DOI: 10.1016/j.mib.2023.102358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 09/17/2023]
Abstract
About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Suzuki S, Yokota K, Igimi S, Kajikawa A. Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances. Sci Rep 2023; 13:15632. [PMID: 37730901 PMCID: PMC10511705 DOI: 10.1038/s41598-023-42840-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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Cerna‐Vargas JP, Sánchez‐Romera B, Matilla MA, Ortega Á, Krell T. Sensing preferences for prokaryotic solute binding protein families. Microb Biotechnol 2023; 16:1823-1833. [PMID: 37547952 PMCID: PMC10443332 DOI: 10.1111/1751-7915.14292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 08/08/2023] Open
Abstract
Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.
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Affiliation(s)
- Jean Paul Cerna‐Vargas
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
- Centro de Biotecnología y Genómica de Plantas CBGPUniversidad Politécnica de Madrid‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPMMadridSpain
| | - Beatriz Sánchez‐Romera
- Scientific Instrumentation ServiceEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of ChemistryUniversity of MurciaMurciaSpain
| | - Tino Krell
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
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Feng H, Fu R, Luo J, Hou X, Gao K, Su L, Xu Y, Miao Y, Liu Y, Xu Z, Zhang N, Shen Q, Xun W, Zhang R. Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria. THE NEW PHYTOLOGIST 2023; 239:2307-2319. [PMID: 37357338 DOI: 10.1111/nph.19086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/27/2023]
Abstract
Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agriculture, Henan University, Zhengzhou, 450046, China
| | - Ruixin Fu
- School of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Jiayu Luo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueqin Hou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kun Gao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lv Su
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Xu
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Yuhua District, Shijiazhuang, 050021, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Duan J, Zhao Q, Wang Y, Chi Z, Li W, Wang X, Liu S, Bi S. The dCache Domain of the Chemoreceptor Tlp1 in Campylobacter jejuni Binds and Triggers Chemotaxis toward Formate. mBio 2023:e0356422. [PMID: 37052512 DOI: 10.1128/mbio.03564-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Chemotaxis is an important virulence factor in some enteric pathogens, and it is involved in the pathogenesis and colonization of the host. However, there is limited knowledge regarding the environmental signals that promote chemotactic behavior and the sensing of these signals by chemoreceptors. To date, there is no information on the ligand molecule that directly binds to and is sensed by Campylobacter jejuni Tlp1, which is a chemoreceptor with a dCache-type ligand-binding domain (LBD). dCache (double Calcium channels and chemotaxis receptor) is the largest group of sensory domains in bacteria, but the dCache-type chemoreceptor that directly binds to formate has not yet been discovered. In this study, formate was identified as a direct-binding ligand of C. jejuni Tlp1 with high sensing specificity. We used the strategy of constructing a functional hybrid receptor of C. jejuni Tlp1 and the Escherichia coli chemoreceptor Tar to screen for the potential ligand of Tlp1, with the binding of formate to Tlp1-LBD being verified using isothermal titration calorimetry. Molecular docking and experimental analyses indicated that formate binds to the membrane-proximal pocket of the dCache subdomain. Chemotaxis assays demonstrated that formate elicits robust attractant responses of the C. jejuni strain NCTC 11168, specifically via Tlp1. The chemoattraction effect of formate via Tlp1 promoted the growth of C. jejuni, especially when competing with Tlp1- or CheY-knockout strains. Our study reveals the molecular mechanisms by which C. jejuni mediates chemotaxis toward formate, and, to our knowledge, is the first report on the high-specificity binding of the dCache-type chemoreceptor to formate as well as the physiological role of chemotaxis toward formate. IMPORTANCE Chemotaxis is important for Campylobacter jejuni to colonize favorable niches in the gastrointestinal tract of its host. However, there is still a lack of knowledge about the ligand molecules for C. jejuni chemoreceptors. The dCache-type chemoreceptor, namely, Tlp1, is the most conserved chemoreceptor in C. jejuni strains; however, the direct-binding ligand(s) triggering chemotaxis has not yet been discovered. In the present study, we found that the ligand that binds directly to Tlp1-LBD with high specificity is formate. C. jejuni exhibits robust chemoattraction toward formate, primarily via Tlp1. Tlp1 is the first reported dCache-type chemoreceptor that specifically binds formate and triggers strong chemotaxis. We further demonstrated that the formate-mediated promotion of C. jejuni growth is correlated with Tlp1-mediated chemotaxis toward formate. Our work provides important insights into the mechanism and physiological function of chemotaxis toward formate and will facilitate further investigations into the involvement of microbial chemotaxis in pathogen-host interactions.
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Affiliation(s)
- Jingjing Duan
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Yuxin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xue Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
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Xu Z, Liu Y, Zhang N, Xun W, Feng H, Miao Y, Shao J, Shen Q, Zhang R. Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes. Curr Opin Microbiol 2023; 72:102269. [PMID: 36682279 DOI: 10.1016/j.mib.2023.102269] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/22/2023]
Abstract
Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.
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Affiliation(s)
- Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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