1
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Ma MY, Hu LL, Xu WY, Zhang W. L-tryptophan anaerobic fermentation for indole acetic acid production: Bacterial enrichment and effects of zero valent iron. BIORESOURCE TECHNOLOGY 2024; 400:130691. [PMID: 38599347 DOI: 10.1016/j.biortech.2024.130691] [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: 01/24/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024]
Abstract
Indole acetic acid (IAA) as a plant hormone, was one of the valuable products of anaerobic fermentation. However, the enriching method remained unknown. Moreover, whether zero valent iron (ZVI) could enhance IAA production was unexplored. In this work, IAA producing bacteria Klebsiella (63 %) was enriched successfully. IAA average production rate and concentration were up to 3 mg/L/h and 56 mg/L. With addition of 1 g/L ZVI, IAA average production rate and concentration was increased for 2 and 3 folds. Mechanisms indicated ZVI increased Na+K+-ATP activity and electron transport activity for 2 folds and 1 fold. Moreover, macro transcription determined indole pyruvate pathway activity like primary-amine oxidase, indole pyruvate decarboxylase and aldehyde dehydrogenase were increased for 146 %, 187 %, and 557 %, respectively. Therefore, ZVI was suitable for enhancement IAA production from mixed culture anaerobic fermentation.
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Affiliation(s)
- Meng-Yao Ma
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Li-Li Hu
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Wen-Yan Xu
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Wei Zhang
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China.
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2
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Benítez SV, Carrasco R, Giraldo JD, Schoebitz M. Microbeads as carriers for Bacillus pumilus: a biofertilizer focus on auxin production. J Microencapsul 2024; 41:170-189. [PMID: 38469757 DOI: 10.1080/02652048.2024.2324812] [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: 10/03/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
The study aimed to develop a solid biofertilizer using Bacillus pumilus, focusing on auxin production to enhance plant drought tolerance. Methods involved immobilising B. pumilus in alginate-starch beads, focusing on microbial concentration, biopolymer types, and environmental conditions. The optimal formulation showed a diameter of 3.58 mm ± 0.18, a uniform size distribution after 15 h of drying at 30 °C, a stable bacterial concentration (1.99 × 109 CFU g-1 ± 1.03 × 109 over 180 days at room temperature), a high auxin production (748.8 µg g-1 ± 10.3 of IAA in 7 days), and a water retention capacity of 37% ± 4.07. In conclusion, this new formulation of alginate + starch + L-tryptophan + B. pumilus has the potential for use in crops due to its compelling water retention, high viability in storage at room temperature, and high auxin production, which provides commercial advantages.
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Affiliation(s)
- Solange V Benítez
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Concepción, Chile
| | - Rocio Carrasco
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Concepción, Chile
| | - Juan D Giraldo
- Escuela de Ingeniería Ambiental, Instituto de Acuicultura, Universidad Austral de Chile, Sede Puerto Montt, Puerto Montt, Chile
| | - Mauricio Schoebitz
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Concepción, Chile
- Laboratory of Biofilms and Environmental Microbiology, Center of Biotechnology, University of Concepción, Concepción, Chile
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3
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Huang HW, Chen MJ. Exploring the Preventive and Therapeutic Mechanisms of Probiotics in Chronic Kidney Disease through the Gut-Kidney Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8347-8364. [PMID: 38571475 PMCID: PMC11036402 DOI: 10.1021/acs.jafc.4c00263] [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: 01/09/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Gut dysbiosis contributes to deterioration of chronic kidney disease (CKD). Probiotics are a potential approach to modulate gut microbiota and gut-derived metabolites to alleviate CKD progression. We aim to provide a comprehensive view of CKD-related gut dysbiosis and a critical perspective on probiotic function in CKD. First, this review addresses gut microbial alterations during CKD progression and the adverse effects associated with the changes in gut-derived metabolites. Second, we conduct a thorough examination of the latest clinical trials involving probiotic intervention to unravel critical pathways via the gut-kidney axis. Finally, we propose our viewpoints on limitations, further considerations, and future research prospects of probiotic adjuvant therapy in alleviating CKD progression. Enhancing our understanding of host-microbe interactions is crucial for gaining precise insights into the mechanisms through which probiotics exert their effects and identifying factors that influence the effectiveness of probiotics in developing strategies to optimize their use and enhance clinical outcomes.
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Affiliation(s)
- Hsiao-Wen Huang
- Department
of Animal Science and Technology, National
Taiwan University, No. 50, Ln. 155, Section 3, Keelung Road, Taipei 10673, Taiwan
| | - Ming-Ju Chen
- Department
of Animal Science and Technology, National
Taiwan University, No. 50, Ln. 155, Section 3, Keelung Road, Taipei 10673, Taiwan
- Center
for Biotechnology, National Taiwan University, No. 81, Changxing Street, Taipei 10672, Taiwan
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4
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Etesami H, Glick BR. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience. Microbiol Res 2024; 281:127602. [PMID: 38228017 DOI: 10.1016/j.micres.2024.127602] [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: 11/29/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.
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Affiliation(s)
- Hassan Etesami
- Soil Science Department, University of Tehran, Tehran, Iran.
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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5
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Ai J, He X, Ren M, Yu T, Liu X, Jiang Y, Li Z, Deng Z. Kaistella yananensis sp. nov., a Novel Indoleacetic Acid-Producing Bacterium Isolated from the Root Nodules of Sophora davidii (Franch.) Skeels. Curr Microbiol 2024; 81:60. [PMID: 38206520 DOI: 10.1007/s00284-023-03578-5] [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: 09/15/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
A novel endophytic bacterium, designated strain BT6-1-3T, was isolated from the root nodules of a leguminous shrub named Sophora davidii (Franch.) Skeels, found growing wild in Yan'an, Shaanxi Province, China. Cells were Gram-staining-negative, non-motile, catalase-positive, oxidase-positive, and did not produce H2S. Strain BT6-1-3T grew at 15-40 °C (optimum 30 °C), at pH 6.0-10.0 (optimum pH 9.0), and with 0-1% (w/v) NaCl (optimum 0.5%). The quinone system was menaquinone 6. The major fatty acids present in BT6-1-3T were iso-C11:0, iso-C15:0, and C16:0. The G+C content of genomic DNA was 39.4 mol% by whole genome sequencing. According to the analysis of 16S rRNA gene sequence, the closest relative was Kaistella montana WG4 (nucleotide identity was 97.6%). The genome of strain BT6-1-3T was sequenced, and the genome similarity was calculated using average nucleotide identity and genome-to-genome distance analysis with the genomes of other strains of Kaistella. Both strongly supported that the strain BT6-1-3T belonged to the genus Kaistella as a representative of a new species. Based on phylogenetic analysis, chemotaxonomic data, and physiological and biochemical characteristics, strain BT6-1-3T represents a new species of the genus Kaistella and is named as Kaistella yananensis sp. nov. Type strain is BT6-1-3T (= NBRC 115452T = CGMCC 1.60032T).
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Affiliation(s)
- Jiamin Ai
- College of Life Science, Northwest A&F University, Yangling, 712100, China
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Xiaolong He
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Mingxia Ren
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Tianfei Yu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Xiaodong Liu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Yingying Jiang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Zhefei Li
- College of Life Science, Northwest A&F University, Yangling, 712100, China.
| | - Zhenshan Deng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
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6
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Xu Y, Guan X, Wang S. Synergistic bactericidal mechanisms of RF energy simultaneously combined with cinnamon essential oil or epsilon-polylysine against Salmonella revealed at cellular and metabolic levels. Int J Food Microbiol 2024; 408:110447. [PMID: 37907022 DOI: 10.1016/j.ijfoodmicro.2023.110447] [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: 07/14/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Abstract
Radio frequency (RF) heating and antimicrobials are considered to be effective methods for inactivating food pathogens. This study explored the bactericidal effects against Salmonella of RF heating combined with two kinds of natural antimicrobials possessing different hydrophobic properties and their synergistic bactericidal mechanisms. Results showed that RF heating caused sublethal damage to bacterial cells and enhanced the interaction of cells and antimicrobials, leading to synergistic bactericidal effects of the simultaneous combination of RF heating and antimicrobials. The combination of RF heating and ε-polylysine (ε-PL) further promoted cell morphological alteration, raised membrane permeability, intracellular adenosine triphosphate (ATP) leakage and intracellular reactive oxygen species (ROS) accumulation compared to individual treatment. The simultaneous combination of RF heating and cinnamon essential oil nanoemulsion (CEON) also further enhanced membrane permeability and ROS accumulation compared to individual treatment, but impacts were less than those in the combination of RF heating and ε-PL. The major synergistic bactericidal mechanism of RF heating and CEON was significantly inhibiting intracellular ATP synthesis. The untargeted metabolomics analysis revealed that the combined treatments enhanced disturbances to multiple intracellular metabolisms compared to individual treatment, thus leading to synergistic bactericidal effects against Salmonella. These results provide an in-depth understanding of the synergistic bactericidal mechanisms of the combination of RF heating and natural antimicrobials from cellular and metabolic levels.
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Affiliation(s)
- Yuanmei Xu
- College of Biological and Food Engineering, Changshu Institute of Technology, 99 South Third Ring Road, Changshu 215500, China
| | - Xiangyu Guan
- College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Shaojin Wang
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling 712100, China; Washington State University, Department of Biological Systems Engineering, Pullman, WA 99164-6120, USA.
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7
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Zhang H, Rong Z, Li Y, Yin Z, Lu C, Zhao H, Kong L, Meng L, Ding X. NIT24 and NIT29-mediated IAA synthesis of Xanthomonas oryzae pv. oryzicola suppresses immunity and boosts growth in rice. MOLECULAR PLANT PATHOLOGY 2024; 25:e13409. [PMID: 38069667 PMCID: PMC10788589 DOI: 10.1111/mpp.13409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024]
Abstract
Auxin plays a pivotal role in the co-evolution of plants and microorganisms. Xanthomonas oryzae pv. oryzicola (Xoc) stands as a significant factor that affects rice yield and quality. However, the current understanding of Xoc's capability for indole 3-acetic acid (IAA) synthesis and its mechanistic implications remains elusive. In this study, we performed a comprehensive genomic analysis of Xoc strain RS105, leading to the identification of two nitrilase enzyme family (NIT) genes, designated as AKO15524.1 and AKO15829.1, subsequently named NIT24 and NIT29, respectively. Our investigation unveiled that the deletion of NIT24 and NIT29 resulted in a notable reduction in IAA synthesis capacity within RS105, thereby impacting extracellular polysaccharide production. This deficiency was partially ameliorated through exogenous IAA supplementation. The study further substantiated that NIT24 and NIT29 have nitrilase activity and the ability to catalyse IAA production in vitro. The lesion length and bacterial population statistics experiments confirmed that NIT24 and NIT29 positively regulated the pathogenicity of RS105, suggesting that NIT24 and NIT29 may regulate Xoc invasion by affecting IAA synthesis. Furthermore, our analysis corroborated mutant strains, RS105_ΔNIT24 and RS105_ΔNIT29, which elicited the outbreak of reactive oxygen species, the deposition of callose and the upregulation of defence-related gene expression in rice. IAA exerted a significant dampening effect on the immune responses incited by these mutant strains in rice. In addition, the absence of NIT24 and NIT29 affected the growth-promoting effect of Xoc on rice. This implies that Xoc may promote rice growth by secreting IAA, thus providing a more suitable microenvironment for its own colonization. In summary, our study provides compelling evidence for the existence of a nitrilase-dependent IAA biosynthesis pathway in Xoc. IAA synthesis-related genes promote Xoc colonization by inhibiting rice immune defence response and affecting rice growth by increasing IAA content in Xoc.
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Affiliation(s)
- Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Zixuan Rong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Haipeng Zhao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Lingguang Kong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Lun Meng
- Shike Modern Agriculture Investment Co., LtdHezeChina
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
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8
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Shinde R, Ayyanath MM, Shukla M, El Kayal W, Saxena P, Subramanian J. Hormonal Interplay Leading to Black Knot Disease Establishment and Progression in Plums. PLANTS (BASEL, SWITZERLAND) 2023; 12:3638. [PMID: 37896101 PMCID: PMC10609688 DOI: 10.3390/plants12203638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
Black Knot (BK) is a deadly disease of European (Prunus domestics) and Japanese (Prunus salicina) plums caused by the hemibiotrophic fungus Apiosporina morbosa. After infection, the appearance of warty black knots indicates a phytohormonal imbalance in infected tissues. Based on this hypothesis, we quantified phytohormones such as indole-3-acetic acid, tryptophan, indoleamines (N-acetylserotonin, serotonin, and melatonin), and cytokinins (zeatin, 6-benzyladenine, and 2-isopentenyladenine) in temporally collected tissues of susceptible and resistant genotypes belonging to European and Japanese plums during of BK progression. The results suggested auxin-cytokinins interplay driven by A. morbosa appears to be vital in disease progression by hampering the plant defense system. Taken together, our results indicate the possibility of using the phytohormone profile as a biomarker for BK resistance in plums.
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Affiliation(s)
- Ranjeet Shinde
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada (M.-M.A.); (M.S.); (P.S.)
| | - Murali-Mohan Ayyanath
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada (M.-M.A.); (M.S.); (P.S.)
| | - Mukund Shukla
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada (M.-M.A.); (M.S.); (P.S.)
| | - Walid El Kayal
- Department of Plant Agriculture, University of Guelph, Vineland Station, ON L0R 2E0, Canada;
- Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Praveen Saxena
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada (M.-M.A.); (M.S.); (P.S.)
| | - Jayasankar Subramanian
- Department of Plant Agriculture, University of Guelph, Vineland Station, ON L0R 2E0, Canada;
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9
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Chen CY, Selvaraj P, Naqvi NI. Functional analysis of auxin derived from a symbiotic mycobiont. FRONTIERS IN PLANT SCIENCE 2023; 14:1216680. [PMID: 37745999 PMCID: PMC10515717 DOI: 10.3389/fpls.2023.1216680] [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: 05/04/2023] [Accepted: 08/16/2023] [Indexed: 09/26/2023]
Abstract
The biosynthesis of auxin or indole-3-acetic acid by microorganisms has a major impact on plant-microbe interactions. Several beneficial microbiota are known to produce auxin, which largely influences root development and growth in the host plants. Akin to findings in rhizobacteria, recent studies have confirmed the production of auxin by plant growth-promoting fungi too. Here, we show that Penicillium citrinum isolate B9 produces auxin as deduced by liquid chromatography tandem-mass spectrometry analysis. Such fungal auxin is secreted and contributes directly to enhanced root and shoot development and overall plant growth in Arabidopsis thaliana. Furthermore, auxin production by P. citrinum likely involves more than one tryptophan-dependent pathway. Using auxin biosynthesis inhibitor L-Kynurenine, we show that the indole-3-pyruvate pathway might be one of the key biosynthetic routes involved in such auxin production. Confocal microscopy of the DR5rev:GFP Arabidopsis reporter line helped demonstrate that P. citrunum B9-derived auxin is biologically active and is able to significantly enhance auxin signaling in roots during such improved root growth and plant development. Furthermore, the phenotypic growth defects arising from impaired auxin signaling in Arabidopsis taa1 mutant or upon L-Kynurenine treatment of wild-type Arabidopsis seedlings could be significantly alleviated by fungus B9-derived auxin, thus suggesting its positive role in plant growth promotion. Collectively, our results provide clear evidence that the production of auxin is one of the main mechanisms involved in induction of the beneficial plant growth by P. citrinum.
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Affiliation(s)
- Cheng-Yen Chen
- Fungal Patho-Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
| | | | - Naweed I. Naqvi
- Fungal Patho-Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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10
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Tang J, Li Y, Zhang L, Mu J, Jiang Y, Fu H, Zhang Y, Cui H, Yu X, Ye Z. Biosynthetic Pathways and Functions of Indole-3-Acetic Acid in Microorganisms. Microorganisms 2023; 11:2077. [PMID: 37630637 PMCID: PMC10459833 DOI: 10.3390/microorganisms11082077] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Indole-3-acetic acid (IAA) belongs to the family of auxin indole derivatives. IAA regulates almost all aspects of plant growth and development, and is one of the most important plant hormones. In microorganisms too, IAA plays an important role in growth, development, and even plant interaction. Therefore, mechanism studies on the biosynthesis and functions of IAA in microorganisms can promote the production and utilization of IAA in agriculture. This mini-review mainly summarizes the biosynthesis pathways that have been reported in microorganisms, including the indole-3-acetamide pathway, indole-3-pyruvate pathway, tryptamine pathway, indole-3-acetonitrile pathway, tryptophan side chain oxidase pathway, and non-tryptophan dependent pathway. Some pathways interact with each other through common key genes to constitute a network of IAA biosynthesis. In addition, functional studies of IAA in microorganisms, divided into three categories, have also been summarized: the effects on microorganisms, the virulence on plants, and the beneficial impacts on plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (J.T.); (L.Z.)
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11
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [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: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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12
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Zhou SP, Tang SQ, Ke X, Zhou HY, Zou SP, Xue YP, Zheng YG. Hyperthermophilic pretreatment significantly accelerates thermophilic composting humification through improving bacterial communities and promoting microbial cooperation. BIORESOURCE TECHNOLOGY 2023:129467. [PMID: 37429549 DOI: 10.1016/j.biortech.2023.129467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Thermophilic composting (TC) can effectively shorten maturity period with satisfactory sanitation. However, the higher energy consumption and lower composts quality limited its widespread application. In this study, hyperthermophilic pretreatment (HP) was introduced as a novel approach within TC, and its effects on humification process and bacterial community during food waste TC was investigated from multiple perspectives. Results showed that a 4-hour pretreatment at 90 °C increased the germination index and humic acid/fulvic acid by 25.52% and 83.08%. Microbial analysis demonstrated that HP stimulated the potential functional thermophilic microbes, and significantly up-regulated the genes related to amino acid biosynthesis. Further network and correlation analysis suggested that pH was the key factor affecting bacterial communities, and higher HP temperatures help to restore bacterial cooperation and showed higher humification degree. In summary, this study contributed to a better understanding of the mechanism towards the accelerated humification by HP.
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Affiliation(s)
- Shi-Peng Zhou
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su-Qin Tang
- Hangzhou Environmental Group Company Limited, Hangzhou 310022, China
| | - Xia Ke
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hai-Yan Zhou
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shu-Ping Zou
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ya-Ping Xue
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yu-Guo Zheng
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
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Martínez-Martínez JG, Rosales-Loredo S, Hernández-Morales A, Arvizu-Gómez JL, Carranza-Álvarez C, Macías-Pérez JR, Rolón-Cárdenas GA, Pacheco-Aguilar JR. Bacterial Communities Associated with the Roots of Typha spp. and Its Relationship in Phytoremediation Processes. Microorganisms 2023; 11:1587. [PMID: 37375088 DOI: 10.3390/microorganisms11061587] [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: 05/12/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation.
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Affiliation(s)
| | - Stephanie Rosales-Loredo
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Alejandro Hernández-Morales
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63173, Mexico
| | - Candy Carranza-Álvarez
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - José Roberto Macías-Pérez
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Gisela Adelina Rolón-Cárdenas
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
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14
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Pintado A, Domínguez-Cerván H, Pastor V, Vincent M, Lee SG, Flors V, Ramos C. Allelic variation in the indoleacetic acid-lysine synthase gene of the bacterial pathogen Pseudomonas savastanoi and its role in auxin production. FRONTIERS IN PLANT SCIENCE 2023; 14:1176705. [PMID: 37346122 PMCID: PMC10280071 DOI: 10.3389/fpls.2023.1176705] [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: 02/28/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Indole-3-acetic acid (IAA) production is a pathogenicity/virulence factor in the Pseudomonas syringae complex, including Pseudomonas savastanoi. P. savastanoi pathovars (pvs.) genomes contain the iaaL gene, encoding an enzyme that catalyzes the biosynthesis of the less biologically active compound 3-indole-acetyl-ϵ-L-lysine (IAA-Lys). Previous studies have reported the identification of IAA-Lys in culture filtrates of P. savastanoi strains isolated from oleander (pv. nerii), but the conversion of IAA into a conjugate was not detectable in olive strains (pv. savastanoi). In this paper, we show the distribution of iaaL alleles in all available P. savastanoi genomes of strains isolated from woody hosts. Most strains encode two different paralogs, except for those isolated from broom (pv. retacarpa), which contain a single allele. In addition to the three previously reported iaaL alleles (iaaL Psv, iaaL Psn and iaaL Pto), we identified iaaL Psf, an exclusive allele of strains isolated from ash (pv. fraxini). We also found that the production of IAA-Lys in P. savastanoi pv. savastanoi and pv. nerii depends on a functional iaaL Psn allele, whereas in pv. fraxini depends on iaaL Psf. The production of IAA-Lys was detected in cultures of an olive strain heterologously expressing IaaLPsn-1, IaaLPsf-1 and IaaLPsf-3, but not when expressing IaaLPsv-1. In addition, Arabidopsis seedlings treated with the strains overproducing the conjugate, and thus reducing the free IAA content, alleviated the root elongation inhibitory effect of IAA. IAA-Lys synthase activity assays with purified allozymes confirmed the functionality and specificity of lysine as a substrate of IaaLPsn-1 and IaaLPsf-3, with IaaLPsf-3 showing the highest catalytic efficiency for both substrates. The IAA-Lys synthase activity of IaaLPsn-1 was abolished by the insertion of two additional tyrosine residues encoded in the inactive allozyme IaaLPsv-1. These results highlight the relevance of allelic variation in a phytohormone-related gene for the modulation of auxin production in a bacterial phytopathogen.
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Affiliation(s)
- Adrián Pintado
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Hilario Domínguez-Cerván
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Victoria Pastor
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I (UJI), Castelló de la Plana, Spain
| | - Marissa Vincent
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Soon Goo Lee
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, United States
| | - Víctor Flors
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I (UJI), Castelló de la Plana, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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15
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Liang X, Zhou K, Li P, Wan D, Liu J, Yi X, Peng Y. Characteristics of endophytic bacteria and active ingredients in the Eucommiae cortex from different origins. Front Microbiol 2023; 14:1164674. [PMID: 37266017 PMCID: PMC10229866 DOI: 10.3389/fmicb.2023.1164674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Objective This study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC. Methods A total of 10 samples of Eucommia ulmoides Oliv. (E. ulmoides) bark were collected from each of the following four regions, namely, Zunyi in Guizhou (GZ), Baokang in Hubei (HUB), Cili in Hunan (HUN), and Loyang in Shaanxi (SX). Subsequently, the contents of the main active ingredients of EC were determined by ultra-performance liquid chromatography (UPLC), and the endophytic bacteria of EC were detected by 16S rRNA sequencing. The relationship between the dominant endophytic bacteria and the active ingredients was investigated by correlation analysis. Results A total of 4,551 different operational taxonomic units (OTUs) were delineated in the four groups of samples, of which 585, 439, 957, and 684 genera were annotated from GZ, HUB, HUN, and SX, respectively. The richness and diversity of endophytic bacteria from different origins were ranked as HUN > SX > GZ or HUB. The analysis demonstrated that there was no significant correlation between the diversity and richness of endophytic bacteria in EC and its active ingredients. Nevertheless, notable variations in the community structures of endophytic bacteria were observed across different origins, and they had a considerable impact on certain active ingredients in EC. Comamonas and Cedecea were the dominant genera. Characteristic bacteria of different origins could be clearly distinguished. Simultaneous, significant correlations had been identified between some characteristic endophytic bacteria derived from different origins and active ingredients of EC. For example, Delftia, a characteristic bacterium from GZ, showed a significant positive correlation with pinoresinol diglucoside. Paenibacillus and Klebsiella, two characteristic bacteria from HUB, exhibited significant positive correlations with geniposidic acid. Thauera, a characteristic bacterium from HUN, demonstrated a significant positive correlation with geniposide. Brevundimonas, a characteristic bacterium from SX, displayed a significant positive correlation with pinoresinol diglucoside. Conclusion There was a complex correlation between EC endophytic bacteria and active ingredient content, while EC endophytic bacteria from different origins had significant differences at the genus level.
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Affiliation(s)
- Xuejuan Liang
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Penghui Li
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Dan Wan
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jing Liu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Yi
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Yanmei Peng
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
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16
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Pantoja-Guerra M, Burkett-Cadena M, Cadena J, Dunlap CA, Ramírez CA. Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01828-x. [PMID: 37138159 DOI: 10.1007/s10482-023-01828-x] [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: 09/22/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 108 CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20-70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain's cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.
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Affiliation(s)
- Manuel Pantoja-Guerra
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia.
- Facultad de Ciencias Agropecuarias, Unilasallista Corporación Universitaria, Caldas - Antioquia, Colombia.
| | | | | | - Christopher A Dunlap
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815 N University, Peoria, IL, USA
| | - Camilo A Ramírez
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia
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17
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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18
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Khianngam S, Meetum P, Chiangmai PN, Tanasupawat S. Identification and Optimisation of Indole-3-Acetic Acid Production of Endophytic Bacteria and Their Effects on Plant Growth. Trop Life Sci Res 2023; 34:219-239. [PMID: 37065794 PMCID: PMC10093774 DOI: 10.21315/tlsr2023.34.1.12] [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: 05/14/2022] [Accepted: 08/24/2022] [Indexed: 04/18/2023] Open
Abstract
Indole-3-acetic acid (IAA) is one of the most physiologically active auxins produced by rhizobacteria and is potentially applied for agriculture. Two endophytic bacteria, VR2 and MG9, isolated from the root of Chrysopogon zizanioides (L.) collected at Cha-Am, and the leaf of Bruguiera cylindrica (L.) Blume collected from a mangrove forest at Ban Laem, Phetchaburi Province, Thailand, were taxonomic characterised based on their phenotypic characteristics and 16S rRNA gene analysis. Strain VR2 was closely related to Enterobacter hormaechei CIP 103441T (99.6% similarity), while strain MG9 was closely related to Bacillus aryabhattai B8W22T (99.9% similarity). Consequently, they were identified as Enterobacter hormaechei and Bacillus aryabhattai, respectively. The IAA production of VR2 and MG9 strains are determined and applied to rice seeds for their root and shoot germination. Strains VR2 and MG9 greatly produced a yield of IAA, 246.00 and 195.55 μg/mL in 1,000 μg/mL of L-tryptophan at pH 6 for 48 h. They showed no significant differences in IAA to root and shoot development. However, the bacterial IAA exhibited potential nearby synthetic IAA, which had a significant effect compared to the control. IAA produced from these two strains might preferably trim down the use of synthetic IAA and could contribute to sustainable agriculture.
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Affiliation(s)
- Saowapar Khianngam
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Phetchaburi Information Technology Campus, Phetchaburi 76120, Thailand
| | - Pimjai Meetum
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Phetchaburi Information Technology Campus, Phetchaburi 76120, Thailand
| | - Pantipa Na Chiangmai
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Phetchaburi Information Technology Campus, Phetchaburi 76120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Corresponding author:
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Orozco-Mosqueda MDC, Santoyo G, Glick BR. Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:606. [PMID: 36771689 PMCID: PMC9921776 DOI: 10.3390/plants12030606] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.
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Affiliation(s)
- Ma. del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México/I.T. Celaya, Celaya 38110, Guanajuato, Mexico
| | - Gustavo Santoyo
- Genomic Diversity Laboratory, Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Michoacan, Mexico
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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20
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Cao Y, He K, Li Q, Chen X, Mo H, Li Z, Ji Q, Li G, Du G, Yang H. Transcriptome analysis of Armillaria gallica 012 m in response to auxin. J Basic Microbiol 2023; 63:17-25. [PMID: 36449692 DOI: 10.1002/jobm.202200463] [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: 07/27/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 12/02/2022]
Abstract
Gastrodia elata is an achlorophyllous and fully mycoheterotrophic orchid which obtains carbon and other nutrients from Armillaria species in its life cycle. Many researchers suggested that plant hormones, as signing molecules, play a central role in the plant-fungi interaction. In the process of Armillaria gallica 012 m cultivation, both exogenous indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) distinctly stimulated the growth of mycelia in solid media. The differential expression genes (DEGs) of A. gallica 012 m with IAA versus blank control (BK) and IBA versus BK were investigated. The results showed that more than 80% of DEGs of the IAA group were coincident with the DEGs of the IBA group, and more than half of upregulated DEGs and most of the downregulated DEGs of the IAA group coincided with those DEGs of the IBA group. Above research implied that A. gallica 012 m could perceive IAA and IBA, and possess similar responses and signaling pathways to IAA and IBA. The overlapping differential genes of the IAA group and IBA group were analyzed by GO term, and the results showed that several DEGs identified were related to biological processes including positive regulation of the biological process and biological process. The downregulated NmrA-like and FKBP_C genes might be benefit to the growth of mycelia. Those results can explain that exiguous IAA and IBA improved the growth of A. gallica to some extent. We speculate that IAA and IBA are signaling molecules, and regulate the expression of growth-related genes of A. gallica 012 m by the same signaling pathway.
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Affiliation(s)
- Yapu Cao
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Kaixiang He
- Department of Chemistry, School of Chemistry and Environment, Yunnan Minzu University, Kunming, China
| | - Qingqing Li
- Life Science College, Southwest Forestry University, Kunming, China.,Kunming Xianghao Technology Co. Ltd., Kunming, China
| | - Xin Chen
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Haiying Mo
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Zhihao Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Qiaolin Ji
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Ganpeng Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Gang Du
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Haiying Yang
- Department of Chemistry, School of Chemistry and Environment, Yunnan Minzu University, Kunming, China
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21
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Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium. Genes (Basel) 2022; 13:genes13122290. [PMID: 36553557 PMCID: PMC9777792 DOI: 10.3390/genes13122290] [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: 10/28/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The bacterium Pseudomonas sp. strain JP233 has been reported to efficiently solubilize sparingly soluble inorganic phosphate, promote plant growth and significantly reduce phosphorus (P) leaching loss from soil. The production of 2-keto gluconic acid (2KGA) by strain JP233 was identified as the main active metabolite responsible for phosphate solubilization. However, the genetic basis of phosphate solubilization and plant-growth promotion remained unclear. As a result, the genome of JP233 was sequenced and analyzed in this study. The JP233 genome consists of a circular chromosome with a size of 5,617,746 bp and a GC content of 62.86%. No plasmids were detected in the genome. There were 5097 protein-coding sequences (CDSs) predicted in the genome. Phylogenetic analyses based on genomes of related Pseudomonas spp. identified strain JP233 as Pseudomonas asiatica. Comparative pangenomic analysis among 9 P. asiatica strains identified 4080 core gene clusters and 111 singleton genes present only in JP233. Genes associated with 2KGA production detected in strain JP233, included those encoding glucose dehydrogenase, pyrroloquinoline quinone and gluoconate dehydrogenase. Genes associated with mechanisms of plant-growth promotion and nutrient acquisition detected in JP233 included those involved in IAA biosynthesis, ethylene catabolism and siderophore production. Numerous genes associated with other properties beneficial to plant growth were also detected in JP233, included those involved in production of acetoin, 2,3-butanediol, trehalose, and resistance to heavy metals. This study provides the genetic basis to elucidate the plant-growth promoting and bio-remediation properties of strain JP233 and its potential applications in agriculture and industry.
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22
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Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [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: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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23
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Rolón-Cárdenas GA, Arvizu-Gómez JL, Soria-Guerra RE, Pacheco-Aguilar JR, Alatorre-Cobos F, Hernández-Morales A. The role of auxins and auxin-producing bacteria in the tolerance and accumulation of cadmium by plants. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:3743-3764. [PMID: 35022877 DOI: 10.1007/s10653-021-01179-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 12/05/2021] [Indexed: 05/16/2023]
Abstract
Cadmium (Cd) is one of the most toxic heavy metals for plant physiology and development. This review discusses Cd effects on auxin biosynthesis and homeostasis, and the strategies for restoring plant growth based on exogenous auxin application. First, the two well-characterized auxin biosynthesis pathways in plants are described, as well as the effect of exogenous auxin application on plant growth. Then, review describes the impacts of Cd on the content, biosynthesis, conjugation, and oxidation of endogenous auxins, which are related to a decrease in root development, photosynthesis, and biomass production. Finally, compelling evidence of the beneficial effects of auxin-producing rhizobacteria in plants exposed to Cd is showed, focusing on photosynthesis, oxidative stress, and production of antioxidant compounds and osmolytes that counteract Cd toxicity, favoring plant growth and improve phytoremediation efficiency. Expanding our understanding of the positive effects of exogenous auxins application and the interactions between bacteria and plants growing in Cd-polluted environments will allow us to propose phytoremediation strategies for restoring environments contaminated with this metal.
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Affiliation(s)
- Gisela Adelina Rolón-Cárdenas
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Avenida Dr. Manuel Nava 6, Zona Universitaria, 78210, San Luis Potosí, San Luis Potosí, México
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, 79060, Ciudad Valles, San Luis Potosí, México
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| | - Ruth Elena Soria-Guerra
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Avenida Dr. Manuel Nava 6, Zona Universitaria, 78210, San Luis Potosí, San Luis Potosí, México
| | | | | | - Alejandro Hernández-Morales
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Avenida Dr. Manuel Nava 6, Zona Universitaria, 78210, San Luis Potosí, San Luis Potosí, México.
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, 79060, Ciudad Valles, San Luis Potosí, México.
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24
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Bellés-Sancho P, Liu Y, Heiniger B, von Salis E, Eberl L, Ahrens CH, Zamboni N, Bailly A, Pessi G. A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:991548. [PMID: 36247538 PMCID: PMC9554594 DOI: 10.3389/fpls.2022.991548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a nifA mutant compared to wild-type nodules. Here, we document the structural changes that a P. phymatum nifA mutant induces in common bean (Phaseolus vulgaris) nodules, eventually leading to hypernodulation. To investigate the role of the P. phymatum iaaMH genes during symbiosis, we monitored their expression in presence and absence of NifA over different stages of the symbiosis. The iaaMH genes were found to be under negative control of NifA in all symbiotic stages. While a P. phymatum iaaMH mutant produced the same number of nodules and nitrogenase activity as the wild-type strain, the nifA mutant produced more nodules than the wild-type that clustered into regularly-patterned root zones. Mutation of the iaaMH genes in a nifA mutant background reduced the presence of these nodule clusters on the root. We further show that the P. phymatum iaaMH genes are located in a region of the symbiotic plasmid with a significantly lower GC content and exhibit high similarity to two genes of the IAM pathway often used by bacterial phytopathogens to deploy IAA as a virulence factor. Overall, our data suggest that the increased abundance of rhizobial auxin in the non-fixing nifA mutant strain enables greater root infection rates and a role for bacterial auxin production in the control of early stage symbiotic interactions.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Elia von Salis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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25
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Pang F, Solanki MK, Wang Z. Streptomyces can be an excellent plant growth manager. World J Microbiol Biotechnol 2022; 38:193. [PMID: 35980475 DOI: 10.1007/s11274-022-03380-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
Abstract
Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.
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Affiliation(s)
- Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-701, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China.
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26
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Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
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Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
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27
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Tan YQ, Wang YN, Feng HY, Guo ZY, Li X, Nie XL, Zhao YY. Host/microbiota interactions-derived tryptophan metabolites modulate oxidative stress and inflammation via aryl hydrocarbon receptor signaling. Free Radic Biol Med 2022; 184:30-41. [PMID: 35367341 DOI: 10.1016/j.freeradbiomed.2022.03.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that induces the expression of a broad range of downstream genes such as cytochromes P450 enzymes and cyclooxygenase-2. Recent research focuses are shifting from AhR activation induced by xenobiotics to its response patterns to physiological ligands that expand our understanding of how endogenous metabolites as ligands to modulate AhR signaling pathway under homeostasis and pathological conditions. With increasing interest in AhR and its endogenous ligands, it would seem advisable to summarize a variety of endogenous ligands especially host/gut microbiota-derived tryptophan metabolites. Mounting evidence has indicated that AhR play a critical role in the regulation of redox homeostasis and immune responses. In this review, we outline the canonical and non-canonical AhR signalling pathway that is mediated by host/gut microbiota-derived tryptophan metabolites. Through several typical endogenous AhR ligands, we investigated the molecular mechanisms of AhR-induced oxidative stress and inflammation in the pathological milieu, including diabetes, diabetic kidney disease and end-stage renal disease. Finally, we summarize and emphasize the limitations and breakthrough of endogenous AhR ligands from host/microbial tryptophan catabolites. This review might provide novel diagnostic and prognostic approach for refractory human diseases and establish new therapeutic strategies for AhR activation.
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Affiliation(s)
- Yue-Qi Tan
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Yan-Ni Wang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Hao-Yu Feng
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Zhi-Yuan Guo
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xia Li
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China; Department of General Practice, Xi'an International Medical Center Hospital, Northwest University, No. 777 Xitai Road, Xi'an, Shaanxi, 710100, China.
| | - Xiao-Li Nie
- Department of Nephrology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, No.13, Shi Liu Gang Road, Haizhu District, Guangzhou, Guangdong, 510315, China.
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
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28
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Zoccarato L, Sher D, Miki T, Segrè D, Grossart HP. A comparative whole-genome approach identifies bacterial traits for marine microbial interactions. Commun Biol 2022; 5:276. [PMID: 35347228 PMCID: PMC8960797 DOI: 10.1038/s42003-022-03184-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
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Affiliation(s)
- Luca Zoccarato
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel.
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, 520-2194, Otsu, Japan
| | - Daniel Segrè
- Departments of Biology, Biomedical Engineering, Physics, Boston University, 02215, Boston, MA, USA
- Bioinformatics Program & Biological Design Center, Boston University, 02215, Boston, MA, USA
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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29
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Wang Y, Xu Y, Xu X, Wang H, Wang D, Yan W, Zhu J, Hao H, Wang G, Cao L, Zhang J. Ginkgo biloba extract ameliorates atherosclerosis via rebalancing gut flora and microbial metabolism. Phytother Res 2022; 36:2463-2480. [PMID: 35312112 DOI: 10.1002/ptr.7439] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/31/2022]
Abstract
The Ginkgo biloba leave extract (GbE) is widely applied in the prevention and treatment of atherosclerotic cardiovascular diseases in clinical practice. However, its mechanism of actions has not been totally elucidated. In this study, we confirmed the beneficial effects of GbE in alleviating hypercholesterolemia, inflammation and atherosclerosis in Ldlr-/- mice, which were fed 12 weeks of Western diet (WD). Moreover, 16S rRNA sequencing revealed that GbE treatment reshaped the WD-perturbed intestinal microbiota, particularly decreased the Firmicutes/Bacteroidetes ratio and elevated the abundance of Akkermansia, Alloprevotella, Alistipes, and Parabacteroides. Furthermore, GbE treatment downregulated the intestinal transcriptional levels of proinflammatory cytokines and enhanced the expression of tight junction proteins, exerting the roles of attenuating the intestinal inflammation as well as repairing the gut barrier. Meanwhile, the targeted metabolomic analysis displayed that GbE treatment significantly reversed the dysfunction of the microbial metabolic phenotypes, including promoting the production of short chain fatty acids, indole-3-acetate and secondary bile acids, which were correlated with the atherosclerotic plaque areas. Finally, we confirmed GbE-altered gut microbiota was sufficient to alleviate atherosclerosis by fecal microbiota transplantation. In summary, our findings provide important insights into the pharmacological mechanism underlying the antiatherogenic efficacy of GbE.
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Affiliation(s)
- Yun Wang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Xu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Hong Wang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Dong Wang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Wenchao Yan
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Jiaying Zhu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Guangji Wang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Lijuan Cao
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Jun Zhang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, Nanjing Medical University, Nanjing, China
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30
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Gilbert S, Poulev A, Chrisler W, Acosta K, Orr G, Lebeis S, Lam E. Auxin-Producing Bacteria from Duckweeds Have Different Colonization Patterns and Effects on Plant Morphology. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060721. [PMID: 35336603 PMCID: PMC8950272 DOI: 10.3390/plants11060721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/30/2022] [Accepted: 02/20/2022] [Indexed: 05/30/2023]
Abstract
The role of auxin in plant-microbe interaction has primarily been studied using indole-3-acetic acid (IAA)-producing pathogenic or plant-growth-promoting bacteria. However, the IAA biosynthesis pathway in bacteria involves indole-related compounds (IRCs) and intermediates with less known functions. Here, we seek to understand changes in plant response to multiple plant-associated bacteria taxa and strains that differ in their ability to produce IRCs. We had previously studied 47 bacterial strains isolated from several duckweed species and determined that 79% of these strains produced IRCs in culture, such as IAA, indole lactic acid (ILA), and indole. Using Arabidopsis thaliana as our model plant with excellent genetic tools, we performed binary association assays on a subset of these strains to evaluate morphological responses in the plant host and the mode of bacterial colonization. Of the 21 tested strains, only four high-quantity IAA-producing Microbacterium strains caused an auxin root phenotype. Compared to the commonly used colorimetric Salkowski assay, auxin concentration determined by LC-MS was a superior indicator of a bacteria's ability to cause an auxin root phenotype. Studies with the auxin response mutant axr1-3 provided further genetic support for the role of auxin signaling in mediating the root morphology response to IAA-producing bacteria strains. Interestingly, our microscopy results also revealed new evidence for the role of the conserved AXR1 gene in endophytic colonization of IAA-producing Azospirillum baldaniorum Sp245 via the guard cells.
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Affiliation(s)
- Sarah Gilbert
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Alexander Poulev
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - William Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Kenneth Acosta
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Sarah Lebeis
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Eric Lam
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
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31
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Dukare A, Mhatre P, Maheshwari HS, Bagul S, Manjunatha BS, Khade Y, Kamble U. Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions. 3 Biotech 2022; 12:57. [PMID: 35186654 PMCID: PMC8817020 DOI: 10.1007/s13205-022-03115-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/12/2022] [Indexed: 12/27/2022] Open
Abstract
Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.
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Affiliation(s)
- Ajinath Dukare
- ICAR-Central Institute for Research on Cotton Technology (CIRCOT), Mumbai, Maharashtra India
| | - Priyank Mhatre
- ICAR-Central Potato Research Institute (Regional Station), Udhagamandalam, Tamil Nadu India
| | - Hemant S. Maheshwari
- ICAR-Indian Institute of Soybean Research (IISR), Indore, Madhya Pradesh India
- Present Address: Ecophysiology of Plants, Faculty of Science and Engineering, GELIFES-Groningen Institute for Evolutionary Life Sciences, The University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Samadhan Bagul
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Anand, Gujarat India
| | - B. S. Manjunatha
- ICAR-National Institute of Natural Fibre Engineering and Technology, Kolkata, West Bengal India
| | - Yogesh Khade
- ICAR- Directorate of Onion and Garlic Research, Pune, Maharashtra India
| | - Umesh Kamble
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana India
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Syrova DS, Shaposhnikov AI, Yuzikhin OS, Belimov AA. Destruction and Transformation of Phytohormones By Microorganisms. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tang Y, Sun J, Dong B, Dai X. Thermal Hydrolysis Pretreatment-Anaerobic Digestion Promotes Plant-Growth Biostimulants Production from Sewage Sludge by Upregulating Aromatic Amino Acids Transformation and Quinones Supply. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1938-1950. [PMID: 35005906 DOI: 10.1021/acs.est.1c06506] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Micromolecular plant-growth biostimulants (micro-PBs) production from sewage sludge is attracting increasing interest, as it is expected to enhance the fertilizing effect of sludge for land application. This study attempted to promote effective micro-PBs production from sewage sludge through thermal hydrolysis pretreatment-anaerobic digestion (THP-AD) and explore the underpinning regulation mechanisms. Results showed that the highest effective micro-PB production in digested sludge was achieved in THP(160 °C)-AD by day 12, with 80.73 mg/kg volatile solid (VS) of phytohormones and 417.75 mg/kg VS of allelochemicals, and these effective micro-PBs all originated from aromatic amino acids (AAAs). The metabolomic and metagenomic results revealed that, as compared with THP(120 °C)-AD and AD without THP, THP(160°C)-AD uniquely upregulated AAAs biosynthesis and consequently improved AAAs metabolism toward effective micro-PBs production. Further exploration of related microbial pathways and metabolites suggested that the upregulated AAAs biosynthesis in THP(160 °C)-AD in the early stage was partially attributed to the enhanced carbohydrate release. More importantly, the results showed that the amount of quinones, which probably facilitate energy generation via acting as electron-transfer mediators, was significantly positively correlated with the abundance of AAAs biosynthesis genes (R2 = 0.93). Hence, the improved initial release and biosynthesis of quinones are critical in enhancing the AAAs biosynthesis in THP(160 °C)-AD. Moreover, the enhanced quinones supply and the consequent active AAAs transformation in THP(160 °C)-AD reinforced the humification process, highly supporting effective micro-PBs stabilization. The important roles of quinones in effective micro-PBs production and stabilization in sludge anaerobic digestion should be considered in technology development for micro-PBs recovery.
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Affiliation(s)
- Yanfei Tang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jing Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Bin Dong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Ong CE, Ahmad R, Goh YK, Azizan KA, Baharum SN, Goh KJ. Growth modulation and metabolic responses of Ganoderma boninense to salicylic acid stress. PLoS One 2021; 16:e0262029. [PMID: 34972183 PMCID: PMC8719765 DOI: 10.1371/journal.pone.0262029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Various phenolic compounds have been screened against Ganoderma boninense, the fungal pathogen causing basal stem rot in oil palms. In this study, we focused on the effects of salicylic acid (SA) on the growth of three G. boninense isolates with different levels of aggressiveness. In addition, study on untargeted metabolite profiling was conducted to investigate the metabolomic responses of G. boninense towards salicylic acid. The inhibitory effects of salicylic acid were both concentration- (P < 0.001) and isolate-dependent (P < 0.001). Also, growth-promoting effect was observed in one of the isolates at low concentrations of salicylic acid where it could have been utilized by G. boninense as a source of carbon and energy. Besides, adaptation towards salicylic acid treatment was evident in this study for all isolates, particularly at high concentrations. In other words, inhibitory effect of salicylic acid treatment on the fungal growth declined over time. In terms of metabolomics response to salicylic acid treatment, G. boninense produced several metabolites such as coumarin and azatyrosine, which suggests that salicylic acid modulates the developmental switch in G. boninense towards the defense mode for its survival. Furthermore, the liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS) analysis showed that the growth of G. boninense on potato dextrose agar involved at least four metabolic pathways: amino acid metabolism, lipid pathway, tryptophan pathway and phenylalanine pathway. Overall, there were 17 metabolites that contributed to treatment separation, each with P<0.005. The release of several antimicrobial metabolites such as eudistomin I may enhance G. boninense's competitiveness against other microorganisms during colonisation. Our findings demonstrated the metabolic versatility of G. boninense towards changes in carbon sources and stress factors. G. boninense was shown to be capable of responding to salicylic acid treatment by switching its developmental stage.
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Affiliation(s)
- Cu Ean Ong
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Rafidah Ahmad
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - You Keng Goh
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Kah Joo Goh
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
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Amelioration of indole acetic acid-induced cytotoxicity in mice using zinc nanoparticles biosynthesized with Ochradenus arabicus leaf extract. Saudi J Biol Sci 2021; 28:7190-7201. [PMID: 34867022 PMCID: PMC8626273 DOI: 10.1016/j.sjbs.2021.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022] Open
Abstract
The diversity of natural phytochemicals represents an unlimited source for discovery and development of new drugs. Ochradenus arabicus, (family: Resedaceae) a notable medicinal plant displays a high content of flavonoid glycosides. This study investigates a possible preventative role of zinc nanoparticles biosynthesized by O. arabicus leaf extracts (OAZnO NPs) in limiting genotoxicity and cytotoxicity caused by indole acetic acid (IAA) in laboratory mice. ZnO NPs were synthesized using O. arabicus leaf extracts and characterized with UV–visible spectroscopy, scanning electron microscopy (SEM) and X-Ray diffraction (XRD). The mice were randomly distributed into the following six groups: control, OAZnO NPs treated (10 mg/kg BW), IAA treated (50 mg/kg BW); simultaneous treatment, pre-treatment, and post-treatment. Reactive oxygen species (ROS), DNA damage, chromosome aberration, and apoptosis were analyzed as toxicity endpoints. IAA exposure significantly induced production of ROS, DNA damage, apoptosis, chromosome aberrations, and micronuclei. Pre-, post-, and simultaneous treatment with OAZnO NPs ameliorated the damage caused by IAA exposure. Exposure to OAZnO NPs alone caused no toxicity for any endpoint based on comparison to controls. This study demonstrated that IAA-induced cytotoxic damage in mice could be ameliorated by treatment with OAZnO NPs. These findings require additional verification in mechanistic and in vitro studies.
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Rodrigues GL, Matteoli FP, Gazara RK, Rodrigues PSL, Dos Santos ST, Alves AF, Pedrosa-Silva F, Oliveira-Pinheiro I, Canedo-Alvarenga D, Olivares FL, Venancio TM. Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus. Microbiol Res 2021; 254:126896. [PMID: 34715447 DOI: 10.1016/j.micres.2021.126896] [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: 05/07/2021] [Revised: 08/11/2021] [Accepted: 10/14/2021] [Indexed: 11/19/2022]
Abstract
Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.
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Affiliation(s)
- Gustavo L Rodrigues
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Rajesh K Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | | | - Samuel T Dos Santos
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil
| | - Alice F Alves
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Isabella Oliveira-Pinheiro
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Daniella Canedo-Alvarenga
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
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Oluwagbemigun K, Anesi A, Clarke G, Schmid M, Mattivi F, Nöthlings U. An Investigation into the Temporal Reproducibility of Tryptophan Metabolite Networks Among Healthy Adolescents. Int J Tryptophan Res 2021; 14:11786469211041376. [PMID: 34594109 PMCID: PMC8477685 DOI: 10.1177/11786469211041376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/01/2021] [Indexed: 01/15/2023] Open
Abstract
Tryptophan and its bioactive metabolites are associated with health conditions such as systemic inflammation, cardiometabolic diseases, and neurodegenerative disorders. There are dynamic interactions among metabolites of tryptophan. The interactions between metabolites, particularly those that are strong and temporally reproducible could be of pathophysiological relevance. Using a targeted metabolomics approach, the concentration levels of tryptophan and 18 of its metabolites across multiple pathways was quantified in 24-hours urine samples at 2 time-points, age 17 years (baseline) and 18 years (follow-up) from 132 (52% female) apparently healthy adolescent participants of the DOrtmund Nutritional and Anthropometric Longitudinally Designed (DONALD) Study. In sex-specific analyses, we applied 2 network approaches, the Gaussian graphical model and Bayesian network to (1) explore the network structure for both time-points, (2) retrieve strongly related metabolites, and (3) determine whether the strongly related metabolites were temporally reproducible. Independent of selected covariates, the 2 network approaches revealed 5 associations that were strong and temporally reproducible. These were novel relationships, between kynurenic acid and indole-3-acetic acid in females and between kynurenic acid and xanthurenic acid in males, as well as known relationships between kynurenine and 3-hydroxykynurenine, and between 3-hydroxykynurenine and 3-hydroxyanthranilic acid in females and between tryptophan and kynurenine in males. Overall, this epidemiological study using network-based approaches shed new light into tryptophan metabolism, particularly the interaction of host and microbial metabolites. The 5 observed relationships suggested the existence of a temporally stable pattern of tryptophan and 6 metabolites in healthy adolescent, which could be further investigated in search of fingerprints of specific physiological states. The metabolites in these relationships may represent a multi-biomarker panel that could be informative for health outcomes.
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Affiliation(s)
- Kolade Oluwagbemigun
- Nutritional Epidemiology, Department of Nutrition and Food Sciences, University of Bonn, Germany
| | - Andrea Anesi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Ireland
- INFANT Research Centre, University College Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Ireland
| | - Matthias Schmid
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, University of Bonn, Germany
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, San Michele all’Adige, Italy
| | - Ute Nöthlings
- Nutritional Epidemiology, Department of Nutrition and Food Sciences, University of Bonn, Germany
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Kunkel BN, Johnson JMB. Auxin Plays Multiple Roles during Plant-Pathogen Interactions. Cold Spring Harb Perspect Biol 2021; 13:a040022. [PMID: 33782029 PMCID: PMC8411954 DOI: 10.1101/cshperspect.a040022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The plant hormone auxin governs many aspects of normal plant growth and development. Auxin also plays an important role in plant-microbe interactions, including interactions between plant hosts and pathogenic microorganisms that cause disease. It is now well established that indole-3-acetic acid (IAA), the most well-studied form of auxin, promotes disease in many plant-pathogen interactions. Recent studies have shown that IAA can act both as a plant hormone that modulates host signaling and physiology to increase host susceptibility and as a microbial signal that directly impacts the pathogen to promote virulence, but large gaps in our understanding remain. In this article, we review recent studies on the roles that auxin plays during plant-pathogen interactions and discuss the virulence mechanisms that many plant pathogens have evolved to manipulate host auxin signaling and promote pathogenesis.
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Affiliation(s)
- Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Joshua M B Johnson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Periphytic microbial response to environmental phosphate bioavailability - relevance to P management in paddy fields. Appl Environ Microbiol 2021; 87:e0120121. [PMID: 34347511 DOI: 10.1128/aem.01201-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Periphyton occurs widely in shallow-water ecosystems such as paddy fields and plays critical parts in regulating local phosphorus cycling. As such, understanding the mechanisms of the biofilm's response to environmental P variability may lead to better perceptions of P utilization and retention in rice farms. Present study aims at exploring the biological and biochemical processes underlying periphyton's P buffering capability through examining changes in community structure, phosphorus uptake and storage, and molecular makeup of exometabolome at different levels of P availability. Under stressed (both excessive and scarce) phosphorus conditions, we found increased populations of the bacterial genus capable of transforming orthophosphate to polyphosphate, as well as mixotrophic algae who can survive through phagotrophy. These results were corroborated by observed polyphosphate buildup under low and high P treatment. Exometabolomic analyses further revealed that periphytic organisms may substitute S-containing lipids for phospholipids, use siderophores to dissolve iron (hydr)oxides to scavenge adsorbed P, and synthesize auxins to resist phosphorus starvation. These findings not only shed light on the mechanistic insights responsible for driving the periphytic P buffer but attest to the ecological roles of periphyton in aiding plants such as rice to overcome P limitations in natural environment. Importance The ability of periphyton to buffer environmental P in shallow aquatic ecosystems may be a natural lesson on P utilization and retention in paddy fields. This work revealed the routes and tools through which periphytic organisms adapt to and regulate ambient P fluctuation. The mechanistic understanding further implicates that the biofilm may serve rice plants to alleviate P stress. Additional results from extracellular metabolite analyses suggest the dissolved periphytic exometabolome can be a valuable nutrient source for soil microbes and plants to reduce biosynthetic costs. These discoveries have the potential to improve our understanding of biogeochemical cycling of phosphorus in general and to refine P management strategies for rice farm in particular.
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Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance. Nat Microbiol 2021; 6:874-884. [PMID: 34017107 DOI: 10.1038/s41564-021-00912-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Antibiotic tolerance, the ability of a typically susceptible microorganism to survive extended periods of exposure to antibiotics, has a critical role in chronic and recurrent bacterial infections, and facilitates the evolution of antibiotic resistance. However, the physiological factors that contribute to the development of antibiotic tolerance, particularly in vivo, are not fully known. Despite the fact that a high-fat diet (HFD) is implicated in several human diseases, the relationship between HFD and antibiotic efficacy is still poorly understood. Here, we evaluated the efficacy of multiple clinically relevant bactericidal antibiotics in HFD-fed mice infected with methicillin-resistant Staphylococcus aureus (MRSA) or Escherichia coli. We found that HFD-fed mice had higher bacterial burdens and these bacteria displayed lower susceptibility to bactericidal antibiotic treatment compared with mice that were fed a standard diet, while microbiota-depleted standard-diet- or HFD-fed mice showed similar susceptibility. Faecal microbiota transplantation from HFD-fed mice impaired antibiotic activity in mice fed a standard diet, indicating that alteration of the gut microbiota and related metabolites in HFD-fed mice may account for the decreased antibiotic activity. 16S rRNA sequencing and metabolomics analysis of faecal samples revealed decreased microbial diversity and differential metabolite profiles in HFD-fed mice. Notably, the tryptophan metabolite indole-3-acetic acid (IAA) was significantly decreased in HFD-fed mice. Further in vitro studies showed that IAA supplementation inhibited the formation of bacterial persisters and promoted the elimination of persisters in combination with antibiotic treatment, potentially through the activation of bacterial metabolic pathways. In vivo, the combination of IAA and ciprofloxacin increased the survival rate of HFD-fed mice infected with MRSA persisters. Overall, our data reveal that a HFD has an antagonistic effect on antibiotic treatment in a mouse model, and this is associated with the alteration of the gut microbiota and IAA production.
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Presence of the Hmq System and Production of 4-Hydroxy-3-Methyl-2-Alkylquinolines Are Heterogeneously Distributed between Burkholderia cepacia Complex Species and More Prevalent among Environmental than Clinical Isolates. Microbiol Spectr 2021; 9:e0012721. [PMID: 34132614 PMCID: PMC8552760 DOI: 10.1128/spectrum.00127-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Burkholderia cepacia complex (Bcc) comprises several species of closely related, versatile bacteria. Some Bcc strains produce 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), analogous to the 4-hydroxy-2-alkylquinolines of Pseudomonas aeruginosa. Using in silico analyses, we previously estimated that the hmqABCDEFG operon, which encodes enzymes involved in the biosynthesis of HMAQs, is carried by about one-third of Bcc strains, with considerable inter- and intraspecies variability. In the present study, we investigated by PCR, using consensus primers, the distribution of hmqABCDEFG in a collection of 312 Bcc strains (222 of clinical and 90 of environmental origins) belonging to 18 Bcc species. We confirmed that this operon is not distributed evenly among Bcc species. Among the 30% of strains bearing the hmqABCDEFG operon, we found that 92% of environmental isolates and 82% of clinically isolated Bcc strains produce levels of HMAQs detectable by liquid chromatography-mass spectrometry in at least one of the tested culture conditions. Among the hmqABCDEFG-positive but HMAQ-negative strains, none expressed the hmqA gene under the specified culture conditions. Interestingly, the hmqABCDEFG operon is more prevalent among plant root environment species (e.g., Burkholderia ambifaria and Burkholderia cepacia) and absent in species commonly found in chronically colonized individuals with cystic fibrosis (e.g., Burkholderia cenocepacia and Burkholderia multivorans), suggesting a role for the Hmq system in niche adaptation. We investigated the impact of the Hmq system on plant growth promotion and found that Pisum sativum root development by B. ambifaria required a functional HMAQ system. IMPORTANCE Environmental bacteria belonging to the various closely related species forming the Burkholderia cepacia complex (Bcc) can infect plants and animals, including humans. Their pathogenicity is regulated by intercellular communication, or quorum sensing, allowing them to collaborate instead of acting individually. Bcc organisms generally exploit interacting quorum sensing systems based on N-acyl-homoserine lactones as signaling molecules. Several Bcc strains also carry an hmqABCDEFG operon responsible for the biosynthesis of 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), molecules analogous to the Pseudomonas quinolone signal (PQS) system of P. aeruginosa. Our finding that the prevalences of the Hmq system and HMAQ production are very different between various Bcc species suggests a key role in niche adaptation or pathogenicity. This is supported by a significant reduction in plant growth promotion in the absence of HMAQ production for a beneficial Bcc strain.
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Ponce GE, Fuse M, Chan A, Connor EF. The Localization of Phytohormones within the Gall-inducing Insect Eurosta solidaginis (Diptera: Tephritidae). ARTHROPOD-PLANT INTERACTIONS 2021; 15:375-385. [PMID: 34149963 PMCID: PMC8211092 DOI: 10.1007/s11829-021-09817-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The phytohormone production hypothesis suggests that organisms, including insects, induce galls by producing and secreting plant growth hormones. Auxins and cytokinins are classes of phytohormones that induce cell growth and cell division, which could contribute to the plant tissue proliferation which constitutes the covering gall. Bacteria, symbiotic with insects, may also play a part in gall induction by insects through the synthesis of phytohormones or other effectors. Past studies have shown that concentrations of cytokinins and auxins in gall-inducing insects are higher than in their host plants. However, these analyses have involved whole-body extractions. Using immunolocalization of cytokinin and auxin, in the gall inducing stage of Eurosta solidaginis, we found both phytohormones to localize almost exclusively to the salivary glands. Co-localization of phytohormone label with a nucleic acid stain in the salivary glands revealed the absence of Wolbachia sp., the bacterial symbiont of E. solidaginis, which suggests that phytohormone production is symbiont independent. Our findings are consistent with the hypothesis that phytohormones are synthesized in and secreted from the salivary glands of E. solidaginis into host-plant tissues for the purpose of manipulating the host plant.
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Affiliation(s)
- Gabriela E Ponce
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Megumi Fuse
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Annette Chan
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
| | - Edward F Connor
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA USA 94132
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Batista BD, Dourado MN, Figueredo EF, Hortencio RO, Marques JPR, Piotto FA, Bonatelli ML, Settles ML, Azevedo JL, Quecine MC. The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom). Arch Microbiol 2021; 203:3869-3882. [PMID: 34013419 DOI: 10.1007/s00203-021-02361-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 12/28/2022]
Abstract
Strains of Bacillus thuringiensis (Bt) are commonly commercialized as bioinoculants for insect pest control, but their benefits go beyond their insecticidal property: they can act as plant growth-promoters. Auxins play a major role in the plant growth promotion. However, the mechanism of auxin production by the Bacilli group, and more specifically by Bt strains, is unclear. In previous work, the plant growth-promoting rhizobacterium (PGPR) B. thuringiensis strain RZ2MS9 increased the corn roots. This drew our attention to the strain's auxin production trait, earlier detected in vitro. Here, we demonstrate that in its genome, RZ2MS9 harbours the complete set of genes required in two pathways that are used for Indole acetic acid (IAA) production. We also detected that the strain produces almost five times more IAA during the stationary phase. The bacterial application increased the shoot dry weight of the Micro-Tom (MT) tomato by 24%. The application also modified MT root architecture, with an increase of 26% in the average lateral root length and inhibition of the axial root. At the cellular level, RZ2MS9-treated MT plants presented elongated root cortical cells with intensified mitotic activity. Altogether, these are the best characterized auxin-associated phenotypes. Besides that, no growth alteration was detected in the auxin-insensitive diageotropic (dgt) plants either with or without the RZ2MS9 inoculation. Our results suggest that auxins play an important role in the ability of B. thuringiensis RZ2MS9 to promote MT growth and provide a better understanding of the auxin production mechanism by a Bt strain.
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Affiliation(s)
- Bruna Durante Batista
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Manuella Nóbrega Dourado
- Department of Microbiology, Biomedicine Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Everthon Fernandes Figueredo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - Renata Ockner Hortencio
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - João Paulo Rodrigues Marques
- Laboratory of Nuclear Instrumentation, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Angelo Piotto
- Department of Crop Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Maria Letícia Bonatelli
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.,Bioinformatics Core, University of California, Davis, CA, USA
| | | | - João Lucio Azevedo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.
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Li M, Li T, Zhou M, Li M, Zhao Y, Xu J, Hu F, Li H. Caenorhabditis elegans Extracts Stimulate IAA Biosynthesis in Arthrobacter pascens ZZ21 via the Indole-3-pyruvic Acid Pathway. Microorganisms 2021; 9:microorganisms9050970. [PMID: 33946196 PMCID: PMC8146544 DOI: 10.3390/microorganisms9050970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Inter-organismal metabolites play important roles in regulating organism behavior and the communication between organisms. Nematodes, the most abundant animals on earth, are crucial participants in soil ecosystems through their interactions with microbes. For example, bacterial-feeding nematodes increase the activity of indole-3-acetic acid (IAA)-producing bacteria and the IAA content in soil. However, the way in which these nematodes interact with bacteria and affect IAA biosynthesis is not well understood. Here, using the model nematode Caenorhabditis elegans and the plant-beneficial bacterium Arthrobacter pascens ZZ21, we examined the effects of nematode excretions or extracts on bacterial IAA biosynthesis. To explore the underlying regulatory mechanism in more detail, we performed transcriptome sequencing and metabolomic analysis. Our findings suggest that C. elegans extracts promote IAA biosynthesis in A. pascens ZZ21 by increasing the expression of genes and the abundance of intermediates involved in the indole-3-pyruvic acid (IPyA) pathway. C. elegans extracts also significantly influenced biosynthetic and metabolic activity in A. pascens ZZ21. Treatment with C. elegans extracts promoted pyruvate metabolism, the citrate cycle (TCA) cycle and the production of some TCA-cycle-related amino acids and inhibited oxidative phosphorylation, which induced the accumulation of reduced nicotinamide adenine dinucleotide (NADH). We propose that the extracts altered the metabolism of A. pascens ZZ21 to help the bacteria resist stress caused by their predator. Our findings indicate that bacterial-feeding nematodes mediate the interaction between nematodes and bacteria via their extracts, providing insights into the ecological function of C. elegans in soil.
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Affiliation(s)
- Mengsha Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
- College of Science & Technology, Ningbo University, Cixi 315300, China
| | - Teng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
| | - Ming Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
| | - Mengdi Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
| | - Yexin Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
| | - Jingjing Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210014, China
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (T.L.); (M.Z.); (M.L.); (Y.Z.); (J.X.); (F.H.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210014, China
- Correspondence: ; Tel.: +86-025-84395374
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Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast. PLoS Genet 2021; 17:e1009414. [PMID: 33690632 PMCID: PMC7978357 DOI: 10.1371/journal.pgen.1009414] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/19/2021] [Accepted: 02/11/2021] [Indexed: 01/13/2023] Open
Abstract
Indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. The capacity to synthesize IAA is also widespread among plant-associated bacterial and fungal species, which may use IAA as an effector molecule to define their relationships with plants or to coordinate their physiological behavior through cell-cell communication. Fungi, including many species that do not entertain a plant-associated life style, are also able to synthesize IAA, but the physiological role of IAA in these fungi has largely remained enigmatic. Interestingly, in this context, growth of the budding yeast Saccharomyces cerevisiae is sensitive to extracellular IAA. Here, we use a combination of various genetic approaches including chemical-genetic profiling, SAturated Transposon Analysis in Yeast (SATAY), and genetic epistasis analyses to identify the mode-of-action by which IAA inhibits growth in yeast. Surprisingly, these analyses pinpointed the target of rapamycin complex 1 (TORC1), a central regulator of eukaryotic cell growth, as the major growth-limiting target of IAA. Our biochemical analyses further demonstrate that IAA inhibits TORC1 both in vivo and in vitro. Intriguingly, we also show that yeast cells are able to synthesize IAA and specifically accumulate IAA upon entry into stationary phase. Our data therefore suggest that IAA contributes to proper entry of yeast cells into a quiescent state by acting as a metabolic inhibitor of TORC1. Auxins are a major group of plant phytohormones that are critical for growth and development. Amongst the auxins, indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. Interestingly, the capacity to synthesize and secrete IAA is also widespread among fungi, including the budding yeast Saccharomyces cerevisiae, but the role of IAA in fungi has largely remained unknown. Here, we confirm an earlier observation that IAA inhibits growth of budding yeast and show by diverse genetic and biochemical means that IAA restrains budding yeast growth by inhibiting the target of rapamycin complex 1 (TORC1), a highly conserved eukaryotic regulator of growth. Intriguingly, budding yeast cells accumulate IAA specifically when limited for nutrients, which suggests that IAA plays a hitherto unknown physiological role in contributing to the establishment of cellular quiescence by acting as a metabolic inhibitor of TORC1.
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Casanova-Sáez R, Mateo-Bonmatí E, Ljung K. Auxin Metabolism in Plants. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a039867. [PMID: 33431579 PMCID: PMC7919392 DOI: 10.1101/cshperspect.a039867] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.
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Affiliation(s)
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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Snak A, Vendruscolo ECG, dos Santos MF, Fiorini A, Mesa D. Genome sequencing and analysis of plant growth-promoting attributes from Leclercia adecarboxylata. Genet Mol Biol 2021; 44:e20200130. [PMID: 33503198 PMCID: PMC7839631 DOI: 10.1590/1678-4685-gmb-2020-0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/11/2020] [Indexed: 11/22/2022] Open
Abstract
Plant growth-promoting bacteria are ecological alternatives for fertilization, mainly for gramineous. Since plant x bacteria interaction is genotype and strain dependent, searching for new strains may contribute to the development of new biofertilizers. We aim to characterize plant growth-promoting capacity of Leclercia adecarboxylata strain Palotina, formerly isolated by our group in corn. A single isolated colony was taken and its genome was sequenced using Illumina technology. The whole genome was compared to other Leclercia adecarboxylata strains, and their biological and growth-promoting traits, such as P solubilization and auxin production, were tested. Following that, a 4.8 Mb genome of L. adecarboxylata strain Palotina was assembled and the functional annotation was carried out. This paper is the first to report the genes associated with plant growth promotion demonstrating in vitro indole acid production by this strain. These results project the endophyte as a potential biofertilizer for further commercial exploitation.
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Affiliation(s)
- Aline Snak
- Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e
Genética, Palotina, PR, Brazil
| | | | | | - Adriana Fiorini
- Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e
Genética, Palotina, PR, Brazil
- Universidade Federal do Paraná, Departamento de Biociências,
Palotina, PR, Brazil
| | - Dany Mesa
- Universidade Federal do Paraná, Departamento de Bioquímica, Centro
Politécnico, Jardim das Américas, Curitiba, PR, Brazil
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Weiten A, Kalvelage K, Becker P, Reinhardt R, Hurek T, Reinhold-Hurek B, Rabus R. Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T. Microb Physiol 2021; 31:16-35. [PMID: 33477134 DOI: 10.1159/000513167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/17/2020] [Indexed: 11/19/2022]
Abstract
The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.
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Affiliation(s)
- Arne Weiten
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kristin Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Patrick Becker
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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Eichmann R, Richards L, Schäfer P. Hormones as go-betweens in plant microbiome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:518-541. [PMID: 33332645 PMCID: PMC8629125 DOI: 10.1111/tpj.15135] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 05/04/2023]
Abstract
The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.
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Affiliation(s)
- Ruth Eichmann
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
| | - Luke Richards
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Patrick Schäfer
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
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Symbiotic Bacterium-Derived Organic Acids Protect Delia antiqua Larvae from Entomopathogenic Fungal Infection. mSystems 2020; 5:5/6/e00778-20. [PMID: 33203688 PMCID: PMC7677000 DOI: 10.1128/msystems.00778-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Colonization resistance, i.e., the protective effects of associated microbiota for the animal host against pathogen infection, has been studied widely over the last 100 years. However, few molecules mediating colonization resistance have been identified. In the symbiosis formed by Delia antiqua and its associated microbes, six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana, providing an ideal model to investigate the chemical mechanism for colonization resistance. Subsequently using this symbiotic system, we first compared effects of the six bacterial species, and one control bacterium (Klebsiella oxytoca) that showed no antifungal effects, on B. bassiana and its infection of D. antiqua Second, metabolomic profiles of the six bacteria and K. oxytoca were compared to identify candidate metabolites that may prevent infection. Third, the concentrations of candidate metabolites in situ from axenic and nonaxenic larvae were determined. Finally, effects of artificial metabolite cocktails on B. bassiana and its infection of D. antiqua larvae were determined. Results showed that compared to K. oxytoca, the six bacteria produced a metabolite cocktail showing inhibitory effects on conidial germination, mycelial growth of B. bassiana, and fungal infection. Our work revealed novel molecules that mediate colonization resistance, which could help in developing chemical mechanisms of colonization resistance. Moreover, this work may aid in discovery and expansion of new bioactive antibiotics, promoting development of prophylactic and therapeutic approaches for treating infectious diseases.IMPORTANCE The protection of associated microbiota for their animal hosts against pathogen infection has been studied widely over the last 100 years. However, how those microbes protect the animal host remains unclear. In former studies, body surface microbes of one insect, Delia antiqua, protected the insect larvae from infection with the entomopathogen Beauveria bassiana By comparing the metabolites produced by microbes that protect the insect and microbes that cannot protect the insect, the question of how the microbes protect the insect is answered. It turns out that body surface bacteria produce a metabolite cocktail that inhibits colonization of B. bassiana and consequently protects the insect. This work reveals novel molecules with antifungal activity, which may aid in discovery and expansion of new prophylactic and therapeutic natural chemicals for treating infectious diseases.
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