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Funnicelli MIG, de Carvalho LAL, Teheran-Sierra LG, Dibelli SC, Lemos EGDM, Pinheiro DG. Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174577. [PMID: 38981540 DOI: 10.1016/j.scitotenv.2024.174577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.
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Affiliation(s)
- Michelli Inácio Gonçalves Funnicelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Lucas Amoroso Lopes de Carvalho
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Luis Guillermo Teheran-Sierra
- Agronomy Research Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, Bogotá 111121, Colombia
| | - Sabrina Custodio Dibelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Molecular Biology Laboratory, Institute for Research in Bioenergy (IPBEN), São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Daniel Guariz Pinheiro
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil.
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Hnamte L, Vanlallawmzuali, Kumar A, Yadav MK, Zothanpuia, Singh PK. An updated view of bacterial endophytes as antimicrobial agents against plant and human pathogens. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100241. [PMID: 39091295 PMCID: PMC11292266 DOI: 10.1016/j.crmicr.2024.100241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024] Open
Abstract
Bacterial endophytes are a crucial component of the phytomicrobiome, playing an essential role in agriculture and industries. Endophytes are a rich source of bioactive compounds, serving as natural antibiotics that can be effective in combating antibiotic resistance in pathogens. These bacteria interact with host plants through various processes such as quorum sensing, chemotaxis, antibiosis, and enzymatic activity. The current paper focuses on how plants benefit extensively from endophytic bacteria and their symbiotic relationship in which the microbes enhance plant growth, nitrogen fixation, increase nutrient uptake, improve defense mechanisms, and act as antimicrobial agents against pathogens. Moreover, it highlights some of the bioactive compounds produced by endophytes.
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Affiliation(s)
- Lalhmangaihmawia Hnamte
- Department of Biotechnology/Life Sciences, Pachhunga University College (A Constituent College of Mizoram University), Aizawl-796001, Mizoram, India
| | - Vanlallawmzuali
- Department of Biotechnology/Life Sciences, Pachhunga University College (A Constituent College of Mizoram University), Aizawl-796001, Mizoram, India
| | - Ajay Kumar
- Amity institute of Biotechnology, Amity University, Noida-201313, India
| | - Mukesh Kumar Yadav
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| | - Zothanpuia
- Department of Biotechnology/Life Sciences, Pachhunga University College (A Constituent College of Mizoram University), Aizawl-796001, Mizoram, India
| | - Prashant Kumar Singh
- Department of Biotechnology/Life Sciences, Pachhunga University College (A Constituent College of Mizoram University), Aizawl-796001, Mizoram, India
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3
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Islam MM, Mandal S. Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp. Arch Microbiol 2024; 206:182. [PMID: 38502250 DOI: 10.1007/s00203-024-03886-9] [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: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.
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Affiliation(s)
- Md Majharul Islam
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Kumari K, Sharma PK, Shikha S, Singh RP. Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16. Funct Integr Genomics 2023; 23:245. [PMID: 37460717 DOI: 10.1007/s10142-023-01161-6] [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: 03/14/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Shweta Shikha
- Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India.
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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Anzuay MS, Prenollio A, Ludueña LM, Morla FD, Cerliani C, Lucero C, Angelini JG, Taurian T. Enterobacter sp. J49: A Native Plant Growth-Promoting Bacteria as Alternative to the Application of Chemical Fertilizers on Peanut and Maize Crops. Curr Microbiol 2023; 80:85. [PMID: 36701020 DOI: 10.1007/s00284-023-03181-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023]
Abstract
In agricultural soils the productivity is determined by several factors and among them are the metabolic activities of the microorganisms that reside in it. The inoculation of plants with these bacteria is an alternative to the use of agrochemicals in crops. In particular, in those soils in which P levels are low, phosphate-solubilizing bacteria became an important group of soil microorganisms. In order to propose a potential P-biofertilizer to replace chemical fertilizers, the objective of this study was to evaluate the response of peanut and maize plants to the inoculation with the phosphate solubilizer Enterobacter sp. J49 individually or in combination with chemical fertilizers on growth, yield, and nutrient contents on peanut and maize plants in field trials. Two field assays in the peanut growing region of Córdoba Province (Argentina) were carried out. The inoculation of peanut with Enterobacter sp. J49 showed an increase in the yield with respect to the other treatments. Maize plants inoculated with this strain, alone or combined with half dose of chemical fertilizer, presented the highest yields. The results indicated that Enterobacter sp. J49 has a growth-promoting effect on the yield of peanut and maize mainly under drought stress. In conclusion, the inoculation with this strain would be a more sustainable agricultural practice for improving yield of peanut and maize crops in Argentinian agricultural area.
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Affiliation(s)
- María Soledad Anzuay
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, 5800, Río Cuarto, Córdoba, Argentina.,Instituto de Investigaciones Agrobiotecnológicas (CONICET, Río Cuarto), Río Cuarto, Argentina
| | - Ariel Prenollio
- Departamento de Producción Vegetal, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Liliana Mercedes Ludueña
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, 5800, Río Cuarto, Córdoba, Argentina.,Instituto de Investigaciones Agrobiotecnológicas (CONICET, Río Cuarto), Río Cuarto, Argentina
| | - Federico Daniel Morla
- Departamento de Producción Vegetal, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,Instituto de Investigaciones Agrobiotecnológicas (CONICET, Río Cuarto), Río Cuarto, Argentina
| | - Cecilia Cerliani
- Departamento de Producción Vegetal, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Cinthia Lucero
- Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Ruta Nacional 35 km 330, 6300, Santa Rosa, La Pampa, Argentina
| | - Jorge Guillermo Angelini
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, 5800, Río Cuarto, Córdoba, Argentina.,Instituto de Investigaciones Agrobiotecnológicas (CONICET, Río Cuarto), Río Cuarto, Argentina
| | - Tania Taurian
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal 3, 5800, Río Cuarto, Córdoba, Argentina. .,Instituto de Investigaciones Agrobiotecnológicas (CONICET, Río Cuarto), Río Cuarto, Argentina.
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Mazoyon C, Hirel B, Pecourt A, Catterou M, Gutierrez L, Sarazin V, Dubois F, Duclercq J. Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea ( Pisum sativum L.) and to Enhance Plant Biomass Production. Microorganisms 2023; 11:microorganisms11010199. [PMID: 36677491 PMCID: PMC9861922 DOI: 10.3390/microorganisms11010199] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.
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Affiliation(s)
- Candice Mazoyon
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Bertrand Hirel
- Unité Mixte de Recherche 1318 INRA-AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique et de l'Environnement (INRAE), 78026 Versailles, France
| | - Audrey Pecourt
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Manuella Catterou
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | | | - Fréderic Dubois
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Jérôme Duclercq
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
- Correspondence: ; Tel.: +33-3-22827612
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Sachman-Ruíz B, Wong-Villarreal A, Aguilar-Marcelino L, Lozano-Aguirre LF, Espinosa-Zaragoza S, Reyes-Reyes AL, Sanzón-Gómez D, Mireles-Arriaga AI, Romero-Tirado R, Rocha-Martínez MK, Pérez-de la Rosa JD, Sánchez-Cruz R, Gómez-Gutiérrez JA. Nematicidal, Acaricidal and Plant Growth-Promoting Activity of Enterobacter Endophytic Strains and Identification of Genes Associated with These Biological Activities in the Genomes. PLANTS (BASEL, SWITZERLAND) 2022; 11:3136. [PMID: 36432865 PMCID: PMC9695364 DOI: 10.3390/plants11223136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/26/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
In the present study, the nematicidal and acaricidal activity of three Enterobacter endophytic strains isolated from Mimosa pudica nodules was evaluated. The percentages of mortality of Enterobacter NOD4 against Panagrellus redivivus was 81.2%, and against Nacobbus aberrans 70.1%, Enterobacter NOD8 72.4% and 62.5%, and Enterobacter NOD10 64.8% and 58.7%, respectively. While against the Tyrophagus putrescentiae mite, the mortality percentages were 68.2% due to Enterobacter NOD4, 64.3% due to Enterobacter NOD8 and 77.8% due to Enterobacter NOD10. On the other hand, the ability of the three Enterobacter strains to produce indole acetic acid and phosphate solubilization, characteristics related to plant growth-promoting bacteria, was detected. Bioinformatic analysis of the genomes showed the presence of genes related to IAA production, phosphate solubilization, and nitrogen fixation. Phylogenetic analyzes of the recA gene, phylogenomics, and average nucleotide identity (ANI) allowed us to identify the strain Enterobacter NOD8 related to E. mori and Enterobacter NOD10 as E. asburiae, while Enterobacter NOD4 was identified as a possible new species of this species. The plant growth-promoting, acaricidal and nematicidal activity of the three Enterobacter strains makes them a potential agent to include in biocontrol alternatives and as growth-promoting bacteria in crops of agricultural interest.
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Affiliation(s)
- Bernardo Sachman-Ruíz
- CENID-Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Jiutepec 62550, Mexico
| | - Arnoldo Wong-Villarreal
- División Agroalimentaria, Universidad Tecnológica de la Selva, Carretera Ocosingo-Altamirano, km 0.5, Ocosingo 29950, Mexico
| | - Liliana Aguilar-Marcelino
- National Center for Disciplinary Research in Animal Health and Safety (INIFAP), Km 11 Federal Road Cuernavaca-Cuautla, Jiutepec 62550, Mexico
| | | | - Saúl Espinosa-Zaragoza
- Facultad de Ciencias Agrícolas, Universidad Autónoma de Chiapas, Huehuetán 30660, Mexico
| | - Ana Laura Reyes-Reyes
- National Institute of Forestry Agricultural and Livestock Research (INIFAP), Campo Experimental Rosario Izapa, Tuxtla Chico 30870, Mexico
| | - Diana Sanzón-Gómez
- Departamento de Agronomía, División Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Irapuato 36500, Mexico
| | - Ana Isabel Mireles-Arriaga
- Departamento de Agronomía, División Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Irapuato 36500, Mexico
| | - Rodrigo Romero-Tirado
- Facultad de Ciencias Agrícolas, Universidad Autónoma de Chiapas, Huehuetán 30660, Mexico
| | - Marisol Karina Rocha-Martínez
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Carretera Federal Cuernavaca-Cuautla No. 8534, Colonia Progreso, Jiutepec 62550, Mexico
| | - Juan Diego Pérez-de la Rosa
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Carretera Federal Cuernavaca-Cuautla No. 8534, Colonia Progreso, Jiutepec 62550, Mexico
| | - Ricardo Sánchez-Cruz
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
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Draft Genome Sequence of Enterobacter mori AYS9, a Potential Plant Growth-Promoting Rhizobacterium. Microbiol Resour Announc 2022; 11:e0100822. [DOI: 10.1128/mra.01008-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we report the draft genome sequence of
Enterobacter mori
AYS9, a rhizobacterium isolated from the rhizosphere of sorghum plants in South Africa. The genome sequence comprised 4,852,175 bp and exhibited a GC content of 55.5% and 4,567 genes, with 4,453 coding sequences, 3 rRNAs, 64 tRNAs, and 1 CRISPR.
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9
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Alves NSF, Kaory Inoue SG, Carneiro AR, Albino UB, Setzer WN, Maia JG, Andrade EH, da Silva JKR. Variation in Peperomia pellucida growth and secondary metabolism after rhizobacteria inoculation. PLoS One 2022; 17:e0262794. [PMID: 35061852 PMCID: PMC8785609 DOI: 10.1371/journal.pone.0262794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/05/2022] [Indexed: 01/31/2023] Open
Abstract
Peperomia pellucida L. Kunth is a herb well-known for its secondary metabolites (SM) with biological potential. In this study, the variations in the SM of P. pellucida during association with rhizobacteria were evaluated. Plants were inoculated with Enterobacter asburiae and Klebsiella variicola, which were identified by sequencing of the 16S rRNA gene. The data were evaluated at 7, 21, and 30-day post inoculation (dpi). Plant-bacteria symbiosis improved plant growth and weight. Total phenolic content and phenylalanine ammonia lyase enzyme activity had a significant increase mainly at 30 dpi. P. pellucida was mainly composed of phenylpropanoids (37.30-52.28%) and sesquiterpene hydrocarbons (39.28-49.42%). The phenylpropanoid derivative 2,4,5-trimethoxy-styrene (ArC2), the sesquiterpene hydrocarbon ishwarane, and the phenylpropanoid dillapiole were the major compounds. Principal component analysis (PCA) of the classes and compounds ≥ 2.0% indicated that plants colonized by E. asburiae had a reduction in the content of sesquiterpene hydrocarbons and an increase in phenylpropanoids and derivatives. Plants treated with this bacterium also had an increase in the content of 2,4,5-trimethoxystyrene at 30 dpi. Plants inoculated with K. variicola had significant increases only in the content of the classes monoterpene hydrocarbons and 'other compounds' (hydrocarbons, esters, ketones, etc.). These data suggest that the production of plant secondary metabolites can be modified depending on the type of rhizobacteria inoculated.
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Affiliation(s)
| | | | - Adriana Ribeiro Carneiro
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Pará,
Belém, Brazil
- Faculdade de Biotecnologia, Universidade Federal do Pará, Belém,
Brazil
| | | | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville,
AL, United States of America
- Aromatic Plant Research Center, Lehi, UT, United States of
America
| | - José Guilherme Maia
- Programa de Pós-Graduação em Química, Universidade Federal do Pará,
Belém, Brazil
| | | | - Joyce Kelly R. da Silva
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Pará,
Belém, Brazil
- Faculdade de Biotecnologia, Universidade Federal do Pará, Belém,
Brazil
- Programa de Pós-Graduação em Química, Universidade Federal do Pará,
Belém, Brazil
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10
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Ali M, Ali Q, Sohail MA, Ashraf MF, Saleem MH, Hussain S, Zhou L. Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective. Int J Mol Sci 2021; 22:ijms221810165. [PMID: 34576331 PMCID: PMC8465699 DOI: 10.3390/ijms221810165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.
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Affiliation(s)
- Mohsin Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Q.A.); (L.Z.)
| | - Muhammad Aamir Sohail
- Center for Excellence in Molecular Plant Sciences, National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China;
| | | | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Punjab, Pakistan;
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Correspondence: (Q.A.); (L.Z.)
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11
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Webster G, Mullins AJ, Cunningham-Oakes E, Renganathan A, Aswathanarayan JB, Mahenthiralingam E, Vittal RR. Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India. FEMS Microbiol Ecol 2021; 96:5876344. [PMID: 32710748 PMCID: PMC7422900 DOI: 10.1093/femsec/fiaa147] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.
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Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Alex J Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Arun Renganathan
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
| | | | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Ravishankar Rai Vittal
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
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12
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Burragoni SG, Jeon J. Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond. Microbiol Res 2021; 245:126691. [PMID: 33508761 DOI: 10.1016/j.micres.2020.126691] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 12/26/2022]
Abstract
Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.
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Affiliation(s)
- Sravanthi Goud Burragoni
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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13
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Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea mays L. var. DKB 177). Microbiol Res 2020; 243:126643. [PMID: 33227680 DOI: 10.1016/j.micres.2020.126643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 11/21/2022]
Abstract
Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.25 %, 30 min), resulting in a reduction of the cultivable-dependent fraction of seed-borne bacteria population, but not significantly detected by real-time PCR, microscopy, and biochemical analysis of the roots on germinated seeds. 16S rRNA sequencing revealed that bacteriome of non-germinated seeds and roots of 5-d germinated seeds exhibited similar diversity and did not differ in the structure concerning seed-disinfection. On the other hand, the relative abundance reduction of the genera f_Enterobacteriaceae_922761 (unassigned genus), Azospirillum, and Acinetobacter in disinfected-seed prior germination seems to display changes in prominence of several new taxa in the roots of germinated seeds. Interestingly, this bacteriome community rebuilt negatively affected the germination speed and growth of maize plantlets. Additionally, bacteriome re-shape increased the maize var. DKB 177 susceptible to the seed-borne plant pathogen Penicillium sp. Such changes in the natural seed-borne composition removed the natural barrier, increasing susceptibility to pathogens, impairing disinfected seeds to germinate, and develop. We conclude that bacteria borne in seeds modulate the relative abundance of taxa colonizing emerged roots, promote germination, seedling growth, and protect the maize against fungal pathogens.
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14
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Li L, Zhang Z, Pan S, Li L, Li X. Characterization and Metabolism Effect of Seed Endophytic Bacteria Associated With Peanut Grown in South China. Front Microbiol 2019; 10:2659. [PMID: 31798570 PMCID: PMC6865467 DOI: 10.3389/fmicb.2019.02659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Endophytes are considered to be excellent biocontrol agents and biofertilizers, and are associated with plant growth promotion and health. In particular, seed-endophytic bacteria benefit the host plant’s progeny via vertical transmission, and can play a role in plant growth and defense. However, seed-associated endophytic bacteria have not been fully explored, with very little known about how they interact with peanut (Arachis hypogaea), for example. Here, 10 genera of endophytic bacteria were isolated from the root tips of peanut seedlings grown either aseptically or in soil. Forty-two bacterial colonies were obtained from peanut seedlings grown in soil, mostly from the genus Bacillus. Eight colonies were obtained from aseptic seedling root tips, including Bacillus sp., Paenibacillus sp., and Pantoea dispersa. Four Bacillus peanut strains GL1–GL4 (B.p.GL1-GL4) produced bio-films, while B.p.GL2 and Paenibacillus glycanilyticus YMR3 (P.g.YMR3) showed strong amylolytic capability, enhanced peanut biomass, and increased numbers of root nodules. Conversely, P. dispersa YMR1 (P.d.YMR1) caused peanut plants to wilt. P.g.YMR3 was distributed mainly around or inside vacuoles and was transmitted to the next generation through gynophores and ovules. Hexanoate, succinate, and jasmonic acid (JA) accumulated in peanut root tips after incubation with P.g.YMR3, but linolenate content decreased dramatically. This suggests that strain P.g.YMR3 increases JA content (14.93-fold change) and modulates the metabolism of peanut to facilitate nodule formation and growth. These findings provide new insight into plant–seed endophytic bacterial interactions in peanut.
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Affiliation(s)
- Limei Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shiyu Pan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyun Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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15
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Makuwa SC, Serepa-Dlamini MH. Data on draft genome sequence of Bacillus sp. strain MHSD28, a bacterial endophyte isolated from Dicoma anomala. Data Brief 2019; 26:104524. [PMID: 31667287 PMCID: PMC6811918 DOI: 10.1016/j.dib.2019.104524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/06/2019] [Accepted: 09/09/2019] [Indexed: 11/26/2022] Open
Abstract
Here, we present the draft genome sequence of Bacillus sp. strain MHSD28 which was sequenced, and assembled with a total length of 5,571,729 bp. The genome has 43 contigs, the largest contig with 1,785,042 bp, N50 of 1,474,247 bp, G + C% content of 35.23%. The strain was isolated from surface sterilized leaves of Dicoma anomala, obtained in Limpopo province, South Africa. The genome has 5792 total genes which include 5701 protein coding sequences (CDS), 192 pseudogenes, 7 rRNA genes with 3 operons (5S, 16S and 23S), 79 tRNA genes and 5 noncoding RNA (ncRNA) genes. This whole genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession number VHIV00000000. The version described in this paper is version VHIV01000000.
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Affiliation(s)
- Sephokoane Cindy Makuwa
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011 Doornfontein 2028, Johannesburg, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011 Doornfontein 2028, Johannesburg, South Africa
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