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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Villanueva-Guerrero A, Nápoles MC, Herrera H. Endophytic Seed-Associated Bacteria as Plant Growth Promoters of Cuban Rice ( Oryza sativa L.). Microorganisms 2023; 11:2317. [PMID: 37764161 PMCID: PMC10537011 DOI: 10.3390/microorganisms11092317] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/19/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Cuban rice cultivars INCA LP-5 and INCA LP-7 are widely distributed in Cuba and Caribbean countries. Although there are studies about rhizospheric bacteria associated with these cultivars, there are no reports about their seed-associated bacteria. This study aimed to isolate endophytic bacteria from rice seeds and select those with the greatest plant growth-promoting traits. A total of nineteen bacterial strains from the genera Pantoea, Bacillus, Paenibacillus, and Pseudomonas were isolated from the husk and endosperm of rice seeds. The strains Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were classified as the most promissory to increase rice growth as they demonstrated the presence of multiple plant growth-promoting traits such as the production of auxins, phosphate, and potassium solubilization, the production of siderophores, and the inhibition of the phytopathogen Pyricularia oryzae. The inoculation of strains of Pantoea sp. and Pseudomonas spp. in rice improves the height, root length, fresh weight, and dry weight of the shoot and root after 21 days post-inoculation in hydroponic assays. This study constitutes the first report on Cuban rice cultivars about the presence of endophytes in seeds and their potential to promote seedling growth. Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were selected as the more promising strains for the development of bio-stimulators or bio-inoculants for Cuban rice crops.
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Affiliation(s)
- Ionel Hernández
- National Institute of Agricultural Science, Plant Physiology and Biochemistry Department, Carretera a Tapaste Km 3 y ½, San José de las Lajas 32700, Mayabeque, Cuba; (R.P.-P.); (M.C.N.)
| | - Cecilia Taulé
- Biological Research Institute Clemente Estable, Microbial Biochemistry and Genomics Department, Avenida Italia 3318, Montevideo 11600, Uruguay; (C.T.); (F.B.); (E.F.)
| | - Reneé Pérez-Pérez
- National Institute of Agricultural Science, Plant Physiology and Biochemistry Department, Carretera a Tapaste Km 3 y ½, San José de las Lajas 32700, Mayabeque, Cuba; (R.P.-P.); (M.C.N.)
| | - Federico Battistoni
- Biological Research Institute Clemente Estable, Microbial Biochemistry and Genomics Department, Avenida Italia 3318, Montevideo 11600, Uruguay; (C.T.); (F.B.); (E.F.)
| | - Elena Fabiano
- Biological Research Institute Clemente Estable, Microbial Biochemistry and Genomics Department, Avenida Italia 3318, Montevideo 11600, Uruguay; (C.T.); (F.B.); (E.F.)
| | - Angela Villanueva-Guerrero
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile;
- Programa de Magister en Manejo de Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - María Caridad Nápoles
- National Institute of Agricultural Science, Plant Physiology and Biochemistry Department, Carretera a Tapaste Km 3 y ½, San José de las Lajas 32700, Mayabeque, Cuba; (R.P.-P.); (M.C.N.)
| | - Héctor Herrera
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile;
- Laboratorio de Ecosistemas y Bosques, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Whole-Genome Sequencing and Annotation of 10 Endophytic and Epiphytic Bacteria Isolated from Lolium arundinaceum. Microbiol Resour Announc 2021; 10:10/19/e00317-21. [PMID: 33986094 PMCID: PMC8142580 DOI: 10.1128/mra.00317-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We report the whole-genome sequence and annotation of 10 endophytic and epiphytic bacteria isolated from the grass Lolium arundinaceum as part of a laboratory exercise in a Fundamentals of Plant Biochemistry and Pathology undergraduate course (BIOL403) at the Rochester Institute of Technology in Rochester, New York. We report the whole-genome sequence and annotation of 10 endophytic and epiphytic bacteria isolated from the grass Lolium arundinaceum as part of a laboratory exercise in a Fundamentals of Plant Biochemistry and Pathology undergraduate course (BIOL403) at the Rochester Institute of Technology in Rochester, New York.
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Heijo G, Taulé C, Mareque C, Stefanello A, Souza EM, Battistoni F. Interaction among endophytic bacteria, sweet sorghum (Sorghum bicolor) cultivars and chemical nitrogen fertilization. FEMS Microbiol Ecol 2021; 97:6007735. [PMID: 33245748 DOI: 10.1093/femsec/fiaa245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/25/2020] [Indexed: 11/14/2022] Open
Abstract
The application of new agricultural technologies to attain sustainable production systems is necessary. The use of plant growth-promoting bacteria to improve plant growth and health has been studied for decades. This work aimed to isolate diazotrophic endophytic bacteria associated with sweet sorghum plants and study the interaction of their inoculation in combination with chemical N-fertilization on different sorghum cultivars. A bacterial collection of 181 isolates was constructed and characterized in vitro and in vivo. From that, the strains Enterobacter sp. UYSB89 and Kosakonia sp. UYSB139 were nifH+, produce IAA, defined as true endophytes and able to promote growth of two sweet sorghum under greenhouse conditions. The evaluated cultivars responded differentially to bacterial inoculation, the nitrogen fertilization doses and their interaction. Thus, plant growth is a multifactorial consequence of the interrelation between crop practices and the plant genotypes. This knowledge is a valuable factor in terms of understanding plant-bacteria endophyte interactions to preserve environmental sustainability during the implementation of agronomic practices.
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Affiliation(s)
- Gabriela Heijo
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Cecilia Taulé
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Cintia Mareque
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Adriano Stefanello
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos Street, Curitiba, Paraná 81531-980, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos Street, Curitiba, Paraná 81531-980, Brazil
| | - Federico Battistoni
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
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Insights into the early stages of plant-endophytic bacteria interaction. World J Microbiol Biotechnol 2021; 37:13. [PMID: 33392741 DOI: 10.1007/s11274-020-02966-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
Abstract
The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.
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Chen Q, Meyer WA, Zhang Q, White JF. 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates. PeerJ 2020; 8:e8417. [PMID: 31942261 PMCID: PMC6956778 DOI: 10.7717/peerj.8417] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.
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Affiliation(s)
- Qiang Chen
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - William A Meyer
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Qiuwei Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - James F White
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Whole-Genome Sequencing of Streptomyces sp. Strain UYFA156, a Cultivar-Specific Plant Growth-Promoting Endophyte of Festuca arundinacea. Microbiol Resour Announc 2019; 8:8/38/e00722-19. [PMID: 31537663 PMCID: PMC6753267 DOI: 10.1128/mra.00722-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces spp. produce many and diverse bioactive metabolites. Plant growth-promoting (PGP) activity by Streptomyces spp. has been reported repeatedly; however, the mechanisms are largely unknown. We report the sequencing of the genome of a PGP endophytic Streptomyces sp. strain, which will contribute to the understanding of the underlying mechanisms for growth promotion. Streptomyces spp. produce many and diverse bioactive metabolites. Plant growth-promoting (PGP) activity by Streptomyces spp. has been reported repeatedly; however, the mechanisms are largely unknown. We report the sequencing of the genome of a PGP endophytic Streptomyces sp. strain, which will contribute to the understanding of the underlying mechanisms for growth promotion.
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Cloning and Expression of the Chitinase Encoded by ChiKJ406136 from Streptomyces Sampsonii (Millard & Burr) Waksman KJ40 and Its Antifungal Effect. FORESTS 2018. [DOI: 10.3390/f9110699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present study demonstrated that the chitinase gene ChiKJ406136 of Streptomyces sampsonii (Millard & Burr) Waksman KJ40 could be cloned using a PCR protocol and expressed in Escherichia coli (Migula) Castellani & Chalmers BL21 (DE3), and the recombinant protein had antifungal effect on four forest pathogens (Cylindrocladium scoparium Morgan, Cryphonectria parasitica (Murrill) Barr, Neofusicoccum parvum Crous, and Fusarium oxysporum Schl.) and also had the biological control effects on Eucalyptus robusta Smith leaf blight, Castanea mollissima BL. blight, Juglans regia L. blight and J. regia root rot. The results showed that ChiKJ406136 was efficiently expressed and a 48 kilodalton (kDa) recombinant protein was obtained. No significant change in protein production was observed in the presence of different concentrations of IPTG (isopropyl-b-D-thio-galactoside). The purified protein yield was greatest in the 150 mmol/L imidazole elution fraction, and the chitinase activities of the crude protein and purified protein solutions were 0.045 and 0.033 U/mL, respectively. The antifungal effects indicated that mycelial cells of the four fungi were disrupted, and the control effects of the chitinase on four forest diseases showed significant differences among the undiluted 10- and 20-fold dilutions and the control. The undiluted solution exhibited best effect. The results of this study provide a foundation for the use of S. sampsonii as a biocontrol agent and provides a new source for the chitinase gene, providing a theoretical basis for its application.
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Faoro H, Rene Menegazzo R, Battistoni F, Gyaneshwar P, do Amaral FP, Taulé C, Rausch S, Gonçalves Galvão P, de Los Santos C, Mitra S, Heijo G, Sheu SY, Chen WM, Mareque C, Zibetti Tadra-Sfeir M, Ivo Baldani J, Maluk M, Paula Guimarães A, Stacey G, de Souza EM, Pedrosa FO, Magalhães Cruz L, James EK. The oil-contaminated soil diazotroph Azoarcus olearius DQS-4 T is genetically and phenotypically similar to the model grass endophyte Azoarcus sp. BH72. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:223-238. [PMID: 27893193 DOI: 10.1111/1758-2229.12502] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/24/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
The genome of Azoarcus olearius DQS-4T , a N2 -fixing Betaproteobacterium isolated from oil-contaminated soil in Taiwan, was sequenced and compared with other Azoarcus strains. The genome sequence showed high synteny with Azoarcus sp. BH72, a model endophytic diazotroph, but low synteny with five non-plant-associated strains (Azoarcus CIB, Azoarcus EBN1, Azoarcus KH32C, A. toluclasticus MF63T and Azoarcus PA01). Average Nucleotide Identity (ANI) revealed that DQS-4T shares 98.98% identity with Azoarcus BH72, which should now be included in the species A. olearius. The genome of DQS-4T contained several genes related to plant colonization and plant growth promotion, such as nitrogen fixation, plant adhesion and root surface colonization. In accordance with the presence of these genes, DQS-4T colonized rice (Oryza sativa) and Setaria viridis, where it was observed within the intercellular spaces and aerenchyma mainly of the roots. Although they promote the growth of grasses, the mechanism(s) of plant growth promotion by A. olearius strains is unknown, as the genomes of DQS-4T and BH72 do not contain genes for indole acetic acid (IAA) synthesis nor phosphate solubilization. In spite of its original source, both the genome and behaviour of DQS-4T suggest that it has the capacity to be an endophytic, nitrogen-fixing plant growth-promoting bacterium.
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Affiliation(s)
- Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
- Laboratory of Gene Expression Regulation, Instituto Carlos Chagas, Fiocruz-PR, Curitiba, Paraná, 81350-010, Brazil
| | - Rodrigo Rene Menegazzo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Federico Battistoni
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | - Fernanda P do Amaral
- Division of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Cecilia Taulé
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Sydnee Rausch
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | | | - Cecilia de Los Santos
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Shubhajit Mitra
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | - Gabriela Heijo
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Shih-Yi Sheu
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, 811, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, 811, Taiwan
| | - Cintia Mareque
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Michelle Zibetti Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - J Ivo Baldani
- Embrapa Agrobiologia, Seropédica, Rio de Janeiro, 23891-000, Brazil
| | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Gary Stacey
- Division of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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