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Humaira Z, Cho D, Peng Y, Avila F, Park YL, Kim CY, Lee J. Demequina capsici sp. nov., a novel plant growth-promoting actinomycete isolated from the rhizosphere of bell pepper (Capsicum annuum). Sci Rep 2024; 14:15830. [PMID: 38982145 PMCID: PMC11233565 DOI: 10.1038/s41598-024-66202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05-80.63% for PMTSA13T and 74.02-80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13T ranged from 19 to 39%, and 19.1-38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to 'carbohydrate metabolism and transport (G)', according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant-microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13T (= KCTC 59028T = GDMCC 1.4451T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.
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Affiliation(s)
- Zalfa Humaira
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea
| | - Donghyun Cho
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Forbes Avila
- Animal Model Research Group, Jeonbuk Branch Institute, Korea Institute of Toxicology, Jeongeup, Jeollabuk-do, 56212, Republic of Korea
- Human and Environmental Toxicology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea
| | - Yu Lim Park
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea.
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Cerezini P, Kuwano BH, Grunvald AK, Hungria M, Nogueira MA. Soybean tolerance to drought depends on the associated Bradyrhizobium strain. Braz J Microbiol 2020; 51:1977-1986. [PMID: 32918241 PMCID: PMC7688821 DOI: 10.1007/s42770-020-00375-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022] Open
Abstract
We evaluated the effect of three different Bradyrhizobium strains inoculated in two soybean genotypes (R01-581F, drought-tolerant, and NA5858RR, drought-sensitive) submitted to drought in two trials conducted simultaneously under greenhouse. The strains (SEMIA 587, SEMIA 5019 (both B. elkanii), and SEMIA 5080 (B. diazoefficiens)) were inoculated individually in each genotype and then submitted to water restriction (or kept well-watered, control) between 45 and 62 days after emergence. No deep changes in plant physiological variables were observed under the moderate water restriction imposed during the first 10 days. Nevertheless, photosynthesis and transpiration decreased after the severe water restriction imposed for further 7 days. Water restriction reduced growth (- 30%) and the number of nodules (- 47% and - 58% for R01-581F and NA5858RR, respectively) of both genotypes, with a negative effect on N-metabolism. The genotype R01-581F inoculated with SEMIA 5019 strain had higher photosynthetic rates compared with NA5858RR, regardless of the Bradyrhizobium strain. On average, R01-581F showed better performance under drought than NA5858RR, with higher number of nodules (51 vs. 38 nodules per plant, respectively) and less accumulation of ureides in petioles (15 μmol g-1 vs. 34 μmol g-1, respectively). Moreover, plants inoculated with SEMIA 5080 had higher glutamine synthetase activity under severe water restriction, especially in the drought-tolerant R01-518F, suggesting maintenance of N metabolism under drought. The Bradyrhizobium strain affects the host plant responses to drought in which the strain SEMIA 5080 improves the drought tolerance of R01-518F genotype.
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Affiliation(s)
- Paula Cerezini
- Department of Agronomy, Universidade Estadual de Londrina, C. Postal 10.011, Londrina, PR, 86057-970, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil
| | - Biana Harumi Kuwano
- Department of Agronomy, Universidade Estadual de Londrina, C. Postal 10.011, Londrina, PR, 86057-970, Brazil
| | - Anna Karolina Grunvald
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil
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Banerjee G, Basak S, Roy T, Chattopadhyay P. Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp. FEMS Microbiol Ecol 2020; 95:5586991. [PMID: 31609448 DOI: 10.1093/femsec/fiz165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/13/2019] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
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Affiliation(s)
- Goutam Banerjee
- Department of Biochemistry, University of Calcutta, West Bengal 700019, India
| | - Swarnendu Basak
- Department of Medical Zoology, Kyung Hee University, School of Medicine, Seoul 02447, Republic of Korea
| | - Tathagato Roy
- Member of Jeevak Herb Welfare Society (registration number S/1L/78148 OF 2010-2011), Santiniketan, 731235, India.,Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, U.S
| | - Pritam Chattopadhyay
- Department of Biotechnology, Gauhati University, Guwahati, Assam 781014, India.,Department of Botany, M.U.C. Women's College, University of Bardhaman, Bardhaman, West Bengal 713104, India
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Carciochi WD, Rosso LHM, Secchi MA, Torres AR, Naeve S, Casteel SN, Kovács P, Davidson D, Purcell LC, Archontoulis S, Ciampitti IA. Soybean yield, biological N 2 fixation and seed composition responses to additional inoculation in the United States. Sci Rep 2019; 9:19908. [PMID: 31882958 PMCID: PMC6934618 DOI: 10.1038/s41598-019-56465-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/05/2019] [Indexed: 12/03/2022] Open
Abstract
It is unclear if additional inoculation with Bradyrhizobia at varying soybean [Glycine max (L.) Merr.] growth stages can impact biological nitrogen fixation (BNF), increase yield and improve seed composition [protein, oil, and amino acid (AA) concentrations]. The objectives of this study were to evaluate the effect of different soybean inoculation strategies (seed coating and additional soil inoculation at V4 or R1) on: (i) seed yield, (ii) seed composition, and (iii) BNF traits [nodule number and relative abundance of ureides (RAU)]. Soybean field trials were conducted in 11 environments (four states of the US) to evaluate four treatments: (i) control without inoculation, (ii) seed inoculation, (iii) seed inoculation + soil inoculation at V4, and (iv) seed inoculation + soil inoculation at R1. Results demonstrated no effect of seed or additional soil inoculation at V4 or R1 on either soybean seed yield or composition. Also, inoculation strategies produced similar values to the non-inoculated control in terms of nodule number and RAU, a reflection of BNF. Therefore, we conclude that in soils with previous history of soybean and under non-severe stress conditions (e.g. high early-season temperature and/or saturated soils), there is no benefit to implementing additional inoculation on soybean yield and seed composition.
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Affiliation(s)
| | | | - Mario A Secchi
- Department of Agronomy, Kansas State University, Manhattan, KS, US
| | | | - Seth Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, US
| | - Shaun N Casteel
- Department of Agronomy, Purdue University, West Lafayette, IN, US
| | - Péter Kovács
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, US
| | - Dan Davidson
- Illinois Soybean Association, Bloomington, IL, US
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, US
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Plant Growth Promoting Rhizobacteria (PGPR) - Prospective and Mechanisms: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.2.34] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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de Souza R, Ambrosini A, Passaglia LM. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 2015; 38:401-19. [PMID: 26537605 PMCID: PMC4763327 DOI: 10.1590/s1415-475738420150053] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/22/2015] [Indexed: 12/12/2022] Open
Abstract
Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.
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Affiliation(s)
- Rocheli de Souza
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciane M.P. Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Siqueira AF, Ormeño-Orrillo E, Souza RC, Rodrigues EP, Almeida LGP, Barcellos FG, Batista JSS, Nakatani AS, Martínez-Romero E, Vasconcelos ATR, Hungria M. Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. BMC Genomics 2014; 15:420. [PMID: 24888481 PMCID: PMC4070871 DOI: 10.1186/1471-2164-15-420] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. RESULTS Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15. CONCLUSIONS Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation and competitiveness.
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Affiliation(s)
- Arthur Fernandes Siqueira
- />Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), C.P. 60001, Londrina, PR 86051-990 Brazil
- />Embrapa Soja, C.P. 231, Londrina, PR 86001-970 Brazil
| | - Ernesto Ormeño-Orrillo
- />Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Rangel Celso Souza
- />Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Petrópolis, RJ 25651-071 Brazil
| | | | - Luiz Gonzaga Paula Almeida
- />Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Petrópolis, RJ 25651-071 Brazil
| | | | - Jesiane Stefânia Silva Batista
- />Department Structural, Molecular and Genetic Biology, Universidade Estadual de Ponta Grossa (UEPG), Av. General Carlos Cavalcanti 4748, Ponta Grossa, PR 84030-900 Brazil
| | | | | | | | - Mariangela Hungria
- />Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), C.P. 60001, Londrina, PR 86051-990 Brazil
- />Embrapa Soja, C.P. 231, Londrina, PR 86001-970 Brazil
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