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Klepa MS, Helene LCF, O´Hara G, Hungria M. Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium
is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains – CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T – previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the
Bradyrhizobium elkanii
supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes – atpD, dnaK, glnII, gyrB, recA and rpoB – did not cluster the strains under study as conspecific to any described
Bradyrhizobium
species. Average nucleotide identity and digital DNA–DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed
Bradyrhizobium
species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.
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Affiliation(s)
- Milena Serenato Klepa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Graham O´Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z. Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica. Syst Appl Microbiol 2022; 45:126337. [DOI: 10.1016/j.syapm.2022.126337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
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3
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Rhem MFK, Silva VC, Dos Santos JMF, Zilli JÉ, James EK, Fragomeni Simon M, Gross E. The large mimosoid genus Inga Mill. (tribe Ingeae, Caesalpinioideae) is nodulated by diverse Bradyrhizobium strains in its main centers of diversity in Brazil. Syst Appl Microbiol 2021; 44:126268. [PMID: 34649028 DOI: 10.1016/j.syapm.2021.126268] [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: 08/19/2020] [Revised: 09/11/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Inga (Caesalpinioideae) is the type genus of the Ingeae tribe in the mimosoid clade. It comprises about 300 species, all trees or treelets, and has an exclusively neotropical distribution, with Brazil as its main center of diversity. In this study, we analyzed the diversity of 40 strains of rhizobia isolated from root nodules collected from ten species of Inga belonging to different types of vegetation in Brazil. Sequences of their housekeeping genes (dnaK, recA, rpoB, gyrB and glnII), 16S rRNA genes, internal transcribed spacer (ITS) regions, as well as their symbiosis-essential genes (nodC and nifH) were used to characterize them genetically. The ability of the rhizobia to form nodules on Inga spp., and on the promiscuous legume siratro (Macroptilium atropurpureum) was also evaluated. A multilocus sequence analysis (MLSA) combined with an analysis of the ITS region showed that the isolates were distributed into four main groups (A-D) within the large genus Bradyrhizobium. Analysis of the nodC and nifH genes showed that the isolates formed a separate branch from all described species of Bradyrhizobium, except for B. ingae. Most of the tested isolates formed nodules on siratro and all isolates tested nodulated Inga spp. Our results suggest a unique co-evolutionary history of Bradyrhizobium and Inga and demonstrate the existence of potential new species of microsymbionts nodulating this important and representative genus of leguminous tree from the Caesalpinioideae mimosoid clade.
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Affiliation(s)
| | - Verônica Cordeiro Silva
- Programa de Pós-Graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | | | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - Eduardo Gross
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.
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Helene LCF, Klepa MS, O'Hara G, Hungria M. Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., isolated from nodules of legumes indigenous to Western Australia. Int J Syst Evol Microbiol 2020; 70:4623-4636. [PMID: 32667875 DOI: 10.1099/ijsem.0.004322] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia, broadly spread in a variety of ecosystems and with remarkable diversity. A polyphasic study was performed to characterize and clarify the taxonomic position of eight bradyrhizobial strains isolated from indigenous legumes to Western Australia. As expected for the genus, the 16S rRNA gene sequences were highly conserved, but the results of multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed three new distinct clades including the following strains: (1) WSM 1744T, WSM 1736 and WSM 1737; (2) WSM 1791T and WSM 1742; and (3) WSM 1741T, WSM 1735 and WSM 1790. The highest ANI values of the three groups in relation to the closest type strains were 92.4, 92.3 and 93.3 %, respectively, below the threshold of species circumscription. The digital DNA-DNA hybridization analysis also confirmed new species descriptions, with less than 52 % relatedness with the closest type strains. The phylogeny of the symbiotic gene nodC clustered the eight strains into the symbiovar retamae, together with seven Bradyrhizobium type strains, sharing from 94.2-98.1 % nucleotide identity (NI), and less than 88.7 % NI with other related strains and symbiovars. Morpho-physiological, phylogenetics, genomic and symbiotic traits were determined for the new groups and our data support the description of three new species, Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., with WSM 1744T (=CNPSo 4013T=LMG 31646T), WSM 1791T (=CNPSo 4014T=LMG 31647T) and WSM 1741T (=CNPSo 4020T=LMG 31651T) designated as type strains, respectively.
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Affiliation(s)
- Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Milena Serenato Klepa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.,Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil.,Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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Begmatov SA, Berestovskaja YY, Vasileva LV, Selitskaya OV. Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030030] [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] Open
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6
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Kong Z, Li L, Wang T, Rong C, Xue Y, Zhang T, Wu J, Li YY. New insights into the cultivation of N, N-dimethylformamide-degrading methanogenic consortium: A long-term investigation on the variation of prokaryotic community inoculated with activated sludge. ENVIRONMENTAL RESEARCH 2020; 182:109060. [PMID: 31884196 DOI: 10.1016/j.envres.2019.109060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/06/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
The cultivation of the N, N-dimethylformamide (DMF)-degrading methanogenic consortium is considered difficult. In this study, an up-flow anaerobic sludge blanket (UASB) was inoculated with activated sludge in order to culture the DMF-degrading anaerobic sludge under a constant DMF concentration of approximately 2000 mg L-1. While the UASB realized a nearly 100% degradation of DMF and a high methane production of 1.03 L d-1 for the first two months, both the removal efficiency and methane production continued to decrease until the end. The characterization of the prokaryotic community reveals that those DMF-hydrolyzing bacteria (DHB) originating from the activated sludge were responsible for the effective degradation of DMF. However, even when fed with a constant concentration of DMF, the DHB kept decreasing all the time while methane-producing archaea were rapidly cultivated. The variation of prokaryotic community suggests that the DHB could not proliferate anaerobically without utilizing the intermediate products from the hydrolysis of DMF, resulting in an unstable DMF-degrading consortium. The cultivation of DHB under the anaerobic condition of the UASB was therefore difficult. The reason it was not possible to culture a DMF-degrading methanogenic consortium in this study is that the DHB are denitrifying bacteria which require nitrate for their cell growth under the anaerobic condition. The solution to maintain the abundance of these DHB is to add doses of nitrate into the system. Nitrate is likely to help these DHB recapture intermediates from methanogens, enabling them to perform a heterotrophic denitrification by using a small proportion of DMF as the carbon source while simultaneously maintaining the cell growth of DHB.
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Affiliation(s)
- Zhe Kong
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Lu Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Tianjie Wang
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Chao Rong
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yi Xue
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Tao Zhang
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Jiang Wu
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan.
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7
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Sharma V, Bhattacharyya S, Kumar R, Kumar A, Ibañez F, Wang J, Guo B, Sudini HK, Gopalakrishnan S, DasGupta M, Varshney RK, Pandey MK. Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and 'Crack-Entry' Legume Groundnut ( Arachis hypogaea L.). PLANTS (BASEL, SWITZERLAND) 2020; 9:E276. [PMID: 32093403 PMCID: PMC7076665 DOI: 10.3390/plants9020276] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as "crack-entry'' mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges.
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Affiliation(s)
- Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Samrat Bhattacharyya
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (M.D.)
- Department of Botany, Sister Nibedita Government General Degree College for Girls, Kolkata 700027, India
| | - Rakesh Kumar
- Department of Life Sciences, Central University of Karnataka, Kadaganchi-585367, India
| | - Ashish Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
- DBT-National Agri-food Biotechnology Institute (NABI), Punjab 140308, India
| | - Fernando Ibañez
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto-5800, Córdoba, Argentina
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 103610, USA;
| | - Baozhu Guo
- Crop Protection and Management Research Unit, United State Department of Agriculture- Agriculture Research Service (USDA-ARS), Tifton, GA 31793, USA;
| | - Hari K. Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (M.D.)
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
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Bradyrhizobium uaiense sp. nov., a new highly efficient cowpea symbiont. Arch Microbiol 2020; 202:1135-1141. [DOI: 10.1007/s00203-020-01827-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 12/24/2022]
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9
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Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species. Syst Appl Microbiol 2020; 43:126053. [PMID: 31937424 DOI: 10.1016/j.syapm.2020.126053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 01/01/2023]
Abstract
Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.
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Root nodules of Genista germanica harbor Bradyrhizobium and Rhizobium bacteria exchanging nodC and nodZ genes. Syst Appl Microbiol 2020; 43:126026. [DOI: 10.1016/j.syapm.2019.126026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022]
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Santos MS, Nogueira MA, Hungria M. Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture. AMB Express 2019; 9:205. [PMID: 31865554 PMCID: PMC6925611 DOI: 10.1186/s13568-019-0932-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022] Open
Abstract
More than one hundred years have passed since the development of the first microbial inoculant for plants. Nowadays, the use of microbial inoculants in agriculture is spread worldwide for different crops and carrying different microorganisms. In the last decades, impressive progress has been achieved in the production, commercialization and use of inoculants. Nowadays, farmers are more receptive to the use of inoculants mainly because high-quality products and multi-purpose elite strains are available at the market, improving yields at low cost in comparison to chemical fertilizers. In the context of a more sustainable agriculture, microbial inoculants also help to mitigate environmental impacts caused by agrochemicals. Challenges rely on the production of microbial inoculants for a broader range of crops, and the expansion of the inoculated area worldwide, in addition to the search for innovative microbial solutions in areas subjected to increasing episodes of environmental stresses. In this review, we explore the world market for inoculants, showing which bacteria are prominent as inoculants in different countries, and we discuss the main research strategies that might contribute to improve the use of microbial inoculants in agriculture.
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Affiliation(s)
- Mariana Sanches Santos
- Embrapa Soja, Cx. Postal 231, Londrina, Paraná 86001-970 Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, Londrina, Paraná 86051-990 Brazil
| | | | - Mariangela Hungria
- Embrapa Soja, Cx. Postal 231, Londrina, Paraná 86001-970 Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, Londrina, Paraná 86051-990 Brazil
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12
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Urquiaga MCDO, Klepa MS, Somasegaran P, Ribeiro RA, Delamuta JRM, Hungria M. Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro. Int J Syst Evol Microbiol 2019; 69:3863-3877. [PMID: 31486763 DOI: 10.1099/ijsem.0.003697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The symbioses between legumes and nitrogen-fixing rhizobia make the greatest contribution to the global nitrogen input via the process of biological nitrogen fixation (BNF). Bradyrhizobium stands out as the main genus nodulating basal Caesalpinioideae. We performed a polyphasic study with 11 strains isolated from root nodules of Chamaecristafasciculata, an annual multi-functional native legume of the USA. In the 16S rRNA gene phylogeny the strains were clustered in the Bradyrhizobium japonicumsuperclade. The results of analysis of the intergenic transcribed spacer (ITS) indicated less than 89.9 % similarity to other Bradyrhizobium species. Multilocus sequence analysis (MLSA) with four housekeeping genes (glnII, gyrB, recA and rpoB) confirmed the new group, sharing less than 95.2 % nucleotide identity with other species. The MLSA with 10 housekeeping genes (atpD, dnaK, gap, glnII, gltA, gyrB, pnp, recA, rpoB and thrC) indicated Bradyrhizobium daqingense as the closest species. Noteworthy, high genetic diversity among the strains was confirmed in the analyses of ITS, MLSA and BOX-PCR. Average nucleotide identity and digital DNA-DNA hybridization values were below the threshold of described Bradyrhizobium species, of 89.7 and 40 %, respectively. In the nifH and nodC phylogenies, the strains were grouped together, but with an indication of horizontal gene transfer, showing higher similarity to Bradyrhizobium arachidis and Bradyrhizobium forestalis. Other phenotypic, genotypic and symbiotic properties were evaluated, and the results altogether support the description of the CNPSo strains as representatives of the new species Bradyrhizobiumfrederickii sp. nov., with CNPSo 3426T (=USDA 10052T=U686T=CL 20T) as the type strain.
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Affiliation(s)
- Maria Clara de Oliveira Urquiaga
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes 70.040-020 Brasília, Distrito Federal, Brazil.,Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil.,Department of Microbiology, Universidade Estadual de Londrina, C.P. 10.011, 86057970, Londrina, Paraná, Brazil
| | - Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul 71605-001 Brasília, Distrito Federal, Brazil.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes 70.040-020 Brasília, Distrito Federal, Brazil
| | | | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul 71605-001 Brasília, Distrito Federal, Brazil
| | - Jakeline Renata Marcon Delamuta
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul 71605-001 Brasília, Distrito Federal, Brazil.,Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Mariangela Hungria
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10.011, 86057970, Londrina, Paraná, Brazil.,Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul 71605-001 Brasília, Distrito Federal, Brazil
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13
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Klepa MS, Urquiaga MCDO, Somasegaran P, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium niftali sp. nov., an effective nitrogen-fixing symbiont of partridge pea [Chamaecrista fasciculata (Michx.) Greene], a native caesalpinioid legume broadly distributed in the USA. Int J Syst Evol Microbiol 2019; 69:3448-3459. [DOI: 10.1099/ijsem.0.003640] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
| | - Maria Clara de Oliveira Urquiaga
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | | | - Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
| | - Mariangela Hungria
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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14
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Klepa MS, Ferraz Helene LC, O’Hara G, Hungria M. Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia. Int J Syst Evol Microbiol 2019; 71:004742. [PMID: 33709900 PMCID: PMC8375429 DOI: 10.1099/ijsem.0.004742] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 01/16/2023] Open
Abstract
Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean (Glycine max) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains-CNPSo 4010T, CNPSo 4016T, and CNPSo 4019T-trapped from Western Australian soils with Glycine clandestina, Glycine tabacina and Glycine max, respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010T and CNPSo 4016T had Bradyrhizobium yuanmingense CCBAU 10071T as the closest species, whereas strain CNPSo 4019T was closer to Bradyrhizobium liaoningense LMG 18230T. The multilocus sequence analysis (MLSA) with five housekeeping genes-dnaK, glnII, gyrB, recA and rpoB-confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA-DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010T and CNPSo 4019T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense, respectively, while strain CNPSo 4016T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium. We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010T (=WSM 4802T=LMG 31645T) isolated from Glycine clandestina, Bradyrhizobium glycinis sp. nov. for CNPSo 4016T (=WSM 4801T=LMG 31649T) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019T (=WSM 4799T=LMG 31650T) isolated from G. max.
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Affiliation(s)
- Milena Serenato Klepa
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
| | - Graham O’Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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15
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Jaiswal SK, Dakora FD. Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa. Front Microbiol 2019; 10:310. [PMID: 30853952 PMCID: PMC6395442 DOI: 10.3389/fmicb.2019.00310] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/05/2019] [Indexed: 11/17/2022] Open
Abstract
Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
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16
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Kong Z, Li L, Li YY. Characterization and variation of microbial community structure during the anaerobic treatment of N, N-dimethylformamide-containing wastewater by UASB with artificially mixed consortium. BIORESOURCE TECHNOLOGY 2018; 268:434-444. [PMID: 30107357 DOI: 10.1016/j.biortech.2018.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 05/11/2023]
Abstract
A lab-scale UASB was operated successfully to anaerobically treat wastewater containing approximately 2000 mg L-1N, N-dimethylformamide (DMF) by artificially mixing anaerobic granular sludge with DMF-degrading activated sludge. DMF was effectively degraded by the UASB under a low OLR of 1.63-4.22 g COD L-1 d-1, with over 96% DMF removal efficiency and a high methane production rate. However, the DMF-degrading ability gradually weakened along with increases in the OLR. The analysis of the microbial community structure by high-throughput sequencing revealed a decline in the abundance of the facultatively anaerobic DMF-hydrolyzing bacteria originating from activated sludge with increasing OLR, further deteriorating the methanogenic degradation of DMF. When the OLR was lowered again, the slow growth of those facultative anaerobes recovered, and slight improvements in the removal were noted. Methylotrophic methanogens utilized the intermediate products from the hydrolysis of DMF, which kept increasing in abundance throughout the entire experimental period.
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Affiliation(s)
- Zhe Kong
- Laboratory of Environmental Protection Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-06, Sendai 980-8579, Miyagi, Japan
| | - Lu Li
- Laboratory of Environmental Protection Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-06, Sendai 980-8579, Miyagi, Japan
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-06, Sendai 980-8579, Miyagi, Japan.
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17
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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18
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Bradyrhizobium forestalis sp. nov., an efficient nitrogen-fixing bacterium isolated from nodules of forest legume species in the Amazon. Arch Microbiol 2018; 200:743-752. [DOI: 10.1007/s00203-018-1486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 01/01/2023]
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19
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de Matos GF, Zilli JE, de Araújo JLS, Parma MM, Melo IS, Radl V, Baldani JI, Rouws LFM. Bradyrhizobium sacchari sp. nov., a legume nodulating bacterium isolated from sugarcane roots. Arch Microbiol 2017; 199:1251-1258. [PMID: 28601967 DOI: 10.1007/s00203-017-1398-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/07/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
Members of the genus Bradyrhizobium are well-known as nitrogen-fixing microsymbionts of a wide variety of leguminous species, but they have also been found in different environments, notably as endophytes in non-legumes such as sugarcane. This study presents a detailed polyphasic characterization of four Bradyrhizobium strains (type strain BR 10280T), previously isolated from roots of sugarcane in Brazil. 16S rRNA sequence analysis, multilocus sequence analysis (MLSA) and analysis of the 16S-23S rRNA internal transcribed spacer showed that these strains form a novel clade close to, but different from B. huanghuaihaiense strain CCBAU 23303T. Average nucleotide identity (ANI) analyses confirmed that BR 10280T represents a novel species. Phylogenetic analysis based on nodC gene sequences also placed the strains close to CCBAU 23303T, but different from this latter strain, the sugarcane strains did not nodulate soybean, although they effectively nodulated Vigna unguiculata, Cajanus cajan and Macroptilium atropurpureum. Physiological traits are in agreement with the placement of the strains in the genus Bradyrhizobium as a novel species for which the name Bradyrhizobium sacchari sp. nov. is proposed.
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Affiliation(s)
- Gustavo Feitosa de Matos
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
- Universidade Federal Rural do Rio de Janeiro, Curso de Pós-graduação em Fitotecnia, Rodovia BR 465 km 07, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | - Jerri Edson Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
| | | | - Marcia Maria Parma
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Itamar Soares Melo
- Embrapa Meio Ambiente, C.P. 69, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Viviane Radl
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landtraße 1, 85764, Oberschleißheim, Germany
| | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, Rio De Janeiro, 23890-000, Brazil
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20
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Cordeiro AB, Ribeiro RA, Helene LCF, Hungria M. Rhizobium esperanzae sp. nov., a N 2 -fixing root symbiont of Phaseolus vulgaris from Mexican soils. Int J Syst Evol Microbiol 2017; 67:3937-3945. [DOI: 10.1099/ijsem.0.002225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrey Barbosa Cordeiro
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020, Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020, Brasília, Distrito Federal, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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21
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Araújo J, Flores-Félix JD, Igual JM, Peix A, González-Andrés F, Díaz-Alcántara CA, Velázquez E. Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan. Int J Syst Evol Microbiol 2017; 67:2236-2241. [PMID: 28671523 DOI: 10.1099/ijsem.0.001932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium, being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, 'Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA-DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense, 'Bradyrhizobium americanum' and Bradyrhizobium daqingense, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium. Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.
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Affiliation(s)
- Juan Araújo
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - César Antonio Díaz-Alcántara
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
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22
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Delamuta JRM, Menna P, Ribeiro RA, Hungria M. Phylogenies of symbiotic genes of Bradyrhizobium symbionts of legumes of economic and environmental importance in Brazil support the definition of the new symbiovars pachyrhizi and sojae. Syst Appl Microbiol 2017; 40:254-265. [PMID: 28647304 DOI: 10.1016/j.syapm.2017.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/19/2017] [Accepted: 04/21/2017] [Indexed: 11/19/2022]
Abstract
Bradyrhizobium comprises most tropical symbiotic nitrogen-fixing strains, but the correlation between symbiotic and core genes with host specificity is still unclear. In this study, the phylogenies of the nodY/K and nifH genes of 45 Bradyrhizobium strains isolated from legumes of economic and environmental importance in Brazil (Arachis hypogaea, Acacia auriculiformis, Glycine max, Lespedeza striata, Lupinus albus, Stylosanthes sp. and Vigna unguiculata) were compared to 16S rRNA gene phylogeny and genetic diversity by rep-PCR. In the 16S rRNA tree, strains were distributed into two superclades-B. japonicum and B. elkanii-with several strains being very similar within each clade. The rep-PCR analysis also revealed high intra-species diversity. Clustering of strains in the nodY/K and nifH trees was identical: 39 strains isolated from soybean grouped with Bradyrhizobium type species symbionts of soybean, whereas five others occupied isolated positions. Only one strain isolated from Stylosanthes sp. showed similar nodY/K and nifH sequences to soybean strains, and it also nodulated soybean. Twenty-one representative strains of the 16S rRNA phylogram were selected and taxonomically classified using a concatenated glnII-recA phylogeny; nodC sequences were also compared and revealed the same clusters as observed in the nodY/K and nifH phylograms. The analyses of symbiotic genes indicated that a large group of strains from the B. elkanii superclade comprised the novel symbiovar sojae, whereas for another group, including B. pachyrhizi, the symbiovar pachyrhizi could be proposed. Other potential new symbiovars were also detected. The co-evolution hypotheses is discussed and it is suggested that nodY/K analysis would be useful for investigating the symbiotic diversity of the genus Bradyrhizobium.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil.
| | - Pâmela Menna
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil.
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil.
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23
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Helene LCF, Delamuta JRM, Ribeiro RA, Hungria M. Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001870] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Jakeline Renata Marçon Delamuta
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil. Arch Microbiol 2017; 199:657-664. [DOI: 10.1007/s00203-017-1340-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446
T
, a Nitrogen-Fixing Symbiont of the Legume Pasture
Stylosanthes guianensis. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00631-16. [PMID: 27365354 PMCID: PMC4929517 DOI: 10.1128/genomea.00631-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bradyrhizobium stylosanthis BR 446T is a nitrogen-fixing symbiont of the tropical legume pasture Stylosanthes guianensis. Its draft genome contains 8,801,717 bp and 8,239 coding sequences (CDSs). Several putative genes that might confer high competitiveness and saprophytic capacity under the stressful conditions of tropical soils were identified in the genome.
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