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Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives. NITROGEN 2023. [DOI: 10.3390/nitrogen4010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Muasya MA, Avontuur JR, Yin Chan W, Venter SN, Steenkamp ET. Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata. Syst Appl Microbiol 2022; 45:126316. [DOI: 10.1016/j.syapm.2022.126316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Klepa MS, Janoni V, Paulitsch F, da Silva AR, do Carmo MRB, Delamuta JRM, Hungria M, da Silva Batista JS. Molecular diversity of rhizobia-nodulating native Mimosa of Brazilian protected areas. Arch Microbiol 2021; 203:5533-5545. [PMID: 34427725 DOI: 10.1007/s00203-021-02537-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 12/29/2022]
Abstract
Symbiotic Paraburkholderia have been increasingly studied in the past 20 years, especially when associated with Mimosa; however, studies with native/endemic species are still scarce. In this study, thirty strains were isolated from root nodules of native Mimosa paranapiacabae and M. micropteris in two locations of the Campos Gerais. The BOX-PCR fingerprinting revealed high genomic diversity, and the 16S rRNA phylogeny clustered the strains in three distinct groups (GI, GII, GIII), with one strain occupying an isolated position. Phylogenetic analysis with four concatenated housekeeping genes (atpD + gltB + gyrB + recA) confirmed the same clusters of 16S rRNA, and the closest species were P. nodosa BR 3437T and P. guartelaensis CNPSo 3008T; this last one isolated from another Mimosa species of the Campos Gerais. The phylogenies of the symbiotic genes nodAC and nifH placed all strains in a well-supported branch with the other species of the symbiovar mimosae. The phylogenetic analyses indicated that the strains represent novel lineages of sv. mimosae and that endemic Mimosa coevolved with indigenous Paraburkholderia in their natural environments.
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Affiliation(s)
- Milena Serenato Klepa
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil.,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86057-970, Brazil.,Embrapa Soja, C.P. 231, Londrina, PR, 86001-970, Brazil
| | - Vanessa Janoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil
| | - Fabiane Paulitsch
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil.,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86057-970, Brazil.,Embrapa Soja, C.P. 231, Londrina, PR, 86001-970, Brazil
| | - Adriane Ribeiro da Silva
- Secretaria da Educação e do Esporte, Governo do Estado do Paraná, NRE Ponta Grossa, Rua Cyro de Lima Garcia, Ponta Grossa, PR, 84050-091, Brazil
| | | | - Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, Londrina, PR, 86001-970, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Distrito Federal, Brasília, 71605-001, Brazil
| | - Mariangela Hungria
- Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10.011, Londrina, Paraná, 86057-970, Brazil.,Embrapa Soja, C.P. 231, Londrina, PR, 86001-970, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Distrito Federal, Brasília, 71605-001, Brazil
| | - Jesiane Stefania da Silva Batista
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil.
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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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Zilli JÉ, de Moraes Carvalho CP, de Matos Macedo AV, de Barros Soares LH, Gross E, James EK, Simon MF, de Faria SM. Nodulation of the neotropical genus Calliandra by alpha or betaproteobacterial symbionts depends on the biogeographical origins of the host species. Braz J Microbiol 2021; 52:2153-2168. [PMID: 34245449 DOI: 10.1007/s42770-021-00570-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/01/2021] [Indexed: 11/26/2022] Open
Abstract
The neotropical genus Calliandra is of great importance to ecology and agroforestry, but little is known about its nodulation or its rhizobia. The nodulation of several species from two restricted diversity centres with native/endemic species (Eastern Brazil and North-Central America) and species widespread in South America, as well as their nodule structure and the molecular characterization of their rhizobial symbionts based on phylogeny of the 16S rRNA, recA and nodC gene, is reported herein. Species representative of different regions were grown in Brazilian soil, their nodulation observed, and their symbionts characterized. Calliandra nodules have anatomy that is typical of mimosoid nodules regardless of the microsymbiont type. The rhizobial symbionts differed according to the geographical origin of the species, i.e. Alphaproteobacteria (Rhizobium) were the exclusive symbionts from North-Central America, Betaproteobacteria (Paraburkholderia) from Eastern Brazil, and a mixture of both nodulated the widespread species. The symbiont preferences of Calliandra species are the result of the host co-evolving with the "local" symbiotic bacteria that thrive in the different edaphoclimatic conditions, e.g. the acidic soils of NE Brazil are rich in acid-tolerant Paraburkholderia, whereas those of North-Central America are typically neutral-alkaline and harbour Rhizobium. It is hypothesized that the flexibility of widespread species in symbiont choice has assisted in their wider dispersal across the neotropics.
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Affiliation(s)
- Jerri Édson Zilli
- Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, 23891-000, Brazil.
| | | | | | | | - Eduardo Gross
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, 45662-900, Bahia, Brazil
| | | | - Marcelo Fragomeni Simon
- Embrapa Recursos Genéticos e Biotecnologia, Cx. Postal 02372, Brasília, DF, 70770-917, Brazil
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Paulitsch F, Dos Reis FB, Hungria M. Twenty years of paradigm-breaking studies of taxonomy and symbiotic nitrogen fixation by beta-rhizobia, and indication of Brazil as a hotspot of Paraburkholderia diversity. Arch Microbiol 2021; 203:4785-4803. [PMID: 34245357 DOI: 10.1007/s00203-021-02466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
Twenty years ago, the first members of the genus Burkholderia capable of nodulating and fixing N2 during symbiosis with leguminous plants were reported. The discovery that β-proteobacteria could nodulate legumes represented a breakthrough event because, for over 100 years, it was thought that all rhizobia belonged exclusively to the α-Proteobacteria class. Over the past 20 years, efforts toward robust characterization of these bacteria with large-scale phylogenomic and taxonomic studies have led to the separation of clinically important and phytopathogenic members of Burkholderia from environmental ones, and the symbiotic nodulating species are now included in the genera Paraburkholderia and Trinickia. Paraburkholderia encompasses the vast majority of β-rhizobia and has been mostly found in South America and South Africa, presenting greater symbiotic affinity with native members of the families Mimosoideae and Papilionoideae, respectively. Being the main center of Mimosa spp. diversity, Brazil is also known as the center of symbiotic Paraburkholderia diversity. Of the 21 symbiotic Paraburkholderia species described to date, 11 have been isolated in Brazil, and others first isolated in different countries have also been found in this country. Additionally, besides the symbiotic N2-fixation capacity of some of its members, Paraburkholderia is considered rich in other beneficial interactions with plants and can promote growth through several direct and indirect mechanisms. Therefore, these bacteria can be considered biological resources employed as environmentally friendly alternatives that could reduce the agricultural dependence on agrochemical inputs.
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Affiliation(s)
- Fabiane Paulitsch
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil.,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70040-020, Brazil
| | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil. .,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.
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Dias MAM, Bomfim CSG, Rodrigues DR, da Silva AF, Santos JCS, do Nascimento TR, Martins LMV, Dantas BF, Ribeiro PRDA, de Freitas ADS, Fernandes-Júnior PI. Paraburkholderia spp. are the main rhizobial microsymbionts of Mimosa tenuiflora (Willd.) Poir. in soils of the Brazilian tropical dry forests (Caatinga biome). Syst Appl Microbiol 2021; 44:126208. [PMID: 33992956 DOI: 10.1016/j.syapm.2021.126208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
Mimosa tenuiflora (Willd.) Poir. is widespread in southern and central American drylands, but little information is available concerning its associated rhizobia. Therefore, this study aimed to characterize M. tenuiflora rhizobia from soils of the tropical dry forests (Caatinga) in Pernambuco State, Brazil, at the molecular and symbiotic levels. Soil samples of pristine Caatinga areas in four municipalities were used to grow M. tenuiflora. First, the bacteria from root nodules were subjected to nodC/nifH gene amplification, and the bacteria positive for both genes had the 16S rRNA gene sequenced. Then, ten strains were evaluated using recA, gyrB, and nodC gene sequences, and seven of them had their symbiotic efficiency assessed. Thirty-two strains were obtained and 22 of them were nodC/nifH positive. Twenty strains clustered within Paraburkholderia and two within Rhizobium by 16S rRNA gene sequencing. The beta-rhizobia were similar to P. phenoliruptrix (12) and P. diazotrophica (8). Both alpha-rhizobia were closely related to R. miluonense. The recA + gyrB phylogenetic analysis clustered four and five strains within the P. phenoliruptrix and P. diazotrophica branches, respectively, but they were somewhat divergent to the 16S rRNA phylogeny. For Rhizobium sp. ESA 637, the recA + gyrB phylogeny clustered the strain with R. jaguaris. The nodC phylogeny indicated that ESA 626, ESA 629, and ESA 630 probably represented a new symbiovar branch. The inoculation assay showed high symbiotic efficiency for all tested strains. The results indicated high genetic diversity and efficiency of M. tenuiflora rhizobia in Brazilian drylands and included P. phenoliruptrix-like bacteria in the list of efficient beta-rhizobia in the Caatinga biome.
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Affiliation(s)
- Marcos André Moura Dias
- Universidade Federal do Vale do São Francisco (Univasf), Colegiado de Farmácia, Petrolina, PE, Brazil
| | | | | | - Aleksandro Ferreira da Silva
- Universidade Federal Rural de Pernambuco (UFRPE), Departamento de Agronomia, Recife, PE, Brazil; Faculdade UniBras, Departamento de Agronomia, Juazeiro, BA, Brazil
| | | | - Tailane Ribeiro do Nascimento
- Universidade do Estado da Bahia (UNEB), Departamento de Tecnologia e Ciências Sociais, R. Edgard Chastinet, s/n, Juazeiro, BA, Brazil
| | - Lindete Míria Vieira Martins
- Universidade do Estado da Bahia (UNEB), Departamento de Tecnologia e Ciências Sociais, R. Edgard Chastinet, s/n, Juazeiro, BA, Brazil
| | | | - Paula Rose de Almeida Ribeiro
- Embrapa Semiárido, Petrolina, PE, Brazil; Fundação de Amparo à Pesquisa do Estado de Pernambuco (Facepe), Recife, PE, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil
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8
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Liu X, You S, Liu H, Yuan B, Wang H, James EK, Wang F, Cao W, Liu ZK. Diversity and Geographic Distribution of Microsymbionts Associated With Invasive Mimosa Species in Southern China. Front Microbiol 2020; 11:563389. [PMID: 33250864 PMCID: PMC7673401 DOI: 10.3389/fmicb.2020.563389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022] Open
Abstract
In order to investigated diversity and geographic distribitution of rhizobia associated with invasive Mimosa species, Mimosa nodules and soils around the plants were sampled from five provinces in southern China. In total, 361 isolates were obtained from Mimosa pudica and Mimosa diplotricha in 25 locations. A multi-locus sequence analysis (MLSA) including 16S rRNA, atpD, dnaK, glnA, gyrB, and recA identified the isolates into eight genospecies corresponding to Paraburkhleria mimosarum, Paraburkholderia phymatum, Paraburkholeria carbensis, Cupriavidus taiwanensis, Cupriavidus sp., Rhizobium altiplani, Rhizobium mesoamericanum, and Rhizobium etli. The majority of the isolates were Cupriavidus (62.6%), followed by Paraburkholderia (33.5%) and Rhizobium (2.9%). Cupriavidus strains were more predominant in nodules of M. diplotricha (76.2) than in M. pudica (59.9%), and the distribution of P. phymatum in those two plant species was reverse (3.4:18.2%). Four symbiotypes were defined among the isolates based upon the phylogeny of nodA-nifH genes, represented by P. mimosarum, P. phymatum–P. caribensis, Cupriavidus spp., and Rhizobium spp. The species affiliation and the symbiotype division among the isolates demonstrated the multiple origins of Mimosa rhizobia in China: most were similar to those found in the original centers of Mimosa plants, but Cupriavidus sp. might have a local origin. The unbalanced distribution of symbionts between the two Mimosa species might be related to the soil pH, organic matter and available nitrogen; Cupriavidus spp. generally dominated most of the soils colonized by Mimosa in this study, but it had a particular preference for neutral-alkaline soils with low fertility whereas. While Paraburkholderia spp. preferred more acidic and fertile soils. The Rhizobium spp. tended to prefer neutral–acidic soils with high fertility soils.
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Affiliation(s)
- Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Shenghao You
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Huajie Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Baojuan Yuan
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Haoyu Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science/Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, China
| | - Weidong Cao
- Institute of Agricultural Resources and Regional Planning of CAAS, Beijing, China
| | - Zhong Kuan Liu
- Institute of Agro-resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Gross E, Dos Reis Junior FB, Avontuur JR, Chan WY, Venter SN, Steenkamp ET. Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae. Syst Appl Microbiol 2020; 44:126152. [PMID: 33276286 DOI: 10.1016/j.syapm.2020.126152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169T (= LMG 31411T; SARCC751T) for this novel species.
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Affiliation(s)
- Lazarus Mavima
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, United States of America
| | - Sofie E De Meyer
- MALDIID Pty Ltd, Murdoch, Western Australia, Australia; Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eduardo Gross
- Universidade Estadual de Santa Cruz, km 16 Rodovia Ilhéus - Itabuna, CEP 45662-900 Ilhéus, BA, Brazil
| | | | - Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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10
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Paulitsch F, Delamuta JRM, Ribeiro RA, da Silva Batista JS, Hungria M. Phylogeny of symbiotic genes reveals symbiovars within legume-nodulating Paraburkholderia species. Syst Appl Microbiol 2020; 43:126151. [PMID: 33171385 DOI: 10.1016/j.syapm.2020.126151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 10/23/2022]
Abstract
Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes. The diversity of genes involved in the nodulation (nodAC) and nitrogen fixation (nifH) abilities was investigated. Only two groups, one containing three Paraburkholderia species symbionts of Mimosa, and another one with P. ribeironis strains presented similar phylogenetic patterns in the analysis of core and symbiotic genes. In three other groups events of horizontal gene transfer of symbiotic genes were detected. Paraburkholderia strains with available genomes were used in the complementary analysis of nifHDK and fixABC and confirmed well-defined phylogenetic positions of symbiotic genes. In all analyses of nod, nif and fix genes the strains were distributed into five clades with high bootstrap support, allowing the proposal of five symbiovars in nodulating nitrogen-fixing Paraburkholderia, designated as mimosae, africana, tropicalis, atlantica and piptadeniae. Phylogenetic inferences within each symbiovar are discussed.
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Affiliation(s)
- Fabiane Paulitsch
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil; Departamento de Microbiologia, 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.
| | - Jakeline Renata Marçon Delamuta
- 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.
| | - Jesiane Stefania da Silva Batista
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Avenida General Carlos Cavalcanti, 4748 - Uvaranas, C.P. 6001, Ponta Grossa, PR 84030‑900, Brazil.
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil; Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, 86057-970 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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11
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Paraburkholderia guartelaensis sp. nov., a nitrogen-fixing species isolated from nodules of Mimosa gymnas in an ecotone considered as a hotspot of biodiversity in Brazil. Arch Microbiol 2019; 201:1435-1446. [PMID: 31428824 DOI: 10.1007/s00203-019-01714-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/14/2019] [Accepted: 08/10/2019] [Indexed: 10/26/2022]
Abstract
A polyphasic approach was used to infer the phylogenetic position of six nitrogen-fixing symbiotic bacteria isolated from Mimosa gymnas nodules grown in an ecotone between the Brazilian biomes of Atlantic Forest and Cerrado, considered as a hotspot of biodiversity. The 16S rRNA gene phylogeny indicated the highest similarity with Paraburkholderia oxyphila (98.7-98.9%), but similar values were found with other Paraburkholderia species. The multilocus sequence analysis (MLSA) of five (recA, gyrB, trpB, gltB, and atpD) housekeeping genes indicated that the CNPSo strains represent a novel lineage, sharing less than 95.7% of nucleotide identity (NI) with other Paraburkholderia species, being more closely related to P. nodosa. Genome parameters were analyzed for strain CNPSo 3008T, and DNA-DNA hybridization revealed a maximum of 55.9% of DNA-DNA relatedness with P. nodosa, while average nucleotide identity with the two closest species was of 93.84% with P. nodosa and of 87.93% with P. mimosarum, both parameters confirming that the strain represents a new species. In the analysis of the nodulation nodC gene, all CNPSo strains showed the highest similarity with P. nodosa, and nodulation tests indicated host specificity with Mimosa. Other phylogenetic, physiological, and chemotaxonomic properties were evaluated. All data obtained support the description of the novel species Paraburkholderia guartelaensis sp. nov., with CNPSo 3008T (= U13000T = G29.01T) indicated as the type strain.
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12
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Beukes CW, Boshoff FS, Phalane FL, Hassen AI, le Roux MM, Stȩpkowski T, Venter SN, Steenkamp ET. Both Alpha- and Beta-Rhizobia Occupy the Root Nodules of Vachellia karroo in South Africa. Front Microbiol 2019; 10:1195. [PMID: 31214140 PMCID: PMC6558075 DOI: 10.3389/fmicb.2019.01195] [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: 08/13/2018] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Vachellia karroo (formerly Acacia karroo) is a wide-spread legume species indigenous to southern Africa. Little is known regarding the identity or diversity of rhizobia that associate with this plant in its native range in South Africa. The aims of this study were therefore: (i) to gather a collection of rhizobia associated with V. karroo from a wide range of geographic locations and biomes; (ii) to identify the isolates and infer their evolutionary relationships with known rhizobia; (iii) to confirm their nodulation abilities by using them in inoculation assays to induce nodules under glasshouse conditions. To achieve these aims, soil samples were collected from 28 locations in seven biomes throughout South Africa, which were then used to grow V. karroo seedlings under nitrogen-free conditions. The resulting 88 bacterial isolates were identified to genus-level using 16S rRNA sequence analysis and to putative species-level using recA-based phylogenetic analyses. Our results showed that the rhizobial isolates represented members of several genera of Alphaproteobacteria (Bradyrhizobium, Ensifer, Mesorhizobium, and Rhizobium), as well as Paraburkholderia from the Betaproteobacteria. Our study therefore greatly increases the known number of Paraburkholderia isolates which can associate with this southern African mimosoid host. We also show for the first time that members of this genus can associate with legumes, not only in the Fynbos biome, but also in the Albany Thicket and Succulent Karoo biomes. Twenty-six putative species were delineated among the 88 isolates, many of which appeared to be new to Science with other likely being conspecific or closely related to E. alkalisoli, M. abyssinicae, M. shonense, and P. tropica. We encountered only a single isolate of Bradyrhizobium, which is in contrast to the dominant association of this genus with Australian Acacia. V. karroo also associates with diverse genera in the Grassland biome where it is quite invasive and involved in bush encroachment. Our findings therefore suggest that V. karroo is a promiscuous host capable of forming effective nodules with both alpha- and beta-rhizobia, which could be a driving force behind the ecological success of this tree species.
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Affiliation(s)
- Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francois S Boshoff
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francina L Phalane
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Ahmed I Hassen
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Marianne M le Roux
- South African National Biodiversity Institute, Pretoria National Botanical Garden, Pretoria, South Africa.,Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Tomasz Stȩpkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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13
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Draft Genome Sequence of Paraburkholderia sp. UYCP14C, a Rhizobium Strain Isolated from Root Nodules of Calliandra parvifolia. Microbiol Resour Announc 2019; 8:8/16/e00173-19. [PMID: 31000547 PMCID: PMC6473141 DOI: 10.1128/mra.00173-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. UYCP14C appears to be a novel species of the plant growth-promoting Paraburkholderia genus.
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14
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Russell SL. Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis. FEMS Microbiol Lett 2019; 366:5289862. [DOI: 10.1093/femsle/fnz013] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/15/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95060; USA
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15
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Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Dos Reis Junior FB, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK. Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera ( Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae. Genes (Basel) 2018; 9:genes9080389. [PMID: 30071618 PMCID: PMC6116057 DOI: 10.3390/genes9080389] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits—diazotrophy and/or symbiotic nodulation, and pathogenesis—were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.
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Affiliation(s)
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Belén Chávez-Ramírez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, 11340 Cd. de Mexico, Mexico.
| | - Chrizelle Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Leah Briscoe
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Noor Khan
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Marta Maluk
- The James Hutton Institute, Dundee DD2 5DA, UK.
| | | | - Ethan Humm
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Monique Arrabit
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Matthew Crook
- 450G Tracy Hall Science Building, Weber State University, Ogden, 84403 UT, USA.
| | - Eduardo Gross
- Center for Electron Microscopy, Department of Agricultural and Environmental Sciences, Santa Cruz State University, 45662-900 Ilheus, BA, Brazil.
| | - Marcelo F Simon
- Embrapa CENARGEN, 70770-917 Brasilia, Distrito Federal, Brazil.
| | | | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ann M Hirsch
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
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