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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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Lopes T, Cardoso P, Matos D, Rocha R, Pires A, Marques P, Figueira E. Graphene oxide influence in soil bacteria is dose dependent and changes at osmotic stress: growth variation, oxidative damage, antioxidant response, and plant growth promotion traits of a Rhizobium strain. Nanotoxicology 2022; 16:549-565. [PMID: 35997812 DOI: 10.1080/17435390.2022.2109528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Climate change events, such as drought, are increasing and soil bacteria can be severely affected. Moreover, the accumulation of emerging pollutants is expected to rapidly increase, and their impact on soil organisms, their interactions, and the services they provide is poorly known. The use of graphene oxide (GO) has been increasing due to its enormous potential for application in several areas and it is expected that concentration in soil will increase in the future, potentially causing disturbances in soil microorganisms not yet identified.Here we show the effects that GO nanosheets can cause on soil bacteria, in particular those that promote plant growth, in control and 10% polyethylene glycol (PEG) conditions. Low concentrations of GO nanosheets did not affect the growth of Rhizobium strain E20-8, but under osmotic stress (PEG) GO decreased bacterial growth even at lower concentrations. GO caused oxidative stress, with antioxidant mechanisms being induced to restrain damage, effectively at lower concentrations, but less effective at higher concentrations, and oxidative damage overcame. Under osmotic stress, alginate and glycine betaine osmoregulated the bacteria. Simultaneous exposure to PEG and GO induced oxidative damage. Plant growth promotion traits (indole acetic acid and siderophores production) were increased by osmotic stress and GO did not disturb these abilities. In the context of climate change, our findings might be relevant as they can form the premises for the implementation of crop production methodologies adapted to the new prevailing conditions, which include the presence of nanoparticles in the soil and more frequent and severe drought.
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Affiliation(s)
- Tiago Lopes
- Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Paulo Cardoso
- Department of Biology & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Diana Matos
- Department of Biology & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Ricardo Rocha
- Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Adília Pires
- Department of Biology & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Paula Marques
- Centre for Mechanical Technology and Automation, Department of Mechanics & TEMA, University of Aveiro, Aveiro, Portugal
| | - Etelvina Figueira
- Department of Biology & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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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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Bellés-Sancho P, Lardi M, Liu Y, Hug S, Pinto-Carbó MA, Zamboni N, Pessi G. Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions. Cells 2021; 10:cells10040952. [PMID: 33924023 PMCID: PMC8073898 DOI: 10.3390/cells10040952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/29/2022] Open
Abstract
Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N2 in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Sebastian Hug
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Marta Adriana Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, CH-8093 Zürich, Switzerland;
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
- Correspondence: ; Tel.: +41-44-63-52904
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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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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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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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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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Paraburkholderia strydomiana sp. nov. and Paraburkholderia steynii sp. nov.: rhizobial symbionts of the fynbos legume Hypocalyptus sophoroides. Antonie van Leeuwenhoek 2019; 112:1369-1385. [DOI: 10.1007/s10482-019-01269-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/22/2019] [Indexed: 02/07/2023]
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11
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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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Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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Silva VC, Alves PAC, Rhem MFK, dos Santos JMF, James EK, Gross E. Brazilian species of Calliandra Benth. (tribe Ingeae) are nodulated by diverse strains of Paraburkholderia. Syst Appl Microbiol 2018; 41:241-250. [DOI: 10.1016/j.syapm.2017.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 11/15/2022]
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Lardi M, Liu Y, Purtschert G, Bolzan de Campos S, Pessi G. Transcriptome Analysis of Paraburkholderia phymatum under Nitrogen Starvation and during Symbiosis with Phaseolus Vulgaris. Genes (Basel) 2017; 8:genes8120389. [PMID: 29244728 PMCID: PMC5748707 DOI: 10.3390/genes8120389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 01/31/2023] Open
Abstract
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils. Among the genes upregulated under nitrogen limitation, we found genes involved in exopolysaccharides production and in motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly upregulated during symbiosis, we identified—besides the nif gene cluster—an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities, suggesting an important role of the cytochrome for respiration inside the nodule. The analysis of mutant strains for the RNA polymerase transcription factor RpoN (σ54) and its activator NifA indicated that—similar to the situation in α-rhizobia—P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Gabriela Purtschert
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
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15
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Porter SS, Faber-Hammond JJ, Friesen ML. Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes. FEMS Microbiol Ecol 2017; 94:4705886. [DOI: 10.1093/femsec/fix168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Joshua J Faber-Hammond
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
- Department of Plant Pathology, Washington State University, P.O. Box 646430 Pullman, WA 99164, USA
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420 Pullman, WA 99164, USA
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de León-Martínez JA, Yañez-Ocampo G, Wong-Villarreal A. Burkholderia species associated with legumes of Chiapas, Mexico, exhibit stress tolerance and growth in aromatic compounds. Rev Argent Microbiol 2017; 49:394-401. [PMID: 28864228 DOI: 10.1016/j.ram.2017.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 02/09/2017] [Accepted: 04/20/2017] [Indexed: 11/18/2022] Open
Abstract
Leguminous plants have received special interest for the diversity of β-proteobacteria in their nodules and are promising candidates for biotechnological applications. In this study, 15 bacterial strains were isolated from the nodules of the following legumes: Indigofera thibaudiana, Mimosa diplotricha, Mimosa albida, Mimosa pigra, and Mimosa pudica, collected in 9 areas of Chiapas, Mexico. The strains were grouped into four profiles of genomic fingerprints through BOX-PCR and identified based on their morphology, API 20NE biochemical tests, sequencing of the 16S rRNA, nifH and nodC genes as bacteria of the Burkholderia genus, genetically related to Burkholderia phenoliruptrix, Burkholderia phymatum, Burkholderia sabiae, and Burkholderia tuberum. The Burkholderia strains were grown under stress conditions with 4% NaCl, 45°C, and benzene presence at 0.1% as the sole carbon source. This is the first report on the isolation of these nodulating species of the Burkholderia genus in legumes in Mexico.
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Affiliation(s)
- José A de León-Martínez
- Instituto de Biociencias, Universidad Autónoma de Chiapas, C.P. 30700 Tapachula, Chiapas, Mexico
| | - Gustavo Yañez-Ocampo
- Laboratorio de Edafología y Ambiente Universidad Autónoma del Estado de México, Instituto Literario 100, C.P. 50000 Toluca, Mexico
| | - Arnoldo Wong-Villarreal
- División Agroalimentaria, Universidad Tecnológica de la Selva, C.P. 29950 Ocosingo, Chiapas, Mexico.
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17
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Lardi M, de Campos SB, Purtschert G, Eberl L, Pessi G. Competition Experiments for Legume Infection Identify Burkholderia phymatum as a Highly Competitive β-Rhizobium. Front Microbiol 2017; 8:1527. [PMID: 28861050 PMCID: PMC5559654 DOI: 10.3389/fmicb.2017.01527] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/28/2017] [Indexed: 01/27/2023] Open
Abstract
Members of the genus Burkholderia (β-proteobacteria) have only recently been shown to be able to establish a nitrogen-fixing symbiosis with several legumes, which is why they are also referred to as β-rhizobia. Therefore, very little is known about the competitiveness of these species to nodulate different legume host plants. In this study, we tested the competitiveness of several Burkholderia type strains (B. diazotrophica, B. mimosarum, B. phymatum, B. sabiae, B. symbiotica and B. tuberum) to nodulate four legumes (Phaseolus vulgaris, Macroptilium atropurpureum, Vigna unguiculata and Mimosa pudica) under our closely defined growth conditions. The assessment of nodule occupancy of these species on different legume host plants revealed that B. phymatum was the most competitive strain in the three papilionoid legumes (bean, cowpea and siratro), while B. mimosarum outcompeted the other strains in mimosa. The analysis of phenotypes known to play a role in nodulation competitiveness (motility, exopolysaccharide production) and additional in vitro competition assays among β-rhizobial strains suggested that B. phymatum has the potential to be a very competitive legume symbiont.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of ZurichZurich, Switzerland
| | | | - Gabriela Purtschert
- Department of Plant and Microbial Biology, University of ZurichZurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of ZurichZurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of ZurichZurich, Switzerland
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18
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Sprent JI, Ardley J, James EK. Biogeography of nodulated legumes and their nitrogen-fixing symbionts. THE NEW PHYTOLOGIST 2017; 215:40-56. [PMID: 28211601 DOI: 10.1111/nph.14474] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Contents 40 I. 40 II. 41 III. 44 IV. 48 V. 49 VI. 49 VII. 52 VIII. 53 53 References 53 SUMMARY: In the last decade, analyses of both molecular and morphological characters, including nodulation, have led to major changes in our understanding of legume taxonomy. In parallel there has been an explosion in the number of genera and species of rhizobia known to nodulate legumes. No attempt has been made to link these two sets of data or to consider them in a biogeographical context. This review aims to do this by relating the data to the evolution of the two partners: it highlights both longitudinal and latitudinal trends and considers these in relation to the location of major land masses over geological time. Australia is identified as being a special case and latitudes north of the equator as being pivotal in the evolution of highly specialized systems in which the differentiated rhizobia effectively become ammonia factories. However, there are still many gaps to be filled before legume nodulation is sufficiently understood to be managed for the benefit of a world in which climate change is rife.
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Affiliation(s)
- Janet I Sprent
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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19
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Dall'Agnol RF, Bournaud C, de Faria SM, Béna G, Moulin L, Hungria M. Genetic diversity of symbiotic Paraburkholderia species isolated from nodules of Mimosa pudica (L.) and Phaseolus vulgaris (L.) grown in soils of the Brazilian Atlantic Forest (Mata Atlântica). FEMS Microbiol Ecol 2017; 93:3045887. [PMID: 28334155 DOI: 10.1093/femsec/fix027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/22/2017] [Indexed: 11/13/2022] Open
Abstract
Some species of the genus Paraburkholderia that are able to nodulate and fix nitrogen in symbiosis with legumes are called β-rhizobia and represent a group of ecological and biotechnological importance. We used Mimosa pudica and Phaseolus vulgaris to trap 427 rhizobial isolates from rhizospheric soil of Mimoseae trees in the Brazilian Atlantic Forest. Eighty-four representative strains were selected according to the 16S rRNA haplotypes and taxonomically characterized using a concatenated 16S rRNA-recA phylogeny. Most strains were assembled in the genus Paraburkholderia, including Paraburkholderia sabiae and Pa. nodosa. Mesorhizobium (α-rhizobia) and Cupriavidus (β-rhizobia) were also isolated, but in smaller proportions. Multilocus sequence analysis and BOX-PCR analyses indicated that six clusters of Paraburkholderia represent potential new species. In the phylogenetic analysis of the nodC gene, the majority of the strains were positioned in the same groups as in the 16S rRNA-recA tree, indicative of stability and vertical inheritance, but we also identified horizontal transfer of nodC in Pa. sabiae. All α- and β-rhizobial species were trapped by both legumes, although preferences of the host plants for specific rhizobial species have been observed.
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Affiliation(s)
- Rebeca Fuzinatto Dall'Agnol
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil.,Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, 86057-970, Londrina, PR, Brazil.,IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France
| | - Caroline Bournaud
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,Embrapa Recursos Genéticos e Biotecnologia, LIMPP Laboratory, C.P. 02372, 70770-917, Brasília, DF, Brazil
| | | | - Gilles Béna
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Mariangela Hungria
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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Biogeographical Patterns of Legume-Nodulating Burkholderia spp.: from African Fynbos to Continental Scales. Appl Environ Microbiol 2016; 82:5099-115. [PMID: 27316955 DOI: 10.1128/aem.00591-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Rhizobia of the genus Burkholderia have large-scale distribution ranges and are usually associated with South African papilionoid and South American mimosoid legumes, yet little is known about their genetic structuring at either local or global geographic scales. To understand variation at different spatial scales, from individual legumes in the fynbos (South Africa) to a global context, we analyzed chromosomal (16S rRNA, recA) and symbiosis (nifH, nodA, nodC) gene sequences. We showed that the global diversity of nodulation genes is generally grouped according to the South African papilionoid or South American mimosoid subfamilies, whereas chromosomal sequence data were unrelated to biogeography. While nodulation genes are structured on a continental scale, a geographic or host-specific distribution pattern was not detected in the fynbos region. In host range experiments, symbiotic promiscuity of Burkholderia tuberum STM678(T) and B phymatum STM815(T) was discovered in selected fynbos species. Finally, a greenhouse experiment was undertaken to assess the ability of mimosoid (Mimosa pudica) and papilionoid (Dipogon lignosus, Indigofera filifolia, Macroptilium atropurpureum, and Podalyria calyptrata) species to nodulate in South African (fynbos) and Malawian (savanna) soils. While the Burkholderia-philous fynbos legumes (D lignosus, I filifolia, and P calyptrata) nodulated only in their native soils, the invasive neotropical species M pudica did not develop nodules in the African soils. The fynbos soil, notably rich in Burkholderia, seems to retain nodulation genes compatible with the local papilionoid legume flora but is incapable of nodulating mimosoid legumes that have their center of diversity in South America. IMPORTANCE This study is the most comprehensive phylogenetic assessment of root-nodulating Burkholderia and investigated biogeographic and host-related patterns of the legume-rhizobial symbiosis in the South African fynbos biome, as well as at global scales, including native species from the South American Caatinga and Cerrado biomes. While a global investigation of the rhizobial diversity revealed distinct nodulation and nitrogen fixation genes among South African and South American legumes, regionally distributed species in the Cape region were unrelated to geographic and host factors.
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De Meyer SE, Briscoe L, Martínez-Hidalgo P, Agapakis CM, de-Los Santos PE, Seshadri R, Reeve W, Weinstock G, O'Hara G, Howieson JG, Hirsch AM. Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:609-619. [PMID: 27269511 DOI: 10.1094/mpmi-05-16-0091-r] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.
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Affiliation(s)
- Sofie E De Meyer
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Leah Briscoe
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
| | | | - Christina M Agapakis
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
| | - Paulina Estrada de-Los Santos
- 3 Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas. Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, México
| | | | - Wayne Reeve
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - George Weinstock
- 5 The Jackson Laboratory for Genomic Medicine, Farmington, CT, U.S.A; and
| | - Graham O'Hara
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John G Howieson
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ann M Hirsch
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
- 6 The Molecular Biology Institute, UCLA, Los Angeles, CA, U.S.A
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Dall'Agnol RF, Plotegher F, Souza RC, Mendes IC, Dos Reis Junior FB, Béna G, Moulin L, Hungria M. Paraburkholderia nodosa is the main N2-fixing species trapped by promiscuous common bean (Phaseolus vulgaris L.) in the Brazilian 'Cerradão'. FEMS Microbiol Ecol 2016; 92:fiw108. [PMID: 27199345 DOI: 10.1093/femsec/fiw108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 11/14/2022] Open
Abstract
The bacterial genus Burkholderia comprises species occupying several habitats, including a group of symbionts of leguminous plants-also called beta-rhizobia-that has been recently ascribed to the new genus Paraburkholderia We used common bean (Phaseolus vulgaris L.) plants to trap rhizobia from an undisturbed soil of the Brazilian Cerrado under the vegetation type 'Cerradão'. Genetic characterization started with the analyses of 181 isolates by BOX-PCR, where the majority revealed unique profiles, indicating high inter- and intra-species diversity. Restriction fragment length polymorphism-PCR of the 16S rRNA of representative strains of the BOX-PCR groups indicated two main clusters, and gene-sequencing analysis identified the minority (27%) as Rhizobium and the majority (73%) as Paraburkholderia Phylogenetic analyses of the 16S rRNA and housekeeping (recA and gyrB) genes positioned all strains of the second cluster in the species P. nodosa, and the phylogeny of a symbiotic gene-nodC-was in agreement with the conserved genes. All isolates were stable vis-à-vis nodulating common bean, but, in general, with a low capacity for fixing N2, although some effective strains were identified. The predominance of P. nodosa might be associated with the edaphic properties of the Cerrado biome, and might represent an important role in terms of maintenance of the ecosystem, which is characterized by acid soils with high saturation of aluminum and low N2 content.
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Affiliation(s)
- Rebeca F Dall'Agnol
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, PR, Brazil
| | - Fábio Plotegher
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil
| | - Renata C Souza
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990, Curitiba, PR, Brazil
| | - Iêda C Mendes
- Department of Soil Microbiology, Embrapa Cerrados, C.P. 08223, 73301-970, Planaltina, DF, Brazil
| | - Fábio B Dos Reis Junior
- Department of Soil Microbiology, Embrapa Cerrados, C.P. 08223, 73301-970, Planaltina, DF, Brazil
| | - Gilles Béna
- IRD, Cirad, University of Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, University of Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Mariangela Hungria
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990, Curitiba, PR, Brazil
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Novel Cupriavidus Strains Isolated from Root Nodules of Native Uruguayan Mimosa Species. Appl Environ Microbiol 2016; 82:3150-3164. [PMID: 26994087 DOI: 10.1128/aem.04142-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/11/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found. IMPORTANCE With the aim of exploring the diversity of rhizobia associated with native Mimosa species, symbionts were isolated from root nodules on five Mimosa species that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genus Mimosa, Brazil and Mexico, where it is mainly associated with Burkholderia and Rhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genus Cupriavidus Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic species C. taiwanensis, but instead they were related to other Cupriavidus species such as C. necator and C. pinatubonensis These data suggest the existence of a higher diversity within beta-rhizobial Cupriavidus than was previously suspected, and that Mimosa spp. from Sierra del Abra de Zabaleta, may be natural reservoirs for novel rhizobia.
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25
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Le Roux JJ, Mavengere NR, Ellis AG. The structure of legume-rhizobium interaction networks and their response to tree invasions. AOB PLANTS 2016; 8:plw038. [PMID: 27255514 PMCID: PMC4940501 DOI: 10.1093/aobpla/plw038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/07/2016] [Indexed: 05/09/2023]
Abstract
Establishing mutualistic interactions in novel environments is important for the successful establishment of some non-native plant species. These associations may, in turn, impact native species interaction networks as non-natives become dominant in their new environments. Using phylogenetic and ecological interaction network approaches we provide the first report of the structure of belowground legume-rhizobium interaction networks and how they change along a gradient of invasion (uninvaded, semi invaded and heavily invaded sites) by Australian Acacia species in South Africa's Cape Floristic Region. We found that native and invasive legumes interact with distinct rhizobial lineages, most likely due to phylogenetic uniqueness of native and invasive host plants. Moreover, legume-rhizobium interaction networks are not nested, but significantly modular with high levels of specialization possibly as a result of legume-rhizobium co-evolution. Although network topology remained constant across the invasion gradient, composition of bacterial communities associated with native legumes changed dramatically as acacias increasingly dominated the landscape. In stark contrast to aboveground interaction networks (e.g. pollination and seed dispersal) we show that invasive legumes do not infiltrate existing native legume-rhizobium networks but rather form novel modules. This absence of mutualist overlap between native and invasive legumes suggests the importance of co-invading rhizobium-acacia species complexes for Acacia invasion success, and argues against a ubiquitous role for the formation and evolutionary refinement of novel interactions.
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Affiliation(s)
- Johannes J Le Roux
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
| | - Natasha R Mavengere
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
| | - Allan G Ellis
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
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Sheu SY, Chen MH, Liu WYY, Andrews M, James EK, Ardley JK, De Meyer SE, James TK, Howieson JG, Coutinho BG, Chen WM. Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia. Int J Syst Evol Microbiol 2015; 65:4716-4723. [DOI: 10.1099/ijsem.0.000639] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven strains, ICMP 19430T, ICMP 19429, ICMP 19431, WSM4637, WSM4638, WSM4639 and WSM4640, were isolated from nitrogen-fixing nodules on roots of the invasive South African legume Dipogon lignosus (subfamily Papilionoideae, tribe Phaseoleae) in New Zealand and Western Australia, and their taxonomic positions were investigated by using a polyphasic approach. All seven strains grew at 10–37 °C (optimum, 25–30 °C), at pH 4.0–9.0 (optimum, pH 6.0–7.0) and with 0–2 % (w/v) NaCl (optimum growth in the absence of NaCl). On the basis of 16S rRNA gene sequence analysis, the strains showed 99.0–99.5 % sequence similarity to the closest type strain, Burkholderia phytofirmans PsJNT, and 98.4–99.7 % sequence similarity to Burkholderia caledonica LMG 19076T. The predominant fatty acids were C18 : 1ω7c (21.0 % of the total fatty acids in strain ICMP 19430T), C16 : 0 (19.1 %), C17 : 0 cyclo (18.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.7 %) and C19 : 0 cyclo ω8c (7.5 %). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was Q-8 and the DNA G+C content of strain ICMP 19430T was 63.2 mol%. The DNA–DNA relatedness of the novel strains with respect to the closest neighbouring members of the genus Burkholderia was 55 % or less. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data, these strains represent a novel symbiotic species in the genus Burkholderia, for which the name Burkholderia dipogonis sp. nov. is proposed, with the type strain ICMP 19430T ( = LMG 28415T = HAMBI 3637T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Ming-Hui Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Wendy Y. Y. Liu
- Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Mitchell Andrews
- Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Euan K. James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Julie K. Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Sofie E. De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | | | - John G. Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Bruna G. Coutinho
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan
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Jiao YS, Liu YH, Yan H, Wang ET, Tian CF, Chen WX, Guo BL, Chen WF. Rhizobial Diversity and Nodulation Characteristics of the Extremely Promiscuous Legume Sophora flavescens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1338-1352. [PMID: 26389798 DOI: 10.1094/mpmi-06-15-0141-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In present study, we report our extensive survey on the diversity and biogeography of rhizobia associated with Sophora flavescens, a sophocarpidine (matrine)-containing medicinal legume. We additionally investigated the cross nodulation, infection pattern, light and electron microscopies of root nodule sections of S. flavescens infected by various rhizobia. Seventeen genospecies of rhizobia belonging to five genera with seven types of symbiotic nodC genes were found to nodulate S. flavescens in natural soils. In the cross-nodulation tests, most representative rhizobia in class α-Proteobacteria, whose host plants belong to different cross-nodulation groups, form effective indeterminate nodules, while representative rhizobia in class β-Proteobacteria form ineffective nodules on S. flavescens. Highly host-specific biovars of Rhizobium leguminosarum (bv. trifolii and bv. viciae) and Rhizobium etli bv. phaseoli could establish symbioses with S. flavescens, providing further evidence that S. flavescens is an extremely promiscuous legume and it does not have strict selectivity on either the symbiotic genes or the species-determining housekeeping genes of rhizobia. Root-hair infection is found as the pattern that rhizobia have gained entry into the curled root hairs. Electron microscopies of ultra-thin sections of S. flavescens root nodules formed by different rhizobia show that the bacteroids are regular or irregular rod shape and nonswollen types. Some bacteroids contain poly-β-hydroxybutyrate (PHB), while others do not, indicating the synthesis of PHB in bacteroids is rhizobia-dependent. The extremely promiscuous symbiosis between S. flavescens and different rhizobia provide us a basis for future studies aimed at understanding the molecular interactions of rhizobia and legumes.
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Affiliation(s)
- Yin Shan Jiao
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Yuan Hui Liu
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Hui Yan
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Chang Fu Tian
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Wen Xin Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Bao Lin Guo
- 3 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Wen Feng Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
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Lemaire B, Van Cauwenberghe J, Verstraete B, Chimphango S, Stirton C, Honnay O, Smets E, Sprent J, James EK, Muasya AM. Characterization of the papilionoid-Burkholderia interaction in the Fynbos biome: The diversity and distribution of beta-rhizobia nodulating Podalyria calyptrata (Fabaceae, Podalyrieae). Syst Appl Microbiol 2015; 39:41-8. [PMID: 26689612 DOI: 10.1016/j.syapm.2015.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 02/04/2023]
Abstract
The South African Fynbos soils are renowned for nitrogen-fixing Burkholderia associated with diverse papilionoid legumes of the tribes Crotalarieae, Hypocalypteae, Indigofereae, Phaseoleae and Podalyrieae. However, despite numerous rhizobial studies in the region, the symbiotic diversity of Burkholderia has not been investigated in relation to a specific host legume and its geographical provenance. This study analyzed the diversity of nodulating strains of Burkholderia from the legume species Podalyria calyptrata. Diverse lineages were detected that proved to be closely related to Burkholderia taxa, originating from hosts in other legume tribes. By analyzing the genetic variation of chromosomal (recA) and nodulation (nodA) sequence data in relation to the sampling sites we assessed the geographical distribution patterns of the P. calyptrata symbionts. Although we found a degree of genetically differentiated rhizobial populations, a correlation between genetic (recA and nodA) and geographic distances among populations was not observed, suggesting high rates of dispersal and rhizobial colonization within Fynbos soils.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa; Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 2435, 3001 Heverlee, Belgium.
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 2435, 3001 Heverlee, Belgium
| | | | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 2435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 2435, 3001 Heverlee, Belgium; Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, The Netherlands
| | - Janet Sprent
- Division of Plant Sciences, University of Dundee at JHI, Dundee DD2 5DA, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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Lemaire B, Van Cauwenberghe J, Chimphango S, Stirton C, Honnay O, Smets E, Muasya AM. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome. FEMS Microbiol Ecol 2015; 91:fiv118. [PMID: 26433010 DOI: 10.1093/femsec/fiv118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, the Netherlands
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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31
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Lemaire B, Dlodlo O, Chimphango S, Stirton C, Schrire B, Boatwright JS, Honnay O, Smets E, Sprent J, James EK, Muasya AM. Symbiotic diversity, specificity and distribution of rhizobia in native legumes of the Core Cape Subregion (South Africa). FEMS Microbiol Ecol 2014; 91:1-17. [DOI: 10.1093/femsec/fiu024] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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