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Claassens R, Venter SN, Beukes CW, Stępkowski T, Chan WY, Steenkamp ET. Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa. Syst Appl Microbiol 2023; 46:126452. [PMID: 37634485 DOI: 10.1016/j.syapm.2023.126452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.
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Affiliation(s)
- Ricu Claassens
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | | | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa; Right to Care, Centurion, Gauteng, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa.
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Klepa MS, Helene LCF, O´Hara G, Hungria M. Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium
is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains – CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T – previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the
Bradyrhizobium elkanii
supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes – atpD, dnaK, glnII, gyrB, recA and rpoB – did not cluster the strains under study as conspecific to any described
Bradyrhizobium
species. Average nucleotide identity and digital DNA–DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed
Bradyrhizobium
species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.
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Affiliation(s)
- Milena Serenato Klepa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Graham O´Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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Adjei JA, Aserse AA, Yli-Halla M, Ahiabor BDK, Abaidoo RC, Lindstrom K. Phylogenetically diverse Bradyrhizobium genospecies nodulate Bambara groundnut (Vigna subterranea L. Verdc) and soybean (Glycine max L. Merril) in the northern savanna zones of Ghana. FEMS Microbiol Ecol 2022; 98:fiac043. [PMID: 35404419 PMCID: PMC9329091 DOI: 10.1093/femsec/fiac043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A total of 102 bacterial strains isolated from nodules of three Bambara groundnut and one soybean cultivars grown in nineteen soil samples collected from northern Ghana were characterized using multilocus gene sequence analysis. Based on a concatenated sequence analysis (glnII-rpoB-recA-gyrB-atpD-dnaK), 54 representative strains were distributed in 12 distinct lineages, many of which were placed mainly in the Bradyrhizobium japonicum and Bradyrhizobium elkanii supergroups. Twenty-four of the 54 representative strains belonged to seven putative novel species, while 30 were conspecific with four recognized Bradyrhizobium species. The nodA phylogeny placed all the representative strains in the cosmopolitan nodA clade III. The strains were further separated in seven nodA subclusters with reference strains mainly of African origin. The nifH phylogeny was somewhat congruent with the nodA phylogeny, but both symbiotic genes were mostly incongruent with the core housekeeping gene phylogeny indicating that the strains acquired their symbiotic genes horizontally from distantly related Bradyrhizobium species. Using redundancy analysis, the distribution of genospecies was found to be influenced by the edaphic factors of the respective sampling sites. In general, these results mainly underscore the high genetic diversity of Bambara groundnut-nodulating bradyrhizobia in Ghanaian soils and suggest a possible vast resource of adapted inoculant strains.
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Affiliation(s)
- Josephine A Adjei
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Aregu A Aserse
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Markku Yli-Halla
- Department of Agricultural Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Benjamin D K Ahiabor
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Robert C Abaidoo
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Kristina Lindstrom
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
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Distribution and biodiversity of rhizobia nodulating Chamaecrista mimosoides in the Shandong peninsula of china. Syst Appl Microbiol 2021; 45:126280. [PMID: 34864282 DOI: 10.1016/j.syapm.2021.126280] [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: 08/07/2021] [Revised: 11/05/2021] [Accepted: 11/14/2021] [Indexed: 10/19/2022]
Abstract
Chamaecrista mimosoides is an annual herb legume widely distributed in tropical and subtropical Asia and Africa. It may have primitive and independently-evolved root nodule types but its rhizobia have not been systematically studied. Therefore, in order to learn the diversity and species affinity of its rhizobia, root nodules were sampled from C. mimosoides plants growing in seven geographical sites along the coast line of Shandong Peninsula, China. A total of 422 rhizobial isolates were obtained from nodules, and they were classified into 28 recA haplotypes. By using multilocus sequence analysis of the concatenated housekeeping genes dnaK, glnII, gyrB, recA and rpoB, the representative strains for these haplotypes were designated as eight defined and five candidate novel genospecies in the genus Bradyrhizobium. Bradyrhizobium elkanii and Bradyrhizobium ferriligni were predominant and universally distributed. The symbiotic genes nodC and nifH of the representative strains showed very similar topology in their phylogenetic trees indicating their co-evolution history. All the representative strains formed effective root nodules in nodulation tests. The correlation between genospecies and soil characteristics analyzed by CANOCO software indicated that available potassium (AK), organic carbon (OC) and available nitrogen (AN) in the soil samples were the main factors affecting the distribution of the symbionts involved in this current study. The study is the first systematic survey of Chamaecrista mimosoides-nodulating rhizobia, and it showed that Chamaecrista spp. were nodulated by bradyrhizobia in natural environments. In addition, the host spectrum of the corresponding rhizobial species was extended, and the study provided novel information on the biodiversity and biogeography of rhizobia.
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5
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Tasiya T, van Zyl E, Coetzee MPA, Stepkowski T, Venter SN, Steenkamp ET. Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns. Mol Phylogenet Evol 2021; 167:107338. [PMID: 34757168 DOI: 10.1016/j.ympev.2021.107338] [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: 07/29/2021] [Revised: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321T and Bradyrhizobium ivorense CI-1BT, while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BBT (SARCC 730T = LMG 31409T), Bradyrhizobium oropedii sp. nov. Pear76T (SARCC 731T = LMG 31408T), and Bradyrhizobium altum sp. nov. Pear77T (SARCC 754T = LMG 31407T) to accommodate three novel species, all of which are symbionts of legumes in South Africa.
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Affiliation(s)
- Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa
| | - Taponeswa Tasiya
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stepkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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6
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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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Culture-independent assessment of the diazotrophic Bradyrhizobium communities in the Pampa and Atlantic Forest Biomes localities in southern Brazil. Syst Appl Microbiol 2021; 44:126228. [PMID: 34265499 DOI: 10.1016/j.syapm.2021.126228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communities inhabiting soils in southern Brazil. The majority of nifD sequences were generated from DNA isolated from tropical-lowland pasture soils, although some soil samples originated from the Campos de Cima da Serra volcanic plateau. In the nifD tree, all the bradyrhizobial sequences comprised 38 clades, including 18 new clades. The sequences generated in this study were resolved into 22 clades and 21 singletons. The nifD bradyrhizobial assemblage contained Azorhizobium and α-proteobacterial methylotrophic genera, suggesting that these genera may have acquired their nif loci from Bradyrhizobium donors. The most common in the lowland pasture soils subclade III.3D branch comprises the isolates of mainly an American origin. On the other hand, subclade III.4, which was earlier detected in Brazil among Bradyrhizobium isolates nodulating native lupins, appears more common in the Campos de Cima da Serra soils. The second-largest group, Clade XXXVIII, has not yet been reported in culture-dependent studies, while another common group called Clade I represents a symbiovar predominating in Australia. The identification of the diverse nifD Clade I haplotypes in the tropical-lowland pastures infested by Australian Acacia spp implies that the introduction of these legumes to southern Brazil has resulted in the dissemination of their bradyrhizobial symbionts.
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Soto-Valenzuela JO, Ormeño-Orrillo E, Zúñiga-Dávila D. Diversidad de rizobios y fijación biológica de nitrógeno en aislados de Clitoria brachystegia, en remanentes de bosque seco tropical de Ecuador y Perú. REV MEX BIODIVERS 2021. [DOI: 10.22201/ib.20078706e.2021.92.3426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Banasiewicz J, Granada CE, Lisboa BB, Grzesiuk M, Matuśkiewicz W, Bałka M, Schlindwein G, Vargas LK, Passaglia LMP, Stępkowski T. Diversity and phylogenetic affinities of Bradyrhizobium isolates from Pampa and Atlantic Forest Biomes. Syst Appl Microbiol 2021; 44:126203. [PMID: 33857759 DOI: 10.1016/j.syapm.2021.126203] [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: 12/02/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
In this work, we investigated Bradyrhizobium strains isolated from soils collected from the rhizosphere of native and exotic legumes species inhabiting two ecoclimatic zones - asubtropical-lowland pasture (Pampa Biome) and a volcanic plateau covered by Araucaria Moist Forests (Atlantic Forest Biome). The rhizobial strains were isolated from the nodules of seven native and one exotic legume species used as rhizobium traps. Single-gene (recA, glnII, dnaK) and combined-gene MLSA analyses (dnaK-glnII-gyrB-recA-rpoB) revealed that nearly 85% of the isolates clustered in B. elkanii supergroup, while the remaining (except for two isolates) in B. japonicum supergroup, albeit, in most cases, separately from the type strains of Bradyrhizobium species. As a symbiotic gene marker, a portion of nifD gene was sequenced for 194 strains. In the nifD-tree, an American branch III.3D (104 isolates), was the most numerous among the isolates. A significant portion of the isolates clustered in American groups; subclade III.4 (40 strains), Clade VII (3 strains), and a new Clade XX (4 strains). Most of the remaining strains belonged to a pantropical III.3C branch (39 isolates). On the other hand, identification of isolates belonging, respectively, to Clade I and Clade II may result of spreading of the Australian (Clade I) and European (Clade II) bradyrhizobia following the introduction of their legume hosts. Our study indicated that the American groups predominated in the symbiotic Bradyrhizobium communities in southern Brazil. However, there is a significant component of exotic lineages, resulting from the dispersal of pantropical Fabaceae taxa and the introduction of exotic legumes.
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Affiliation(s)
- Joanna Banasiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Camille E Granada
- Universidade do Vale do Taquari - UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil
| | - Bruno B Lisboa
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Małgorzata Grzesiuk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Weronika Matuśkiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Mateusz Bałka
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Gilson Schlindwein
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciano K Vargas
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul., Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
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10
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Ramoneda J, Roux JJL, Frossard E, Frey B, Gamper HA. Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop. FEMS Microbiol Ecol 2021; 96:5874250. [PMID: 32691840 DOI: 10.1093/femsec/fiaa145] [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: 01/16/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
There is interest in understanding how cultivation, plant genotype, climate and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities can be revealed, which is of particular interest for bacteria such as rhizobia. Here, we determined the structure of root nodule bacterial communities of rooibos (Aspalathus linearis), a leguminous shrub endemic to South Africa. We related the community dissimilarities of the root nodule bacteria of 18 paired cultivated and wild rooibos populations to pairwise geographical distances, plant ecophysiological characteristics and soil physicochemical parameters. Using next-generation sequencing data, we identified region-, cultivation- and farm-specific operational taxonomic units for four distinct classes of root nodule bacterial communities, dominated by members of the genus Mesorhizobium. We found that while bacterial richness was locally increased by organic cultivation, strong biogeographical differentiation in the bacterial communities of wild rooibos disappeared with cultivation of one single cultivar across its entire cultivation range. This implies that expanding rooibos farming has the potential to endanger wild rooibos populations through the homogenisation of root nodule bacterial diversity.
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Affiliation(s)
- Josep Ramoneda
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Johannes J Le Roux
- Department of Biological Sciences, Macquarie University, Balaclava Rd, Macquarie Park NSW 2109, Sydney, Australia
| | - Emmanuel Frossard
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hannes Andres Gamper
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland.,Faculty of Science and Technology, Free University of Bolzen-Bolzano, Piazza Università, 1, 39100 Bolzano BZ, Italy
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11
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Ramoneda J, Le Roux JJ, Frossard E, Frey B, Gamper HA. Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop. FEMS Microbiol Ecol 2020; 96:5828728. [PMID: 32364226 DOI: 10.1093/femsec/fiaa083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.
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Affiliation(s)
- Josep Ramoneda
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Johannes J Le Roux
- Department of Biological Sciences, Macquarie University, Balaclava Rd, Macquarie Park NSW 2109, Sydney, Australia
| | - Emmanuel Frossard
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hannes Andres Gamper
- Faculty of Science and Technology, Free University of Bolzen-Bolzano,Piazza Università, 1, 39100 Bolzano BZ, Italy
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12
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Cabral Michel D, Martins da Costa E, Azarias Guimarães A, Soares de Carvalho T, Santos de Castro Caputo P, Willems A, de Souza Moreira FM. Bradyrhizobium campsiandrae sp. nov., a nitrogen-fixing bacterial strain isolated from a native leguminous tree from the Amazon adapted to flooded conditions. Arch Microbiol 2020; 203:233-240. [PMID: 32857180 DOI: 10.1007/s00203-020-02022-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/23/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023]
Abstract
The nitrogen-fixing bacterial strain UFLA 01-1174T was isolated from nodules of Campsiandra laurilifolia Benth. originating from the Amazon region, Brazil. Its taxonomic position was defined using a polyphasic approach. Analysis of the 16S rRNA gene placed the strain in the Bradyrhizobium genus, the closest species being B. guangdongense CCBAU 51649T and B. guangzhouense CCBAU 51670T, both with 99.8% similarity. Multilocus sequence analysis (MLSA) of recA, gyrB, glnII, rpoB, atpD, and dnaK indicated that UFLA 01-1174T is a new species, most closely related to B. stylosanthis BR 446T (94.4%) and B. manausense BR 3351T (93.7%). Average nucleotide identity (ANI) differentiated UFLA 01-1174T from the closest species with values lower than 90%. The G + C content in the DNA of UFLA 01-1174T is 63.6 mol%. Based on this data, we conclude that the strain represents a new species. The name proposed is Bradyrhizobium campsiandrae, with UFLA 01-1174T (= INPA 394BT = LMG 10099T) as type strain.
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Affiliation(s)
- Daniele Cabral Michel
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Elaine Martins da Costa
- Universidade Federal Do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | - Amanda Azarias Guimarães
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Teotonio Soares de Carvalho
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Polyane Santos de Castro Caputo
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fatima Maria de Souza Moreira
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil.
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13
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Symbiotic, phenotypic and genotypic characterization of Bradyrhizobium sp. nodulating Spartium junceum L. from Bejaia, northeastern Algeria. Symbiosis 2020. [DOI: 10.1007/s13199-020-00679-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Boudehouche W, Parker MA, Boulila F. Relationships of Bradyrhizobium strains nodulating three Algerian Genista species. Syst Appl Microbiol 2020; 43:126074. [PMID: 32169316 DOI: 10.1016/j.syapm.2020.126074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
The Mediterranean world is the cradle for the diversification of a large number of plant species, including legumes belonging to the Tribe Genisteae. Nodule bacteria from three species of Genista legumes indigenous to northwestern Africa (G. ferox, G. numidica, G. tricuspidata) were sampled across a 150km region of Algeria in order to investigate symbiotic relationships. Partial 23S rRNA sequences from 107 isolates indicated that Bradyrhizobium was the predominant symbiont genus (96% of isolates), with the remainder belonging to Rhizobium or Mesorhizobium. A multilocus sequence analysis on 46 Bradyrhizobium strains using seven housekeeping (HK) genes showed that strains were differentiated into multiple clades with affinities to seven species: B. canariense (17 isolates), B. japonicum (2), B. ottawaense (2), B. cytisi/B. rifense (9), 'B. valentinum' (5), and B. algeriense (11). Extensive discordance between the HK gene phylogeny and a tree for four loci in the symbiosis island (SI) region implied that horizontal transfer of SI loci has been common. Cases of close symbiont relationship across pairs of legumes hosts were evident, with 33% of isolates having as their closest relative a strain sampled from a different Genista species. Nevertheless, tree permutation tests also showed that there was substantial host-related phylogenetic clustering. Thus, each of the three Genista hosts utilized a measurably different array of bacterial lineages.
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Affiliation(s)
- Wafa Boudehouche
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
| | - Matthew A Parker
- Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Farida Boulila
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
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15
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Abstract
AbstractWe isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.
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16
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol 2019; 42:427-439. [PMID: 31031014 DOI: 10.1016/j.syapm.2019.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023]
Abstract
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels.
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Affiliation(s)
- Juanita R Avontuur
- 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
| | - Chrizelle W Beukes
- 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 0110, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Poland
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - 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. http://emma.steenkamp.up.ac.za
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17
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Jaiswal SK, Dakora FD. Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa. Front Microbiol 2019; 10:310. [PMID: 30853952 PMCID: PMC6395442 DOI: 10.3389/fmicb.2019.00310] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/05/2019] [Indexed: 11/17/2022] Open
Abstract
Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
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18
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Grönemeyer JL, Reinhold-Hurek B. Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource. Front Microbiol 2018; 9:2194. [PMID: 30294308 PMCID: PMC6158577 DOI: 10.3389/fmicb.2018.02194] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023] Open
Abstract
Making use of biological nitrogen fixation (BNF) with pulses and green manure legumes can help to alleviate nitrogen deficiencies and increase soil fertility, problems faced particularly in smallholder agriculture in Subsahara Africa (SSA). The isolation of indigenous rhizobia provides a basis for the formulation of rhizobial inoculants. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Here we discuss global species discovery of Bradyrhizobium spp. Although recently the number of validly published Bradyrhizobium species is rapidly increasing, their diversity in SSA is not well-represented. We summarize the recent knowledge on species diversity in the Bradyrhizobium yuanmingense lineage to which most SSA isolates belong, and their biogeographic distribution and adaptations. Most indigenous rhizobia appear to differ from species found on other continents. We stress that an as yet hidden diversity may be a rich resource for inoculant development in future. As some species are exceptionally temperature tolerant, they may be potential biofertilizer candidates for global warming scenarios.
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Affiliation(s)
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, Center for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
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19
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Rathi S, Tak N, Bissa G, Chouhan B, Ojha A, Adhikari D, Barik SK, Satyawada RR, Sprent JI, James EK, Gehlot HS. Selection of Bradyrhizobium or Ensifer symbionts by the native Indian caesalpinioid legume Chamaecrista pumila depends on soil pH and other edaphic and climatic factors. FEMS Microbiol Ecol 2018; 94:5089966. [DOI: 10.1093/femsec/fiy180] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/01/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sonam Rathi
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Nisha Tak
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Garima Bissa
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Bhawana Chouhan
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Archana Ojha
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Dibyendu Adhikari
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Saroj K Barik
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Rama Rao Satyawada
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Janet I Sprent
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hukam S Gehlot
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
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20
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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21
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Dludlu MN, Chimphango SBM, Stirton CH, Muasya AM. Differential Preference of Burkholderia and Mesorhizobium to pH and Soil Types in the Core Cape Subregion, South Africa. Genes (Basel) 2017; 9:genes9010002. [PMID: 29271943 PMCID: PMC5793155 DOI: 10.3390/genes9010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/02/2022] Open
Abstract
Over 760 legume species occur in the ecologically-heterogeneous Core Cape Subregion (CCR) of South Africa. This study tested whether the main symbionts of CCR legumes (Burkholderia and Mesorhizobium) are phylogenetically structured by altitude, pH and soil types. Rhizobial strains were isolated from field nodules of diverse CCR legumes and sequenced for 16S ribosomic RNA (rRNA), recombinase A (recA) and N-acyltransferase (nodA). Phylogenetic analyses were performed using Bayesian and maximum likelihood techniques. Phylogenetic signals were determined using the D statistic for soil types and Pagel’s λ for altitude and pH. Phylogenetic relationships between symbionts of the narrowly-distributed Indigofera superba and those of some widespread CCR legumes were also determined. Results showed that Burkholderia is restricted to acidic soils, while Mesorhizobium occurs in both acidic and alkaline soils. Both genera showed significant phylogenetic clustering for pH and most soil types, but not for altitude. Therefore, pH and soil types influence the distribution of Burkholderia and Mesorhizobium in the CCR. All strains of Indigofera superba were identified as Burkholderia, and they were nested within various clades containing strains from outside its distribution range. It is, therefore, hypothesized that I. superba does not exhibit rhizobial specificity at the intragenic level. Implications for CCR legume distributions are discussed.
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Affiliation(s)
- Meshack Nkosinathi Dludlu
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa.
| | - Samson B M Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa.
| | - Charles H Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa.
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa.
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22
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Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindström K. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11 T and Bradyrhizobium yuanmingense CCBAU 10071 T. Stand Genomic Sci 2017; 12:74. [PMID: 29225730 PMCID: PMC5717998 DOI: 10.1186/s40793-017-0283-x] [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: 08/29/2017] [Accepted: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain 10.1601/nm.1463 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of 10.1601/nm.24498 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T. The genes encoding for nodulation and nitrogen fixation in ERR11T showed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating 10.1601/nm.27386 10.1601/strainfinder?urlappend=%3Fid%3DLMG+26795 T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T are organized in a similar way to the homologous genes identified in the genomes of 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T, 10.1601/nm.25806 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/nm.1462 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11T also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the 10.1601/nm.25806 branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to 10.1601/nm.25806 branch (10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 (58.5%), followed by 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 or 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11T is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of 10.1601/nm.30737 sp. nov. with strain ERR11T (10.1601/strainfinder?urlappend=%3Fid%3DHAMBI+3532 T=10.1601/strainfinder?urlappend=%3Fid%3DLMG+30162 T) as the type strain.
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Affiliation(s)
- Aregu Amsalu Aserse
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - William B Whitman
- Department of Microbiology, Biological Sciences, University of Georgia, Athens, USA
| | - Kristina Lindström
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
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Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland. Syst Appl Microbiol 2017; 40:482-491. [DOI: 10.1016/j.syapm.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/24/2017] [Accepted: 09/20/2017] [Indexed: 01/27/2023]
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