1
|
Young JPW, Moeskjær S, Afonin A, Rahi P, Maluk M, James EK, Cavassim MIA, Rashid MHO, Aserse AA, Perry BJ, Wang ET, Velázquez E, Andronov EE, Tampakaki A, Flores Félix JD, Rivas González R, Youseif SH, Lepetit M, Boivin S, Jorrin B, Kenicer GJ, Peix Á, Hynes MF, Ramírez-Bahena MH, Gulati A, Tian CF. Defining the Rhizobium leguminosarum Species Complex. Genes (Basel) 2021; 12:111. [PMID: 33477547 PMCID: PMC7831135 DOI: 10.3390/genes12010111] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
Collapse
Affiliation(s)
| | - Sara Moeskjær
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Afonin
- Laboratory for Genetics of Plant-Microbe Interactions, ARRIAM, Pushkin, 196608 Saint-Petersburg, Russia;
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India;
| | - Marta Maluk
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; (M.M.); (E.K.J.)
| | - Euan K. James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; (M.M.); (E.K.J.)
| | - Maria Izabel A. Cavassim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - M. Harun-or Rashid
- Biotechnology Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh 2202, Bangladesh;
| | - Aregu Amsalu Aserse
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Benjamin J. Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad De México 11340, Mexico;
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain; (E.V.); (R.R.G.)
| | - Evgeny E. Andronov
- Department of Microbial Monitoring, ARRIAM, Pushkin, 196608 Saint-Petersburg, Russia;
| | - Anastasia Tampakaki
- Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece;
| | - José David Flores Félix
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal;
| | - Raúl Rivas González
- Departamento de Microbiología y Genética, Universidad de Salamanca, Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain; (E.V.); (R.R.G.)
| | - Sameh H. Youseif
- Department of Microbial Genetic Resources, National Gene Bank (NGB), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Marc Lepetit
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, 06903 Sophia Antipolis, France;
| | - Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR INRAE-IRD-CIRAD-UM2-SupAgro, Campus International de Baillarguet, TA-A82/J, CEDEX 05, 34398 Montpellier, France;
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK;
| | - Gregory J. Kenicer
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), 37008 Salamanca, Spain;
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
| | - Martha Helena Ramírez-Bahena
- Departamento de Didáctica de las Matemáticas y de las Ciencias Experimentales. Universidad de Salamanca, 37008 Salamanca, Spain;
| | - Arvind Gulati
- Microbial Prospection, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176 061, India;
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| |
Collapse
|
2
|
Youseif SH, Abd El-Megeed FH, Mohamed AH, Ageez A, Veliz E, Martínez-Romero E. Diverse Rhizobium strains isolated from root nodules of Trifolium alexandrinum in Egypt and symbiovars. Syst Appl Microbiol 2020; 44:126156. [PMID: 33232849 DOI: 10.1016/j.syapm.2020.126156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022]
Abstract
Berseem clover (T. alexandrinum) is the main forage legume crop used as animal feed in Egypt. Here, eighty rhizobial isolates were isolated from root nodules of berseem clover grown in different regions in Egypt and were grouped by RFLP-16S rRNA ribotyping. Representative isolates were characterized using phylogenetic analyses of the 16S rRNA, rpoB, glnA, pgi, and nodC genes. We also investigated the performance of these isolates using phenotypic tests and nitrogen fixation efficiency assays. The majority of strains (<90%) were closely related to Rhizobium aegyptiacum and Rhizobium aethiopicum and of the remaining strains, six belonged to the Rhizobium leguminosarum genospecies complex and only one strain was assigned to Agrobacterium fabacearum. Despite their heterogeneous chromosomal background, most of the strains shared nodC gene alleles corresponding to symbiovar trifolii. Some of the strains closely affiliated to R. aegyptiacum and R. aethiopicum had superior nodulation and nitrogen fixation capabilities in berseem clover, compared to the commercial inoculant (Okadein®) and N-added treatments. R. leguminosarum strain NGB-CR 17 that harbored a nodC allele typical of symbiovar viciae, was also able to form an effective symbiosis with clover. Two strains with nodC alleles of symbiovar trifolii, R. aegyptiacum strains NGB-CR 129 and 136, were capable of forming effective nodules in Phaseolus vulgaris in axenic greenhouse conditions. This adds the symbiovar trifolii which is well-established in the Egyptian soils to the list of symbiovars that form nodules in P. vulgaris.
Collapse
Affiliation(s)
- Sameh H Youseif
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt.
| | - Fayrouz H Abd El-Megeed
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Akram H Mohamed
- Department of Microbial Genetic Resources, National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Amr Ageez
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt; Faculty of Biotechnology, MSA University, 6 October City, Egypt
| | - Esteban Veliz
- Department of Plant Biology, University of California, Davis, Life Sciences Addition, 1 Shields Ave., Davis, CA, 95616, USA
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, UNAM Cuernavaca, Morelos, Mexico
| |
Collapse
|
3
|
El-Batanony NH, Castellano-Hinojosa A, Correa-Galeote D, Bedmar EJ. Phylogenetic diversity of bacterial strains from root nodules of legumes grown wild in Egypt. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
4
|
Rajnovic I, Ramírez-Bahena MH, Sánchez-Juanes F, González-Buitrago JM, Kajic S, Peix Á, Velázquez E, Sikora S. Phylogenetic diversity of rhizobia nodulating Phaseolus vulgaris in Croatia and definition of the symbiovar phaseoli within the species Rhizobium pisi. Syst Appl Microbiol 2019; 42:126019. [PMID: 31635886 DOI: 10.1016/j.syapm.2019.126019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/27/2022]
Abstract
Phaseolus vulgaris is a legume indigenous to America which is currently cultivated in Europe including countries located at the Southeast of this continent, such as Croatia, where several local landraces are cultivated, most of them of Andean origin. In this work we identify at species and symbiovar levels several fast-growing strains able to form effective symbiosis with P. vulgaris in different Croatian soils. The identification at species level based on MALDI-TOF MS and core gene sequence analysis showed that most of these strains belong to the species R. leguminosarum, R. hidalgonense and R. pisi. In addition, several strains belong to putative new species phylogenetically close to R. ecuadorense and R. sophoriradicis. All Croatian strains belong to the symbiovar phaseoli and harbour the α and γ nodC alleles typical for American strains of this symbiovar. Nevertheless, most of Croatian strains harboured the γ nodC gene allele supporting its Andean origin since it is also dominant in other European countries, where Andean cultivars of P. vulgaris are traditionally cultivated, as occurs in Spain. The only strains harbouring the α nodC allele belong to R. hidalgonense and R. pisi, this last only containing the symbiovars viciae and trifolii to date. This is the first report about the presence in Europe of the species R. hidalgonense, the nodulation of P. vulgaris by R. pisi and the existence of the symbiovar phaseoli within this species. These results significantly increase the knowledge of the biogeography of Rhizobium-P. vulgaris symbiosis.
Collapse
Affiliation(s)
- Ivana Rajnovic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | | | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - José-Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - Sanja Kajic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain.
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain; Departmento de Microbiología y Genética and CIALE, Universidad de Salamanca, Salamanca, Spain
| | - Sanja Sikora
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
5
|
Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines. Microbiol Resour Announc 2018; 7:MRA00903-18. [PMID: 30533911 PMCID: PMC6256449 DOI: 10.1128/mra.00903-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/24/2018] [Indexed: 11/20/2022] Open
Abstract
Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna, Philippines. Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna, Philippines. The 7.07-Mb complete genome comprises three replicons, one chromosome, and two plasmids, with a G+C content of 59.4% and 6,720 protein-coding genes. The genome encodes gene clusters supporting rhizosphere processes, plant symbiosis, and secondary bioactive metabolites.
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique. Appl Environ Microbiol 2018; 84:AEM.01712-17. [PMID: 29101189 PMCID: PMC5752868 DOI: 10.1128/aem.01712-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/19/2017] [Indexed: 11/22/2022] Open
Abstract
Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes. IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.
Collapse
|
8
|
Molecular diversity and phylogeny of indigenous Rhizobium leguminosarum strains associated with Trifolium repens plants in Romania. Antonie van Leeuwenhoek 2017; 111:135-153. [DOI: 10.1007/s10482-017-0934-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/20/2017] [Indexed: 11/30/2022]
|
9
|
Kutkowska J, Marek-Kozaczuk M, Wielbo J, Wójcik M, Urbanik-Sypniewska T. Electrophoretic profiles of lipopolysaccharides from Rhizobium strains nodulating Pisum sativum do not reflect phylogenetic relationships between these strains. Arch Microbiol 2017; 199:1011-1021. [PMID: 28386666 PMCID: PMC5548859 DOI: 10.1007/s00203-017-1374-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 11/03/2022]
Abstract
Rhizobia that nodulate peas comprise a heterogeneous group of bacteria. The aim of this study was to investigate the relationship between phylogeny and electrophoretic and hydroxy fatty acid lipopolysaccharide (LPS) profiles of pea microsymbionts. Based on amplified fragment length polymorphism (AFLP) fingerprinting data, the pea microsymbionts were grouped into two clusters distinguished at 58% similarity level. Based on the concatenated 16S rRNA, recA, and atpD housekeeping gene data, the microsymbionts appeared to be most closely related to Rhizobium leguminosarum biovars viciae and trifolii. Applying cluster analysis to their LPS electrophoretic profiles, the strains were assigned to two major groups with different banding patterns. All hydroxy fatty acids common to R. leguminosarum and R. etli were detected in each examined strain. Differences in the proportions of 3- to ω-1 hydroxy fatty acids allowed us to distinguish two groups of strains. This classification did not overlap with one based on LPS electrophoretic profiles. No clear correlation was apparent between the genetic traits and LPS profiles of the pea nodule isolates.
Collapse
Affiliation(s)
- Jolanta Kutkowska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Wójcik
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | | |
Collapse
|
10
|
Marek-Kozaczuk M, Wdowiak-Wróbel S, Kalita M, Chernetskyy M, Deryło K, Tchórzewski M, Skorupska A. Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens. Antonie van Leeuwenhoek 2017; 110:1729-1744. [PMID: 28791535 PMCID: PMC5676844 DOI: 10.1007/s10482-017-0922-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/29/2017] [Indexed: 11/28/2022]
Abstract
Trifolium rubens L., commonly known as the red feather clover, is capable of symbiotic interactions with rhizobia. Up to now, no specific symbionts of T. rubens and their symbiotic compatibility with Trifolium spp. have been described. We characterized the genomic diversity of T. rubens symbionts by analyses of plasmid profiles and BOX-PCR. The phylogeny of T. rubens isolates was inferred based on the nucleotide sequences of 16S rRNA and two core genes (atpD, recA). The nodC phylogeny allowed classification of rhizobia nodulating T. rubens as Rhizobium leguminosarum symbiovar trifolii (Rlt). The symbiotic efficiency of the Rlt isolates was determined on four clover species: T. rubens, T. pratense, T. repens and T. resupinatum. We determined that Rlt strains formed mostly inefficient symbiosis with their native host plant T. rubens and weakly effective (sub-optimal) symbiosis with T. repens and T. pratense. The same Rlt strains were fully compatible in the symbiosis with T. resupinatum. T. rubens did not exhibit strict selectivity in regard to the symbionts and rhizobia closely related to Rhizobium grahamii, Rhizobium galegae and Agrobacterium radiobacter, which did not nodulate Trifolium spp., were found amongst T. rubens nodule isolates.
Collapse
Affiliation(s)
- Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Mykhaylo Chernetskyy
- The Botanic Garden of Maria Curie-Skłodowska University, Sławinkowska 3, 20-810, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| |
Collapse
|
11
|
Jaiswal SK, Msimbira LA, Dakora FD. Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa. Syst Appl Microbiol 2017; 40:215-226. [PMID: 28372899 PMCID: PMC5460907 DOI: 10.1016/j.syapm.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/05/2017] [Accepted: 02/12/2017] [Indexed: 11/30/2022]
Abstract
Groundnut is an economically important N2-fixing legume that can contribute about 100–190 kg N ha−1 to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.
Collapse
Affiliation(s)
- Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
| | - Levini A Msimbira
- Department of Crop Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
| |
Collapse
|
12
|
Analysis of rhizobial endosymbionts of Vicia, Lathyrus and Trifolium species used to maintain mountain firewalls in Sierra Nevada National Park (South Spain). Syst Appl Microbiol 2017; 40:92-101. [DOI: 10.1016/j.syapm.2016.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
|
13
|
Zinga MK, Jaiswal SK, Dakora FD. Presence of diverse rhizobial communities responsible for nodulation of common bean (Phaseolus vulgaris) in South African and Mozambican soils. FEMS Microbiol Ecol 2016; 93:fiw236. [PMID: 27915286 DOI: 10.1093/femsec/fiw236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/22/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
The diversity and phylogeny of root-nodule bacteria isolated from common bean grown in Mozambique and different provinces of South Africa was studied by restriction fragment length polymorphism (RFLP) and phylogenetic analysis. The combined restriction banding pattern of 16S rRNA and nifH profile-generated dendrogram grouped all test isolates into four major clusters with XXI restriction groups and three clusters with VIII restriction groups. Location-based clustering was observed with the 16S rRNA RFLP analysis. Phylogenetic analysis of 16S rRNA, glnII, gyrB and gltA sequences showed that common bean was nodulated specifically by Rhizobium etli in Mozambican soils, and by a diverse group of Rhizobium species in South African soils (e.g. R. etli, R. phaseoli, R. sophoriradicis, R. leucaenae and novel group of Rhizobium spp.). Isolates from the Eastern Cape region of South Africa were dominated by R. leucaenae Overall, the results suggested high nodulation promiscuity of common bean grown in Southern Africa. The nifH and nodC sequence analysis classified all the test isolates with R. etli group, except for isolates TUTPVSA117, TUTPVSA114 and TUTPVSA110 which delineated with R. tropici group. This finding was inconsistent with the phylogram of the housekeeping genes, and is probably an indication of horizontal gene transfer among the Rhizobium isolates tested.
Collapse
Affiliation(s)
- Mwajuma K Zinga
- Department of Crop Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
| | - Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0001, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0001, South Africa
| |
Collapse
|
14
|
Sami D, Mokhtar R, Peter M, Mohamed M. Rhizobium leguminosarum symbiovar trifolii, Ensifer numidicus and Mesorhizobium amorphae symbiovar ciceri (or Mesorhizobium loti) are new endosymbiotic bacteria of Lens culinaris Medik. FEMS Microbiol Ecol 2016; 92:fiw118. [PMID: 27267929 DOI: 10.1093/femsec/fiw118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 11/13/2022] Open
Abstract
A total of 142 rhizobial bacteria were isolated from root nodules of Lens culinaris Medik endemic to Tunisia and they belonged to the species Rhizobium leguminosarum, and for the first time to Ensifer and Mesorhizobium, genera never previously described as microsymbionts of lentil. Phenotypically, our results indicate that L. culinaris Medik strains showed heterogenic responses to the different phenotypic features and they effectively nodulated their original host. Based on the concatenation of the 16S rRNA with relevant housekeeping genes (glnA, recA, dnaK), rhizobia that nodulate lentil belonged almost exclusively to the known R. leguminosarum sv. viciae. Interestingly, R. leguminosarum sv. trifolii, Ensifer numidicus (10 isolates) and Mesorhizobium amorphae (or M. loti) (9 isolates) isolates species, not considered, up to now, as a natural symbiont of lentil are reported. The E. numidicus and M. amorphae (or M. loti) strains induced fixing nodules on Medicago sativa and Cicer arietinum host plants, respectively. Symbiotic gene phylogenies showed that the E. numidicus, new symbiont of lentil, markedly diverged from strains of R. leguminosarum, the usual symbionts of lentil, and converged to the symbiovar meliloti so far described within E. meliloti Indeed, the nodC and nodA genes from the M. amorphae showed more than 99% similarity with respect to those from M. mediterraneum, the common chickpea nodulating species, and would be included in the new infrasubspecific division named M. amorphae symbiovar ciceri, or to M. loti, related to the strains able to effectively nodulate C. arietinum host plant. On the basis of these data, R. leguminosarum sv. trifolii (type strain LBg3 (T)), M. loti or M. amorphae sv. ciceri (type strain LB4 (T)) and E. numidicus (type strain LBi2 (T)) are proposed as new symbionts of L. culinaris Medik.
Collapse
Affiliation(s)
- Dhaoui Sami
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Rejili Mokhtar
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Mergaert Peter
- Institute for IntegrativeBiology of the Cell, Centre National de la Recherche Scientifique, Avenue de la Terrasse Bât. 34, 91198 Gif-sur-Yvette, France
| | - Mars Mohamed
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| |
Collapse
|
15
|
Remigi P, Zhu J, Young JPW, Masson-Boivin C. Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts. Trends Microbiol 2015; 24:63-75. [PMID: 26612499 DOI: 10.1016/j.tim.2015.10.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/08/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait.
Collapse
Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France; New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Jun Zhu
- Department of Microbiology, Nanjing Agricultural University, Nanjing, China; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| |
Collapse
|
16
|
Kumar Meena R, Kumar Singh R, Pal Singh N, Kumari Meena S, Singh Meena V. Isolation of low temperature surviving plant growth – promoting rhizobacteria (PGPR) from pea (Pisum sativum L.) and documentation of their plant growth promoting traits. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.08.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Van Cauwenberghe J, Verstraete B, Lemaire B, Lievens B, Michiels J, Honnay O. Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales. Syst Appl Microbiol 2014; 37:613-21. [DOI: 10.1016/j.syapm.2014.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/04/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
|
18
|
Near-full length sequencing of 16S rDNA and RFLP indicates that Rhizobium etli is the dominant species nodulating Egyptian winter Berseem clover (Trifolium alexandrinum L.). Syst Appl Microbiol 2014; 37:121-8. [DOI: 10.1016/j.syapm.2013.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/10/2013] [Accepted: 08/16/2013] [Indexed: 11/23/2022]
|
19
|
Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiol Res 2014; 169:2-17. [DOI: 10.1016/j.micres.2013.09.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/24/2022]
|