1
|
Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J, Young P. Guidelines for the description of rhizobial symbiovars. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743471 DOI: 10.1099/ijsem.0.006373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Rhizobia are bacteria that form nitrogen-fixing nodules in legume plants. The sets of genes responsible for both nodulation and nitrogen fixation are carried in plasmids or genomic islands that are often mobile. Different strains within a species sometimes have different host specificities, while very similar symbiosis genes may be found in strains of different species. These specificity variants are known as symbiovars, and many of them have been given names, but there are no established guidelines for defining or naming them. Here, we discuss the requirements for guidelines to describe symbiovars, propose a set of guidelines, provide a list of all symbiovars for which descriptions have been published so far, and offer a mechanism to maintain a list in the future.
Collapse
Affiliation(s)
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
| | | | | | | | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
2
|
Borhani B, Khodakaramian G, Velázquez E. Diversity and phylogeny of the bacterial strains isolated from nodules of fenugreek (Trigonella foenum-graecum L.) in Iran. FEMS Microbiol Lett 2022; 369:6590815. [PMID: 35604871 DOI: 10.1093/femsle/fnac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/22/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The diversity of fenugreek (Trigonella foenum-graecum L.) microsymbionts has been barely studied even though it is of great interest for being a spice and a medicinal plant. Here we analyzed fifty-nine bacterial strains isolated from fenugreek nodules originating from different geographic and climatic areas of Iran. Most of these strains exhibit phenotypic characteristics compatible with rhizobia and they nodulate fenugreek. Analysis of the recA and atpD genes shows that representative strains of ERIC-BOX-PCR groups cluster with the type strains of Ensifer meliloti and Ensifer kummerowiae as well as with strains capable of nodulating different Trigonella species found in other countries. The closeness of E. meliloti and E. kummerowiae suggests there is a need to revise the taxonomic status of the latter species. The nodC gene analysis shows that most Trigonella-nodulating strains belong to the symbiovar meliloti except those nodulating Trigonella arcuata in China, which belong to the symbiovar rigiduloides. This analysis shows that the type strains of E. kummerowiae, E. meliloti and E. medicae belonged to three well-defined groups within the symbiovar meliloti, with the Iranian strains belonging to the E. kummerowiae subgroup. The small group of strains unable to nodulate fenugreek isolated in this study belong to Enterobacter cloacae, reported for the first time as being a possible endophyte of fenugreek nodules.
Collapse
Affiliation(s)
- Behzad Borhani
- Department of Plant Protection, Faculty of Agriculture, Buali Sina University, Hamedan, 65178-38695, Iran
| | - Gholam Khodakaramian
- Department of Plant Protection, Faculty of Agriculture, Buali Sina University, Hamedan, 65178-38695, Iran
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca 37001, Spain.,Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain.,Unidad Asociada USAL-IRNASA (CSIC), Salamanca, Spain
| |
Collapse
|
3
|
Khairnar M, Hagir A, Parmar K, Sayyed RZ, James EK, Rahi P. Phylogenetic diversity and plant growth-promoting activities of rhizobia nodulating fenugreek (Trigonella foenum-graecum Linn.) cultivated in different agroclimatic regions of India. FEMS Microbiol Ecol 2022; 98:6526309. [PMID: 35142840 DOI: 10.1093/femsec/fiac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/15/2021] [Accepted: 02/08/2022] [Indexed: 11/15/2022] Open
Abstract
Fenugreek (Trigonella foenum-graecum Linn.), is an extensively cultivated legume crop used as a herb, spice, and traditional medicine in India. The symbiotic efficiency and plant growth-promoting potential of fenugreek rhizobia depend on the symbiont strain and environmental factors. We isolated 176 root-nodulating bacteria from fenugreek cultivated in different agroclimatic regions of India. MALDI-TOF MS-based identification and phylogenetic analyses based on 16S rRNA and five housekeeping genes classified the fenugreek-rhizobia as Ensifer (Sinorhizobium) meliloti. However, the strains represent separate sub-lineages of E. meliloti, distinct from all reported sub-lineages across the globe. We also observed the spatial distribution of fenugreek rhizobia, as the three sub-lineages of E. meliloti recorded during this study were specific to their respective agroclimatic regions. According to the symbiotic gene (nodC and nifH) phylogenies, all three sub-lineages of E. meliloti harboured symbiotic genes similar to symbiovar meliloti; as with the housekeeping genes, these also revealed a spatial distribution for different clades of sv. meliloti. The strains could nodulate fenugreek plants and they showed plant growth-promoting potential. Significant differences were found in the plant growth parameters in response to inoculation with the various strains, suggesting strain-level differences. This study demonstrates that fenugreek rhizobia in India are diverse and spatially distributed in different agro-climatic regions.
Collapse
Affiliation(s)
- Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Ashwini Hagir
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Krupa Parmar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Riyazali Zafarali Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science, and Commerce College, Shahada 425409, India
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| |
Collapse
|
4
|
Ilahi H, Hsouna J, Ellouze W, Gritli T, Chihaoui SA, Barhoumi F, Najib Elfeddy M, Bachkouel S, Ouahmane L, Tambong JT, Mnasri B. Phylogenetic study of rhizobia nodulating pea (Pisum sativum) isolated from different geographic locations in Tunisia. Syst Appl Microbiol 2021; 44:126221. [PMID: 34119907 DOI: 10.1016/j.syapm.2021.126221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Nodulated Pisum sativum plants showed the presence of native rhizobia in 16 out of 23 soil samples collected especially in northern and central Tunisia. A total of 130 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, dnaK and glnII) assigned 35 isolates to Rhizobium laguerreae, R. ruizarguesonis, Agrobacterium radiobacter, Ensifer meliloti and two putative genospecies. R. laguerreae was the most dominant species nodulating P. sativum with 63%. The isolates 21PS7 and 21PS15 were assigned to R. ruizarguesonis, and this is the first report of this species in Tunisia. Two putative new lineages were identified, since strains 25PS6, 10PS4 and 12PS15 clustered distinctly from known rhizobia species but within the R. leguminosarum complex (Rlc) with the most closely related species being R. indicum with 96.4% sequence identity. Similarly, strains 16PS2, 3PS9 and 3PS18 showed 97.4% and 97.6% similarity with R. sophorae and R. laguerreae, respectively. Based on 16S-23S intergenic spacer (IGS) fingerprinting, there was no clear association between the strains and their geographic locations. According to nodC and nodA phylogenies, strains of Rlc species and, interestingly, strain 8PS18 identified as E. meliloti, harbored the symbiotic genes of symbiovar viciae and clustered in two different clades showing heterogeneity within the symbiovar. All these strains nodulated and fixed nitrogen with pea plants. However, the strains belonging to A. radiobacter and the two remaining strains of E. meliloti were unable to nodulate P. sativum, suggesting that they were non-symbiotic strains. The results of this study further suggest that the Tunisian Rhizobium community is more diverse than previously reported.
Collapse
Affiliation(s)
- Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario L0R 2E0, Canada
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Mohamed Najib Elfeddy
- Phytobacteriology Laboratory, Plant Protection Research Unit, CRRA Marrakesh, National Institute for Agronomical Research, Marrakesh 40000, Morocco
| | - Sarra Bachkouel
- Research Support and Technology Transfer Unity, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - James T Tambong
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia.
| |
Collapse
|
5
|
Kang W, Jiang Z, Chen Y, Wu F, Liu C, Wang H, Shi S, Zhang XX. Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level. BMC Plant Biol 2020; 20:293. [PMID: 32590947 PMCID: PMC7318466 DOI: 10.1186/s12870-020-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/18/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness. RESULTS Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants. CONCLUSIONS Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.
Collapse
Affiliation(s)
- Wenjuan Kang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
| | - Zhehao Jiang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yonggang Chen
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Fang Wu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chang Liu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Haifang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
- Key Laboratory of Grassland Ecosystem of the Chinese Ministry of Education, Lanzhou, 730070, China.
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
| |
Collapse
|
6
|
Tounsi-hammami S, Le Roux C, Dhane-fitouri S, De Lajudie P, Duponnois R, Ben Jeddi F. Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils. Syst Appl Microbiol 2019; 42:448-56. [DOI: 10.1016/j.syapm.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 11/30/2022]
|
7
|
Tong W, Li X, Huo Y, Zhang L, Cao Y, Wang E, Chen W, Tao S, Wei G. Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris. Syst Appl Microbiol 2018; 41:300-310. [PMID: 29576402 DOI: 10.1016/j.syapm.2018.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.
Collapse
Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyun Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
8
|
Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata. J Sci Food Agric 2017; 97:4314-4325. [PMID: 28220509 DOI: 10.1002/jsfa.8281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in European soils. The aim of this study was to study the genetic and phenotypic diversity of indigenous cowpea-nodulating rhizobia in Greece. RESULTS The genetic diversity of indigenous rhizobia associated with cowpea was investigated through a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into three groups. Based on the analysis of the 16S rRNA genes, IGS and on the concatenation of six housekeeping genes (recA, glnII, gyrB, truA, thrA and SMc00019), rhizobial isolates were classified within the species Ensifer fredii. However, symbiotic gene phylogenies, based on nodC, nifH and rhcRST genes, showed that the Ensifer isolates are markedly diverged from type and reference strains of E. fredii and formed one clearly separate cluster. The E. fredii strains were able to nodulate and fix nitrogen in cowpea but not in soybean and common bean. CONCLUSION The present study showed that cowpea is nodulated under field conditions by fast-growing rhizobia belonging to the species E. fredii. Based on the phylogenies, similarity levels of symbiotic genes and the host range, the Ensifer isolates may constitute a new symbiovar for which the name 'aegeanense' is proposed. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Christos T Fotiadis
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| |
Collapse
|
9
|
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
Collapse
Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| |
Collapse
|
10
|
León-Barrios M, Pérez-Yépez J, Dorta P, Garrido A, Jiménez C. Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis. Syst Appl Microbiol 2017; 40:171-178. [PMID: 28216096 DOI: 10.1016/j.syapm.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N2-fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9.
Collapse
Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain.
| | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Paola Dorta
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Garrido
- Granja Agrícola Experimental, Área de Agricultura y Ganadería, Cabildo de Lanzarote, Canary Islands, Spain
| | - Concepción Jiménez
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| |
Collapse
|
11
|
Viollet A, Pivato B, Mougel C, Cleyet-Marel JC, Gubry-Rangin C, Lemanceau P, Mazurier S. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza 2017; 27:23-33. [PMID: 27549437 DOI: 10.1007/s00572-016-0730-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/11/2016] [Indexed: 05/20/2023]
Abstract
Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.
Collapse
Affiliation(s)
- Amandine Viollet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Barbara Pivato
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Christophe Mougel
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
- INRA, UMR1349 IGEPP, 35653, Le Rheu, France
| | - Jean-Claude Cleyet-Marel
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Cécile Gubry-Rangin
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France.
| |
Collapse
|
12
|
Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Alías-Villegas C, Cubo MT, Lara-Dampier V, Bellogín RA, Camacho M, Temprano F, Espuny MR. Rhizobial strains isolated from nodules of Medicago marina in southwest Spain are abiotic-stress tolerant and symbiotically diverse. Syst Appl Microbiol 2015; 38:506-14. [DOI: 10.1016/j.syapm.2015.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/05/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
|
14
|
Ramírez-Bahena MH, Vargas M, Martín M, Tejedor C, Velázquez E, Peix Á. Alfalfa microsymbionts from different ITS and nodC lineages of Ensifer meliloti and Ensifer medicae symbiovar meliloti establish efficient symbiosis with alfalfa in Spanish acid soils. Appl Microbiol Biotechnol 2015; 99:4855-65. [DOI: 10.1007/s00253-014-6347-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 10/24/2022]
|
15
|
Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Cevallos MÁ, Lozano L, Castro-Mondragón J, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E. Genomic basis of symbiovar mimosae in Rhizobium etli. BMC Genomics 2014; 15:575. [PMID: 25005495 PMCID: PMC4125696 DOI: 10.1186/1471-2164-15-575] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 07/01/2014] [Indexed: 11/25/2022] Open
Abstract
Background Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. Results We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved. Conclusions The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-575) contains supplementary material, which is available to authorized users.
Collapse
|