1
|
van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
Collapse
Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- 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.
| |
Collapse
|
2
|
Brahim Mahamat O, Younes S, Otchom BB, Franzel S, Ouchar Mahamat Hidjazi AD, Soumaya EI. A Review on Medicinal and Ethnomedicinal Uses, Biological Features, and Phytochemical Constituents of Sesbania sesban L. Merr., A Nitrogen-Fixing Plant Native to the Republic of Chad. ScientificWorldJournal 2024; 2024:1225999. [PMID: 38268744 PMCID: PMC10807938 DOI: 10.1155/2024/1225999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
This study reports on a literature review of the leguminous tree Sesbania sesban (L.) Merr which is found in the N'djamena region, the Republic of Chad. The study focused on S. sesban's medicinal and ethnomedicinal uses, biological features, and phytochemical constituents to assist in future evaluations. A literature review was conducted using academic websites, such as Science Direct and Springer, online international plant databases, and data from national herbaria. S. sesban is a perennial shrub or tree that measures 3-4 m in height. This species is becoming rare in N'djamena but can be found in the rainy season, while in winter, it occurs mainly in ponds (called the Chadian dialect "Bouta") and on the shores of the Chari and Logone rivers. The local inhabitants in Chad use the species as medicine, livestock feed, and fuelwood and for improving soil fertility and repelling desert encroachment. Traditional healers use its leaves to treat breast cancer and edema. S. sesban is an essential species native to the Republic of Chad that needs conservation and valorization. Viewing its importance and rarity in N'djamena , a strategy for replanting the species in gardens, homes, and fields around N'djamena and other regions of Chad is recommended.
Collapse
Affiliation(s)
- Ousman Brahim Mahamat
- Laboratory of Biology, Ecology and Health, Faculty of Sciences, Abdelmalek Essaâdi University, Tetouan, Morocco
- National Federation Associations of Healers and Practitioners of Medicine, The Ministry of Public Health of Chad, N'Djamena, Chad
| | - Saoud Younes
- Laboratory of Biology, Ecology and Health, Faculty of Sciences, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Brahim Boy Otchom
- Faculty of Human Health Sciences (FSSH), University of N'Djamena, N'Djamena, Chad
- Toumaï University of N'Djamena, N'Djamena, Chad
| | | | - Al-Djazouli Ouchar Mahamat Hidjazi
- Faculty of Exact Applied Sciences, Department of Earth Sciences, N'Djamena University, N'Djamena, Chad
- Laboratory of Geology and Oceanology, Geology Department, Faculty of Sciences, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - El ismaili Soumaya
- Laboratory of Innovative Technologies, Civil Engineering Department, National School of Applied Sciences ENSA-Tangier, Abdelmalek Essaâdi University, Tetouan, Morocco
| |
Collapse
|
3
|
Colombi E, Hill Y, Lines R, Sullivan JT, Kohlmeier MG, Christophersen CT, Ronson CW, Terpolilli JJ, Ramsay JP. Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer. Microb Genom 2023; 9:mgen000918. [PMID: 36748564 PMCID: PMC9973854 DOI: 10.1099/mgen.0.000918] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.
Collapse
Affiliation(s)
- Elena Colombi
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia.,Present address: School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Yvette Hill
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - MacLean G Kohlmeier
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Claus T Christophersen
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jason J Terpolilli
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Joshua P Ramsay
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| |
Collapse
|
4
|
Choudhary S, Tak N, Bissa G, Chouhan B, Choudhary P, Sprent JI, James EK, Gehlot HS. The widely distributed legume tree Vachellia (Acacia) nilotica subsp. indica is nodulated by genetically diverse Ensifer strains in India. Symbiosis 2020; 80:15-31. [DOI: 10.1007/s13199-019-00658-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
5
|
Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
Collapse
Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| |
Collapse
|
6
|
Beukes CW, Boshoff FS, Phalane FL, Hassen AI, le Roux MM, Stȩpkowski T, Venter SN, Steenkamp ET. Both Alpha- and Beta-Rhizobia Occupy the Root Nodules of Vachellia karroo in South Africa. Front Microbiol 2019; 10:1195. [PMID: 31214140 PMCID: PMC6558075 DOI: 10.3389/fmicb.2019.01195] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Vachellia karroo (formerly Acacia karroo) is a wide-spread legume species indigenous to southern Africa. Little is known regarding the identity or diversity of rhizobia that associate with this plant in its native range in South Africa. The aims of this study were therefore: (i) to gather a collection of rhizobia associated with V. karroo from a wide range of geographic locations and biomes; (ii) to identify the isolates and infer their evolutionary relationships with known rhizobia; (iii) to confirm their nodulation abilities by using them in inoculation assays to induce nodules under glasshouse conditions. To achieve these aims, soil samples were collected from 28 locations in seven biomes throughout South Africa, which were then used to grow V. karroo seedlings under nitrogen-free conditions. The resulting 88 bacterial isolates were identified to genus-level using 16S rRNA sequence analysis and to putative species-level using recA-based phylogenetic analyses. Our results showed that the rhizobial isolates represented members of several genera of Alphaproteobacteria (Bradyrhizobium, Ensifer, Mesorhizobium, and Rhizobium), as well as Paraburkholderia from the Betaproteobacteria. Our study therefore greatly increases the known number of Paraburkholderia isolates which can associate with this southern African mimosoid host. We also show for the first time that members of this genus can associate with legumes, not only in the Fynbos biome, but also in the Albany Thicket and Succulent Karoo biomes. Twenty-six putative species were delineated among the 88 isolates, many of which appeared to be new to Science with other likely being conspecific or closely related to E. alkalisoli, M. abyssinicae, M. shonense, and P. tropica. We encountered only a single isolate of Bradyrhizobium, which is in contrast to the dominant association of this genus with Australian Acacia. V. karroo also associates with diverse genera in the Grassland biome where it is quite invasive and involved in bush encroachment. Our findings therefore suggest that V. karroo is a promiscuous host capable of forming effective nodules with both alpha- and beta-rhizobia, which could be a driving force behind the ecological success of this tree species.
Collapse
Affiliation(s)
- Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francois S Boshoff
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francina L Phalane
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Ahmed I Hassen
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Marianne M le Roux
- South African National Biodiversity Institute, Pretoria National Botanical Garden, Pretoria, South Africa.,Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Tomasz Stȩpkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
7
|
Salmi A, Boulila F, Bourebaba Y, Le Roux C, Belhadi D, de Lajudie P. Phylogenetic diversity of Bradyrhizobium strains nodulating Calicotome spinosa in the Northeast of Algeria. Syst Appl Microbiol 2018; 41:452-9. [DOI: 10.1016/j.syapm.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
|
8
|
Kalita M, Małek W. Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland. Syst Appl Microbiol 2017; 40:482-91. [DOI: 10.1016/j.syapm.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/24/2017] [Accepted: 09/20/2017] [Indexed: 01/27/2023]
|
9
|
Degefu T, Wolde-Meskel E, Rasche F. Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia. Int J Syst Evol Microbiol 2017; 68:449-460. [PMID: 29143730 DOI: 10.1099/ijsem.0.002486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δ15N analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I-IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δ15N-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ15N=0.73) and GN102 (δ15N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.
Collapse
Affiliation(s)
- Tulu Degefu
- School of Applied Natural Sciences, Applied Biology Program, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593 Stuttgart, Germany
| |
Collapse
|
10
|
Degefu T, Wolde-meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40:205-214. [DOI: 10.1016/j.syapm.2017.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
|
11
|
Varun M, Ogunkunle CO, D'Souza R, Favas P, Paul M. Identification of Sesbania sesban (L.) Merr. as an Efficient and Well Adapted Phytoremediation Tool for Cd Polluted Soils. Bull Environ Contam Toxicol 2017; 98:867-873. [PMID: 28456824 DOI: 10.1007/s00128-017-2094-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 07/28/2016] [Accepted: 04/21/2017] [Indexed: 06/07/2023]
Abstract
A pot experiment was carried out to assess Cd uptake and accumulation efficiency of Sesbania sesban. Plants were grown in soil spiked with 25, 50, 100, 150, 200, 250, and 300 mg/kg Cd. After 120 days, plants were harvested and analyzed for Cd content. A steady increase in Cd accumulation with increasing metal concentration in soil was observed for all treatments. Accumulation of Cd was greatest in roots (86.7 ± 6.3 mg/kg), followed by stem (18.59 ± 1.9 mg/kg), and leaf (3.16 ± 1.1 mg/kg). Chlorophyll content declined with increasing Cd concentration, while proline and protein content increased as compared to control. At higher Cd levels, root, shoot length, and biomass were all significantly reduced (p ≤ 0.001). An increase in total protein along with greater A250/A280 value suggested an increase in metal-protein complexes. Considering the rapid growth, high biomass, accumulation efficiency, and adaptive properties, this plant could be used as a valuable tool for the phytoremediation of Cd contaminated soils.
Collapse
Affiliation(s)
- Mayank Varun
- Department of Botany, St. John's College, Agra, Uttar Pradesh, 282 002, India.
| | - Clement O Ogunkunle
- Environmental Biology Unit, Department of Plant Biology, University of Ilorin, Ilorin, 240003, Nigeria
| | - Rohan D'Souza
- Department of Botany, St. John's College, Agra, Uttar Pradesh, 282 002, India
| | - Paulo Favas
- School of Life Sciences and the Environment, University of Trás-os-Montes e Alto Douro, 5001-801, Vila Real, Portugal
- Faculty of Sciences and Technology, MARE - Marine and Environmental Sciences Centre, University of Coimbra, 3004-517, Coimbra, Portugal
| | - Manoj Paul
- Department of Botany, St. John's College, Agra, Uttar Pradesh, 282 002, India
| |
Collapse
|
12
|
Tena W, Wolde-Meskel E, Degefu T, Walley F. Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinum L.) in soils from southern and central Ethiopia. Can J Microbiol 2017; 63:690-707. [PMID: 28499096 DOI: 10.1139/cjm-2016-0776] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I-IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.
Collapse
Affiliation(s)
- Wondwosen Tena
- a Department of Plant Science, Debre Berhan University, P.O. Box 445, Debre Berhan, Ethiopia
| | | | - Tulu Degefu
- c Department of Biology, Hawassa University, P.O. Box 05, Hawassa, Ethiopia
| | - Fran Walley
- d Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| |
Collapse
|
13
|
de Oliveira-Francesquini JP, Hungria M, Savi DC, Glienke C, Aluizio R, Kava V, Galli-Terasawa LV. Differential colonization by bioprospected rhizobial bacteria associated with common bean in different cropping systems. Can J Microbiol 2017; 63:682-689. [PMID: 28376308 DOI: 10.1139/cjm-2016-0784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we evaluated the diversity of rhizobia isolated from root nodules on common bean (Phaseolus vulgaris) derived from Andean and Mesoamerican centers and grown under field and greenhouse conditions. Genetic characterization of isolates was performed by sequencing analyses of the 16S rRNA gene and 2 housekeeping genes, recA and glnII, and by the amplification of nifH. Symbiotic efficiency was evaluated by examining nodulation, plant biomass production, and plant nitrogen (N) accumulation. The influence of the environment was observed in nodulation capacity, where Rhizobium miluonense was dominant under greenhouse conditions and the Rhizobium acidisoli group prevailed under field conditions. However, strain LGMB41 fit into a separate group from the type strain of R. acidisoli in terms of multilocus phylogeny, implying that it could belong to a new species. Rhizobium miluonense LGMB73 showed the best symbiotic efficiency performance, i.e., with the highest shoot-N content (77.7 mg/plant), superior to the commercial standard strain (56.9 mg/plant). Biodiversity- and bioprospecting-associated studies are important to better understand ecosystems and to develop more effective strategies to improve plant growth using a N-fixation process.
Collapse
Affiliation(s)
| | | | - Daiani Cristina Savi
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Chirlei Glienke
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Rodrigo Aluizio
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Vanessa Kava
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | | |
Collapse
|
14
|
Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
|
15
|
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
|
16
|
Mousavi SA, Li L, Wei G, Räsänen L, Lindström K. Evolution and taxonomy of native mesorhizobia nodulating medicinal Glycyrrhiza species in China. Syst Appl Microbiol 2016; 39:260-265. [DOI: 10.1016/j.syapm.2016.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022]
|
17
|
Affiliation(s)
- Susana Rodríguez‐Echeverría
- CFE‐Centre for Functional Ecology Department of Life Sciences University of Coimbra Calçada Martim de Freitas 3000‐456 Coimbra Portugal
| | - Yudi M. Lozano
- Estación Experimental de Zonas Áridas Consejo Superior de Investigaciones Científicas Carretera de Sacramento s/n E‐04120 La Cañada de San Urbano Almería Spain
| | - Richard D. Bardgett
- Faculty of Life Sciences The University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT UK
| |
Collapse
|
18
|
Ji Z, Yan H, Cui Q, Wang E, Chen W, Chen W. Genetic divergence and gene flow among Mesorhizobium strains nodulating the shrub legume Caragana. Syst Appl Microbiol 2015; 38:176-83. [DOI: 10.1016/j.syapm.2015.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 11/16/2022]
|
19
|
Bakhoum N, Galiana A, Le Roux C, Kane A, Duponnois R, Ndoye F, Fall D, Noba K, Sylla SN, Diouf D. Phylogeny of nodulation genes and symbiotic diversity of Acacia senegal (L.) Willd. and A. seyal (Del.) Mesorhizobium strains from different regions of Senegal. Microb Ecol 2015; 69:641-651. [PMID: 25315832 DOI: 10.1007/s00248-014-0507-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 09/26/2014] [Indexed: 06/04/2023]
Abstract
Acacia senegal and Acacia seyal are small, deciduous legume trees, most highly valued for nitrogen fixation and for the production of gum arabic, a commodity of international trade since ancient times. Symbiotic nitrogen fixation by legumes represents the main natural input of atmospheric N2 into ecosystems which may ultimately benefit all organisms. We analyzed the nod and nif symbiotic genes and symbiotic properties of root-nodulating bacteria isolated from A. senegal and A. seyal in Senegal. The symbiotic genes of rhizobial strains from the two Acacia species were closed to those of Mesorhizobium plurifarium and grouped separately in the phylogenetic trees. Phylogeny of rhizobial nitrogen fixation gene nifH was similar to those of nodulation genes (nodA and nodC). All A. senegal rhizobial strains showed identical nodA, nodC, and nifH gene sequences. By contrast, A. seyal rhizobial strains exhibited different symbiotic gene sequences. Efficiency tests demonstrated that inoculation of both Acacia species significantly affected nodulation, total dry weight, acetylene reduction activity (ARA), and specific acetylene reduction activity (SARA) of plants. However, these cross-inoculation tests did not show any specificity of Mesorhizobium strains toward a given Acacia host species in terms of infectivity and efficiency as stated by principal component analysis (PCA). This study demonstrates that large-scale inoculation of A. senegal and A. seyal in the framework of reafforestation programs requires a preliminary step of rhizobial strain selection for both Acacia species.
Collapse
Affiliation(s)
- Niokhor Bakhoum
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, BP 5005, Dakar, Senegal,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Pérez-Yépez J, Armas-Capote N, Velázquez E, Pérez-Galdona R, Rivas R, León-Barrios M. Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 2014; 37:553-9. [DOI: 10.1016/j.syapm.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
|
21
|
Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia. Appl Microbiol Biotechnol 2013; 97:10117-34. [PMID: 24196581 DOI: 10.1007/s00253-013-5248-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
Abstract
Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.
Collapse
Affiliation(s)
- Aregu Amsalu Aserse
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, P.O. Box 56, 00014, Finland,
| | | | | | | | | |
Collapse
|
22
|
Xu KW, Penttinen P, Chen YX, Zou L, Zhou T, Zhang X, Hu C, Liu F. Polyphasic characterization of rhizobia isolated from Leucaena leucocephala from Panxi, China. World J Microbiol Biotechnol 2013; 29:2303-15. [PMID: 23749221 DOI: 10.1007/s11274-013-1396-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
Leucaena leucocephala was introduced into Panxi, Sichuan, China, in the 1980s and 1990s for afforestation and preventing water loss and soil erosion in this area. The co-introduction of rhizobial symbionts of introduced plants has drawn attention since they may influence local soil communities. We studied the phylogenetic position of the L. leucocephala isolates and assessed if the rhizobia were introduced together with the host to Panxi, Sichuan, China. The glnII and atpD genes of fifteen representative isolates were sequenced and analyzed, and applied multilocus sequence analyses in which the housekeeping genes recA, glnII and atpD were included. Furthermore, we estimated the within species diversity directly with 23S rDNA and IGS RFLP and indirectly through phenotypic analysis of forty L. leucocephala isolates. The isolates represented seven species and 38 diversified strains in the genera Ensifer, Mesorhizobium, Bradyrhizobium and Rhizobium. The within species diversity of the Ensifer isolates was large, proposing a potential to occupy novel niches. There was not conclusive evidence to show that any of the strains would have been co-introduced with L. leucocephala. On the contrary, we came to a conclusion that the possible introduction should not be inferred from sequence data alone.
Collapse
|
23
|
Degefu T, Wolde-meskel E, Frostegård Å. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia. Syst Appl Microbiol 2013; 36:272-80. [PMID: 23643092 DOI: 10.1016/j.syapm.2013.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/16/2013] [Accepted: 03/25/2013] [Indexed: 11/17/2022]
Abstract
The taxonomic diversity of thirty-seven Rhizobium strains, isolated from nodules of leguminous trees and herbs growing in Ethiopia, was studied using multilocus sequence analyses (MLSA) of six core and two symbiosis-related genes. Phylogenetic analysis based on the 16S rRNA gene grouped them into five clusters related to nine Rhizobium reference species (99-100% sequence similarity). In addition, two test strains occupied their own independent branches on the phylogenetic tree (AC86a2 along with R. tibeticum; 99.1% similarity and AC100b along with R. multihospitium; 99.5% similarity). One strain from Milletia ferruginea was closely related (>99%) to the genus Shinella, further corroborating earlier findings that nitrogen-fixing bacteria are distributed among phylogenetically unrelated taxa. Sequence analyses of five housekeeping genes also separated the strains into five well-supported clusters, three of which grouped with previously studied Ethiopian common bean rhizobia. Three of the five clusters could potentially be described into new species. Based on the nifH genes, most of the test strains from crop legumes were closely related to several strains of Ethiopian common bean rhizobia and other symbionts of bean plants (R. etli and R. gallicum sv. phaseoli). The grouping of the test strains based on the symbiosis-related genes was not in agreement with the housekeeping genes, signifying differences in their evolutionary history. Our earlier studies revealing a large diversity of Mesorhizobium and Ensifer microsymbionts isolated from Ethiopian legumes, together with the results from the present analysis of Rhizobium strains, suggest that this region might be a potential hotspot for rhizobial biodiversity.
Collapse
Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
| | | | | |
Collapse
|
24
|
Degefu T, Wolde-meskel E, Frostegård Å. Phylogenetic multilocus sequence analysis identifies seven novel Ensifer genospecies isolated from a less-well-explored biogeographical region in East Africa. Int J Syst Evol Microbiol 2012; 62:2286-95. [DOI: 10.1099/ijs.0.039230-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The diversity of 71 rhizobial strains belonging to the genus
Ensifer
, isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined
Ensifer
species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within
Ensifer
for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of
Ensifer
in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.
Collapse
|
25
|
Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A, Frostegård Å. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2012; 63:1746-1753. [PMID: 22941297 DOI: 10.1099/ijs.0.044032-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.
Collapse
Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Endalkachew Wolde-Meskel
- School of Plant and Horticultural Sciences, Hawassa University, PO Box 5, Hawassa, Ethiopia.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Binbin Liu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| |
Collapse
|
26
|
Ramírez-Bahena MH, Hernández M, Peix Á, Velázquez E, León-Barrios M. Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov. Syst Appl Microbiol 2012; 35:334-41. [DOI: 10.1016/j.syapm.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/25/2012] [Accepted: 05/06/2012] [Indexed: 10/28/2022]
|
27
|
Fterich A, Mahdhi M, Lafuente A, Pajuelo E, Caviedes MA, Rodriguez-Llorente ID, Mars M. Taxonomic and symbiotic diversity of bacteria isolated from nodules of Acacia tortilis subsp. raddiana in arid soils of Tunisia. Can J Microbiol 2012; 58:738-51. [PMID: 22616625 DOI: 10.1139/w2012-048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A collection of rhizobia isolated from Acacia tortilis subsp. raddiana nodules from various arid soils in Tunisia was analyzed for their diversity at both taxonomic and symbiotic levels. The isolates were found to be phenotypically diverse. The majority of the isolates tolerated 3% NaCl and grew at 40 °C. Genetic characterization emphasized that most of the strains (42/50) belong to the genus Ensifer, particularly the species Ensifer meliloti, Ensifer garamanticus, and Ensifer numidicus. Symbiotic properties of isolates showed diversity in their capacity to nodulate their host plant and to fix atmospheric nitrogen. The most effective isolates were closely related to E. garamanticus. Nodulation tests showed that 3 strains belonging to Mesorhizobium genus failed to renodulate their host plant, which is surprising for symbiotic rhizobia. Furthermore, our results support the presence of non-nodulating endophytic bacteria belonging to the Acinetobacter genus in legume nodules.
Collapse
Affiliation(s)
- A Fterich
- Laboratoire de biotechnologies végétales appliquées à l'amélioration des cultures, Faculté des sciences de Gabès, Université de Gabès, Cité Erriadh, Zrig 6072 Gabès, Tunisia
| | | | | | | | | | | | | |
Collapse
|
28
|
Rashid MH, Schäfer H, Gonzalez J, Wink M. Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol 2012; 35:98-109. [DOI: 10.1016/j.syapm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 11/23/2022]
|
29
|
Aserse AA, Räsänen LA, Assefa F, Hailemariam A, Lindström K. Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. Syst Appl Microbiol 2012; 35:120-31. [DOI: 10.1016/j.syapm.2011.11.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/22/2011] [Accepted: 11/24/2011] [Indexed: 11/24/2022]
|
30
|
Stępkowski T, Zak M, Moulin L, Króliczak J, Golińska B, Narożna D, Safronova VI, Mądrzak CJ. Bradyrhizobium canariense and Bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in Europe. Syst Appl Microbiol 2011; 34:368-75. [PMID: 21514760 DOI: 10.1016/j.syapm.2011.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 02/26/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
Abstract
Forty three Bradyrhizobium strains isolated in Poland from root nodules of lupin species (Lupinus albus, L. angustifolius and L. luteus), and pink serradella (Ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpD, glnII and recA) and nodulation (nodA) gene sequences. Additionally, seven strains originating from root-nodules of yellow serradella (O. compressus) from Asinara Island (Italy) were included in this study. Phylogenetic trees revealed that 15 serradella strains, including all yellow serradella isolates, and six lupin strains grouped in Bradyrhizobium canariense (BC) clade, whereas eight strains from pink serradella and 15 lupin strains were assigned to Bradyrhizobium japonicum (BJ1). Apparently, these species are the two dominant groups in soils of central Europe, in the nodules of lupin and serradella plants. Only three strains belonged to other chromosomal lineages: one formed a cluster that was sister to B. canariense, one strain grouped outside the branch formed by B. japonicum super-group, and one strain occupied a distant position in the genus Bradyrhizobium, clustering with strains of the Rhodopseudomonas genus. All strains in nodulation nodA gene tree grouped in a cluster referred to as Clade II, which is in line with earlier data on this clade dominance among Bradyrhizobium strains in Europe. The nodA tree revealed four well-supported subgroups within Clade II (II.1-II.4). Interestingly, all B. canariense strains clustered in subgroup II.1 whereas B. japonicum strains dominated subgroups II.2-II.4.
Collapse
Affiliation(s)
- Tomasz Stępkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Noskowskiego 12/14, Poland
| | | | | | | | | | | | | | | |
Collapse
|