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Hsouna J, Gritli T, Ilahi H, Han JC, Ellouze W, Zhang XX, Mansouri M, Rahi P, El Idrissi MM, Lamrabet M, Courty PE, Wipf D, Bekki A, Tambong JT, Mnasri B. Rhizobium aouanii sp. nov., efficient nodulating rhizobia isolated from Acacia saligna roots in Tunisia. Int J Syst Evol Microbiol 2024; 74. [PMID: 39235833 PMCID: PMC11376454 DOI: 10.1099/ijsem.0.006515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024] Open
Abstract
Three bacterial strains, 1AS14IT, 1AS12I and 6AS6, isolated from root nodules of Acacia saligna, were characterized using a polyphasic approach. Phylogenetic analysis based on rrs sequences placed all three strains within the Rhizobium leguminosarum complex. Further phylogeny, based on 1 756 bp sequences of four concatenated housekeeping genes (recA, atpD, glnII and gyrB), revealed their distinction from known rhizobia species of the R. leguminosarum complex (Rlc), forming a distinct clade. The closest related species, identified as Rhizobium laguerreae, with a sequence identity of 96.4% based on concatenated recA-atpD-glnII-gyrB sequences. The type strain, 1AS14IT, showed average nucleotide identity (ANI) values of 94.9, 94.3 and 94.1% and DNA-DNA hybridization values of 56.1, 57.4 and 60.0% with the type strains of closest known species: R. laguerreae, Rhizobium acaciae and 'Rhizobium indicum', respectively. Phylogenomic analyses using 81 up-to-date bacteria core genes and the Type (Strain) Genome Server pipeline further supported the uniqueness of strains 1AS14IT, 1AS12I and 6AS6. The relatedness of the novel strains to NCBI unclassified Rhizobium sp. (396 genomes) and metagenome-derived genomes showed ANI values from 76.7 to 94.8% with a species-level cut-off of 96%, suggesting that strains 1AS14I, 1AS12I and 6AS6 are a distinct lineage. Additionally, differentiation of strains 1AS14IT, 1AS12I and 6AS6 from their closest phylogenetic neighbours was achieved using phenotypic, physiological and fatty acid content analyses. Based on the genomic, phenotypic and biochemical data, we propose the establishment of a novel rhizobial species, Rhizobium aouanii sp. nov., with strain 1AS14IT designated as the type strain (=DSM 113914T=LMG 33206T). This study contributes to the understanding of microbial diversity in nitrogen-fixing symbioses, specifically within Acacia saligna ecosystems in Tunisia.
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Affiliation(s)
- Jihed Hsouna
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
- University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Houda Ilahi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Jia-Cheng Han
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, 4902 Victoria Avenue North, Vineland Station, Ontario, L0R 2E0, Canada
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Maroua Mansouri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Praveen Rahi
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur (CRBIP), Paris, France
| | - Mustapha Missbah El Idrissi
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco
| | - Mouad Lamrabet
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco
| | - Pierre Emmanuel Courty
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Daniel Wipf
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Abdelkader Bekki
- Biotechnology of Rhizobia and Plant Breeding Laboratory, Department of Biotechnology, Faculty of Sciences, University of Oran1, Sénia, Algeria
| | - James T Tambong
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
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Shi N, He T, Qin H, Wang Z, You S, Wang E, Hu G, Wang F, Yu M, Liu X, Liu Z. Microvirga sesbaniae sp. nov. and Microvirga yunnanensis sp. nov., Pink-Pigmented Bacteria Isolated from Root Nodules of Sesbania cannabina (Retz.) Poir. Microorganisms 2024; 12:1558. [PMID: 39203400 PMCID: PMC11356035 DOI: 10.3390/microorganisms12081558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Four pigment-producing rhizobial strains nodulating Sesbania cannabina (Retz.) Poir. formed a unique group in genus Microvirga in the phylogeny of a 16S rRNA gene and five housekeeping genes (gyrB, recA, dnaK, glnA, and atpD) in a genome analysis, phenotypic characteristics analysis, and chemotaxonomic analysis. These four strains shared as high as 99.3% similarity with Microvirga tunisiensis LmiM8T in the 16S rRNA gene sequence and, in an MLSA, were subdivided into two clusters, ANI (genome average nucleotide) and dDDH (digital DNA-DNA hybridization) which shared sequence similarities lower than the species thresholds with each other and with the reference strains for related Microvirga species. The polar lipids elucidated that phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin were the main components for strain SWF67558T and for strain HBU65207T, with the exception of PC. SWF67558T and HBU65207T strains had similar predominant cellular fatty acids, including C16:0, C18:0, summed feature 2, and summed feature8, but with different contents. In addition, all the four novel strains produced pink-pigment, and the main coloring material extract from strain SWF67558T was identified as zeaxanthin, which presented antioxidant ability and reduction power. With all the phylogenetic and phenotypic divergency, we proposed these pink-pigmented symbiotic bacteria as two novel species, named Microvirga sesbaniae sp. nov. and Microvirga yunnanensis sp. nov., with SWF67558T (=KCTC82331T=GDMCC1.2024T) and HBU65207T (=KCTC92125T=GDMCC1.2023T) as the type strains, respectively.
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Affiliation(s)
- Nan Shi
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Teng He
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Huifang Qin
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Ziye Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Shenghao You
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Entao Wang
- Affiliation Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City 11340, Mexico;
| | - Guoli Hu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming 650224, China;
| | - Miao Yu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Research Center of Microbial Breeding and Conservation, Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (N.S.); (T.H.); (H.Q.); (Z.W.); (S.Y.); (G.H.); (M.Y.)
| | - Zhenyu Liu
- Institute of Agro-Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
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Kaziūnienė J, Pini F, Shamshitov A, Razbadauskienė K, Frercks B, Gegeckas A, Mažylytė R, Lapinskienė L, Supronienė S. Genetic Characterization of Rhizobium spp. Strains in an Organic Field Pea ( Pisum sativum L.) Field in Lithuania. PLANTS (BASEL, SWITZERLAND) 2024; 13:1888. [PMID: 39065414 PMCID: PMC11280047 DOI: 10.3390/plants13141888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Biological nitrogen fixation in legume plants depends on the diversity of rhizobia present in the soil. Rhizobial strains exhibit specificity towards host plants and vary in their capacity to fix nitrogen. The increasing interest in rhizobia diversity has prompted studies of their phylogenetic relations. Molecular identification of Rhizobium is quite complex, requiring multiple gene markers to be analysed to distinguish strains at the species level or to predict their host plant. In this research, 50 rhizobia isolates were obtained from the root nodules of five different Pisum sativum L. genotypes ("Bagoo", "Respect", "Astronaute", "Lina DS", and "Egle DS"). All genotypes were growing in the same field, where ecological farming practices were applied, and no commercial rhizobia inoculants were used. The influence of rhizobial isolates on pea root nodulation and dry biomass accumulation was determined. 16S rRNA gene, two housekeeping genes recA and atpD, and symbiotic gene nodC were analysed to characterize rhizobia population. The phylogenetic analysis of 16S rRNA gene sequences showed that 46 isolates were linked to Rhizobium leguminosarum; species complex 1 isolate was identified as Rhizobium nepotum, and the remaining 3 isolates belonged to Rahnella spp., Paenarthrobacter spp., and Peribacillus spp. genera. RecA and atpD gene analysis showed that the 46 isolates identified as R. leguminosarum clustered into three genospecies groups (B), (E) and (K). Isolates that had the highest influence on plant dry biomass accumulation clustered into the (B) group. NodC gene phylogenetic analysis clustered 46 R. leguminosarum isolates into 10 groups, and all isolates were assigned to the R. leguminosarum sv. viciae.
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Affiliation(s)
- Justina Kaziūnienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Akademija, Lithuania (S.S.)
| | - Francesco Pini
- Department of Biology, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Arman Shamshitov
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Akademija, Lithuania (S.S.)
| | - Kristyna Razbadauskienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Akademija, Lithuania (S.S.)
| | - Birutė Frercks
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, LT-54333 Babtai, Lithuania
| | - Audrius Gegeckas
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Raimonda Mažylytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Laura Lapinskienė
- Department of Biology, Faculty of Natural Sciences, Vytautas Magnus University, 53361 Kaunas, Lithuania
| | - Skaidrė Supronienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Akademija, Lithuania (S.S.)
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Kozlova AP, Muntyan VS, Vladimirova ME, Saksaganskaia AS, Kabilov MR, Gorbunova MK, Gorshkov AN, Grudinin MP, Simarov BV, Roumiantseva ML. Soil Giant Phage: Genome and Biological Characteristics of Sinorhizobium Jumbo Phage. Int J Mol Sci 2024; 25:7388. [PMID: 39000497 PMCID: PMC11242549 DOI: 10.3390/ijms25137388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage-microbe interactions with nitrogen-fixing symbiotic microorganisms.
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Affiliation(s)
- Alexandra P Kozlova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Victoria S Muntyan
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Maria E Vladimirova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Alla S Saksaganskaia
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Maria K Gorbunova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Andrey N Gorshkov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia
| | - Mikhail P Grudinin
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia
| | - Boris V Simarov
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Marina L Roumiantseva
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
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Kirichek EA, Flores-Félix JD, Velázquez E, Tsyganova AV, Tsyganov VE. Whole-genome sequence of six Rhizobium laguerreae strains. Microbiol Resour Announc 2024; 13:e0027924. [PMID: 38767349 PMCID: PMC11237489 DOI: 10.1128/mra.00279-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Rhizobium laguerreae is regarded as a promising candidate for biofertilization of legume plants worldwide through its high efficiency in symbiosis. In this paper, we report high-quality sequences of six R. laguerreae strains with total genome completeness from 93.5% to 97.5%.
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Affiliation(s)
- Evgenii A. Kirichek
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - José D. Flores-Félix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Salamanca, Spain
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
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Jithesh T, James EK, Iannetta PPM, Howard B, Dickin E, Monaghan JM. Recent progress and potential future directions to enhance biological nitrogen fixation in faba bean ( Vicia faba L.). PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2024; 5:e10145. [PMID: 38779338 PMCID: PMC11109504 DOI: 10.1002/pei3.10145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The necessity for sustainable agricultural practices has propelled a renewed interest in legumes such as faba bean (Vicia faba L.) as agents to help deliver increased diversity to cropped systems and provide an organic source of nitrogen (N). However, the increased cultivation of faba beans has proven recalcitrant worldwide as a result of low yields. So, it is hoped that increased and more stable yields would improve the commercial success of the crop and so the likelihood of cultivation. Enhancing biological N fixation (BNF) in faba beans holds promise not only to enhance and stabilize yields but also to increase residual N available to subsequent cereal crops grown on the same field. In this review, we cover recent progress in enhancing BNF in faba beans. Specifically, rhizobial inoculation and the optimization of fertilizer input and cropping systems have received the greatest attention in the literature. We also suggest directions for future research on the subject. In the short term, modification of crop management practices such as fertilizer and biochar input may offer the benefits of enhanced BNF. In the long term, natural variation in rhizobial strains and faba bean genotypes can be harnessed. Strategies must be optimized on a local scale to realize the greatest benefits. Future research must measure the most useful parameters and consider the economic cost of strategies alongside the advantages of enhanced BNF.
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Affiliation(s)
- Tamanna Jithesh
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
| | | | - Pietro P. M. Iannetta
- The James Hutton InstituteDundeeUK
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina (CBFQ), Laboratório Associado, Escola Superior de BiotecnologiaPortoPortugal
| | - Becky Howard
- Processors and Growers Research OrganisationPeterboroughUK
| | - Edward Dickin
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
| | - James M. Monaghan
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
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Rivera Ortuña FN, Guevara-Luna J, Yan J, Lopez Amezcua E, Arroyo-Herrera I, Li Y, Vásquez-Murrieta MS, Rojas Arellano D, Wang ET. Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils. Arch Microbiol 2024; 206:281. [PMID: 38805057 DOI: 10.1007/s00203-024-03989-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.
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Affiliation(s)
- Flor N Rivera Ortuña
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Joseph Guevara-Luna
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Jun Yan
- National Observation Station of Hailun Agro-Ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Eloisa Lopez Amezcua
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Ivan Arroyo-Herrera
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Yan Li
- College of Life Science, Yantai University, Shandong Province, Yantai City, 264005, China
| | - Maria Soledad Vásquez-Murrieta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Danae Rojas Arellano
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México.
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8
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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] [Abstract] [Key Words] [MESH Headings] [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.
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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.
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9
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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; 74:006373. [PMID: 38743471 PMCID: PMC11165908 DOI: 10.1099/ijsem.0.006373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/25/2024] [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.
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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
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10
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Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF. Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species. BMC Genomics 2024; 25:419. [PMID: 38684951 PMCID: PMC11057113 DOI: 10.1186/s12864-024-10333-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUD The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.
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Affiliation(s)
- Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China.
| | - Tingyan Guo
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, México
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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11
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Dolatabad HK, Mahjenabadi VAJ. Geographical and climatic distribution of lentil-nodulating rhizobia in Iran. FEMS Microbiol Ecol 2024; 100:fiae046. [PMID: 38587812 PMCID: PMC11044965 DOI: 10.1093/femsec/fiae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Lentil is one of the most important legumes cultivated in various provinces of Iran. However, there is limited information about the symbiotic rhizobia of lentils in this country. In this study, molecular identification of lentil-nodulating rhizobia was performed based on 16S-23S rRNA intergenic spacer (IGS) and recA, atpD, glnII, and nodC gene sequencing. Using PCR-RFLP analysis of 16S-23S rRNA IGS, a total of 116 rhizobia isolates were classified into 20 groups, leaving seven strains unclustered. Phylogenetic analysis of representative isolates revealed that the rhizobia strains belonged to Rhizobium leguminosarum and Rhizobium laguerreae, and the distribution of the species is partially related to geographical location. Rhizobium leguminosarum was the dominant species in North Khorasan and Zanjan, while R. laguerreae prevailed in Ardabil and East Azerbaijan. The distribution of the species was also influenced by agroecological climates; R. leguminosarum thrived in cold semiarid climates, whereas R. laguerreae adapted to humid continental climates. Both species exhibited equal dominance in the Mediterranean climate, characterized by warm, dry summers and mild, wet winters, in Lorestan and Kohgiluyeh-Boyer Ahmad provinces.
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Affiliation(s)
- Hossein Kari Dolatabad
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
| | - Vahid Alah Jahandideh Mahjenabadi
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
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12
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Janczarek M, Kozieł M, Adamczyk P, Buczek K, Kalita M, Gromada A, Mordzińska-Rak A, Polakowski C, Bieganowski A. Symbiotic efficiency of Rhizobium leguminosarum sv. trifolii strains originating from the subpolar and temperate climate regions. Sci Rep 2024; 14:6264. [PMID: 38491088 PMCID: PMC10943007 DOI: 10.1038/s41598-024-56988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Red clover (Trifolium pratense L.) is a forage legume cultivated worldwide. This plant is capable of establishing a nitrogen-fixing symbiosis with Rhizobium leguminosarum symbiovar trifolii strains. To date, no comparative analysis of the symbiotic properties and heterogeneity of T. pratense microsymbionts derived from two distinct geographic regions has been performed. In this study, the symbiotic properties of strains originating from the subpolar and temperate climate zones in a wide range of temperatures (10-25 °C) have been characterized. Our results indicate that all the studied T. pratense microsymbionts from two geographic regions were highly efficient in host plant nodulation and nitrogen fixation in a wide range of temperatures. However, some differences between the populations and between the strains within the individual population examined were observed. Based on the nodC and nifH sequences, the symbiotic diversity of the strains was estimated. In general, 13 alleles for nodC and for nifH were identified. Moreover, 21 and 61 polymorphic sites in the nodC and nifH sequences were found, respectively, indicating that the latter gene shows higher heterogeneity than the former one. Among the nodC and nifH alleles, three genotypes (I-III) were the most frequent, whereas the other alleles (IV-XIII) proved to be unique for the individual strains. Based on the nodC and nifH allele types, 20 nodC-nifH genotypes were identified. Among them, the most frequent were three genotypes marked as A (6 strains), B (5 strains), and C (3 strains). Type A was exclusively found in the temperate strains, whereas types B and C were identified in the subpolar strains. The remaining 17 genotypes were found in single strains. In conclusion, our data indicate that R. leguminosarum sv. trifolii strains derived from two climatic zones show a high diversity with respect to the symbiotic efficiency and heterogeneity. However, some of the R. leguminosarum sv. trifolii strains exhibit very good symbiotic potential in the wide range of the temperatures tested; hence, they may be used in the future for improvement of legume crop production.
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Affiliation(s)
- Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
| | - Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Paulina Adamczyk
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Katarzyna Buczek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Anna Gromada
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Aleksandra Mordzińska-Rak
- Department of Biochemistry and Molecular Biology, Faculty of Medical Studies, Medical University in Lublin, 1 Chodźki, 20-093, Lublin, Poland
| | - Cezary Polakowski
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, 4 Doświadczalna, 20-290, Lublin, Poland
| | - Andrzej Bieganowski
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, 4 Doświadczalna, 20-290, Lublin, Poland
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13
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Figueroa III JL, Dhungel E, Bellanger M, Brouwer CR, White III RA. MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life. Bioinformatics 2024; 40:btae119. [PMID: 38426351 PMCID: PMC10955254 DOI: 10.1093/bioinformatics/btae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/22/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
MOTIVATION MetaCerberus is a massively parallel, fast, low memory, scalable annotation tool for inference gene function across genomes to metacommunities. MetaCerberus provides an elusive HMM/HMMER-based tool at a rapid scale with low memory. It offers scalable gene elucidation to major public databases, including KEGG (KO), COGs, CAZy, FOAM, and specific databases for viruses, including VOGs and PHROGs, from single genomes to metacommunities. RESULTS MetaCerberus is 1.3× as fast on a single node than eggNOG-mapper v2 on 5× less memory using an exclusively HMM/HMMER mode. In a direct comparison, MetaCerberus provides better annotation of viruses, phages, and archaeal viruses than DRAM, Prokka, or InterProScan. MetaCerberus annotates more KOs across domains when compared to DRAM, with a 186× smaller database, and with 63× less memory. MetaCerberus is fully integrated for automatic analysis of statistics and pathways using differential statistic tools (i.e. DESeq2 and edgeR), pathway enrichment (GAGE R), and pathview R. MetaCerberus provides a novel tool for unlocking the biosphere across the tree of life at scale. AVAILABILITY AND IMPLEMENTATION MetaCerberus is written in Python and distributed under a BSD-3 license. The source code of MetaCerberus is freely available at https://github.com/raw-lab/metacerberus compatible with Python 3 and works on both Mac OS X and Linux. MetaCerberus can also be easily installed using bioconda: mamba create -n metacerberus -c bioconda -c conda-forge metacerberus.
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Affiliation(s)
- Jose L Figueroa III
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| | - Eliza Dhungel
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
| | - Madeline Bellanger
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| | - Cory R Brouwer
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
| | - Richard Allen White III
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
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14
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Danilova N, Galieva G, Kuryntseva P, Selivanovskaya S, Galitskaya P. Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce ( Lactuca sativa L.). Microorganisms 2023; 11:2828. [PMID: 38137972 PMCID: PMC10746115 DOI: 10.3390/microorganisms11122828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.
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Affiliation(s)
| | | | | | | | - Polina Galitskaya
- Institute of Environmental Sciences, Kazan Federal University, Kazan 420008, Russia; (N.D.); (G.G.); (P.K.); (S.S.)
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15
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Romanenko L, Otstavnykh N, Tanaka N, Kurilenko V, Svetashev V, Tekutyeva L, Mikhailov V, Isaeva M. Characterization and Genomic Analysis of Fererhizobium litorale gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore. Microorganisms 2023; 11:2385. [PMID: 37894043 PMCID: PMC10609224 DOI: 10.3390/microorganisms11102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576T and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576T and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692T, 96.9% to Ensifer adhaerens NBRC 100388T, and 96.8% to Pararhizobium giardinii NBRC 107135T. The ANI values between strain KMM 9576T and Ensifer adhaerens NBRC 100388T, Sinorhizobium fredii USDA 205T, Pararhizobium giardinii NBRC 107135T, and Rhizobium leguminosarum NBRC 14778T were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576T and Rhizobium leguminosarum NBRC 14778T and 'Rhizobium album' NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576T) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C18:1ω7c as the dominant fatty acid followed by 11-methyl C18:1ω7c and C19:0 cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576T and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576T (=NRIC 0957T).
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan;
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Vasily Svetashev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Liudmila Tekutyeva
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnaya St. 42, Volno-Nadezhdinskoye, Primorsky krai, Vladivostok 692481, Russia;
| | - Valery Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
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Li X, Li Z. What determines symbiotic nitrogen fixation efficiency in rhizobium: recent insights into Rhizobium leguminosarum. Arch Microbiol 2023; 205:300. [PMID: 37542687 DOI: 10.1007/s00203-023-03640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
| | - Zhangqun Li
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China
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Ma T, Xue H, Piao C, Jiang N, Li Y. Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov. Front Microbiol 2023; 14:1207256. [PMID: 37601364 PMCID: PMC10434624 DOI: 10.3389/fmicb.2023.1207256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).
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Affiliation(s)
| | | | | | | | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
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18
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Zhang J, Wang N, Li S, Brunel B, Wang J, Feng Y, Yang T, Zong X. Genotypic composition and performance of pea-nodulating rhizobia from soils outside the native plant-host range. Front Microbiol 2023; 14:1201140. [PMID: 37469428 PMCID: PMC10353855 DOI: 10.3389/fmicb.2023.1201140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 07/21/2023] Open
Abstract
Cultivated soils need to shelter suitable rhizobia for legume cropping, especially in areas outside of the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with Pisum sativum L. in soils of Hebei Province, a region that has recently experienced an expansion of pea production in China. A total of 43 rhizobial isolates were obtained from root-nodules and characterized genetically and symbiotically. The isolates discriminated into 12 genotypes as defined by PCR-RFLP of IGS DNA. Multiple locus sequence analysis (MLSA) based on the 16S rRNA, recA, atpD and gyrB of representative strains placed them into five clusters of four defined species (R. sophorae, R. indicum, R. changzhiense, and R. anhuiense) and a novel Rhizobium genospecies. R. sophorae was the dominant group (58%) followed by R. indicum (23%). The other groups composed of R. changzhiense (14%), R. anhuiense (1 isolate) and the new genospecies (1 isolate), were minor and site-specific. Based on nodC phylogeny, all representatives were intermingled within the symbiovar viciae with R. sophorae and R. changzhiense being a new record. All the tested strains showed efficient symbiotic fixation on pea plants, with half of them exhibiting better plant biomass performance. This suggests that the pea-nodulating rhizobia in Hebei Province form a specific community of efficient symbiotic rhizobia on pea, distinct from those reported in other countries.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
- Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou, Henan Province, China
| | - Nan Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Brigitte Brunel
- LSTM, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, IRD, Montpellier, France
| | - Jingqi Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Yufeng Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, China
| | - Tao Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuxiao Zong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Young JPW, Jorrin B, Moeskjær S, James EK. Rhizobium brockwellii sp. nov., Rhizobium johnstonii sp. nov. and Rhizobium beringeri sp. nov., three genospecies within the Rhizobium leguminosarum species complex. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486744 DOI: 10.1099/ijsem.0.005979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Genomic evidence indicates that the
Rhizobium leguminosarum
species complex comprises multiple distinct species, perhaps 18 or more. Of the five earliest genospecies (gs) to be described, only two have formal names: R. leguminosarum sensu stricto (gsE) and
Rhizobium ruizarguesonis
(gsC). Here, we provide formal descriptions and names for the other three genospecies, based on the publicly available genome sequences for multiple strains of each species: Rhizobium brockwellii sp. nov. (gsA, 37 strains, type strain CC275eT=LMG 6122T = ICMP 2163T=NZP 561T = PDDCC 2163T=HAMBI 13T), Rhizobium johnstonii sp. nov. (gsB, 54 strains, type strain 3841T = LMG 32736T=DSM 114642T) and Rhizobium beringeri sp. nov. (gsD, 8 strains, type strain SM51T = LMG 32895T = DSM 115206T). Each species forms a well-supported clade in a phylogeny based on 120 concatenated core genes. All strains have average nucleotide identity (ANI) above 96 % with the relevant type strain and below 96 % with all other type strains. Each species is characterised by a number of genes that are absent or rare in other species.
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Affiliation(s)
- J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Beatriz Jorrin
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Sara Moeskjær
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Euan K James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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20
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Ballesteros-Gutiérrez M, Albareda M, Barbas C, López-Gonzálvez Á, Dunn MF, Palacios JM. A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/ Pisum sativum system. Front Microbiol 2023; 14:1182563. [PMID: 37260681 PMCID: PMC10228743 DOI: 10.3389/fmicb.2023.1182563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.
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Affiliation(s)
- Marta Ballesteros-Gutiérrez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Coral Barbas
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Ángeles López-Gonzálvez
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Michael F. Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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21
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Xavier GR, Jesus EDC, Dias A, Coelho MRR, Molina YC, Rumjanek NG. Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:954. [PMID: 36840302 PMCID: PMC9962295 DOI: 10.3390/plants12040954] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.
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Affiliation(s)
| | | | - Anelise Dias
- Departamento de Fitotecnia, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, UFRRJ, Rodovia BR-465, Km 7, Seropédica 23890-000, RJ, Brazil
| | | | - Yulimar Castro Molina
- Programa de Pós-graduação em Microbiologia Agrícola, Universidade Federal de Lavras, UFLA, Trevo Rotatório Professor Edmir Sá Santos, Lavras 37203-202, MG, Brazil
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22
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Competitiveness and Phylogenetic Relationship of Rhizobial Strains with Different Symbiotic Efficiency in Trifolium repens: Conversion of Parasitic into Non-Parasitic Rhizobia by Natural Symbiotic Gene Transfer. BIOLOGY 2023; 12:biology12020243. [PMID: 36829520 PMCID: PMC9953144 DOI: 10.3390/biology12020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
Abstract
In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.
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23
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Mahdhi A, Mars M, Rejili M. Members of Ensifer and Rhizobium genera are new bacterial endosymbionts nodulating Pisum sativum (L.). FEMS Microbiol Ecol 2023; 99:fiad001. [PMID: 36597782 DOI: 10.1093/femsec/fiad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
A total of 84 Pisum sativum legume nodulating bacteria (LNB) were isolated from seven geographical sites from southern Tunisia. Phylogenetic analyses based on partial sequences of 16S rRNA gene and the housekeeping genes glnII, and recA grouped strains into six clusters, four of which belonged to the genus Rhizobium and two to the Ensifer genus. Among Rhizobium clusters, 41 strains were affiliated to Rhizobium leguminosarum, two strains to R. pisi, two strains to R. etli, and interestingly two strains belonged to previously undescribed Rhizobium species. The remaining two strains were closely related to Ensifer medicae (two strains) and Ensifer meliloti (two strains). A symbiotic nodC gene-based phylogeny and host specificity test showed that all Rhizobium strains nodulating pea belonged to the symbiovar viciae, whereas the Ensifer strains were associated with the symbiovar meliloti never described to date. All strains under investigation differed in the number of induced root nodules and the effectiveness of atmospheric nitrogen fixation. The R. leguminosarum PsZA23, R. leguminosarum PsGBL42, and E. medicae PsTA22a, forming the most effective symbiosis with the plant host, are potential candidates for inoculation programs.
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Affiliation(s)
- A Mahdhi
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - M Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - M Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
- Department of Life Sciences, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
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24
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Kosolapova AO, Belousov MV, Sulatsky MI, Tsyganova AV, Sulatskaya AI, Bobylev AG, Shtark OY, Tsyganov VE, Volkov KV, Zhukov VA, Tikhonovich IA, Nizhnikov AA. RopB protein of Rhizobium leguminosarum bv. viciae adopts amyloid state during symbiotic interactions with pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1014699. [PMID: 36388578 PMCID: PMC9650718 DOI: 10.3389/fpls.2022.1014699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Amyloids represent protein aggregates with highly ordered fibrillar structure associated with the development of various disorders in humans and animals and involved in implementation of different vital functions in all three domains of life. In prokaryotes, amyloids perform a wide repertoire of functions mostly attributed to their interactions with other organisms including interspecies interactions within bacterial communities and host-pathogen interactions. Recently, we demonstrated that free-living cells of Rhizobium leguminosarum, a nitrogen-fixing symbiont of legumes, produce RopA and RopB which form amyloid fibrils at cell surface during the stationary growth phase thus connecting amyloid formation and host-symbiont interactions. Here we focused on a more detailed analysis of the RopB amyloid state in vitro and in vivo, during the symbiotic interaction between R. leguminosarum bv. viciae with its macrosymbiont, garden pea (Pisum sativum L.). We confirmed that RopB is the bona fide amyloid protein since its fibrils exhibit circular x-ray reflections indicating its cross-β structure specific for amyloids. We found that fibrils containing RopB and exhibiting amyloid properties are formed in vivo at the surface of bacteroids of R. leguminosarum extracted from pea nodules. Moreover, using pea sym31 mutant we demonstrated that formation of extracellular RopB amyloid state occurs at different stages of bacteroid development but is enhanced in juvenile symbiosomes. Proteomic screening of potentially amyloidogenic proteins in the nodules revealed the presence of detergent-resistant aggregates of different plant and bacterial proteins including pea amyloid vicilin. We demonstrated that preformed vicilin amyloids can cross-seed RopB amyloid formation suggesting for probable interaction between bacterial and plant amyloidogenic proteins in the nodules. Taken together, we demonstrate that R. leguminosarum bacteroids produce extracellular RopB amyloids in pea nodules in vivo and these nodules also contain aggregates of pea vicilin amyloid protein, which is able to cross-seed RopB fibrillogenesis in vitro. Thus, we hypothesize that plant nodules contain a complex amyloid network consisting of plant and bacterial amyloids and probably modulating host-symbiont interactions.
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Affiliation(s)
- Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | | | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
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25
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Bartoli C, Boivin S, Marta M, Gris C, Gasciolli V, Gaston M, Auriac MC, Debellé F, Cottret L, Carlier A, Masson-Boivin C, Lepetit M, Lefebvre B. Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development. Environ Microbiol 2022; 24:5509-5523. [PMID: 35920038 DOI: 10.1111/1462-2920.16148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots, and found a low diversity of Rlv compared to that observed in the Rlv species complex. We tested the ability of a subset of these Rlv for wheat root colonization when co-inoculated with other Rlv. Only a few strains, including those isolated from wheat roots, and one strain isolated from pea nodules, were efficient in colonizing roots in co-inoculation conditions, while all the strains tested in single strain inoculation conditions were found to colonize the surface and interior of roots. Furthermore, Rlv strains isolated from wheat roots were able to stimulate root development and early arbuscular mycorrhizal fungi colonization. These responses were strain and host genotype dependent. Our results suggest that wheat can be an alternative host for Rlv; nevertheless, there is a strong competition between Rlv strains for wheat root colonization. In addition, we showed that Rlv are endophytic wheat root bacteria with potential ability to modify wheat development.
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Affiliation(s)
- Claudia Bartoli
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.,LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes INRAE, IRD, CIRAD, University of Montpellier, Montpellier SupAgro Montpellier, France
| | - Marchetti Marta
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Mégane Gaston
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Marie-Christine Auriac
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.,FRAIB-TRI Imaging Platform Facilities, Université de Toulouse, CNRS, 24 chemin de Borderouge, Castanet-Tolosan, France
| | - Frédéric Debellé
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Aurélien Carlier
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes INRAE, IRD, CIRAD, University of Montpellier, Montpellier SupAgro Montpellier, France.,Institut Sophia Agrobiotech INRAE, CNRS, University Côte d'azur, Sophia Antipolis, France
| | - Benoit Lefebvre
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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26
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Relevance of prokaryotic subspecies in the age of genomics. New Microbes New Infect 2022; 48:101024. [PMID: 36176539 PMCID: PMC9513812 DOI: 10.1016/j.nmni.2022.101024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
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27
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Kozieł M, Kalita M, Janczarek M. Genetic diversity of microsymbionts nodulating Trifolium pratense in subpolar and temperate climate regions. Sci Rep 2022; 12:12144. [PMID: 35840628 PMCID: PMC9287440 DOI: 10.1038/s41598-022-16410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.
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Affiliation(s)
- Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
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28
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Hsouna J, Gritli T, Ilahi H, Ellouze W, Mansouri M, Chihaoui SA, Bouhnik O, Missbah El Idrissi M, Abdelmoumen H, Wipf D, Courty PE, Bekki A, Tambong JT, Mnasri B. Genotypic and symbiotic diversity studies of rhizobia nodulating Acacia saligna in Tunisia reveal two novel symbiovars within the Rhizobium leguminosarum complex and Bradyrhizobium. Syst Appl Microbiol 2022; 45:126343. [PMID: 35759954 DOI: 10.1016/j.syapm.2022.126343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/08/2022] [Accepted: 06/12/2022] [Indexed: 11/15/2022]
Abstract
Acacia saligna is an invasive alien species that has the ability to establish symbiotic relationships with rhizobia. In the present study, genotypic and symbiotic diversity of native rhizobia associated with A. saligna in Tunisia were studied. A total of 100 bacterial strains were selected and three different ribotypes were identified based on rrs PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, gyrB and glnII) assigned 30 isolates to four putative new lineages and a single strain to Sinorhizobium meliloti. Thirteen slow-growing isolates representing the most dominant IGS (intergenic spacer) profile clustered distinctly from known rhizobia species within Bradyrhizobium with the closest related species being Bradyrhizobium shewense and Bradyrhizobium niftali, which had 95.17% and 95.1% sequence identity, respectively. Two slow-growing isolates, 1AS28L and 5AS6L, had B. frederekii as their closest species with a sequence identity of 95.2%, an indication that these strains could constitute a new lineage. Strains 1AS14I, 1AS12I and 6AS6 clustered distinctly from known rhizobia species but within the Rhizobium leguminosarum complex (Rlc) with the most closely related species being Rhizobium indicum with 96.3% sequence identity. Similarly, the remaining 11 strains showed 96.9 % and 97.2% similarity values with R. changzhiense and R. indicum, respectively. Based on nodC and nodA phylogenies and cross inoculation tests, these 14 strains of Rlc species clearly diverged from strains of Sinorhizobium and Rlc symbiovars, and formed a new symbiovar for which the name sv. "salignae" is proposed. Bacterial strains isolated in this study that were taxonomically assigned to Bradyrhizobium harbored different symbiotic genes and the data suggested a new symbiovar, for which sv. "cyanophyllae" is proposed. Isolates formed effective nodules on A. saligna.
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Affiliation(s)
- Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Houda Ilahi
- 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, 4902 Victoria Avenue North, Vineland Station, Ontario L0R 2E0, Canada.
| | - Maroua Mansouri
- 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
| | - Omar Bouhnik
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Mustapha Missbah El Idrissi
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Daniel Wipf
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Abdelkader Bekki
- Laboratory of Rhizobia Biotechnology and Plant Breeding, University Oran1, Es Senia 31000, Algeria
| | - James T Tambong
- Agriculture and Agri-Food Canada, 960 Carling Avenue, 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.
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Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.
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Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
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Yurgel SN, Ajeethan N, Smertenko A. Response of Plant-Associated Microbiome to Plant Root Colonization by Exogenous Bacterial Endophyte in Perennial Crops. Front Microbiol 2022; 13:863946. [PMID: 35479645 PMCID: PMC9037143 DOI: 10.3389/fmicb.2022.863946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
The application of bacterial inoculums for improving plant growth and production is an important component of sustainable agriculture. However, the efficiency of perennial crop inoculums depends on the ability of the introduced endophytes to exert an impact on the host-plant over an extended period of time. This impact might be evaluated by the response of plant-associated microbiome to the inoculation. In this study, we monitored the effect of a single bacterial strain inoculation on the diversity, structure, and cooperation in plant-associated microbiome over 1-year period. An endophyte (RF67) isolated from Vaccinium angustifolium (wild blueberry) roots and annotated as Rhizobium was used for the inoculation of 1-year-old Lonicera caerulea (Haskap) plants. A significant level of bacterial community perturbation was detected in plant roots after 3 months post-inoculation. About 23% of root-associated community variation was correlated with an application of the inoculant, which was accompanied by increased cooperation between taxa belonging to Proteobacteria and Actinobacteriota phyla and decreased cooperation between Firmicutes in plant roots. Additionally, a decrease in bacterial Shannon diversity and an increase in the relative abundances of Rhizobiaceae and Enterobacteriaceae were detected in the roots of inoculated plants relative to the non-inoculated control. A strong effect of the inoculation on the bacterial cooperation was also detected after 1 year of plant field growth, whereas no differences in bacterial community composition and also alpha and beta diversities were detected between bacterial communities from inoculated and non-inoculated roots. These findings suggest that while exogenous endophytes might have a short-term effect on the root microbiome structure and composition, they can boost cooperation between plant-growth-promoting endophytes, which can exist for the extended period of time providing the host-plant with long-lasting beneficial effects.
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Affiliation(s)
- Svetlana N. Yurgel
- Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United States
| | - Nivethika Ajeethan
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Department of Biosystems Technology, Faculty of Technology, University of Jaffna, Kilinochchi, Sri Lanka
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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Draft Genome Sequence of Rhizobium ruizarguesonis (Rhizobium leguminosarum) Strain 1TK341. Microbiol Resour Announc 2022; 11:e0102321. [PMID: 35297685 PMCID: PMC9022549 DOI: 10.1128/mra.01023-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium ruizarguesonis (Rhizobium leguminosarum) strain 1TK341 was isolated from pink nodules of fixation-negative mutant line P61 of pea (Pisum sativum L.) grown in soil. Here, we report the draft genome sequence of the strain.
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Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F, diCenzo GC. Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation. Int J Syst Evol Microbiol 2022; 72:005243. [PMID: 35238735 PMCID: PMC9558580 DOI: 10.1099/ijsem.0.005243] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022] Open
Abstract
The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. The most problematic is Rhizobium , which is notorious for being highly paraphyletic, as most newly described species in the family are assigned to this genus without consideration of their proximity to existing genera, or the need to create novel genera. Moreover, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae , wherein genera are defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86 %. We further propose that additional genomic or phenotypic evidence can justify division of species into separate genera even if they share greater than 86 % cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into Xaviernesmea gen. nov. Data is also provided to support the formation of Peteryoungia aggregata comb. nov., Endobacterium yantingense comb. nov., Neorhizobium petrolearium comb. nov., Pararhizobium arenae comb. nov., Pseudorhizobium tarimense comb. nov. and Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. Despite pairwise cpAAI values for all Ensifer species and all Sinorhizobium species being >86 %, additional genomic and phenotypic data suggest that they significantly differ in their biology and ecology. We therefore propose emended descriptions of Ensifer and Sinorhizobium , which we argue should be considered as separate genera.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute for Plant Protection in Horticulture and Forests, Braunschweig, Germany
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Florent Lassalle
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - George C. diCenzo
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
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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] [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.
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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
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Zhang J, Li S, Wang N, Yang T, Brunel B, Andrews M, Zong X, Wang E. Rhizobium sophorae is the dominant rhizobial symbiont of Vicia faba L. In North China. Syst Appl Microbiol 2021; 45:126291. [PMID: 34968802 DOI: 10.1016/j.syapm.2021.126291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 11/27/2022]
Abstract
Faba bean (Vicia faba L.) is a major introduced grain-legume crop cultivated in China. In this study, rhizobia that nodulated faba bean grown in soils from three sites in North China (Hebei Province) were isolated and characterized. Firstly, isolates were categorized into genotypes by ribosomal IGS PCR-RFLP analysis, then representatives of the different IGS genotypes were further identified by phylogenetic analyses of 16S rRNA, housekeeping (atpD, recA) and nodulation (nodC) gene sequences. Rhizobial distribution based on the IGS genotype was related to the different soil physicochemical features by redundancy analysis. IGS typing and phylogenetic analyses of 16S rRNA and concatenated housekeeping gene sequences affiliated the 103 rhizobial strains isolated into four Rhizobium species/genospecies. A total of 69 strains of 3 IGS types were assigned to R. sophorae, 20 isolates of 5 IGS types to R. changzhiense and 9 isolates of 3 IGS types to R. indicum. The representative strain of the five remaining isolates (1 IGS type) was clearly separated from all Rhizobium type strains and was most closely related to defined genospecies according to the recently described R. leguminosarum species complex. Rhizobium sophorae strains (67% of total isolates) were common in all sites and shared an identical nodC sequence typical of faba bean symbionts belonging to symbiovar viciae. In this first study of rhizobia nodulating faba bean in Hebei Province, China, R. sophorae was found to be the dominant symbiont in contrast to other countries.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province 450000, PR China; Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, Henan Province, PR China.
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province 450000, PR China
| | - Nan Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province 450000, PR China
| | - Tao Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Brigitte Brunel
- LSTM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Xuxiao Zong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México, D. F, Mexico
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35
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Nombre Rodríguez-Navarro D, Lorite MJ, Temprano Vera FJ, Camacho M. Selection and characterization of Spanish Trifolium-nodulating rhizobia for pasture inoculation. Syst Appl Microbiol 2021; 45:126290. [PMID: 34999517 DOI: 10.1016/j.syapm.2021.126290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022]
Abstract
Identification of elite nitrogen-fixing rhizobia strains is a continuous and never ending effort, since new legume species can be cultivated in different agro systems or are introduced into new areas. This current study reports on the taxonomic affiliation and symbiotic proficiency of nine strains of Trifolium-nodulating rhizobia isolated from different pasture areas in Spain, as well as three Rhizobium leguminosarum bv. trifolii reference strains, on eleven Trifolium species. Based on 16S rRNA gene sequences the strains belonged to the R. leguminosarum species complex. Additional phylogenetic analyses of the housekeeping genes recA, atpD and rpoB showed the strains were closely related to the species R. leguminosarum, R. laguerreae, R. indicum, R. ruizarguesonis or R. acidisoli. In addition, three strains had no clear affiliation and could represent putative new species, although two of the reference strains were positioned close to R. ruizarguesonis. nodC gene phylogeny allowed the discrimination between strains isolated from annual or perennial Trifolium species and placed all of them in the symbiovar trifolii. Neither geographic origin nor host-plant species could be correlated with the taxonomic affiliation of the strains and a high degree of phenotypic diversity was found among this set of strains. The strong interaction of plant species with the rhizobial strains found for biological nitrogen fixation (BNF) was noteworthy, and allowed the identification of rhizobial strains with a maximum proficiency for certain trefoil species. Several strains showed high BNF potential with a wide range of clover species, which made them valuable strains for inoculant manufacturers and they would be particularly useful for inoculation of seed mixtures in natural or cultivated pastures.
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Affiliation(s)
| | - María J Lorite
- Dpto. Microbiología y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | - María Camacho
- IFAPA Centro Las Torres, Crta Sevilla-Cazalla Km 12, 2, 41200 Seville, Spain
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Riah N, de Lajudie P, Béna G, Heulin K, Djekoun A. Variability in symbiotic efficiency with respect to the growth of pea and lentil inoculated with various rhizobial genotypes originating from sub-humid and semi-arid regions of eastern Algeria. Symbiosis 2021. [DOI: 10.1007/s13199-021-00821-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Boivin S, Mahé F, Debellé F, Pervent M, Tancelin M, Tauzin M, Wielbo J, Mazurier S, Young P, Lepetit M. Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae. FRONTIERS IN PLANT SCIENCE 2021; 12:719987. [PMID: 34567032 PMCID: PMC8457355 DOI: 10.3389/fpls.2021.719987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
Abstract
Legumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv. A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum, Vicia faba, and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frederic Mahé
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frédéric Debellé
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, University of Toulouse, Castanet-Tolosan, France
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Mathilde Tancelin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Sylvie Mazurier
- Agroecology, AgroSup Dijon, INRAE, University Burgundy Franche-Comté, Dijon, France
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Institut Sophia Agrobiotech, INRAE, CNRS, Côte d’Azur University, Sophia-Antipolis, France
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38
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Gnangui SLE, Fossou RK, Ebou A, Amon CER, Koua DK, Kouadjo CGZ, Cowan DA, Zézé A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire. Microorganisms 2021; 9:microorganisms9091842. [PMID: 34576737 PMCID: PMC8472840 DOI: 10.3390/microorganisms9091842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023] Open
Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
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Affiliation(s)
- Sara Laetitia Elphège Gnangui
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Correspondence:
| | - Anicet Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Dominique Kadio Koua
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Claude Ghislaine Zaka Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, 01 Abidjan 1740, Côte d’Ivoire;
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
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39
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Cavassim MIA, Andersen SU, Bataillon T, Schierup MH. Recombination facilitates adaptive evolution in rhizobial soil bacteria. Mol Biol Evol 2021; 38:5480-5490. [PMID: 34410427 PMCID: PMC8662638 DOI: 10.1093/molbev/msab247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.
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Affiliation(s)
- Maria Izabel A Cavassim
- Bioinformatics Research Centre, Aarhus University, Aarhus, 8000, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, 8000, Denmark
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40
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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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] [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.
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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.
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Rahal S, Chekireb D. Diversity of rhizobia and non-rhizobia endophytes isolated from root nodules of Trifolium sp. growing in lead and zinc mine site Guelma, Algeria. Arch Microbiol 2021; 203:3839-3849. [PMID: 34003331 DOI: 10.1007/s00203-021-02362-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
High concentrations of heavy metals in mine soil disturb the interactions between legumes and microorganisms leading to select strains adapted to these specific conditions. In this work, we analyzed the diversity of fifty strains isolated from Trifolium sp. nodules growing on Pb-Zn mine soil, in the Northeastern of Algeria and highlighted their potential symbiotic traits. The phylogeny of the 16S rRNA gene sequences revealed a high bacterial diversity with a predominance of non-rhizobial endophytes. The identified isolates belong to the thirteen following genera Cupriavidus, Pseudomonas, Bacillus, Acinetobacter, Enterobacter, Roseomonas, Paracoccus, Frondihabitans, Microbacterium, Kocuria, Providencia, Micrococcus and Staphylococcus. Regarding rhizobial strains, only isolates affiliated to Rhizobium genus were obtained. The symbiotic gene nodC and the nitrogen fixation gene nifH present showed that Rhizobium isolates belonged to the symbiovar trifolii. In addition to bacterial, one yeast strain was isolated and identified as Rhodotorula mucilaginosa by sequencing the internal transcribed spacer (ITS) region.
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Affiliation(s)
- Sarah Rahal
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Sciences, Department of Biochemistry, University Badji Mokhtar Annaba, B.P. 12, Sidi Amar, 23200, Annaba, Algeria.
| | - Djamel Chekireb
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Sciences, Department of Biochemistry, University Badji Mokhtar Annaba, B.P. 12, Sidi Amar, 23200, Annaba, Algeria.
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Thomas GH. Microbial Musings – April 2021. Microbiology (Reading) 2021; 167. [PMID: 33945459 PMCID: PMC8289222 DOI: 10.1099/mic.0.001061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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de Lajudie P, Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020. Int J Syst Evol Microbiol 2021; 71:004784. [PMID: 33956594 PMCID: PMC8289204 DOI: 10.1099/ijsem.0.004784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/20/2021] [Indexed: 02/04/2023] Open
Affiliation(s)
- Philippe de Lajudie
- IRD, University of Montpellier, CIRAD, INRAE, SupAgro, LSTM, Montpellier, France
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Finland
- Department of Biology, University of Turku, Finland
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Efstathiadou E, Ntatsi G, Savvas D, Tampakaki AP. Genetic characterization at the species and symbiovar level of indigenous rhizobial isolates nodulating Phaseolus vulgaris in Greece. Sci Rep 2021; 11:8674. [PMID: 33883620 PMCID: PMC8060271 DOI: 10.1038/s41598-021-88051-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Phaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. This is the first report on the characterization of bean-nodulating rhizobia at the species and symbiovar level in Greece. The goals of this research were to isolate and characterize rhizobia nodulating local common bean genotypes grown in five different edaphoclimatic regions of Greece with no rhizobial inoculation history. The genetic diversity of the rhizobial isolates was assessed by BOX-PCR and the phylogenetic affiliation was assessed by multilocus sequence analysis (MLSA) of housekeeping and symbiosis-related genes. A total of fifty fast-growing rhizobial strains were isolated and representative isolates with distinct BOX-PCR fingerpriniting patterns were subjected to phylogenetic analysis. The strains were closely related to R. anhuiense, R. azibense, R. hidalgonense, R. sophoriradicis, and to a putative new genospecies which is provisionally named as Rhizobium sp. I. Most strains belonged to symbiovar phaseoli carrying the α-, γ-a and γ-b alleles of nodC gene, while some of them belonged to symbiovar gallicum. To the best of our knowledge, it is the first time that strains assigned to R. sophoriradicis and harbored the γ-b allele were found in European soils. All strains were able to re-nodulate their original host, indicating that they are true microsymbionts of common bean.
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Affiliation(s)
- Evdoxia Efstathiadou
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece.
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Fields B, Moffat EK, Friman VP, Harrison E. The impact of intra-specific diversity in the rhizobia-legume symbiosis. MICROBIOLOGY-SGM 2021; 167. [PMID: 33829985 PMCID: PMC8289218 DOI: 10.1099/mic.0.001051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhizobia - nitrogen-fixing, root-nodulating bacteria - play a critical role in both plant ecosystems and sustainable agriculture. Rhizobia form intracellular infections within legumes roots where they produce plant accessible nitrogen from atmospheric nitrogen and thus reduce the reliance on industrial inputs. The rhizobia-legume symbiosis is often treated as a pairwise relationship between single genotypes, both in research and in the production of rhizobial inoculants. However in nature individual plants are infected by a high diversity of rhizobia symbionts. How this diversity affects productivity within the symbiosis is unclear. Here, we use a powerful statistical approach to assess the impact of diversity within the Rhizobium leguminosarum - clover symbiosis using a biodiversity-ecosystem function framework. Statistically, we found no significant impact of rhizobium diversity. However this relationship was weakly positive - rather than negative - indicating that there is no significant cost to increasing inoculant diversity. Productivity was influenced by the identity of the strains within an inoculant; strains with the highest individual performance showed a significant positive contribution within mixed inoculants. Overall, inoculant effectiveness was best predicted by the individual performance of the best inoculant member, and only weakly predicted by the worst performing member. Collectively, our data suggest that the Rhizobium leguminosarum - clover symbiosis displays a weak diversity-function relationship, but that inoculant performance can be improved through the inclusion of high performing strains. Given the wide environmental dependence of rhizobial inoculant quality, multi-strain inoculants could be highly successful as they increase the likelihood of including a strain well adapted to local conditions across different environments.
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Affiliation(s)
- Bryden Fields
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Emma K Moffat
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Hailu Gunnabo A, Geurts R, Wolde-meskel E, Degefu T, E. Giller K, van Heerwaarden J. Phylogeographic distribution of rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. FEMS Microbiol Ecol 2021; 97:fiab046. [PMID: 33724341 PMCID: PMC8016211 DOI: 10.1093/femsec/fiab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/13/2021] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobiumphaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection.
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Affiliation(s)
- Ashenafi Hailu Gunnabo
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Endalkachew Wolde-meskel
- World Agroforestry Centre (ICRAF), c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, 4 Ethiopia
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, Ethiopia
| | - Ken E. Giller
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Joost van Heerwaarden
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
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Selection of Rhizobium strains for inoculation of Lithuanian Pisum sativum breeding lines. Symbiosis 2021. [DOI: 10.1007/s13199-021-00747-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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