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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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Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
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Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
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Tang M, Wang H, Qi X, He T, Zhang B, Wang E, Yu M, Wang B, Wang F, Liu Z, Liu X. Diversification of Sinorhizobium populations associated with Medicago polymorpha and Medicago lupulina in purple soil of China. Front Microbiol 2023; 13:1055694. [PMID: 36687603 PMCID: PMC9846747 DOI: 10.3389/fmicb.2022.1055694] [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: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S-23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.
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Affiliation(s)
- Mingxing Tang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Haoyu Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Xin Qi
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Teng He
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Bin Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Miao Yu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Beinan Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China
| | - Fang Wang
- Key Laboratory of State Forestry Administration for Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming City, China
| | - Zhongkuan Liu
- Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China,*Correspondence: Zhongkuan Liu, ; Xiaoyun Liu,
| | - Xiaoyun Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding City, China,*Correspondence: Zhongkuan Liu, ; Xiaoyun Liu,
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Castellano-Hinojosa A, Mora C, Strauss SL. Native Rhizobia Improve Plant Growth, Fix N 2, and Reduce Greenhouse Emissions of Sunnhemp More than Commercial Rhizobia Inoculants in Florida Citrus Orchards. PLANTS (BASEL, SWITZERLAND) 2022; 11:3011. [PMID: 36432740 PMCID: PMC9695096 DOI: 10.3390/plants11223011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Sunnhemp (Crotalaria juncea L.) is an important legume cover crop used in tree cropping systems, where there is increased interest by growers to identify rhizobia to maximize soil nitrogen (N) inputs. We aimed to isolate and identify native rhizobia and compare their capabilities with non-native rhizobia from commercial inoculants to fix atmospheric dinitrogen (N2), produce and reduce nitrous oxide (N2O), and improve plant growth. Phylogenetic analyses of sequences of the 16S rRNA and recA, atpD, and glnII genes showed native rhizobial strains belonged to Rhizobium tropici and the non-native strain to Bradyrhizobium japonicum. Plant nodulation tests, sequencing of nodC and nifH genes, and the acetylene-dependent ethylene production assay confirmed the capacity of all strains to nodulate sunnhemp and fix N2. Inoculation with native rhizobial strains resulted in significant increases in root and shoot weight and total C and N contents in the shoots, and showed greater N2-fixation rates and lower emissions of N2O compared to the non-native rhizobium. Our results suggest that native rhizobia improve plant growth, fix N2, and reduce greenhouse emissions of sunnhemp more than commercial rhizobia inoculants in Florida citrus orchards.
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Rajnovic I, Ramírez-Bahena MH, Kajic S, Igual JM, Peix Á, Velázquez E, Sikora S. Rhizobium croatiense sp. nov. and Rhizobium redzepovicii sp. nov., two new species isolated from nodules of Phaseolus vulgaris in Croatia. Syst Appl Microbiol 2022; 45:126317. [DOI: 10.1016/j.syapm.2022.126317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Žalnėravičius R, Paškevičius A, Samukaitė-Bubnienė U, Ramanavičius S, Vilkienė M, Mockevičienė I, Ramanavičius A. Microbial Fuel Cell Based on Nitrogen-Fixing Rhizobium anhuiense Bacteria. BIOSENSORS 2022; 12:bios12020113. [PMID: 35200373 PMCID: PMC8869864 DOI: 10.3390/bios12020113] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 06/01/2023]
Abstract
In this study, the nitrogen-fixing, Gram-negative soil bacteria Rhizobium anhuiense was successfully utilized as the main biocatalyst in a bacteria-based microbial fuel cell (MFC) device. This research investigates the double-chambered, H-type R. anhuiense-based MFC that was operated in modified Norris medium (pH = 7) under ambient conditions using potassium ferricyanide as an electron acceptor in the cathodic compartment. The designed MFC exhibited an open-circuit voltage (OCV) of 635 mV and a power output of 1.07 mW m-2 with its maximum power registered at 245 mV. These values were further enhanced by re-feeding the anode bath with 25 mM glucose, which has been utilized herein as the main carbon source. This substrate addition led to better performance of the constructed MFC with a power output of 2.59 mW m-2 estimated at an operating voltage of 281 mV. The R. anhuiense-based MFC was further developed by improving the charge transfer through the bacterial cell membrane by applying 2-methyl-1,4-naphthoquinone (menadione, MD) as a soluble redox mediator. The MD-mediated MFC device showed better performance, resulting in a slightly higher OCV value of 683 mV and an almost five-fold increase in power density to 4.93 mW cm-2. The influence of different concentrations of MD on the viability of R. anhuiense bacteria was investigated by estimating the optical density at 600 nm (OD600) and comparing the obtained results with the control aliquot. The results show that lower concentrations of MD, ranging from 1 to 10 μM, can be successfully used in an anode compartment in which R. anhuiense bacteria cells remain viable and act as a main biocatalyst for MFC applications.
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Affiliation(s)
- Rokas Žalnėravičius
- Centre for Physical Sciences and Technology, Sauletekio Av. 3, LT-10257 Vilnius, Lithuania; (R.Ž.); (U.S.-B.); (S.R.)
| | - Algimantas Paškevičius
- Laboratory of Biodeterioration Research, Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania;
| | - Urtė Samukaitė-Bubnienė
- Centre for Physical Sciences and Technology, Sauletekio Av. 3, LT-10257 Vilnius, Lithuania; (R.Ž.); (U.S.-B.); (S.R.)
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Institute of Chemistry, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
| | - Simonas Ramanavičius
- Centre for Physical Sciences and Technology, Sauletekio Av. 3, LT-10257 Vilnius, Lithuania; (R.Ž.); (U.S.-B.); (S.R.)
| | - Monika Vilkienė
- Lithuanian Research Centre for Agriculture and Forestry, Instituto Av.1, Akademija, LT-58344 Kedainiai, Lithuania; (M.V.); (I.M.)
| | - Ieva Mockevičienė
- Lithuanian Research Centre for Agriculture and Forestry, Instituto Av.1, Akademija, LT-58344 Kedainiai, Lithuania; (M.V.); (I.M.)
| | - Arūnas Ramanavičius
- Centre for Physical Sciences and Technology, Sauletekio Av. 3, LT-10257 Vilnius, Lithuania; (R.Ž.); (U.S.-B.); (S.R.)
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Institute of Chemistry, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
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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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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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Efstathiadou E, Savvas D, Tampakaki AP. Genetic diversity and phylogeny of indigenous rhizobia nodulating faba bean (Vicia faba L.) in Greece. Syst Appl Microbiol 2020; 43:126149. [PMID: 33161357 DOI: 10.1016/j.syapm.2020.126149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/19/2020] [Accepted: 09/19/2020] [Indexed: 12/16/2022]
Abstract
The genetic diversity and phylogeny of fast-growing rhizobia isolated from root nodules of Vicia faba grown in different geographical regions of Greece were assessed. Although Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia spp. in European soils, there is no available information on native rhizobia nodulating faba bean in Greece. Seventy bacterial strains were isolated and grouped into sixteen distinct profiles based on BOX-PCR fingerprinting. The phylogenetic affiliation was further defined by sequence analysis of the rrs and multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and gyrB). Fifty-eight isolates were affiliated with recently described genospecies gsF-2, represented by R. laguerreae FB206T, whereas six isolates were closely related to gsB and two isolates might belong to gsA. Two isolates assigned to R. hidalgonense and another two non-nodulating strains could not be assigned to any validly defined species and possibly belong to a new rhizobial lineage. Interestingly, R. laguerreae strains were commonly found at all sampling sites, suggesting that they could be the main symbionts of faba beans in Greek soils. According to the phylogenies of two symbiosis-related genes (nodC and nifH), all nodulating isolates belonged to symbiovar (sv.) viciae harboring four distinct nodC gene haplotypes and they were grouped into two clades together with strains assigned to R. laguerreae and genospecies of R. leguminosarum isolated from other countries and continents. This is the first report that R. hidalgonense strains belong to sv. viciae. No correlation was observed between the nodC haplotypes, geographic origin and chromosomal background of the isolates in the study.
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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
| | - 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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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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Zhang J, Xu Y, Liang S, Ma X, Lu Z, Sun P, Zhang H, Sun F. Synergistic effect of Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1 on the growth of the microbiota in the black soil of Northeast China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110079. [PMID: 31841891 DOI: 10.1016/j.ecoenv.2019.110079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
The application of Atrazine in soil has always been a main problem in agriculture because its residuals may maintain in the soil for a long term. In this paper, two strains of Atrazine degrading bacteria (Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1) were used to make biological compound microbial inoculum to repair the Atrazine contaminated typical black soil in Northeast China. Grain chaff was chosen as the optimal carrier material for microbial inoculum. The dynamic changes of Atrazine were detected by gas chromatography. The half-life of Atrazine in soil containing microbial inoculum was shortened from 9.8 d to 4.2 d. The Atrazine sensitive crops grown in the repaired soil showed increased stem length, root length, and emergence rate. The effects of microbial remediation on the original bacterial and fungal biota in the typical black soil in Northeast China were analyzed using the metagenomic approach. Results showed that Atrazine inhibited the original bacteria and fungi populations. The total numbers of bacterial and fungal species in the soil were partially recovered by adding the microbial inoculum. Two genera (Sphingosinicella and Sphingomonas) were the dominant bacteria. The beneficial bacterial biota was recovered and the number of species of the beneficial bacteria was higher than that in the original soil after adding the microbial inoculum. The dominant fungi included genera Guehomyces and Chaetomella. There was a total of 113 unclassified fungal genera (22.6% of 499), indicating the potential utility of the unclassified fungal species in the assessment of the soil contamination by Atrazine.
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Affiliation(s)
- Jinpeng Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Yuncheng Xu
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Shuang Liang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Xiulan Ma
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Zhongbin Lu
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Peng Sun
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Hao Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China.
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, 30043, USA.
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12
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Tong W, Li X, Wang E, Cao Y, Chen W, Tao S, Wei G. Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts. BMC Genomics 2020; 21:186. [PMID: 32106817 PMCID: PMC7047383 DOI: 10.1186/s12864-020-6578-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 02/13/2020] [Indexed: 01/02/2023] Open
Abstract
Background Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts. Results Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions. Conclusions The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.
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Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México D.F, Mexico
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Shiheng Tao
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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13
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Gunnabo AH, Geurts R, Wolde-Meskel E, Degefu T, Giller KE, van Heerwaarden J. Genetic Interaction Studies Reveal Superior Performance of Rhizobium tropici CIAT899 on a Range of Diverse East African Common Bean (Phaseolus vulgaris L.) Genotypes. Appl Environ Microbiol 2019; 85:e01763-19. [PMID: 31562174 PMCID: PMC6881787 DOI: 10.1128/aem.01763-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023] Open
Abstract
We studied symbiotic performance of factorial combinations of diverse rhizobial genotypes (GR) and East African common bean varieties (GL) that comprise Andean and Mesoamerican genetic groups. An initial wide screening in modified Leonard jars (LJ) was followed by evaluation of a subset of strains and genotypes in pots (contained the same, sterile medium) in which fixed nitrogen was also quantified. An additive main effect and multiplicative interaction (AMMI) model was used to identify the contribution of individual strains and plant genotypes to the GL × GR interaction. Strong and highly significant GL × GR interaction was found in the LJ experiment but with little evidence of a relation to genetic background or growth habits. The interaction was much weaker in the pot experiment, with all bean genotypes and Rhizobium strains having relatively stable performance. We found that R. etli strain CFN42 and R. tropici strains CIAT899 and NAK91 were effective across bean genotypes but with the latter showing evidence of positive interaction with two specific bean genotypes. This suggests that selection of bean varieties based on their response to inoculation is possible. On the other hand, we show that symbiotic performance is not predicted by any a priori grouping, limiting the scope for more general recommendations. The fact that the strength and pattern of GL × GR depended on growing conditions provides an important cautionary message for future studies.IMPORTANCE The existence of genotype-by-strain (GL × GR) interaction has implications for the expected stability of performance of legume inoculants and could represent both challenges and opportunities for improvement of nitrogen fixation. We find that significant genotype-by-strain interaction exists in common bean (Phaseolus vulgaris L.) but that the strength and direction of this interaction depends on the growing environment used to evaluate biomass. Strong genotype and strain main effects, combined with a lack of predictable patterns in GL × GR, suggests that at best individual bean genotypes and strains can be selected for superior additive performance. The observation that the screening environment may affect experimental outcome of GL × GR means that identified patterns should be corroborated under more realistic conditions.
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Affiliation(s)
- A H Gunnabo
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
| | - R Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University and Research, Wageningen, The Netherlands
| | - E Wolde-Meskel
- World Agroforestry Centre (ICRAF), Addis Ababa, Ethiopia
| | - T Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - K E Giller
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
| | - J van Heerwaarden
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
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14
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Rajnovic I, Ramírez-Bahena MH, Sánchez-Juanes F, González-Buitrago JM, Kajic S, Peix Á, Velázquez E, Sikora S. Phylogenetic diversity of rhizobia nodulating Phaseolus vulgaris in Croatia and definition of the symbiovar phaseoli within the species Rhizobium pisi. Syst Appl Microbiol 2019; 42:126019. [PMID: 31635886 DOI: 10.1016/j.syapm.2019.126019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/27/2022]
Abstract
Phaseolus vulgaris is a legume indigenous to America which is currently cultivated in Europe including countries located at the Southeast of this continent, such as Croatia, where several local landraces are cultivated, most of them of Andean origin. In this work we identify at species and symbiovar levels several fast-growing strains able to form effective symbiosis with P. vulgaris in different Croatian soils. The identification at species level based on MALDI-TOF MS and core gene sequence analysis showed that most of these strains belong to the species R. leguminosarum, R. hidalgonense and R. pisi. In addition, several strains belong to putative new species phylogenetically close to R. ecuadorense and R. sophoriradicis. All Croatian strains belong to the symbiovar phaseoli and harbour the α and γ nodC alleles typical for American strains of this symbiovar. Nevertheless, most of Croatian strains harboured the γ nodC gene allele supporting its Andean origin since it is also dominant in other European countries, where Andean cultivars of P. vulgaris are traditionally cultivated, as occurs in Spain. The only strains harbouring the α nodC allele belong to R. hidalgonense and R. pisi, this last only containing the symbiovars viciae and trifolii to date. This is the first report about the presence in Europe of the species R. hidalgonense, the nodulation of P. vulgaris by R. pisi and the existence of the symbiovar phaseoli within this species. These results significantly increase the knowledge of the biogeography of Rhizobium-P. vulgaris symbiosis.
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Affiliation(s)
- Ivana Rajnovic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | | | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - José-Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - Sanja Kajic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain.
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain; Departmento de Microbiología y Genética and CIALE, Universidad de Salamanca, Salamanca, Spain
| | - Sanja Sikora
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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15
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Benjelloun I, Thami Alami I, Douira A, Udupa SM. Phenotypic and Genotypic Diversity Among Symbiotic and Non-symbiotic Bacteria Present in Chickpea Nodules in Morocco. Front Microbiol 2019; 10:1885. [PMID: 31620094 PMCID: PMC6759536 DOI: 10.3389/fmicb.2019.01885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/30/2019] [Indexed: 11/19/2022] Open
Abstract
Environmental pollution problems and increased demand for green technologies in production are forcing farmers to introduce agricultural practices with a lower impact on the environment. Chickpea (Cicer arietinum) in arid and semi-arid environments is frequently affected by harsh environmental stresses such as heat, drought and salinity, which limit its growth and productivity and affect biological nitrogen fixation ability of rhizobia. Climate change had further aggravated these stresses. Inoculation with appropriate stress tolerant rhizobia is necessary for an environmentally friendly and sustainable agricultural production. In this study, endophytic bacteria isolated from chickpea nodules from different soil types and regions in Morocco, were evaluated for their phenotypic and genotypic diversity in order to select the most tolerant ones for further inoculation of this crop. Phenotypic characterization of 135 endophytic bacteria from chickpea nodules showed a wide variability for tolerance to heavy metals and antibiotics, variable response to extreme temperatures, salinity, pH and water stress. 56% of isolates were able to nodulate chickpea. Numerical analysis of rep-PCR results showed that nodulating strains fell into 22 genotypes. Sequencing of 16S rRNA gene of endophytic bacteria from chickpea nodules revealed that 55% of isolated bacteria belong to Mesorhizobium genus. Based on MLSA of core genes (recA, atpD, glnII and dnaK), tasted strains were distributed into six clades and were closely related to Mesorhizobium ciceri, Mesorhizobium opportunistum, Mesorhizobium qingshengii, and Mesorhizobium plurifarium. Most of nodulating strains were belonging to a group genetically distinct from reference Mesorhizobium species. Three isolates belong to genus Burkholderia of the class β- proteobacteria, and 55 other strains belong to the class γ- proteobacteria. Some of the stress tolerant isolates have great potential for further inoculation of chickpea in the arid and semiarid environments to enhance biological nitrogen fixation and productivity in the context of climate change adaptation and mitigation.
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Affiliation(s)
- Imane Benjelloun
- Department of Microbiology, National Institute of Agronomical Research, Rabat, Morocco
- Department of Biology, Faculty of Sciences, Ibn Tofail University, Kenitra, Morocco
- ICARDA-INRA Cooperative Research Project, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Imane Thami Alami
- Department of Microbiology, National Institute of Agronomical Research, Rabat, Morocco
| | - Allal Douira
- Department of Biology, Faculty of Sciences, Ibn Tofail University, Kenitra, Morocco
| | - Sripada M. Udupa
- ICARDA-INRA Cooperative Research Project, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
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16
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Bouznif B, Guefrachi I, Rodríguez de la Vega RC, Hungria M, Mars M, Alunni B, Shykoff JA. Phylogeography of the Bradyrhizobium spp. Associated With Peanut, Arachis hypogaea: Fellow Travelers or New Associations? Front Microbiol 2019; 10:2041. [PMID: 31551977 PMCID: PMC6737463 DOI: 10.3389/fmicb.2019.02041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
Legume plants have colonized almost all terrestrial biotopes. Their ecological success is partly due to the selective advantage provided by their symbiotic association with nitrogen-fixing bacteria called rhizobia, which allow legumes to thrive on marginal lands and nitrogen depleted soils where non-symbiotic plants cannot grow. Additionally, their symbiotic capacities result in a high protein content in their aerial parts and seeds. This interesting nutritional value has led to the domestication and agricultural exploitation of several legumes grown for seeds and/or fodder for human and domestic animal consumption. Several cultivated legume species are thus grown far beyond their natural geographic range. Other legume species have become invasives, spreading into new habitats. The cultivation and establishment of legume species outside of their original range requires either that they are introduced or cultivated along with their original symbiotic partner or that they find an efficient symbiotic partner in their introduced habitat. The peanut, Arachis hypogaea, a native of South America, is now cultivated throughout the world. This species forms root nodules with Bradyrhizobium, but it is unclear whether these came with the seeds from their native range or were acquired locally. Here we propose to investigate the phylogeography of Bradyrhizobium spp. associated with a number of different wild and cultivated legume species from a range of geographical areas, including numerous strains isolated from peanut roots across the areas of peanut cultivation. This will allow us to address the question of whether introduced/cultivated peanuts associate with bacteria from their original geographic range, i.e., were introduced together with their original bacterial symbionts, or whether they acquired their current associations de novo from the bacterial community within the area of introduction. We will base the phylogenetic analysis on sequence data from both housekeeping and core genes and a symbiotic gene (nif). Differences between the phylogenetic signal of symbiotic and non-symbiotic genes could result from horizontal transfer of symbiosis capacity. Thus this study will also allow us to elucidate the processes by which this symbiotic association has evolved within this group of Bradyrhizobium spp.
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Affiliation(s)
- Besma Bouznif
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Ibtissem Guefrachi
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | | | | | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Benoit Alunni
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Jacqui Anne Shykoff
- Écologie, Systématique et Évolution, CNRS, University Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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17
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Huo Y, Tong W, Wang J, Wang F, Bai W, Wang E, Shi P, Chen W, Wei G. Rhizobium chutanense sp. nov., isolated from root nodules of Phaseolus vulgaris in China. Int J Syst Evol Microbiol 2019; 69:2049-2056. [PMID: 31091180 DOI: 10.1099/ijsem.0.003430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, rod-shaped bacterial strains (C5T and C16), isolated from root nodules of Phaseolus vulgaris L. in Jiangxi Province, PR China, were characterized by using a polyphasic taxonomical approach. The phylogenetic analysis of the 16S rRNA gene and three concatenated housekeeping genes (recA-glnII-atpD) revealed that C5T and C16 were members of the genus Rhizobium, yet were distinct from known species. The case for strain C5T representing a novel species was supported by genomic results. Pairwise digital DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. The genome-based phylogenetic tree reconstructed by using the up-to-date bacterial core gene set consisting of 92 genes showed that the strains formed a monophyletic branch, further supporting this result. The symbiotic genes of nodC and nifH were identified in both strains; each could nodulate Phaseolus vulgaris and Glycine max but not Leucaena leucocephala, Pisum sativum or Medicago sativa plants. Major cellular fatty acids of C5T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 58.8 %), C18 : 1 ω7c 11-methyl (14.2 %) and C18 : 0 (8.1 %). The DNA G+C content of C5T was 61.4 mol%. Based on these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Rhizobium chutanense sp. nov. The type strain is C5T (=CCTCC AB 2018143T=LMG 30777T).
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Affiliation(s)
- Yunyun Huo
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Wenjun Tong
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Juanjuan Wang
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Fang Wang
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Wenqing Bai
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Entao Wang
- 3Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico
| | - Peng Shi
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
| | - Weimin Chen
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
| | - Gehong Wei
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Shaanxi, PR China
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Shaanxi, PR China
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18
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González V, Santamaría RI, Bustos P, Pérez-Carrascal OM, Vinuesa P, Juárez S, Martínez-Flores I, Cevallos MÁ, Brom S, Martínez-Romero E, Romero D. Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters. Front Microbiol 2019; 10:910. [PMID: 31114559 PMCID: PMC6503217 DOI: 10.3389/fmicb.2019.00910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 01/07/2023] Open
Abstract
The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.
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Affiliation(s)
- Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rosa Isela Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Susana Brom
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Ji Z, Liu T, Zhang J, Yan H, Wang E, Cui Q, Chen W, Chen W. Genetic divergence among Bradyrhizobium strains nodulating wild and cultivated Kummerowia spp. in China. Syst Appl Microbiol 2018; 42:223-231. [PMID: 30343835 DOI: 10.1016/j.syapm.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
Distribution of rhizobial species is affected by geographical isolation and selected by leguminous hosts, however, little is known about the molecular evolution of rhizobia nodulating the same legume in different eco-environments. In present study, the microevolution of Bradyrhizobium associated with the leguminous grass Kummerowia grown in exurban areas and cultivated in urban areas in China was investigated. Total 14 genospecies, including seven new groups, were identified based on a concatenated sequence analysis of taxonomic markers (SMc00019, truA and thrA) for 94 representative strains. Results demonstrated that lower levels of nucleotide diversity were found in the strains isolated from urban areas compared with those isolated from exurban areas, based on the evolutional analyses of three housekeeping genes (atpD, glnII and recA), two symbiosis-related genes (nodC and nifH), and the taxonomic markers. Moreover, compared with urban areas, gene exchange and recombination occurred more frequently among the genospecies isolated from exurban areas, regardless of the geographical distribution. Finally, the evolutionary lineage of Bradyrhizobium strains isolated from urban areas was independent of that of the strains isolated from exurban areas. In summary, the evolutionary history of Kummerowia bradyrhizobia may have been gradually segregated to different evolutionary lineages, irrespective of distinct biogeography.
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Affiliation(s)
- Zhaojun Ji
- College of Life Science and Horqin Plant Stress Biology Research Institute, Inner Mongolia University for the Nationalities, Tongliao 028042, Inner Mongolia, China; State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Tianyan Liu
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Jixing Zhang
- College of Life Science and Horqin Plant Stress Biology Research Institute, Inner Mongolia University for the Nationalities, Tongliao 028042, Inner Mongolia, China
| | - Hui Yan
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Qingguo Cui
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenxin Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China.
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