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Aslam MM, Fritschi FB, Di Z, Wang G, Li H, Lam HM, Waseem M, Weifeng X, Zhang J. Overexpression of LaGRAS enhances phosphorus acquisition via increased root growth of phosphorus-deficient white lupin. PHYSIOLOGIA PLANTARUM 2023; 175:e13962. [PMID: 37343119 DOI: 10.1111/ppl.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
The GRAS transcription factors play an indispensable role in plant growth and responses to environmental stresses. The GRAS gene family has extensively been explored in various plant species; however, the comprehensive investigation of GRAS genes in white lupin remains insufficient. In this study, bioinformatics analysis of white lupin genome revealed 51 LaGRAS genes distributed into 10 distinct phylogenetic clades. Gene structure analyses revealed that LaGRAS proteins were considerably conserved among the same subfamilies. Notably, 25 segmental duplications and a single tandem duplication showed that segmental duplication was the major driving force for the expansion of GRAS genes in white lupin. Moreover, LaGRAS genes exhibited preferential expression in young cluster root and mature cluster roots and may play key roles in nutrient acquisition, particularly phosphorus (P). To validate this, RT-qPCR analysis of white lupin plants grown under +P (normal P) and -P (P deficiency) conditions elucidated significant differences in the transcript level of GRAS genes. Among them, LaGRAS38 and LaGRAS39 were identified as potential candidates with induced expression in MCR under -P. Additionally, white lupin transgenic hairy root overexpressing OE-LaGRAS38 and OE-LaGRAS39 showed increased root growth, and P concentration in root and leaf compared to those with empty vector control, suggesting their role in P acquisition. We believe this comprehensive analysis of GRAS members in white lupin is a first step in exploring their role in the regulation of root growth, tissue development, and ultimately improving P use efficiency in legume crops under natural environments.
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Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Felix B Fritschi
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Zhang Di
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Muhammad Waseem
- College of Horticulture, Hainan University, Haikou, China
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Xu Weifeng
- College of Agriculture, Yangzhou University, Yangzhou, China
- Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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2
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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3
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Bromfield ESP, Cloutier S, Wasai-Hara S, Minamisawa K. Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel
Bradyrhizobium
lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit (rps) gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named
Bradyrhizobium
species with
B. japonicum
USDA 6T as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome blast distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4T, 323S2, 1S5 and 38S5T have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4T and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5T (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names Bradyrhizobium barranii sp. nov. subsp. barranii subsp. nov. (sv. glycinearum) and Bradyrhizobium barranii sp. nov. subsp. apii subsp. nov. (sv. septentrionale) are proposed with strain 144S4T (=LMG 31552T=HAMBI 3722T) as the species type strain and type strain of subsp. barranii subsp. nov., and strain 38S5T (=LMG 31556T=HAMBI 3721T) as the type strain of subsp. apii subsp. nov.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sawa Wasai-Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8604, Japan
- Graduate School of Life Sciences, Tohoku University,, Katahira, Aoba-ku, Sendai 980–8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University,, Katahira, Aoba-ku, Sendai 980–8577, Japan
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Phylogenetic and symbiotic diversity of Lupinus albus and L. angustifolius microsymbionts in the maamora forest, morocco. Syst Appl Microbiol 2022; 45:126338. [DOI: 10.1016/j.syapm.2022.126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022]
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5
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Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana). PLANTS 2022; 11:plants11070990. [PMID: 35406970 PMCID: PMC9002731 DOI: 10.3390/plants11070990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/25/2022]
Abstract
The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.
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Alkemade JA, Nazzicari N, Messmer MM, Annicchiarico P, Ferrari B, Voegele RT, Finckh MR, Arncken C, Hohmann P. Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1011-1024. [PMID: 34988630 PMCID: PMC8942938 DOI: 10.1007/s00122-021-04014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 05/11/2023]
Abstract
GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
| | | | - Barbara Ferrari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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7
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Castellano-Hinojosa A, Correa-Galeote D, Ramírez-Bahena MH, Tortosa G, González-López J, Bedmar EJ, Peix Á. Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870578 DOI: 10.1099/ijsem.0.005120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to 'A. deltaense' YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium. Whole genome average nucleotide identity and digital DNA-DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10-42 °C, pH 5.0-10.0 and with 0.0-0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium, for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain.,Department of Microbiology, Faculty of Pharmacy, University of Granada. Campus Cartuja, 18071-Granada, Spain
| | - David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | | | - Germán Tortosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | - Jesús González-López
- Department of Microbiology, Faculty of Pharmacy, University of Granada. Campus Cartuja, 18071-Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, 18080-Granada, Spain
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [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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9
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Salmi A, Boulila F. Heavy metals multi-tolerant Bradyrhizobium isolated from mercury mining region in Algeria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112547. [PMID: 33839604 DOI: 10.1016/j.jenvman.2021.112547] [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: 12/25/2020] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Heavy metals accumulation in the environment has led to a decrease in the capacity of ecosystems to sustain life as human, animal and plant health is threatened. To remedy this problem, rhizoremediation has been suggested as a solution. Legumes and rhizobia symbiotic association has captivated attention due to its involvement in the restoration of heavy-metal-contaminated sites. Thus, the aim of this study was to isolate and characterize the strains nodulating Calicotome spinosa plant that naturally occurred in two Algerian mercury mines. Fifty-four bacterial strains were isolated, then grouped into sixteen distinct BOX-PCR patterns and were genetically identified as belonging to the Bradyrhizobium genus. The studied strains were able to induce nodules on Retama monosperma, R. reatam, Lupinus albus, while no nodulation was observed in Glycine max, their symbiotic capacity was confirmed by amplifying the nodC gene. The phylogenetic analysis based on the nodC has grouped this Bradyrhizobium strains to either symbiovar genistearum or retamae. The isolates revealed diversity in terms of NaCl; pH tolerance, and phosphate solubilization. Production of siderophores was negative for these strains. All the isolated Bradyrhizobium were tolerant to both Zn and Pb in contrast they were sensitive to Cu and Cd. Interestingly, 43% of strains were tolerant to high Hg levels. Hence, some strains displayed multiple tolerances to heavy metals. Therefore, this is the first time we identify Bradyrhizobium strains originating from a North African mercury mine. This study could help to select mercury and other heavy metal-tolerant rhizobia showing an interesting potential to be used as inoculants to remediate the heavy metal soil accumulation.
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Affiliation(s)
- Adouda Salmi
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
| | - Farida Boulila
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria
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10
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Alkemade JA, Messmer MM, Arncken C, Leska A, Annicchiarico P, Nazzicari N, Książkiewicz M, Voegele RT, Finckh MR, Hohmann P. A High-Throughput Phenotyping Tool to Identify Field-Relevant Anthracnose Resistance in White Lupin. PLANT DISEASE 2021; 105:1719-1727. [PMID: 33337235 DOI: 10.1094/pdis-07-20-1531-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The seed- and air-borne pathogen Colletotrichum lupini, the causal agent of lupin anthracnose, is the most important disease in white lupin (Lupinus albus) worldwide and can cause total yield loss. The aims of this study were to establish a reliable high-throughput phenotyping tool to identify anthracnose resistance in white lupin germplasm and to evaluate a genomic prediction model, accounting for previously reported resistance quantitative trait loci, on a set of independent lupin genotypes. Phenotyping under controlled conditions, performing stem inoculation on seedlings, showed to be applicable for high throughput, and its disease score strongly correlated with field plot disease assessments (r = 0.95, P < 0.0001) and yield (r = -0.64, P = 0.035). Traditional one-row field disease phenotyping showed no significant correlation with field plot disease assessments (r = 0.31, P = 0.34) and yield (r = -0.45, P = 0.17). Genomically predicted resistance values showed no correlation with values observed under controlled or field conditions, and the parental lines of the recombinant inbred line population used for constructing the prediction model exhibited a resistance pattern opposite to that displayed in the original (Australian) environment used for model construction. Differing environmental conditions, inoculation procedures, or population structure may account for this result. Phenotyping a diverse set of 40 white lupin accessions under controlled conditions revealed eight accessions with improved resistance to anthracnose. The standardized area under the disease progress curves (sAUDPC) ranged from 2.1 to 2.8, compared with the susceptible reference accession with a sAUDPC of 3.85. These accessions can be incorporated into white lupin breeding programs. In conclusion, our data support stem inoculation-based disease phenotyping under controlled conditions as a time-effective approach to identify field-relevant resistance, which can now be applied to further identify sources of resistance and their underlying genetics.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Agata Leska
- Getreidezüchtung Peter Kunz (gzpk), Feldbach, Switzerland
| | | | - Nelson Nazzicari
- CREA, Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | | | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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11
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Bouhnik O, Lamin H, Alami S, Bennis M, Ouajdi M, Bellaka M, El Antry S, Abbas Y, Abdelmoumen H, Bedmar EJ, El Idrissi MM. The endemic Chamaecytisus albidus is nodulated by symbiovar genistearum of Bradyrhizobium in the Moroccan Maamora Forest. Syst Appl Microbiol 2021; 44:126197. [PMID: 33838436 DOI: 10.1016/j.syapm.2021.126197] [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: 06/19/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 10/21/2022]
Abstract
Out of 54 isolates from root nodules of the Moroccan-endemic Chamaecytisus albidus plants growing in soils from the Maamora cork oak forest, 44 isolates formed nodules when used to infect their original host plant. A phenotypic analysis showed the metabolic diversity of the strains that used different carbohydrates and amino acids as sole carbon and nitrogen sources. The isolates grew on media with pH values ranging from 6 to 8. However, they did not tolerate high temperatures or drought and they did not grow on media with salt concentrations higher than 85 mM. REP-PCR fingerprinting grouped the strains into 12 clusters, of which representative strains were selected for ARDRA and rrs analyses. The rrs gene sequence analysis indicated that all 12 strains were members of the genus Bradyrhizobium and their phylogeny showed that they were grouped into two different clusters. Two strains from each group were selected for multilocus sequence analysis (MLSA) using atpD, recA, gyrB and glnII housekeeping genes. The inferred phylogenetic trees confirmed that the strains clustered into two divergent clusters. Strains CM55 and CM57 were affiliated to the B. canariense/B. lupini group, whereas strains CM61 and CM64 were regrouped within the B. cytisi/B. rifense lineage. The analysis of the nodC symbiotic gene affiliated the strains to the symbiovar genistearum. The strains were also able to nodulate Retama monosperma, Lupinus luteus and Cytisus monspessulanus, but not Phaseolus vulgaris or Glycine max. Inoculation tests with C. albidus showed that some strains could be exploited as efficient inocula that could be used to improve plant growth in the Maamora forest.
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Affiliation(s)
- Omar Bouhnik
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Hanane Lamin
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Soufiane Alami
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Meryeme Bennis
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Mohammed Ouajdi
- Centre de Recherche Forestière, Département des Eaux et Forêts, Avenue Omar Ibn El Khattab, BP 763, Rabat-Agdal 10050, Morocco
| | - M'hamed Bellaka
- Centre de Recherche Forestière, Département des Eaux et Forêts, Avenue Omar Ibn El Khattab, BP 763, Rabat-Agdal 10050, Morocco
| | - Salwa El Antry
- Centre de Recherche Forestière, Département des Eaux et Forêts, Avenue Omar Ibn El Khattab, BP 763, Rabat-Agdal 10050, Morocco
| | - Younes Abbas
- Faculté Polydiciplinaire, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Eulogio J Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, CSIC Estación Experimental del Zaidín, Apartado Postal 419, 18080 Granada, Spain
| | - Mustapha Missbah El Idrissi
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco.
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12
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Mannaa M, Han G, Jeon HW, Kim J, Kim N, Park AR, Kim JC, Seo YS. Influence of Resistance-Inducing Chemical Elicitors against Pine Wilt Disease on the Rhizosphere Microbiome. Microorganisms 2020; 8:microorganisms8060884. [PMID: 32545246 PMCID: PMC7356868 DOI: 10.3390/microorganisms8060884] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/24/2022] Open
Abstract
Pine wilt disease (PWD) caused by Bursaphelenchus xylophilus is a major threat to pine forests worldwide. Induction of resistance is a promising and safe management option that should be investigated in relation to its possible influence on the pine tree ecosystem, including the surrounding microbial communities. In this study, two main resistance-inducing chemical elicitors, methyl salicylic acid (MeSA) and acibenzolar-s-methyl (ASM), were tested for their control efficiency against PWD and their influence on the rhizosphere microbial composition. Foliar treatment of pine seedlings with the chemical elicitors resulted in a reduction in PWD severity, with ASM showing better control efficacy, reaching up to 73% compared to the untreated control. Moreover, bacterial community analysis of the rhizosphere revealed significant changes in several microbial taxa that were present at low relative abundance. In particular, ASM treatment resulted in a significant increase in specific microbial taxa, including members of the Rhodanobacter, Devosia, Bradyrhizobium, Acidibacter, Mesorhizobium, and Hyphomicrobium genera, which are known to play ecological and plant growth-promoting roles. Furthermore, chitinolytic bacteria were shown to be reduced in response to treatment with both MeSA and ASM. Altogether, the present findings demonstrate the occurrence of significant alterations in several ecologically important microbial taxa after treatment with resistance-inducing chemicals. As compared to MeSA treatment, ASM treatment was more effective at suppressing PWD and resulted in more beneficial changes in rhizosphere microbial composition.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.); (N.K.)
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.); (N.K.)
| | - Hee Won Jeon
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Junheon Kim
- Forest Insect Pests and Diseases Division, National Institute of Forest Science, Seoul 02455, Korea;
| | - Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.); (N.K.)
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.); (N.K.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
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13
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Kosmachevskaya OV, Osipov EV, Van Chi T, Mai PTT, Topunov AF. Effect of Cultivation Conditions on Poly(3-hydroxybutyrate) Synthesis by Nodule Bacteria Rhizobium phaseoli. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s000368382001010x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Kalita M, Małek W, Coutinho TA. Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus. Syst Appl Microbiol 2020; 43:126056. [PMID: 31987702 DOI: 10.1016/j.syapm.2020.126056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.
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Affiliation(s)
- Michał Kalita
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland.
| | - Wanda Małek
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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15
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Root nodules of Genista germanica harbor Bradyrhizobium and Rhizobium bacteria exchanging nodC and nodZ genes. Syst Appl Microbiol 2020; 43:126026. [DOI: 10.1016/j.syapm.2019.126026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022]
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16
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Ramírez-Bahena MH, Flores-Félix JD, Velázquez E, Peix Á. The Mimosoid tree Leucaena leucocephala can be nodulated by the symbiovar genistearum of Bradyrhizobium canariense. Syst Appl Microbiol 2019; 43:126041. [PMID: 31767155 DOI: 10.1016/j.syapm.2019.126041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/16/2022]
Abstract
Leucaena leucocephala is a Mimosoid legume tree indigenous to America that has spread to other continents, although it is not still present in some European countries such as Portugal. Nevertheless, we found that this legume can be nodulated in this country by slow-growing rhizobial strains which were identified as Bradyrhizobium canariense trough the analysis of the core genes recA and glnII. The analysis of the symbiotic gene nodC showed that these strains belong to the symbiovar genistearum, which commonly nodulates Genistoid legumes. Although two strains nodulating L. leucocephala in China and Brazil were classified within the genus Bradyrhizobium, they belong to undescribed species and to the symbiovars glycinearum and tropici, respectively. Therefore, we report here for the first time the ability of L. leucocephala to establish symbiosis with strains of B. canariense sv genistearum confirming the high promiscuity of L. leucocephala, that allows it to establish symbiosis with rhizobia native to different continents increasing its invasiveness potential.
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Affiliation(s)
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias(CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias(CIALE), Universidad de Salamanca, Edificio Departamental de Biología, Lab 209. Av. Doctores de la Reina S/N, 37007 Salamanca, Spain; Unidad Asociada Grupo de Interacción planta-microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain
| | - 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.
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17
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Obando M, Correa-Galeote D, Castellano-Hinojosa A, Gualpa J, Hidalgo A, Alché JD, Bedmar E, Cassán F. Analysis of the denitrification pathway and greenhouse gases emissions in Bradyrhizobium sp. strains used as biofertilizers in South America. J Appl Microbiol 2019; 127:739-749. [PMID: 30803109 DOI: 10.1111/jam.14233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 02/19/2019] [Indexed: 02/02/2023]
Abstract
AIMS Greenhouse gases are considered as potential atmospheric pollutants, with agriculture being one of the main emission sources. The practice of inoculating soybean seeds with Bradyrhizobium sp. might contribute to nitrous oxide (N2 O) emissions. We analysed this capacity in five of the most used strains of Bradyrhizobium sp. in South America. METHODS AND RESULTS We analysed the denitrification pathway and N2 O production by Bradyrhizobium japonicum E109 and CPAC15, Bradyrhizobium diazoefficiens CPAC7 and B. elkanii SEMIA 587 and SEMIA 5019, both in free-living conditions and in symbiosis with soybean. The in silico analysis indicated the absence of nosZ genes in B. japonicum and the presence of all denitrification genes in B. diazoefficiens strains, as well as the absence of nirK, norC and nosZ genes in B. elkanii. The in planta analysis confirmed N2 O production under saprophytic conditions or symbiosis with soybean root nodules. In the case of symbiosis, up to 26.1 and 18.4 times higher in plants inoculated with SEMIA5019 and E109, respectively, than in those inoculated with USDA110. CONCLUSIONS The strains E109, SEMIA 5019, CPAC15 and SEMIA 587 showed the highest N2 O production both as free-living cells and in symbiotic conditions in comparison with USDA110 and CPAC7, which do have the nosZ gene. Although norC and nosZ could not be identified in silico or in vitro in SEMIA 587 and SEMIA 5019, these strains showed the capacity to produce N2 O in our experimental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to analyse and confirm the incomplete denitrification capacity and N2 O production in four of the five most used strains of Bradyrhizobium sp. for soybean inoculation in South America.
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Affiliation(s)
- M Obando
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - D Correa-Galeote
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - A Castellano-Hinojosa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - J Gualpa
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - A Hidalgo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - J D Alché
- Departamento de Protection Vegetal, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - E Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - F Cassán
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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18
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Rejili M, Msaddak A, Filali I, Benabderrahim MA, Mars M, Marín M. New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils. FEMS Microbiol Ecol 2019; 95:5537381. [DOI: 10.1093/femsec/fiz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTThirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.
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Affiliation(s)
- 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
| | - A Msaddak
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - I Filali
- College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh PO Box 84428, Saudi Arabia
| | - M A Benabderrahim
- Arid and Oases Cropping Laboratory, Arid Area Institute, Gabes 6051, 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 Marín
- Institute of Genetics, Ludwig Maximilians University of Munich (LMU), Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
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19
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Kong Z, Li L, Kato H, Zhang T, Xue Y, Li YY. Dissection and characterization of the prokaryotic community during the long-term operation of a submerged anaerobic membrane bioreactor for the anaerobic treatment of N, N-dimethylformamide-containing wastewater with a co-cultured inoculum. BIORESOURCE TECHNOLOGY 2019; 282:482-493. [PMID: 30897486 DOI: 10.1016/j.biortech.2019.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
A submerged anaerobic membrane bioreactor (SAnMBR) was operated for the anaerobic treatment of wastewater containing approximately 2000 mg L-1N, N-dimethylformamide (DMF). Inoculated with a co-cultured inoculum, the SAnMBR obtained an excellent DMF removal under a low organic loading rate (OLR) of 3.14-4.16 g COD L-1 d-1. However, the elevation of OLR limited hydrolysis. While the co-cultured inoculum initially contains abundant DMF-hydrolyzing bacteria with potential to hydrolyze DMF into intermediates, such as Paracoccus, Hyphomicrobium, Burkholderia, Catellibacterium, Bacillus and Bradyrhizobium, since these bacteria are facultative anaerobes which survive anaerobically, they kept decaying rather than proliferating, resulting in the weakening of the DMF-hydrolyzing ability. Each re-inoculation of new sludge only temporarily revitalized hydrolysis activity for a short period. Due to the lack of nitrate, these bacteria were unable to proliferate. This suggests that a small dose of nitrate would help to enrich these bacteria and establish a stable DMF-degrading consortium.
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Affiliation(s)
- Zhe Kong
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Lu Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Hiroyuki Kato
- The Japan Institute of Wastewater Engineering and Technology, Suido-Cho Bld 7F, 3-1 Suido-Cho, Shinjuku Ward, Tokyo 162-0811, Japan
| | - Tao Zhang
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yi Xue
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan.
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20
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol 2019; 42:427-439. [PMID: 31031014 DOI: 10.1016/j.syapm.2019.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023]
Abstract
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels.
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Affiliation(s)
- Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort 0110, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Poland
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Stephanus N Venter
- 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. http://emma.steenkamp.up.ac.za
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21
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Jaiswal SK, Dakora FD. Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa. Front Microbiol 2019; 10:310. [PMID: 30853952 PMCID: PMC6395442 DOI: 10.3389/fmicb.2019.00310] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/05/2019] [Indexed: 11/17/2022] Open
Abstract
Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Faculty of Science, Tshwane University of Technology, Pretoria, South Africa
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22
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Phylogenetic diversity of Bradyrhizobium strains nodulating Calicotome spinosa in the Northeast of Algeria. Syst Appl Microbiol 2018; 41:452-459. [DOI: 10.1016/j.syapm.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
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23
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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Talyzin VV, Bashirova NF, Kosmachevskaya OV, Punina NV, Arabova LI, Tikhomirova NV, Topunov AF. Methemoglobin Reductase of Bacteria and Bacteroids Bradyrhizobium lupini: Purification and Properties. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818010131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland. Syst Appl Microbiol 2017; 40:482-491. [DOI: 10.1016/j.syapm.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/24/2017] [Accepted: 09/20/2017] [Indexed: 01/27/2023]
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26
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Msaddak A, Rejili M, Durán D, Rey L, Imperial J, Palacios JM, Ruiz-Argüeso T, Mars M. Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils. FEMS Microbiol Ecol 2017; 93:3828104. [PMID: 28505340 DOI: 10.1093/femsec/fix068] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/12/2017] [Indexed: 11/14/2022] Open
Abstract
The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga.
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Affiliation(s)
- Abdelhakim Msaddak
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain.,CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Jose Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Tomas Ruiz-Argüeso
- CSIC and Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA)-Faculty of Sciences of Gabès, Erriadh, Zrig 6072, Tunisia
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485-2494. [PMID: 28771120 DOI: 10.1099/ijsem.0.002144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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Araújo J, Flores-Félix JD, Igual JM, Peix A, González-Andrés F, Díaz-Alcántara CA, Velázquez E. Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan. Int J Syst Evol Microbiol 2017; 67:2236-2241. [PMID: 28671523 DOI: 10.1099/ijsem.0.001932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium, being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, 'Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA-DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense, 'Bradyrhizobium americanum' and Bradyrhizobium daqingense, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium. Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.
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Affiliation(s)
- Juan Araújo
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas. (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - César Antonio Díaz-Alcántara
- Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
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Beligala DH, Michaels HJ, Devries M, Phuntumart V. Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.711063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Ramírez-Bahena MH, Flores-Félix JD, Chahboune R, Toro M, Velázquez E, Peix A. Bradyrhizobium centrosemae (symbiovar centrosemae) sp. nov., Bradyrhizobium americanum (symbiovar phaseolarum) sp. nov. and a new symbiovar (tropici) of Bradyrhizobium viridifuturi establish symbiosis with Centrosema species native to America. Syst Appl Microbiol 2016; 39:378-83. [DOI: 10.1016/j.syapm.2016.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/30/2016] [Accepted: 06/03/2016] [Indexed: 11/26/2022]
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32
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Diversity of Bradyrhizobium strains nodulating Lupinus micranthus on both sides of the Western Mediterranean: Algeria and Spain. Syst Appl Microbiol 2016; 39:266-274. [DOI: 10.1016/j.syapm.2016.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/17/2022]
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33
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Jones FP, Clark IM, King R, Shaw LJ, Woodward MJ, Hirsch PR. Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison. Sci Rep 2016; 6:25858. [PMID: 27162150 PMCID: PMC4861915 DOI: 10.1038/srep25858] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/25/2016] [Indexed: 11/28/2022] Open
Abstract
The slow-growing genus Bradyrhizobium is biologically important in soils, with different representatives found to perform a range of biochemical functions including photosynthesis, induction of root nodules and symbiotic nitrogen fixation and denitrification. Consequently, the role of the genus in soil ecology and biogeochemical transformations is of agricultural and environmental significance. Some isolates of Bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to form nodules. Here we present the genome and gene annotations of two such free-living Bradyrhizobium isolates, named G22 and BF49, from soils with differing long-term management regimes (grassland and bare fallow respectively) in addition to carbon metabolism analysis. These Bradyrhizobium isolates are the first to be isolated and sequenced from European soil and are the first free-living Bradyrhizobium isolates, lacking both nodulation and nitrogen fixation genes, to have their genomes sequenced and assembled from cultured samples. The G22 and BF49 genomes are distinctly different with respect to size and number of genes; the grassland isolate also contains a plasmid. There are also a number of functional differences between these isolates and other published genomes, suggesting that this ubiquitous genus is extremely heterogeneous and has roles within the community not including symbiotic nitrogen fixation.
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Affiliation(s)
- Frances Patricia Jones
- Department of AgroEcology, Rothamsted Research, Harpenden, AL5 2JQ, UK.,Department of Geography and Environmental Science, University of Reading, Reading, RG6 6AH, UK
| | - Ian M Clark
- Department of AgroEcology, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Robert King
- Department of Computational and Systems Biology, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Liz J Shaw
- Department of Geography and Environmental Science, University of Reading, Reading, RG6 6AH, UK
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, University of Reading, Reading, RG6 6AH, UK
| | - Penny R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, AL5 2JQ, UK
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Li YH, Wang R, Zhang XX, Young JPW, Wang ET, Sui XH, Chen WX. Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut. Int J Syst Evol Microbiol 2015; 65:4655-4661. [DOI: 10.1099/ijsem.0.000629] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.
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Affiliation(s)
- Yong Hua Li
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Rui Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | | | - En Tao Wang
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Xin Hua Sui
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Wen Xin Chen
- State Key Lab for Agro-Biotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
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