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Rajkumari J, Katiyar P, Dheeman S, Pandey P, Maheshwari DK. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 2022; 38:206. [PMID: 36008736 DOI: 10.1007/s11274-022-03370-w] [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: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Prashant Katiyar
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India
| | - Shrivardhan Dheeman
- Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India.
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Mohamad R, Willems A, Le Quéré A, Prevent M, Maynaud G, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium ventifaucium sp. nov. and Mesorhizobium escarrei sp. nov., two novel root-nodulating species isolated from Anthyllis vulneraria. Syst Appl Microbiol 2022; 45:126341. [DOI: 10.1016/j.syapm.2022.126341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 10/18/2022]
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Zaw M, Rathjen JR, Zhou Y, Ryder MH, Denton MD. Rhizobial diversity is associated with inoculation history at a two-continent scale. FEMS Microbiol Ecol 2022; 98:6567838. [PMID: 35416244 PMCID: PMC9329089 DOI: 10.1093/femsec/fiac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
Abstract
A total of 120 Mesorhizobium strains collected from the central dry zone of Myanmar were analyzed in a pot experiment to evaluate nodulation and symbiotic effectiveness (SE%) in chickpea plants. Phylogenetic analyses revealed all strains belonged to the genus Mesorhizobium according to 16–23S rDNA IGS and the majority of chickpea nodulating rhizobia in Myanmar soils were most closely related to M. gobiense, M. muleiense, M. silamurunense, M. tamadayense and M. temperatum. Around two-thirds of the Myanmar strains (68%) were most closely related to Indian strain IC-2058 (CA-181), which is also most closely related to M. gobiense. There were no strains that were closely related to the cognate rhizobial species to nodulate chickpea: M. ciceri and M. mediterraneum. Strains with diverse 16S–23S rDNA IGS shared similar nodC and nifH gene sequences with chickpea symbionts. Detailed sequence analysis of nodC and nifH found that the strains in Myanmar were somewhat divergent from the group including M. ciceri and were more closely related to M. muleiense and IC-2058. A cross-continent analysis between strains isolated in Australia compared with Myanmar found that there was little overlap in species, where Australian soils were dominated with M. ciceri, M. temperatum and M. huakuii. The only co-occurring species found in both Myanmar and Australia were M. tamadayense and M. silumurunense. Continued inoculation with CC1192 may have reduced diversity of chickpea strains in Australian soils. Isolated strains in Australian and Myanmar had similar adaptive traits, which in some cases were also phylogenetically related. The genetic discrepancy between chickpea nodulating strains in Australia and Myanmar is not only due to inoculation history but to adaptation to soil conditions and crop management over a long period, and there has been virtually no loss of symbiotic efficiency over this time in strains isolated from soils in Myanmar.
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Affiliation(s)
- Myint Zaw
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA5064, Australia.,Yezin Agricultural University, Yezin, Naypyidaw 15013, Myanmar
| | - Judith R Rathjen
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA5064, Australia
| | - Yi Zhou
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA5064, Australia
| | - Maarten H Ryder
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA5064, Australia
| | - Matthew D Denton
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA5064, Australia
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Maitra S, Brestic M, Bhadra P, Shankar T, Praharaj S, Palai JB, Shah MMR, Barek V, Ondrisik P, Skalický M, Hossain A. Bioinoculants-Natural Biological Resources for Sustainable Plant Production. Microorganisms 2021; 10:51. [PMID: 35056500 PMCID: PMC8780112 DOI: 10.3390/microorganisms10010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.
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Affiliation(s)
- Sagar Maitra
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Preetha Bhadra
- Department of Biotechnology, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India;
| | - Tanmoy Shankar
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Subhashisa Praharaj
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Jnana Bharati Palai
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | | | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Peter Ondrisik
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Milan Skalický
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Akbar Hossain
- Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh;
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Muleta A, Tesfaye K, Assefa F, Greenlon A, Riely BK, Carrasquilla-Garcia N, Gai Y, Haileslassie T, Cook DR. Genomic diversity and distribution of Mesorhizobium nodulating chickpea (Cicer arietinum L.) from low pH soils of Ethiopia. Syst Appl Microbiol 2021; 45:126279. [PMID: 34839036 DOI: 10.1016/j.syapm.2021.126279] [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] [Received: 03/13/2021] [Revised: 10/26/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Chickpea is the third most important grain legume worldwide. This is due in part to its high protein content that results from its ability to acquire bioavailable nitrogen when colonized by diverse, nitrogen fixing Mesorhizobium species. However, the diversity and distribution of mesorhizobia communities may depend on their adaptation to soil conditions. Therefore, this study was initiated in order to isolate and investigate the diversity and taxonomic identities of chickpea-nodulating Mesorhizobium species from low pH soils of Ethiopia. A total of 81 rhizobia strains were isolated from chickpea nodules harvested from low pH soils throughout Ethiopia, and their genomes were sequenced and assembled. Considering a representative set of the best-sequenced 81 genomes, the average sequence depth was 30X, with estimated average genome sizes of approximately 7 Mbp. Annotation of the assembled genome predicted an average of 7,453 protein-coding genes. Concatenation of 400 universal PhyloPhlAn conserved genes present in the genomes of all 81 strains allowed detailed phylogenetic analysis, from which eight well-supported species were identified, including M.opportunistum, M.australicum, Mesorhizobium sp. LSJC280BOO, M.wenxiniae, M.amorphae, M.loti and M.plurifarium, as well as a novel species. Phylogenetic reconstructions based on the symbiosis-related (nodC and nifH) genes were different from the core genes and consistent with horizontal transfer of the symbiotic island. The two major genomic groups, M.plurifarium and M.loti, were widely distributed in almost all the sites. The geographic pattern of genomic diversity indicated there was no relationship between geographic and genetic distance (r = 0.01, p > 0.01). In conclusion, low pH soils in Ethiopia harbored a diverse group of Mesorhizobium species, several of which were not previously known to nodulate chickpea.
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Affiliation(s)
- Atsede Muleta
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Kassahun Tesfaye
- Institutes of Biotechnology, Addis Ababa University, P.O Box 1176, Addis Ababa, Ethiopia; Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Fassil Assefa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Alex Greenlon
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Brendan K Riely
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Yunpeng Gai
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
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Diversity of rhizobial and non-rhizobial bacteria nodulating wild ancestors of grain legume crop plants. Int Microbiol 2021; 24:207-218. [PMID: 33423098 DOI: 10.1007/s10123-020-00158-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
Chickpeas, lentils, and peas are the oldest grain legume species that spread to other regions after their first domestication in Fertile Crescent, and they could reveal the rhizobial evolution in relation to the microsymbionts of wild species in this region. This study investigated the phenotypic and genotypic diversity of the nodule-forming rhizobial bacteria recovered from Pisum sativum subsp., Cicer pinnatifidum, and Lens culinaris subsp. orientalis exhibiting natural distribution in the Gaziantep province of Turkey. PCA analyses of rhizobial isolates, which were tested to be highly resistant to stress conditions, showed that especially pH and salt concentrations had an important effect on these bacteria. Phylogenetic analysis based on 16S rRNA determined that these wild species were nodulated by at least 7 groups including Rhizobium and non-Rhizobium. The largest group comprised of Rhizobium leguminosarum and Rhizobium sp. while R. pusense, which was previously determined as non-symbiotic species, was found to nodulate C. pinnatifidum and L. culinaris subsp. orientalis. In recent studies, Klebsiella sp., which is stated to be able to nodulate different species, strong evidences have been obtained in present study exhibiting that Klebsiella sp. can nodulate C. pinnatifidum and Pseudomonas sp. was able to nodulate C. pinnatifidum and P. sativum subsp. Additionally, L. culinaris subsp. orientalis unlike other plant species, was nodulated by Burkholderia sp. and Serratia sp. associated isolates. Some isolates could not be characterized at the species level since the 16S rRNA sequence similarity rate was low and the fact that they were in a separate group supported with high bootstrap values in the phylogenetic tree may indicate that these isolates could be new species. The REP-PCR fingerprinting provided results supporting the existence of new species nodulating wild ancestors.
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Abstract
AbstractLegume genotype (GL) x rhizobium genotype (GR) interaction in chickpea was studied using a genetically diverse set of accessions and rhizobium strains in modified Leonard Jars. A subset of effective GL x GR combinations was subsequently evaluated in a pot experiment to identify combinations of chickpea genotypes and rhizobium strains with stable and superior symbiotic performance. A linear mixed model was employed to analyse the occurrence of GL x GR interaction and an additive main effects and multiplicative interaction (AMMI) model was used to study patterns in the performance of genotype-strain combinations. We found statistically significant interaction in jars in terms of symbiotic effectiveness that was entirely due to the inclusion of one of the genotypes, ICC6263. No interaction was found in a subsequent pot experiment. The presence of two genetic groups (Kabuli and Desi genepools) did not affect interaction with Mesorhizobium strains. With the exception of a negative interaction with genotype ICC6263 in the jar experiment, the type strain Mesorhizobium ciceri LMG 14989 outperformed or equalled other strains on all chickpea genotypes in both jar and pot experiments. Similar to earlier reports in common bean, our results suggest that efforts to find more effective strains may be more rewarding than aiming for identification of superior combinations of strains and genotypes.
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Zhang J, Shang Y, Liu C, Brunel B, Wang E, Li S, Peng S, Guo C, Chen W. Mesorhizobium jarvisii is a dominant and widespread species symbiotically efficient on Astragalus sinicus L. in the Southwest of China. Syst Appl Microbiol 2020; 43:126102. [PMID: 32847794 DOI: 10.1016/j.syapm.2020.126102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 11/18/2022]
Abstract
In order to identify rhizobia of Astragalus sinicus L. and estimate their geographic distribution in the Southwest China, native rhizobia nodulating A. sinicus were isolated and their genetic diversity were studied at 13 sites cultivated in four Chinese provinces. A total of 451 rhizobial isolates were trapped with A. sinicus plants from soils and classified into 8 different genotypes defined by PCR-based restriction fragment length polymorphism (RFLP) of 16S-23S rRNA intergenic spacer (IGS). Twenty-one representative strains were further identified into three defined Mesorhizobium species by phylogenetic analyses of 16S rRNA genes and housekeeping genes (glnII and atpD). M. jarvisii was dominant accounting for 76.3% of the total isolates, 22.8% of the isolates were identified as M. huakuii and five strains belonged to M. qingshengii. All representatives were assigned to the symbiovar astragali by sharing high nodC sequence similarities of more than 99%. Furthermore, the biogeography distribution of these rhizobial genotypes and species was mainly affected by contents of available phosphorus, available potassium, total salts and pH in soils. The most remarkable point was the identification of M. jarvisii as a widespread and predominant species of A. sinicus in southwest of China. These results revealed a novel geographic pattern of rhizobia associated with A. sinicus in China.
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MESH Headings
- Astragalus Plant/microbiology
- Astragalus Plant/physiology
- China
- DNA, Bacterial/genetics
- Genes, Bacterial
- Genes, rRNA
- Genetic Variation
- Mesorhizobium/classification
- Mesorhizobium/genetics
- Mesorhizobium/isolation & purification
- Mesorhizobium/physiology
- Phylogeny
- Plant Root Nodulation
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Root Nodules, Plant/microbiology
- Soil/chemistry
- Soil Microbiology
- Symbiosis/genetics
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, PR China; Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, Henan Province, PR China.
| | - Yimin Shang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, PR China
| | - Chunzeng Liu
- Institute of Plant Nutrition and Resource Environment, Henan Academy of Agricultural Sciences, Zhengzhou 450000, Henan Province, PR China
| | - Brigitte Brunel
- LSTM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11340, Ciudad de México, Mexico
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, PR China
| | - Shanshan Peng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, PR China
| | - Chen Guo
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, PR China; Research and Innovation Center of Chunlun Group, Fuzhou, 350007, PR China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, 100193, PR China
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Zhang J, Peng S, Shang Y, Brunel B, Li S, Zhao Y, Liu Y, Chen W, Wang E, Singh RP, James EK. Genomic diversity of chickpea-nodulating rhizobia in Ningxia (north central China) and gene flow within symbiotic Mesorhizobium muleiense populations. Syst Appl Microbiol 2020; 43:126089. [PMID: 32690192 DOI: 10.1016/j.syapm.2020.126089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/28/2022]
Abstract
Diversity and taxonomic affiliation of chickpea rhizobia were investigated from Ningxia in north central China and their genomic relationships were compared with those from northwestern adjacent regions (Gansu and Xinjiang). Rhizobia were isolated from root-nodules after trapping by chickpea grown in soils from a single site of Ningxia and typed by IGS PCR-RFLP. Representative strains were phylogenetically analyzed on the basis of the 16S rRNA, housekeeping (atpD, recA and glnII) and symbiosis (nodC and nifH) genes. Genetic differentiation and gene flow were estimated among the chickpea microsymbionts from Ningxia, Gansu and Xinjiang. Fifty chickpea rhizobial isolates were obtained and identified as Mesorhizobium muleiense. Their symbiosis genes nodC and nifH were highly similar (98.4 to 100%) to those of other chickpea microsymbionts, except for one representative strain (NG24) that showed low nifH similarities with all the defined Mesorhizobium species. The rhizobial population from Ningxia was genetically similar to that from Gansu, but different from that in Xinjiang as shown by high chromosomal gene flow/low differentiation with the Gansu population but the reverse with the Xinjiang population. This reveals a biogeographic pattern with two main populations in M. muleiense, the Xinjiang population being chromosomally differentiated from Ningxia-Gansu one. M. muleiense was found as the sole main chickpea-nodulating rhizobial symbiont of Ningxia and it was also found in Gansu sharing alkaline-saline soils with Ningxia. Introduction of chickpea in recently cultivated areas in China seems to select from alkaline-saline soils of M. muleiense that acquired symbiotic genes from symbiovar ciceri.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, P.R. China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Henan Province, 450000, P.R. China; Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, Henan Province, P.R. China.
| | - Shanshan Peng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, P.R. China
| | - Yimin Shang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, P.R. China
| | - Brigitte Brunel
- LSTM, Univ Montpellier, CIRAD, INRAe, Institut Agro, IRD, Montpellier, France
| | - Shuo Li
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, P.R. China
| | - Yongfeng Zhao
- Guyuan Branch of Ningxia Academy of Agricultural and Forestry Sciences, Guyuan 756000, Ningxia Province, P.R. China
| | - Yifei Liu
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, 450000, P.R. China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, P.R. China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México, D. F., México
| | - Raghvendra Pratap Singh
- Department of Research and Development, Biotechnology, Uttaranchal University, Dehradun-248007, India
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Estrella MJ, Fontana MF, Cumpa Velásquez LM, Torres Tejerizo GA, Diambra L, Hansen LH, Pistorio M, Sannazzaro AI. Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina. Syst Appl Microbiol 2020; 43:126044. [DOI: 10.1016/j.syapm.2019.126044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
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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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12
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traG Gene Is Conserved across Mesorhizobium spp. Able to Nodulate the Same Host Plant and Expressed in Response to Root Exudates. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3715271. [PMID: 30834262 PMCID: PMC6374801 DOI: 10.1155/2019/3715271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 11/22/2022]
Abstract
Evidences for an involvement of the bacterial type IV secretion system (T4SS) in the symbiotic relationship between rhizobia and legumes have been pointed out by several recent studies. However, information regarding this secretion system in Mesorhizobium is still very scarce. The aim of the present study was to investigate the phylogeny and expression of the traG gene, which encodes a substrate receptor of the T4SS. In addition, the occurrence and genomic context of this and other T4SS genes, namely, genes from tra/trb and virB/virD4 complexes, were also analyzed in order to unveil the structural and functional organization of T4SS in mesorhizobia. The location of the T4SS genes in the symbiotic region of the analyzed rhizobial genomes, along with the traG phylogeny, suggests that T4SS genes could be horizontally transferred together with the symbiosis genes. Regarding the T4SS structural organization in Mesorhizobium, the virB/virD4 genes were absent in all chickpea (Cicer arietinum L.) microsymbionts and in the Lotus symbiont Mesorhizobium japonicum MAFF303099T. Interestingly, the presence of genes belonging to another secretion system (T3SS) was restricted to these strains lacking the virB/virD4 genes. The traG gene expression was detected in M. mediterraneum Ca36T and M. ciceri LMS-1 strains when exposed to chickpea root exudates and also in the early nodules formed by M. mediterraneum Ca36T, but not in older nodules. This study contributes to a better understanding of the importance of T4SS in mutualistic symbiotic bacteria.
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Sannazzaro AI, Torres Tejerizo G, Fontana MF, Cumpa Velásquez LM, Hansen LH, Pistorio M, Estrella MJ. Mesorhizobium sanjuanii sp. nov., isolated from nodules of Lotus tenuis in the saline-alkaline lowlands of Flooding Pampa, Argentina. Int J Syst Evol Microbiol 2018; 68:2936-2942. [DOI: 10.1099/ijsem.0.002924] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A. I. Sannazzaro
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - G. Torres Tejerizo
- 2IBBM (Instituto de Biotecnología y Biología Molecular), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - M. F. Fontana
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - L. M. Cumpa Velásquez
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - L. H. Hansen
- 3Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - M. Pistorio
- 2IBBM (Instituto de Biotecnología y Biología Molecular), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - M. J. Estrella
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
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14
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Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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15
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Chen YX, Zou L, Penttinen P, Chen Q, Li QQ, Wang CQ, Xu KW. Faba Bean ( Vicia faba L.) Nodulating Rhizobia in Panxi, China, Are Diverse at Species, Plant Growth Promoting Ability, and Symbiosis Related Gene Levels. Front Microbiol 2018; 9:1338. [PMID: 29973926 PMCID: PMC6019463 DOI: 10.3389/fmicb.2018.01338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023] Open
Abstract
We isolated 65 rhizobial strains from faba bean (Vicia faba L.) from Panxi, China, studied their plant growth promoting ability with nitrogen free hydroponics, genetic diversity with clustered analysis of combined ARDRA and IGS-RFLP, and phylogeny by sequence analyses of 16S rRNA gene, three housekeeping genes and symbiosis related genes. Eleven strains improved the plant shoot dry mass significantly comparing to that of not inoculated plants. According to the clustered analysis of combined ARDRA and IGS-RFLP the isolates were genetically diverse. Forty-one of 65 isolates represented Rhizobium anhuiense, and the others belonged to R. fabae, Rhizobium vallis, Rhizobium sophorae, Agrobacterium radiobacter, and four species related to Rhizobium and Agrobacterium. The isolates carried four and five genotypes of nifH and nodC, respectively, in six different nifH-nodC combinations. When looking at the species-nifH-nodC combinations it is noteworthy that all but two of the six R. anhuiense isolates were different. Our results suggested that faba bean rhizobia in Panxi are diverse at species, plant growth promoting ability and symbiosis related gene levels.
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Affiliation(s)
- Yuan X Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lan Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental & Resource Sciences, Zhejiang Agriculture & Forestry University, Lin'an, China.,Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qi Q Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Chang Q Wang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Kai W Xu
- College of Resources, Sichuan Agricultural University, Chengdu, China
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16
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Tong W, Li X, Huo Y, Zhang L, Cao Y, Wang E, Chen W, Tao S, Wei G. Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris. Syst Appl Microbiol 2018; 41:300-310. [PMID: 29576402 DOI: 10.1016/j.syapm.2018.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.
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Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyun Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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17
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Sharma A, Bandamaravuri KB, Sharma A, Arora DK. Phenotypic and molecular assessment of chickpea rhizobia from different chickpea cultivars of India. 3 Biotech 2017; 7:327. [PMID: 28955624 DOI: 10.1007/s13205-017-0952-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 09/07/2017] [Indexed: 12/01/2022] Open
Abstract
In the present study, heterogeneity in natural chickpea rhizobia populations associated with 18 different chickpea (Cicer arientinum) cultivars of India was investigated. Physiological diversity of 20 chickpea rhizobia was characterized based on phenotypic parameters such as Bromothymol blue (BTB) test, pH, temperature and salinity tolerance. Based on response to BTB test and pH tolerance, all chickpea rhizobia were further divided into slow growers/alkali producers (14 isolates) and fast growers/acid producers (6 isolates). The temperature (upto 40 °C) and salinity (NaCl) tolerance (upto 6%) tests provided a wide description of physiological diversity among the rhizobial isolates. The intrinsic antibiotic resistance of each isolate against 14 different antibiotics distinguished all chickpea rhizobia into five clades at the level of 80% similarity coefficient. Further, based on UPGMA phylogeny of carbon utilization profile, all isolates were dispersed into six clusters at the level of 85% similarity coefficient, which indicated a remarkable variability among the rhizobia. The evaluation of nodule-forming efficiency of all isolates revealed that the isolate ACR15 was more competent for nodule formation than all other isolates. The representative strain from each carbon metabolic cluster was further subjected for molecular identification through 16S rRNA gene characterization. Neighbour-joining method-based phylogeny of 16S rRNA gene sequence revealed a high degree of species diversity among the isolates. Further, the prominent nodule-forming isolate such as ACR15 was identified as Mesorhizobium ciceri, while other isolates showed similarity with other species of Mesorhizobium genus. The present study contributed to the knowledge that besides M. ciceri and M. mediterraneum, chickpea can also be nodulated by many other native chickpea rhizobia which indicates the impact of exploration of promising native populations. These findings may support the further investigation of symbiotic as well as stress responsive genes of chickpea rhizobia leading to develop more effective inoculant strains for wide agricultural applications.
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Affiliation(s)
- Anu Sharma
- National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nathbhanjan, Uttar Pradesh India
| | - Kishore Babu Bandamaravuri
- National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nathbhanjan, Uttar Pradesh India
| | - Anjana Sharma
- Department of Biological Sciences, Rani Durga Vati University, Jabalpur, Madhya Pradesh India
| | - Dillip K Arora
- National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nathbhanjan, Uttar Pradesh India
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18
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Cyanobacterial and rhizobial inoculation modulates the plant physiological attributes and nodule microbial communities of chickpea. Arch Microbiol 2017; 199:1311-1323. [PMID: 28669069 DOI: 10.1007/s00203-017-1405-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/06/2017] [Accepted: 06/24/2017] [Indexed: 10/19/2022]
Abstract
The present investigation aimed to understand the influence of two plant growth promoting cyanobacterial formulations (Anabaena-Mesorhizobium ciceri biofilm and Anabaena laxa), along with Mesorhizobium ciceri, on the symbiotic performance of five each of desi- and kabuli-chickpea cultivars. Inoculation with cyanobacterial formulations led to significant interactions with different cultivars, in terms of fresh weight and number of nodules, the concentration of nodular leghemoglobin, and the number of pods. The inoculant A. laxa alone was superior in its performance, recording 30-50% higher values than uninoculated control, and led to significantly higher nodule number per plant and fresh root weight, relative to the M. ciceri alone. Highest nodule numbers were recorded in the kabuli cultivars BG256 and BG1003. The kabuli cultivar BG1108 treated with the biofilmed Anabaena-M. ciceri inoculant recorded the highest concentration of leghemoglobin in nodules. These inoculants also stimulated the elicitation of defense- and pathogenesis-related enzymes in both the desi and kabuli cultivars, by two to threefolds. The analyses of Denaturing Gradient Gel Electrophoresis (DGGE) profiles revealed that microbial communities in nodules were highly diverse, with about 23 archaeal, 9 bacterial, and 13 cyanobacterial predominant phylotypes observed in both desi and kabuli cultivars, and influenced by the inoculants. Our findings illustrate that the performance of the chickpea plants may be significantly modulated by the microbial communities in the nodule, which may contribute towards improved plant growth and metabolic activity of nodules. This emphasizes the promise of cyanobacterial inoculants in improving the symbiotic performance of chickpea.
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19
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Tena W, Wolde-Meskel E, Degefu T, Walley F. Genetic and phenotypic diversity of rhizobia nodulating chickpea (Cicer arietinum L.) in soils from southern and central Ethiopia. Can J Microbiol 2017; 63:690-707. [PMID: 28499096 DOI: 10.1139/cjm-2016-0776] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forty-two chickpea-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations of Ethiopia and were characterized on the basis of 76 phenotypic traits. Furthermore, 18 representative strains were selected and characterized using multilocus sequence analyses of core and symbiotic gene loci. Numerical analysis of the phenotypic characteristics grouped the 42 strains into 4 distinct clusters. The analysis of the 16S rRNA gene of the 18 strains showed that they belong to the Mesorhizobium genus. On the basis of the phylogenetic tree constructed from the combined genes sequences (recA, atpD, glnII, and gyrB), the test strains were distributed into 4 genospecies (designated as genospecies I-IV). Genospecies I, II, and III could be classified with Mesorhizobium ciceri, Mesorhizobium abyssinicae, and Mesorhizobium shonense, respectively, while genospecies IV might represent an unnamed Mesorhizobium genospecies. Phylogenetic reconstruction based on the symbiosis-related (nifH and nodA) genes supported a single cluster together with a previously described symbiont of chickpea (M. ciceri and Mesorhizobium mediterraneum). Overall, our results corroborate earlier findings that Ethiopian soils harbor phylogenetically diverse Mesorhizobium species, justifying further explorative studies. The observed differences in symbiotic effectiveness indicated the potential to select effective strains for use as inoculants and to improve the productivity of chickpea in the country.
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Affiliation(s)
- Wondwosen Tena
- a Department of Plant Science, Debre Berhan University, P.O. Box 445, Debre Berhan, Ethiopia
| | | | - Tulu Degefu
- c Department of Biology, Hawassa University, P.O. Box 05, Hawassa, Ethiopia
| | - Fran Walley
- d Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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20
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de Oliveira-Francesquini JP, Hungria M, Savi DC, Glienke C, Aluizio R, Kava V, Galli-Terasawa LV. Differential colonization by bioprospected rhizobial bacteria associated with common bean in different cropping systems. Can J Microbiol 2017; 63:682-689. [PMID: 28376308 DOI: 10.1139/cjm-2016-0784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we evaluated the diversity of rhizobia isolated from root nodules on common bean (Phaseolus vulgaris) derived from Andean and Mesoamerican centers and grown under field and greenhouse conditions. Genetic characterization of isolates was performed by sequencing analyses of the 16S rRNA gene and 2 housekeeping genes, recA and glnII, and by the amplification of nifH. Symbiotic efficiency was evaluated by examining nodulation, plant biomass production, and plant nitrogen (N) accumulation. The influence of the environment was observed in nodulation capacity, where Rhizobium miluonense was dominant under greenhouse conditions and the Rhizobium acidisoli group prevailed under field conditions. However, strain LGMB41 fit into a separate group from the type strain of R. acidisoli in terms of multilocus phylogeny, implying that it could belong to a new species. Rhizobium miluonense LGMB73 showed the best symbiotic efficiency performance, i.e., with the highest shoot-N content (77.7 mg/plant), superior to the commercial standard strain (56.9 mg/plant). Biodiversity- and bioprospecting-associated studies are important to better understand ecosystems and to develop more effective strategies to improve plant growth using a N-fixation process.
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Affiliation(s)
| | | | - Daiani Cristina Savi
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Chirlei Glienke
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Rodrigo Aluizio
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Vanessa Kava
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
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21
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Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
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22
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León-Barrios M, Pérez-Yépez J, Dorta P, Garrido A, Jiménez C. Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis. Syst Appl Microbiol 2017; 40:171-178. [PMID: 28216096 DOI: 10.1016/j.syapm.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N2-fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9.
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Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain.
| | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Paola Dorta
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Garrido
- Granja Agrícola Experimental, Área de Agricultura y Ganadería, Cabildo de Lanzarote, Canary Islands, Spain
| | - Concepción Jiménez
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
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Remigi P, Zhu J, Young JPW, Masson-Boivin C. Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts. Trends Microbiol 2015; 24:63-75. [PMID: 26612499 DOI: 10.1016/j.tim.2015.10.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/08/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait.
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Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France; New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Jun Zhu
- Department of Microbiology, Nanjing Agricultural University, Nanjing, China; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
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Isolation of salt-tolerant mutants of Mesorhizobium ciceri strain Rch125 and identification of genes involved in salt sensitivity. Symbiosis 2015. [DOI: 10.1007/s13199-015-0357-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gnat S, Małek W, Oleńska E, Wdowiak-Wróbel S, Kalita M, Łotocka B, Wójcik M. Phylogeny of Symbiotic Genes and the Symbiotic Properties of Rhizobia Specific to Astragalus glycyphyllos L. PLoS One 2015; 10:e0141504. [PMID: 26496493 PMCID: PMC4619719 DOI: 10.1371/journal.pone.0141504] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/08/2015] [Indexed: 11/21/2022] Open
Abstract
The phylogeny of symbiotic genes of Astragalus glycyphyllos L. (liquorice milkvetch) nodule isolates was studied by comparative sequence analysis of nodA, nodC, nodH and nifH loci. In all these genes phylograms, liquorice milkvetch rhizobia (closely related to bacteria of three species, i.e. Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium ciceri) formed one clearly separate cluster suggesting the horizontal transfer of symbiotic genes from a single ancestor to the bacteria being studied. The high sequence similarity of the symbiotic genes of A. glycyphyllos rhizobia (99-100% in the case of nodAC and nifH genes, and 98-99% in the case of nodH one) points to the relatively recent (in evolutionary scale) lateral transfer of these genes. In the nodACH and nifH phylograms, A. glycyphyllos nodule isolates were grouped together with the genus Mesorhizobium species in one monophyletic clade, close to M. ciceri, Mesorhizobium opportunistum and Mesorhizobium australicum symbiovar biserrulae bacteria, which correlates with the close relationship of these rhizobia host plants. Plant tests revealed the narrow host range of A. glycyphyllos rhizobia. They formed effective symbiotic interactions with their native host (A. glycyphyllos) and Amorpha fruticosa but not with 11 other fabacean species. The nodules induced on A. glycyphyllos roots were indeterminate with apical, persistent meristem, an age gradient of nodule tissues and cortical vascular bundles. To reflect the symbiosis-adaptive phenotype of rhizobia, specific for A. glycyphyllos, we propose for these bacteria the new symbiovar "glycyphyllae", based on nodA and nodC genes sequences.
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Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, University of Life Sciences, 13 Akademicka st. 20–950 Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, University of Maria Curie-Skłodowska, 19 Akademicka st., 20–033 Lublin, Poland
| | - Ewa Oleńska
- Department of Genetics and Evolution, University of Białystok, 1J Ciołkowskiego st., 15–245 Białystok, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, University of Maria Curie-Skłodowska, 19 Akademicka st., 20–033 Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, University of Maria Curie-Skłodowska, 19 Akademicka st., 20–033 Lublin, Poland
| | - Barbara Łotocka
- Department of Botany, Warsaw University of Life Sciences—SGGW, 159 Nowoursynowska st., 02–766 Warsaw, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, University of Maria Curie-Skłodowska, 19 Akademicka st., 20–033 Lublin, Poland
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Lemaire B, Van Cauwenberghe J, Chimphango S, Stirton C, Honnay O, Smets E, Muasya AM. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome. FEMS Microbiol Ecol 2015; 91:fiv118. [PMID: 26433010 DOI: 10.1093/femsec/fiv118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, the Netherlands
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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Xu KW, Zou L, Penttinen P, Wang K, Heng NN, Zhang XP, Chen Q, Zhao K, Chen YX. Symbiotic effectiveness and phylogeny of rhizobia isolated from faba bean (Vicia faba L.) in Sichuan hilly areas, China. Syst Appl Microbiol 2015; 38:515-23. [DOI: 10.1016/j.syapm.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 11/26/2022]
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Singh RP, Manchanda G, Singh RN, Srivastava AK, Dubey RC. Selection of alkalotolerant and symbiotically efficient chickpea nodulating rhizobia from North-West Indo Gangetic Plains. J Basic Microbiol 2015; 56:14-25. [DOI: 10.1002/jobm.201500267] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/16/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Raghvendra Pratap Singh
- National Bureau of Agriculturally Important Microorganisms (ICAR); Kushmaur, Kaithauli; Maunath Bhanjan Uttar Pradesh India
- Department of Botany and Microbiology; Gurukul Kangri University; Haridwar Uttrakhand India
| | | | - Ram Nageena Singh
- National Bureau of Agriculturally Important Microorganisms (ICAR); Kushmaur, Kaithauli; Maunath Bhanjan Uttar Pradesh India
| | - Alok Kumar Srivastava
- National Bureau of Agriculturally Important Microorganisms (ICAR); Kushmaur, Kaithauli; Maunath Bhanjan Uttar Pradesh India
| | - R. C. Dubey
- Department of Botany and Microbiology; Gurukul Kangri University; Haridwar Uttrakhand India
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Cicer canariense, an endemic legume to the Canary Islands, is nodulated in mainland Spain by fast-growing strains from symbiovar trifolii phylogenetically related to Rhizobium leguminosarum. Syst Appl Microbiol 2015; 38:346-50. [DOI: 10.1016/j.syapm.2015.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 11/21/2022]
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Ji Z, Yan H, Cui Q, Wang E, Chen W, Chen W. Genetic divergence and gene flow among Mesorhizobium strains nodulating the shrub legume Caragana. Syst Appl Microbiol 2015; 38:176-83. [DOI: 10.1016/j.syapm.2015.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 11/16/2022]
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Bakhoum N, Galiana A, Le Roux C, Kane A, Duponnois R, Ndoye F, Fall D, Noba K, Sylla SN, Diouf D. Phylogeny of nodulation genes and symbiotic diversity of Acacia senegal (L.) Willd. and A. seyal (Del.) Mesorhizobium strains from different regions of Senegal. MICROBIAL ECOLOGY 2015; 69:641-651. [PMID: 25315832 DOI: 10.1007/s00248-014-0507-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 09/26/2014] [Indexed: 06/04/2023]
Abstract
Acacia senegal and Acacia seyal are small, deciduous legume trees, most highly valued for nitrogen fixation and for the production of gum arabic, a commodity of international trade since ancient times. Symbiotic nitrogen fixation by legumes represents the main natural input of atmospheric N2 into ecosystems which may ultimately benefit all organisms. We analyzed the nod and nif symbiotic genes and symbiotic properties of root-nodulating bacteria isolated from A. senegal and A. seyal in Senegal. The symbiotic genes of rhizobial strains from the two Acacia species were closed to those of Mesorhizobium plurifarium and grouped separately in the phylogenetic trees. Phylogeny of rhizobial nitrogen fixation gene nifH was similar to those of nodulation genes (nodA and nodC). All A. senegal rhizobial strains showed identical nodA, nodC, and nifH gene sequences. By contrast, A. seyal rhizobial strains exhibited different symbiotic gene sequences. Efficiency tests demonstrated that inoculation of both Acacia species significantly affected nodulation, total dry weight, acetylene reduction activity (ARA), and specific acetylene reduction activity (SARA) of plants. However, these cross-inoculation tests did not show any specificity of Mesorhizobium strains toward a given Acacia host species in terms of infectivity and efficiency as stated by principal component analysis (PCA). This study demonstrates that large-scale inoculation of A. senegal and A. seyal in the framework of reafforestation programs requires a preliminary step of rhizobial strain selection for both Acacia species.
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Affiliation(s)
- Niokhor Bakhoum
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, BP 5005, Dakar, Senegal,
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Rouhrazi K, Khodakaramian G. Phenotypic and genotypic diversity of root-nodulating bacteria isolated from chickpea (Cicer arietinum L.) in Iran. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1062-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity.
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Pérez-Yépez J, Armas-Capote N, Velázquez E, Pérez-Galdona R, Rivas R, León-Barrios M. Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 2014; 37:553-9. [DOI: 10.1016/j.syapm.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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Bahulikar RA, Torres-Jerez I, Worley E, Craven K, Udvardi MK. Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern Oklahoma. Appl Environ Microbiol 2014; 80:5636-43. [PMID: 25002418 PMCID: PMC4178587 DOI: 10.1128/aem.02091-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 11/20/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial C4 grass native to North America that is being developed as a feedstock for cellulosic ethanol production. Industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. A potential sustainable alternative source of nitrogen is biological nitrogen fixation. As a step in this direction, we studied the diversity of nitrogen-fixing bacteria (NFB) associated with native switchgrass plants from the tallgrass prairie of northern Oklahoma (United States), using a culture-independent approach. DNA sequences from the nitrogenase structural gene, nifH, revealed over 20 putative diazotrophs from the alpha-, beta-, delta-, and gammaproteobacteria and the firmicutes associated with roots and shoots of switchgrass. Alphaproteobacteria, especially rhizobia, predominated. Sequences derived from nifH RNA indicated expression of this gene in several bacteria of the alpha-, beta-, delta-, and gammaproteobacterial groups associated with roots. Prominent among these were Rhizobium and Methylobacterium species of the alphaproteobacteria, Burkholderia and Azoarcus species of the betaproteobacteria, and Desulfuromonas and Geobacter species of the deltaproteobacteria.
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Affiliation(s)
- Rahul A Bahulikar
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Ivone Torres-Jerez
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Eric Worley
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Kelly Craven
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
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Li C, Lai Q, Li G, Liu Y, Sun F, Shao Z. Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments. PLoS One 2014; 9:e101394. [PMID: 25019154 PMCID: PMC4096408 DOI: 10.1371/journal.pone.0101394] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022] Open
Abstract
Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.
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Affiliation(s)
- Chongping Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guizhen Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- * E-mail:
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Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Cevallos MÁ, Lozano L, Castro-Mondragón J, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E. Genomic basis of symbiovar mimosae in Rhizobium etli. BMC Genomics 2014; 15:575. [PMID: 25005495 PMCID: PMC4125696 DOI: 10.1186/1471-2164-15-575] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 07/01/2014] [Indexed: 11/25/2022] Open
Abstract
Background Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. Results We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved. Conclusions The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-575) contains supplementary material, which is available to authorized users.
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Armas-Capote N, Pérez-Yépez J, Martínez-Hidalgo P, Garzón-Machado V, del Arco-Aguilar M, Velázquez E, León-Barrios M. Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands). Syst Appl Microbiol 2014; 37:140-8. [DOI: 10.1016/j.syapm.2013.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 11/16/2022]
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Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiol Res 2014; 169:2-17. [DOI: 10.1016/j.micres.2013.09.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/24/2022]
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