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NIANG D, GUEDDOU A, NIANG N, NZEPANG D, SAMBOU A, DIOUF A, ZAIYA AZ, CISSOKO M, GULLY D, NGUEPJOP JR, SVISTOONOFF S, FONCEKA D, HOCHER V, DIOUF D, FALL S, TISA LS. Permanent draft genome sequence of Bradyrhizobium vignae, strain ISRA 400, an elite nitrogen-fixing bacterium, isolated from the groundnut growing area in Senegal. J Genomics 2023; 11:52-57. [PMID: 37915957 PMCID: PMC10615618 DOI: 10.7150/jgen.88302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
A new Bradyrhizobium vignae strain called ISRA400 was isolated from groundnut (Arachis hypogaea L.) root nodules obtained by trapping the bacteria from soil samples collected in the Senegalese groundnut basin. In this study, we present the draft genome sequence of this strain ISRA400, which spans approximatively 7.9 Mbp and exhibits a G+C content of 63.4%. The genome analysis revealed the presence of 48 tRNA genes and one rRNA operon (16S, 23S, and 5S). The nodulation test revealed that this strain ISRA400 significantly improves the nodulation parameters and chlorophyll content of the Arachis hypogaea variety Fleur11. These findings suggest the potential of Bradyrhizobium vignae strain ISRA400 as an effective symbiotic partner for improving the growth and productivity of groundnut crop.
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Affiliation(s)
- Diariatou NIANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Abdellatif GUEDDOU
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Nogaye NIANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Darius NZEPANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Aissatou SAMBOU
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
| | - Adama DIOUF
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Arlette Z ZAIYA
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Present address: Institute of Agricultural Research for Development (IRAD), Yaounde, Cameroon
| | - Maimouna CISSOKO
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Djamel GULLY
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Joel-Romaric NGUEPJOP
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
- CIRAD, UMRAGAP, CIRAD/Univ Montpellier/ INRAE, Institut Agro, F-34398 Montpellier, France
| | - Sergio SVISTOONOFF
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Daniel FONCEKA
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
- CIRAD, UMRAGAP, CIRAD/Univ Montpellier/ INRAE, Institut Agro, F-34398 Montpellier, France
| | - Valérie HOCHER
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Diégane DIOUF
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Université du Sine Saloum El Hadj Ibrahima Niass (USSEIN), UFR Sciences sociales et environnementales, Centre d'Excellence Africain "Agriculture pour la Sécurité Alimentaire et Nutritionnelle" (CEA-AGRISAN), Kaolack
| | - Saliou FALL
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Louis S. TISA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Avontuur JR, Wilken PM, Palmer M, Coetzee MPA, Stępkowski T, Venter SN, Steenkamp ET. Complex evolutionary history of photosynthesis in Bradyrhizobium. Microb Genom 2023; 9:001105. [PMID: 37676703 PMCID: PMC10569730 DOI: 10.1099/mgen.0.001105] [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: 05/16/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.
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Affiliation(s)
- Juanita R. Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P. Markus Wilken
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Martin P. A. Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warszawa, Poland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Paudel D, Wang L, Poudel R, Acharya JP, Victores S, de Souza CHL, Rios E, Wang J. Elucidating the effects of organic vs. conventional cropping practice and rhizobia inoculation on rhizosphere microbial diversity and yield of peanut. ENVIRONMENTAL MICROBIOME 2023; 18:60. [PMID: 37464442 DOI: 10.1186/s40793-023-00517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/09/2023] [Indexed: 07/20/2023]
Abstract
Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial diversity and activity in the rhizosphere that influences plant health, nutrition, and crop yield, as well as soil quality and soil fertility. However, our understanding of the complex effects of microbial diversity and rhizobia inoculation on crop yields of different peanut cultivars under organic versus conventional farming systems is extremely limited. In this research, we studied the impacts of conventional vs. organic cultivation practices and inoculation with commercial vs. single strain inoculum on peanut yield and soil microbial diversity of five peanut cultivars. The experiment was set up in the field following a split-split-plot design. Our results from the 16 S microbiome sequencing showed considerable variations of microbial composition between the cultivation types and inoculum, indicating a preferential association of microbes to peanut roots with various inoculum and cropping system. Alpha diversity indices (chao1, Shannon diversity, and Simpson index) of soil microbiome were generally higher in plots with organic than conventional inorganic practices. The cultivation type and inoculum explained significant differences among bacterial communities. Taxonomic classification revealed two phyla, TM6 and Firmicutes were significantly represented in inorganic as compared to organic soil, where significant phyla were Armatimonadetes, Gemmatimonadetes, Nitrospirae, Proteobacteria, Verrucomicrobia, and WS3. Yields in the organic cultivation system decreased by 10-93% of the yields in the inorganic cultivation system. Cultivar G06 and T511 consistently showed relative high yields in both organic and inorganic trials. Our results show significant two-way interactions between cultivation type and genotype for most of the trait data collected. Therefore, it is critical for farmers to choose varieties based on their cultivation practices. Our results showed that bacterial structure was more uniform in organic fields and microbial diversity in legumes was reduced in inorganic fields. This research provided guides for farmers and scientists to improve peanut yield while promoting microbial diversity and increasing sustainability.
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Affiliation(s)
- Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ravin Poudel
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Janam P Acharya
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | | | | | - Esteban Rios
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA.
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Zhao Z, Wang Y, Peng Z, Luo Z, Zhao M, Wang J. Allelic expression of AhNSP2-B07 due to parent of origin affects peanut nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193465. [PMID: 37426991 PMCID: PMC10325728 DOI: 10.3389/fpls.2023.1193465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 07/11/2023]
Abstract
Legumes are well-known for establishing a symbiotic relationship with rhizobia in root nodules to fix nitrogen from the atmosphere. The nodulation signaling pathway 2 (NSP2) gene plays a critical role in the symbiotic signaling pathway. In cultivated peanut, an allotetraploid (2n = 4x = 40, AABB) legume crop, natural polymorphisms in a pair of NSP2 homoeologs (Na and Nb) located on chromosomes A08 and B07, respectively, can cause loss of nodulation. Interestingly, some heterozygous (NBnb) progeny produced nodules, while some others do not, suggesting non-Mendelian inheritance in the segregating population at the Nb locus. In this study, we investigated the non-Mendelian inheritance at the NB locus. Selfing populations were developed to validate the genotypical and phenotypical segregating ratios. Allelic expression was detected in roots, ovaries, and pollens of heterozygous plants. Bisulfite PCR and sequencing of the Nb gene in gametic tissue were performed to detect the DNA methylation variations of this gene in different gametic tissues. The results showed that only one allele at the Nb locus expressed in peanut roots during symbiosis. In the heterozygous (Nbnb) plants, if dominant allele expressed, the plants produced nodules, if recessive allele expressed, then no nodules were produced. qRT-PCR experiments revealed that the expression of Nb gene in the ovary was extremely low, about seven times lower than that in pollen, regardless of genotypes or phenotypes of the plants at this locus. The results indicated that Nb gene expression in peanut depends on the parent of origin and is imprinted in female gametes. However, no significant differences of DNA methylation level were detected between these two gametic tissues by bisulfite PCR and sequencing. The results suggested that the remarkable low expression of Nb in female gametes may not be caused by DNA methylation. This study provided a unique genetic basis of a key gene involved in peanut symbiosis, which could facilitate understanding the regulation of gene expression in symbiosis in polyploid legumes.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Yichun Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
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Zhao Z, Wang L, Kelley K, Jones JB, Tillman B, Wang J. GFP labeling of a Bradyrhizobium strain and an attempt to track the crack entry process during symbiosis with peanuts. World J Microbiol Biotechnol 2023; 39:219. [PMID: 37269424 DOI: 10.1007/s11274-023-03665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Compared to the well-studied model legumes, where symbiosis is established via root hair entry, the peanut is infected by Bradyrhizobium through the crack entry, which is less common and not fully understood. Crack entry is, however, considered a primitive symbiotic infection pathway, which could be potentially utilized for engineering non-legume species with nitrogen fixation ability. We utilized a fluorescence-labeled Bradyrhizobium strain to help in understanding the crack entry process at the cellular level. A modified plasmid pRJPaph-bjGFP, harboring the codon-optimized GFP gene and tetracycline resistance gene, was created and conjugated into Bradyrhizobium strain Lb8, an isolate from peanut nodules, through tri-parental mating. Microscopic observation and peanut inoculation assays confirmed the successful GFP tagging of Lb8, which is capable of generating root nodules. A marking system for peanut root potential infection sites and an optimized sample preparation protocol for cryostat sectioning was developed. The feasibility of using the GFP-tagged Lb8 for observing crack entry was examined. GFP signal was detected at the nodule primordial stage and the following nodule developmental stages with robust GFP signals observed in infected cells in the mature nodules. Spherical bacteroids in the root tissue were visualized at the nodules' inner cortex under higher magnification, reflecting the trace along the rhizobial infection path. The GFP labeled Lb8 can serve as an essential tool for plant-microbe studies between the cultivated peanut and Bradyrhizobium, which could facilitate further study of the crack entry process during the legume-rhizobia symbiosis.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Karen Kelley
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Jeffrey B Jones
- Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Plant Pathology Department, University of Florida, Gainesville, FL, 32610, USA
| | - Barry Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.
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Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
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Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
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Ghantasala S, Roy Choudhury S. Nod factor perception: an integrative view of molecular communication during legume symbiosis. PLANT MOLECULAR BIOLOGY 2022; 110:485-509. [PMID: 36040570 DOI: 10.1007/s11103-022-01307-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Compatible interaction between rhizobial Nod factors and host receptors enables initial recognition and signaling events during legume-rhizobia symbiosis. Molecular communication is a new paradigm of information relay, which uses chemical signals or molecules as dialogues for communication and has been witnessed in prokaryotes, plants as well as in animal kingdom. Understanding this fascinating relay of signals between plants and rhizobia during the establishment of a synergistic relationship for biological nitrogen fixation represents one of the hotspots in plant biology research. Predominantly, their interaction is initiated by flavonoids exuding from plant roots, which provokes changes in the expression profile of rhizobial genes. Compatible interactions promote the secretion of Nod factors (NFs) from rhizobia, which are recognised by cognate host receptors. Perception of NFs by host receptors initiates the symbiosis and ultimately leads to the accommodation of rhizobia within root nodules via a series of mutual exchange of signals. This review elucidates the bacterial and plant perspectives during the early stages of symbiosis, explicitly emphasizing the significance of NFs and their cognate NF receptors.
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Affiliation(s)
- Swathi Ghantasala
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
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Ngwenya ZD, Mohammed M, Jaiswal SK, Dakora FD. Phylogenetic relationships among Bradyrhizobium species nodulating groundnut (Arachis hypogea L.), jack bean (Canavalia ensiformis L.) and soybean (Glycine max Merr.) in Eswatini. Sci Rep 2022; 12:10629. [PMID: 35739215 PMCID: PMC9226157 DOI: 10.1038/s41598-022-14455-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
This study assessed the genetic diversity and phylogenetic relationships of rhizobial isolates obtained from root nodules of groundnut, jack bean and soybean planted in different locations within Eswatini. Seventy-six rhizobial isolates were studied using ERIC-PCR (enterobacterial repetitive intergenic consensus) fingerprinting and PCR amplification of 16S rRNA, housekeeping genes (atpD, dnaK, glnll and rpoB) and symbiotic genes (nifH and nodC). The dendrogram generated from the ERIC-PCR banding patterns grouped the test rhizobial isolates into 16 major clusters (Cluster I-XVI), with three isolates, namely TUTAHeS60, TUTGMeS3 and TUTAHeS127, forming outgroups of Clusters IV, VI and IX, respectively. Furthermore, the 76 test isolates were grouped into 56 ERIC-PCR types at 70% similarity level. The phylogenetic analysis of the 16S rRNA gene and multilocus sequence analysis of four housekeeping (atpD, dnaK, glnII and rpoB) and two symbiotic (nifH and nodC) genes showed that all three legumes (groundnut, jack bean and soybean) were nodulated by bacterial symbionts belonging to the genus Bradyrhizobium, with some isolates exhibiting high divergence from the known reference type strains. The results also showed that B. arachidis, B. iriomotense and B. canariense were the closest type strains to the groundnut isolates, while B. pachyrhizi and B. elkanii were the closest relatives to the bacterial symbionts associated with the nodulation of both jack bean and soybean. This study is the first report to describe of the bacterial symbionts nodulating jack bean in African soils.
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Affiliation(s)
- Zanele D Ngwenya
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 001, South Africa
| | - Mustapha Mohammed
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 001, South Africa
- Department of Crop Science, University for Development Studies, P.O. Box 1350, Tamale, Ghana
| | - Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 001, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Private Bag X680, Pretoria, 001, South Africa.
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Shu H, Luo Z, Peng Z, Wang J. The application of CRISPR/Cas9 in hairy roots to explore the functions of AhNFR1 and AhNFR5 genes during peanut nodulation. BMC PLANT BIOLOGY 2020; 20:417. [PMID: 32894045 PMCID: PMC7487912 DOI: 10.1186/s12870-020-02614-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 08/19/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Peanut is an important legume crop growing worldwide. With the published allotetraploid genomes, further functional studies of the genes in peanut are very critical for crop improvement. CRISPR/Cas9 system is emerging as a robust tool for gene functional study and crop improvement, which haven't been extensively utilized in peanut yet. Peanut plant forms root nodules to fix nitrogen through a symbiotic relationship with rhizobia. In model legumes, the response of plants to rhizobia is initiated by Nod factor receptors (NFRs). However, information about the function of NFRs in peanut is still limited. In this study, we applied the CRISPR/Cas9 tool in peanut hairy root transformation system to explore the function of NFR genes. RESULTS We firstly identified four AhNFR1 genes and two AhNFR5 genes in cultivated peanut (Tifrunner). The gene expression analysis showed that the two AhNFR1 and two AhNFR5 genes had high expression levels in nodulating (Nod+) line E5 compared with non-nodulating (Nod-) line E4 during the process of nodule formation, suggesting their roles in peanut nodulation. To further explore their functions in peanut nodulation, we applied CRISPR technology to create knock-out mutants of AhNFR1 and AhNFR5 genes using hairy root transformation system. The sequencing of these genes in transgenic hairy roots showed that the selected AhNFR1 and AhNFR5 genes were successfully edited by the CRISPR system, demonstrating its efficacy for targeted mutation in allotetraploid peanut. The mutants with editing in the two AhNFR5 genes showed Nod- phenotype, whereas mutants with editing in the two selected AhNFR1 genes could still form nodules after rhizobia inoculation. CONCLUSIONS This study showed that CRISPR-Cas9 could be used in peanut hairy root transformation system for peanut functional genomic studies, specifically on the gene function in roots. By using CRISPR-Cas9 targeting peanut AhNFR genes in hairy root transformation system, we validated the function of AhNFR5 genes in nodule formation in peanut.
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Affiliation(s)
- Hongmei Shu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
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