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Shah I, Sarim KM, Sikka VK, Dudeja SS, Gahlot DK. Developed Rhizobium Strains Enhance Soil Fertility and Yield of Legume Crops in Haryana, India. J Basic Microbiol 2024:e2400327. [PMID: 39021277 DOI: 10.1002/jobm.202400327] [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: 06/02/2024] [Revised: 06/17/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
Three strains of Gram-negative bacterium, Rhizobium, were developed by gamma (γ)-irradiation random mutagenesis. The developed strains were evaluated for their augmented features for symbiotic association, nitrogen fixation, and crop yield of three leguminous plants-chickpea, field-pea, and lentil-in agricultural fields of the northern Indian state of Haryana. Crops treated with developed mutants exhibited significant improvement in plant features and the yield of crops when compared to the control-uninoculated crops and crops grown with indigenous or commercial crop-specific strains of Rhizobium. This improvement was attributed to generated mutants, MbPrRz1 (on chickpea), MbPrRz2 (on lentil), and MbPrRz3 (on field-pea). Additionally, the cocultured symbiotic response of MbPrRz1 and MbPrRz2 mutants was found to be more pronounced on all three crops. The statistical analysis using Pearson's correlation coefficients revealed that nodulation and plant biomass were the most related parameters of crop yield. Among the effectiveness of developed mutants, MbPrRz1 yielded the best results for all three tested crops. Moreover, the developed mutants enhanced macro- and micronutrients of the experimental fields when compared with fields harboring the indigenous rhizobial community. These developed mutants were further genetically characterized, predominantly expressing nitrogen fixation marker, nifH, and appeared to belong to Mesorhizobium ciceri (MbPrRz1) and Rhizobium leguminosarum (both MbPrRz2 and MbPrRz3). In summary, this study highlights the potential of developed Rhizobium mutants as effective biofertilizers for sustainable agriculture, showcasing their ability to enhance symbiotic relationships, crop yield, and soil fertility.
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Affiliation(s)
- Ikbal Shah
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
- Department of Microbiology, OM Sterling Global University, Hisar, India
| | - Khan M Sarim
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, India
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Virendra K Sikka
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
| | - Surjit S Dudeja
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, India
| | - Dharmender K Gahlot
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
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2
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Liu J, Wang M, Zhao Y, Cao K, He L, Hao X, Suo R, Zhang H, Wang X. Transcriptomics and metabolomics profiling reveals involvement of flavonoids in early nodulation of Caucasian clover (Trifolium ambiguum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108050. [PMID: 37812991 DOI: 10.1016/j.plaphy.2023.108050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/21/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Caucasian clover (Trifolium ambiguum) is a perennial rooted and tillering leguminous forage with strong adaptability, outstanding stress tolerance and other preferable traits. However, the specificity with rhizobia limits the extended application of Caucasian clover. Therefore, it is important to study the changes of genes and metabolites in the early process of nodulation in Caucasian clover to improve its nodulation and nitrogen fixation ability. In this study, we used Caucasian clover as the experimental material to investigate its nodulation mechanism using transcriptomic and metabolomic approaches, such that to break the nitrogen fixation barrier for the promotion of Caucasian clover. Metabolomic and transcriptomic profiling revealed that both DAMs and DEGs were significantly enriched in the phenylpropanoid and flavonoid biosynthetic pathways, with DEGs showing up-regulation at 3 days and 6 days post inoculation (dpi) with rhizobia, and some DEGs showing down-regulation at 9 dpi. Accumulation of flavonoids was significantly increased at both 3 dpi and 6 dpi, and some compounds were significantly decreased at 9 dpi. A total of 35 DEGs were involved in flavonoid synthesis by WGCNA analysis, among which HCT, CCR, COMT and F3H played an important role. This study provides insights in understanding the molecular mechanism of nodulation and nitrogen fixation in Caucasian clover.
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Affiliation(s)
- Jiawei Liu
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China
| | - Mingjiu Wang
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China.
| | - Yan Zhao
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China.
| | - Kefan Cao
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China
| | - Lijun He
- College of Agriculture, Inner Mongolia Agricultural University, 275 East Academy Street, Saihan District, Hohhot 010019, PR China
| | - Xinyan Hao
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China
| | - Rongzhen Suo
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China
| | - Huimin Zhang
- Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, 29 Eerduosi East Street, Saihan District, Hohhot 010011, PR China
| | - Xiaolong Wang
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, 2 Yihe Street, Longsha District, Qiqihar 161005, PR China
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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Rhizobium leguminosarum bv. trifolii NodD2 Enhances Competitive Nodule Colonization in the Clover-Rhizobium Symbiosis. Appl Environ Microbiol 2020; 86:AEM.01268-20. [PMID: 32651206 DOI: 10.1128/aem.01268-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Establishment of the symbiotic relationship that develops between rhizobia and their legume hosts is contingent upon an interkingdom signal exchange. In response to host legume flavonoids, NodD proteins from compatible rhizobia activate expression of nodulation genes that produce lipochitin oligosaccharide signaling molecules known as Nod factors. Root nodule formation commences upon legume recognition of compatible Nod factor. Rhizobium leguminosarum was previously considered to contain one copy of nodD; here, we show that some strains of the Trifolium (clover) microsymbiont R. leguminosarum bv. trifolii contain a second copy designated nodD2. nodD2 genes were present in 8 out of 13 strains of R. leguminosarum bv. trifolii, but were absent from the genomes of 16 R. leguminosarum bv. viciae strains. Analysis of single and double nodD1 and nodD2 mutants in R. leguminosarum bv. trifolii strain TA1 revealed that NodD2 was functional and enhanced nodule colonization competitiveness. However, NodD1 showed significantly greater capacity to induce nod gene expression and infection thread formation. Clover species are either annual or perennial and this phenological distinction is rarely crossed by individual R. leguminosarum bv. trifolii microsymbionts for effective symbiosis. Of 13 strains with genome sequences available, 7 of the 8 effective microsymbionts of perennial hosts contained nodD2, whereas the 3 microsymbionts of annual hosts did not. We hypothesize that NodD2 inducer recognition differs from NodD1, and NodD2 functions to enhance competition and effective symbiosis, which may discriminate in favor of perennial hosts.IMPORTANCE Establishment of the rhizobium-legume symbiosis requires a highly specific and complex signal exchange between both participants. Rhizobia perceive legume flavonoid compounds through LysR-type NodD regulators. Often, rhizobia encode multiple copies of nodD, which is one determinant of host specificity. In some species of rhizobia, the presence of multiple copies of NodD extends their symbiotic host-range. Here, we identified and characterized a second copy of nodD present in some strains of the clover microsymbiont Rhizobium leguminosarum bv. trifolii. The second nodD gene contributed to the competitive ability of the strain on white clover, an important forage legume. A screen for strains containing nodD2 could be utilized as one criterion to select strains with enhanced competitive ability for use as inoculants for pasture production.
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Rhizobium-Legume Symbiosis: Molecular Determinants and Geospecificity. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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6
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Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils. Syst Appl Microbiol 2019; 42:448-456. [DOI: 10.1016/j.syapm.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 11/30/2022]
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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: 6] [Impact Index Per Article: 1.2] [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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8
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Marek-Kozaczuk M, Wdowiak-Wróbel S, Kalita M, Chernetskyy M, Deryło K, Tchórzewski M, Skorupska A. Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens. Antonie van Leeuwenhoek 2017; 110:1729-1744. [PMID: 28791535 PMCID: PMC5676844 DOI: 10.1007/s10482-017-0922-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/29/2017] [Indexed: 11/28/2022]
Abstract
Trifolium rubens L., commonly known as the red feather clover, is capable of symbiotic interactions with rhizobia. Up to now, no specific symbionts of T. rubens and their symbiotic compatibility with Trifolium spp. have been described. We characterized the genomic diversity of T. rubens symbionts by analyses of plasmid profiles and BOX-PCR. The phylogeny of T. rubens isolates was inferred based on the nucleotide sequences of 16S rRNA and two core genes (atpD, recA). The nodC phylogeny allowed classification of rhizobia nodulating T. rubens as Rhizobium leguminosarum symbiovar trifolii (Rlt). The symbiotic efficiency of the Rlt isolates was determined on four clover species: T. rubens, T. pratense, T. repens and T. resupinatum. We determined that Rlt strains formed mostly inefficient symbiosis with their native host plant T. rubens and weakly effective (sub-optimal) symbiosis with T. repens and T. pratense. The same Rlt strains were fully compatible in the symbiosis with T. resupinatum. T. rubens did not exhibit strict selectivity in regard to the symbionts and rhizobia closely related to Rhizobium grahamii, Rhizobium galegae and Agrobacterium radiobacter, which did not nodulate Trifolium spp., were found amongst T. rubens nodule isolates.
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Affiliation(s)
- Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Mykhaylo Chernetskyy
- The Botanic Garden of Maria Curie-Skłodowska University, Sławinkowska 3, 20-810, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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Cúcio C, Engelen AH, Costa R, Muyzer G. Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific. Front Microbiol 2016; 7:440. [PMID: 27065991 PMCID: PMC4815253 DOI: 10.3389/fmicb.2016.00440] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.
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Affiliation(s)
- Catarina Cúcio
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Aschwin H. Engelen
- Marine Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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Gordon BR, Klinger CR, Weese DJ, Lau JA, Burke PV, Dentinger BTM, Heath KD. Decoupled genomic elements and the evolution of partner quality in nitrogen-fixing rhizobia. Ecol Evol 2016; 6:1317-27. [PMID: 27087920 PMCID: PMC4775534 DOI: 10.1002/ece3.1953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 01/24/2023] Open
Abstract
Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long-term impacts of global changes, such as increased N (nitrogen) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or HGT (horizontal gene transfer). In a previous work using the legume/rhizobia mutualism, we demonstrated that long-term nitrogen fertilization caused the evolution of less-mutualistic rhizobia. Here, we use our 63 previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N fertilization. We find evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and suggest MoFe subunit interaction sites in the evolution of less-mutualistic rhizobia. These results provide insight into the mechanisms behind the evolutionary response of rhizobia to long-term N fertilization, and we discuss the implications of our results for the evolution of the mutualism.
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Affiliation(s)
- Benjamin R. Gordon
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | - Christie R. Klinger
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | - Dylan J. Weese
- Department of BiologySt. Ambrose University518 West Locust StDavenportIowa52803
| | - Jennifer A. Lau
- Kellogg Biological Station and Department of Plant BiologyMichigan State University3700 E. Gull Lake DriveHickory CornersMichigan49060
| | - Patricia V. Burke
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
| | | | - Katy D. Heath
- Department of Plant BiologyUniversity of Illinois Urbana‐Champaign505 S. Goodwin Ave.UrbanaIllinois61801
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12
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Hood G, Karunakaran R, Downie JA, Poole P. MgtE From Rhizobium leguminosarum Is a Mg²⁺ Channel Essential for Growth at Low pH and N2 Fixation on Specific Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1281-1287. [PMID: 26422403 DOI: 10.1094/mpmi-07-15-0166-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
MgtE is predicted to be a Rhizobium leguminosarum channel and is essential for growth when both Mg²⁺ is limiting and the pH is low. N₂was only fixed at 8% of the rate of wild type when the crop legume Pisum sativum was inoculated with an mgtE mutant of R. leguminosarum and, although bacteroids were present, they were few in number and not fully developed. R. leguminosarum MgtE was also essential for N₂fixation on the native legume Vicia hirsuta but not when in symbiosis with Vicia faba. The importance of MgtE and the relevance of the contrasting phenotypes is discussed.
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Affiliation(s)
- Graham Hood
- 1 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Ramakrishnan Karunakaran
- 1 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - J Allan Downie
- 1 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Philip Poole
- 1 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
- 2 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
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13
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Influence of Rhizobia Inoculation on Biomass Gain and Tissue Nitrogen Content of Leucaena leucocephala Seedlings under Drought. FORESTS 2015. [DOI: 10.3390/f6103686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Lira MA, Nascimento LRS, Fracetto GGM. Legume-rhizobia signal exchange: promiscuity and environmental effects. Front Microbiol 2015; 6:945. [PMID: 26441880 PMCID: PMC4561803 DOI: 10.3389/fmicb.2015.00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/27/2015] [Indexed: 12/29/2022] Open
Abstract
Although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. Although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. This relative disparity in current knowledge is also apparent in the research on the effects of environmental stress on signal exchange; cool-climate stresses, such as low-soil temperature, comprise a relatively large body of research, whereas high-temperature stresses and drought are not nearly as well understood. Both tropical legumes and their environmental stress-induced effects are increasingly important due to global population growth (the demand for protein), climate change (increasing temperatures and more extreme climate behavior), and urbanization (and thus heavy metals). This knowledge gap for both legumes and their environmental stresses is compounded because whereas most temperate legume-rhizobia symbioses are relatively specific and cultivated under relatively stable environments, the converse is true for tropical legumes, which tend to be promiscuous, and grow in highly variable conditions. This review will clarify some of this missing information and highlight fields in which further research would benefit our current knowledge.
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Affiliation(s)
- Mario A. Lira
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
| | - Luciana R. S. Nascimento
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
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Structural analysis of succinoglycan oligosaccharides from Sinorhizobium meliloti strains with different host compatibility phenotypes. J Bacteriol 2013; 195:2032-8. [PMID: 23457246 DOI: 10.1128/jb.00009-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti NRG247 has a Fix(+) phenotype on Medicago truncatula A20 and is Fix(-) on M. truncatula A17, and the phenotype is reversed with S. meliloti NRG185. As the succinoglycan was shown to impact host specificity, an analysis of the succinoglycan oligosaccharides produced by each strain was conducted. The symbiotically active succinoglycan trimeric oligosaccharides (STOs) from the two S. meliloti strains were compared by chromatography and mass spectrometry, and the analysis of the S. meliloti NRG247 oligosaccharides showed that this strain produces an abundance of STO trimer 1 (T1), containing no succinate (i.e., three nonsuccinylated repeats), yet the low-molecular-weight pool contained no nonsuccinylated monomers (potential repeats). This showed that STO T1 is likely to be the active signal on M. truncatula A20 and that the biosynthesis of the STOs is not a random polymerization of the monomer population. The results also suggest that the fully succinylated STO T7 is required for the infection of M. truncatula A17.
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Melino VJ, Drew EA, Ballard RA, Reeve WG, Thomson G, White RG, O'Hara GW. Identifying abnormalities in symbiotic development between Trifolium spp. and Rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes. ANNALS OF BOTANY 2012; 110:1559-72. [PMID: 22989463 PMCID: PMC3503493 DOI: 10.1093/aob/mcs206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/15/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Legumes overcome nitrogen limitations by entering into a mutualistic symbiosis with N(2)-fixing bacteria (rhizobia). Fully compatible associations (effective) between Trifolium spp. and Rhizobium leguminosarum bv. trifolii result from successful recognition of symbiotic partners in the rhizosphere, root hair infection and the formation of nodules where N(2)-fixing bacteroids reside. Poorly compatible associations can result in root nodule formation with minimal (sub-optimal) or no (ineffective) N(2)-fixation. Despite the abundance and persistence of strains in agricultural soils which are poorly compatible with the commercially grown clover species, little is known of how and why they fail symbiotically. The aims of this research were to determine the morphological aberrations occurring in sub-optimal and ineffective clover nodules and to determine whether reduced bacteroid numbers or reduced N(2)-fixing activity is the main cause for the Sub-optimal phenotype. METHODS Symbiotic effectiveness of four Trifolium hosts with each of four R. leguminosarum bv. trifolii strains was assessed by analysis of plant yields and nitrogen content; nodule yields, abundance, morphology and internal structure; and bacteroid cytology, quantity and activity. KEY RESULTS Effective nodules (Nodule Function 83-100 %) contained four developmental zones and N(2)-fixing bacteroids. In contrast, Sub-optimal nodules of the same age (Nodule Function 24-57 %) carried prematurely senescing bacteroids and a small bacteroid pool resulting in reduced shoot N. Ineffective-differentiated nodules carried bacteroids aborted at stage 2 or 3 in differentiation. In contrast, bacteroids were not observed in Ineffective-vegetative nodules despite the presence of bacteria within infection threads. CONCLUSIONS Three major responses to N(2)-fixation incompatibility between Trifolium spp. and R. l. trifolii strains were found: failed bacterial endocytosis from infection threads into plant cortical cells, bacteroid differentiation aborted prematurely, and a reduced pool of functional bacteroids which underwent premature senescence. We discuss possible underlying genetic causes of these developmental abnormalities and consider impacts on N(2)-fixation of clovers.
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Affiliation(s)
- V. J. Melino
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA 6150, Australia
| | - E. A. Drew
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA 5001, Australia
| | - R. A. Ballard
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA 5001, Australia
| | - W. G. Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA 6150, Australia
| | - G. Thomson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA 6150, Australia
| | - R. G. White
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - G. W. O'Hara
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA 6150, Australia
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Terpolilli JJ, Hood GA, Poole PS. What determines the efficiency of N(2)-fixing Rhizobium-legume symbioses? Adv Microb Physiol 2012; 60:325-89. [PMID: 22633062 DOI: 10.1016/b978-0-12-398264-3.00005-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biological nitrogen fixation is vital to nutrient cycling in the biosphere and is the major route by which atmospheric dinitrogen (N(2)) is reduced to ammonia. The largest single contribution to biological N(2) fixation is carried out by rhizobia, which include a large group of both alpha and beta-proteobacteria, almost exclusively in association with legumes. Rhizobia must compete to infect roots of legumes and initiate a signaling dialog with host plants that leads to nodule formation. The most common form of infection involves the growth of rhizobia down infection threads which are laid down by the host plant. Legumes form either indeterminate or determinate types of nodules, with these groups differing widely in nodule morphology and often in the developmental program by which rhizobia form N(2) fixing bacteroids. In particular, indeterminate legumes from the inverted repeat-lacking clade (IRLC) (e.g., peas, vetch, alfalfa, medics) produce a cocktail of antimicrobial peptides which cause endoreduplication of the bacterial genome and force rhizobia into a nongrowing state. Bacteroids often become dependent on the plant for provision of key cofactors, such as homocitrate needed for nitrogenase activity or for branched chain amino acids. This has led to the suggestion that bacteroids at least from the IRLC can be considered as ammoniaplasts, where they are effectively facultative plant organelles. A low O(2) tension is critical both to induction of genes needed for N(2) fixation and to the subsequent exchange of nutrient between plants and bacteroids. To achieve high rates of N(2) fixation, the legume host and Rhizobium must be closely matched not only for infection, but for optimum development, nutrient exchange, and N(2) fixation. In this review, we consider the multiple steps of selection and bacteroid development and how these alter the overall efficiency of N(2) fixation.
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Affiliation(s)
- Jason J Terpolilli
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
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Abstract
Legume plants are able to engage in root nodule symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia. This mutualistic association is highly specific, such that each rhizobial species/strain interacts with only a specific group of legumes, and vice versa. Symbiosis specificity can occur at multiple phases of the interaction, ranging from initial bacterial attachment and infection to late nodule development associated with nitrogen fixation. Genetic control of symbiosis specificity is complex, involving fine-tuned signal communication between the symbiotic partners. Here we review our current understanding of the mechanisms used by the host and bacteria to choose their symbiotic partners, with a special focus on the role that the host immunity plays in controlling the specificity of the legume - rhizobial symbiosis.
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Affiliation(s)
- Dong Wang
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
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Sant'Anna FH, Almeida LGP, Cecagno R, Reolon LA, Siqueira FM, Machado MRS, Vasconcelos ATR, Schrank IS. Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense. BMC Genomics 2011; 12:409. [PMID: 21838888 PMCID: PMC3169532 DOI: 10.1186/1471-2164-12-409] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 08/12/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species. RESULTS Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order. CONCLUSION The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle.
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Affiliation(s)
- Fernando H Sant'Anna
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av, Bento Gonçalves, 9500 Campus do Vale, Porto Alegre, RS, Brazil
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Provorov NA, Vorobyov NI. Simulation of evolution implemented in the mutualistic symbioses towards enhancing their ecological efficiency, functional integrity and genotypic specificity. Theor Popul Biol 2010; 78:259-69. [DOI: 10.1016/j.tpb.2010.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 08/26/2010] [Accepted: 08/31/2010] [Indexed: 11/28/2022]
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Koch M, Delmotte N, Rehrauer H, Vorholt JA, Pessi G, Hennecke H. Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:784-90. [PMID: 20459317 DOI: 10.1094/mpmi-23-6-0784] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Rhizobia are able to infect legume roots, elicit root nodules, and live therein as endosymbiotic, nitrogen-fixing bacteroids. Host recognition and specificity are the results of early programming events in bacteria and plants, in which important signal molecules play key roles. Here, we introduce a new aspect of this symbiosis: the adaptive response to hosts. This refers to late events in bacteroids in which specific genes are transcribed and translated that help the endosymbionts to meet the disparate environmental requirements imposed by the hosts in which they live. The host-adaptation concept was elaborated with Bradyrhizobium japonicum and three different legumes (soybean, cowpea, and siratro). Transcriptomes and proteomes in root-nodule bacteroids were analyzed and compared, and genes and proteins were identified which are specifically induced in only one of the three hosts. We focused on those determinants that were congruent in the two data sets of host-specific transcripts and proteins: seven for soybean, five for siratro, and two for cowpea. One gene cluster for a predicted ABC-type transporter, differentially expressed in siratro, was deleted in B. japonicum. The respective mutant had a symbiotic defect on siratro rather than on soybean or cowpea. This result demonstrates the value of the applied approach and corroborates the host-specific adaptation concept.
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Affiliation(s)
- Marion Koch
- Institute of Microbiology, ETH, Zurich, Switzerland
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Cloning and Characterization of a Plasmid Encoded ACC Deaminase from an Indigenous Pseudomonas fluorescens FY32. Curr Microbiol 2010; 61:37-43. [DOI: 10.1007/s00284-009-9573-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
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Sabir JSM, El-Bestawy E. Enhancement of nodulation by some arid climate strains of Rhizobium leguminosarum biovar trifolii using protoplast fusion. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9922-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lei X, Wang ET, Chen WF, Sui XH, Chen WX. Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China. Arch Microbiol 2008; 190:657-71. [DOI: 10.1007/s00203-008-0418-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Revised: 07/10/2008] [Accepted: 07/14/2008] [Indexed: 11/24/2022]
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Brito B, Toffanin A, Prieto RI, Imperial J, Ruiz-Argüeso T, Palacios JM. Host-dependent expression of Rhizobium leguminosarum bv. viciae hydrogenase is controlled at transcriptional and post-transcriptional levels in legume nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:597-604. [PMID: 18393619 DOI: 10.1094/mpmi-21-5-0597] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The legume host affects the expression of Rhizobium leguminosarum hydrogenase activity in root nodules. High levels of symbiotic hydrogenase activity were detected in R. leguminosarum bacteroids from different hosts, with the exception of lentil (Lens culinaris). Transcription analysis showed that the NifA-regulated R. leguminosarum hydrogenase structural gene promoter (P(1)) is poorly induced in lentil root nodules. Replacement of the P(1) promoter by the FnrN-dependent promoter of the fixN gene restored transcription of hup genes in lentil bacteroids, but not hydrogenase activity. In the P(fixN)-hupSL strain, additional copies of the hup gene cluster and nickel supplementation to lentil plants increased bacteroid hydrogenase activity. However, the level of activity in lentil still was significantly lower than in pea bacteroids, indicating that an additional factor is impairing hydrogenase expression inside lentil nodules. Immunological analysis revealed that lentil bacteroids contain reduced levels of both hydrogenase structural subunit HupL and nickel-binding protein HypB. Altogether, results indicate that hydrogenase expression is affected by the legume host at the level of both transcription of hydrogenase structural genes and biosynthesis or stability of nickel-related proteins HypB and HupL, and suggest the existence of a plant-dependent mechanism that affects hydrogenase activity during the symbiosis by limiting nickel availability to the bacteroid.
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Affiliation(s)
- Belén Brito
- Departamento de Biotecnología, Escuela Técnica Superior Ingenieros Agrónomos, Universidad Politécnica de Madrid (UPM), Spain
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