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Vaccaro F, Passeri I, Ajijah N, Bettini P, Courty PE, Dębiec-Andrzejewska K, Joshi N, Kowalewska Ł, Stasiuk R, Musiałowski M, Pranaw K, Mengoni A. Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species. Microbiol Res 2024; 285:127768. [PMID: 38820702 DOI: 10.1016/j.micres.2024.127768] [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: 02/08/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible molecular interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the biology of symbiotic nitrogen fixation bacteria. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 ×4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a generalized rhizobia genotype x fungal genotype interaction, including synergistic, neutral and antagonistic effects on alfalfa symbiotic phenotypes. Differential expression of a high number of genes was shown in rhizobia strains with up to 25% of total genes differentially expressed upon treatment of cultures with fungal spent media. Percentages over total genes and type of genes differentially expressed changed according to both fungal species and rhizobial strain. To support the hypothesis of a relevant rhizobia genotype x fungal genotype interaction, a nested Likelihood Ratio Test indicated that the model considering the fungus-rhizobium interaction explained 23.4% of differentially expressed genes. Our results provide insights into molecular interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.
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Affiliation(s)
| | | | - Nur Ajijah
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | | | | | | | - Namrata Joshi
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Łucja Kowalewska
- Department of Plant Anatomy and Cytology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Marcin Musiałowski
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland; School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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Response of intercropped barley and fenugreek to mono- and co-inoculation with Sinorhizobium meliloti F42 and Variovorax paradoxus F310 under contrasting agroclimatic regions. Arch Microbiol 2021; 203:1657-1670. [PMID: 33433645 DOI: 10.1007/s00203-020-02180-8] [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: 11/23/2020] [Revised: 12/21/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
In the present research, we aimed to select efficient rhizobia and plant growth-promoting rhizobacteria (PGPR) from fenugreek nodules and assess their performance as bio-inoculum for intercropped fenugreek and barley. Inoculation effects with selected bacteria were investigated firstly on fenugreek plants under greenhouse experiment and secondly on intercropped fenugreek and barley under three different agro-environmental conditions for two consecutive years. Sinorhizobium meliloti F42 was selected due to its ability to nodulate fenugreek and effectively improve plant growth. Among non-nodulating endophytic bacteria, Variovorax paradoxus F310 strain was selected regarding its plant growth-promoting traits showed in vitro and confirmed in vivo under greenhouse experiment. Field inoculation trials revealed a significant improvement in fenugreek nodulation (up to + 97%) as well as in soil enzymes activities (up to + 209%), shoot N content (up to + 18%), shoot dry weight (up to + 40%), photosynthetic assimilation (up to + 34%) and chlorophyll content of both intercropped plants in response to the mono-inoculation with Sinorhizobium meliloti F42, compared to the un-inoculated treatment at the SBR and JBS sites. Variovorax paradoxus F310 inoculation significantly increased shoot P content of both intercropped plants at the three experimental sites compared to the un-inoculated treatment (up to + 48%). It was shown that bacterial inoculation was more efficient at the low-rainfall region than the high-rainfall region. The co-inoculation with Sinorhizobium meliloti F42 and Variovorax paradoxus F310 resulted in a significant reduction in fenugreek nodulation and shoot N content. This survey showed the benefits of rhizobial and PGPR inoculation as efficient bio-inoculums to promote the cereal-legume intercropping system and highlights the influence of site-specific environmental factors on Rhizobium-PGPR-plant interactions.
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Draft Genome Sequence of Sinorhizobium meliloti Strain CXM1-105. Microbiol Resour Announc 2019; 8:MRA01621-18. [PMID: 30643907 PMCID: PMC6328680 DOI: 10.1128/mra.01621-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 12/11/2018] [Indexed: 12/04/2022] Open
Abstract
Sinorhizobium meliloti is a Gram-negative bacterium which fixes atmospheric nitrogen in symbiosis with Medicago spp. We report the draft genome sequence of S. meliloti strain CXM1-105, associated with nodules of Medicago sativa subsp. Sinorhizobium meliloti is a Gram-negative bacterium which fixes atmospheric nitrogen in symbiosis with Medicago spp. We report the draft genome sequence of S. meliloti strain CXM1-105, associated with nodules of Medicago sativa subsp. varia (Martyn) Arcang.
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Draft Genome Sequence of Sinorhizobium meliloti Strain AK170. Microbiol Resour Announc 2019; 8:MRA01571-18. [PMID: 30637407 PMCID: PMC6318378 DOI: 10.1128/mra.01571-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 11/20/2022] Open
Abstract
Root nodule bacteria of Sinorhizobium meliloti species live in a symbiotic relationship with alfalfa plants. We report here the draft genome sequence of S. meliloti strain AK170, recovered from nodules of Medicago orthoceras (Kar. Root nodule bacteria of Sinorhizobium meliloti species live in a symbiotic relationship with alfalfa plants. We report here the draft genome sequence of S. meliloti strain AK170, recovered from nodules of Medicago orthoceras (Kar. & Kir.) growing in an area impacted by salinization.
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Roumiantseva ML, Saksaganskaia AS, Muntyan VS, Cherkasova ME, Simarov BV. Structural Polymorphism of Sinorhizobium meliloti Genes Related to Virulence and Salt Tolerance. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418050083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Checcucci A, Azzarello E, Bazzicalupo M, De Carlo A, Emiliani G, Mancuso S, Spini G, Viti C, Mengoni A. Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene? Front Genet 2017; 8:6. [PMID: 28194158 PMCID: PMC5276845 DOI: 10.3389/fgene.2017.00006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/13/2017] [Indexed: 11/13/2022] Open
Abstract
Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.
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Affiliation(s)
- Alice Checcucci
- Department of Biology, University of Florence Sesto Fiorentino, Italy
| | - Elisa Azzarello
- Department of Agri-food Production and Environmental Science, University of Florence Florence, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Florence Sesto Fiorentino, Italy
| | - Anna De Carlo
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Valorizzazione del Legno e delle Specie Arboree Florence, Italy
| | - Giovanni Emiliani
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Valorizzazione del Legno e delle Specie Arboree Florence, Italy
| | - Stefano Mancuso
- Department of Agri-food Production and Environmental Science, University of Florence Florence, Italy
| | - Giulia Spini
- Department of Agri-food Production and Environmental Science, University of Florence Florence, Italy
| | - Carlo Viti
- Department of Agri-food Production and Environmental Science, University of Florence Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence Sesto Fiorentino, Italy
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Muntyan VS, Cherkasova ME, Andronov EE, Simarov BV, Roumiantseva ML. Occurrence of islands in genomes of Sinorhizobium meliloti native isolates. RUSS J GENET+ 2016. [DOI: 10.1134/s102279541608010x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Donnarumma F, Bazzicalupo M, Blažinkov M, Mengoni A, Sikora S, Babić KH. Biogeography of Sinorhizobium meliloti nodulating alfalfa in different Croatian regions. Res Microbiol 2014; 165:508-16. [DOI: 10.1016/j.resmic.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/11/2014] [Indexed: 11/16/2022]
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