Group leader: Jose Manuel Palacios Alberti - Professor

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Pea root nodules

The association between legume plants and a group of alpha-proteobacteria, collectively known as rhizobia, allows the reduction of atmospheric nitrogen into ammonia in specialized organs called root nodules. This symbiotic nitrogen fixation is carried out by the nitrogenase enzymatic complex synthesized by endosymbiotic Rhizobium cells called bacteroids, which are fed with organic acids derived from plant photosynthate. The Rhizobium-legume symbiosis provides a non-polluting source of nitrogen for legume crops, and constitutes a key component for the development of sustainable agriculture.

Intensive research carried out in many labs during the last decades has revealed a sophisticate exchange of signals involved in specific recognition and metabolic adaptation of both partners. Our lab has been working for a number of years in the study of traits involved in the establishment and functioning of this diazotrophic symbiotic association, providing new data on the characterization of metalloenzymes relevant for the symbiotic process, such as [NiFe] hydrogenase, on mechanisms of nickel provision for hydrogenase biosynthesis and metal homeostasis, and on the description of novel rhizobia specific for different legumes. Our current work aims at progressing along some basic questions regarding the Rhizobium-legume symbiosis:


  • How do rhizobia adapt to specific conditions within the nodule?
  • How does the host plant control bacteria behaviour within the nodule?
  • What is the potential of novel Rhizobium-legume symbiotic systems?


We are developing our work along two main research lines:

1) Determinants of the efficiency and specificity of the symbiosis.


Effect of hse mutation on symbiosis with pea plants

The output of the Rhizobium-legume symbiosis is the result of a delicate balance between both partners, with multiple adaptations involved in both plant and bacteria.  The identification of both plant and bacterial determinants involved in this process will contribute to the elucidation of the fine-tuning of both symbionts to accommodate to each other. A combination of transcriptomic and proteomic analysis of bacteroids induced in two different legumes (pea and lentil) has been set up to study host-dependent bacterial traits.


Our working hypothesis is that differential sets of plant-dependent compounds/conditions control the activity of the bacteria in a host-specific way. We are in the process of identifying rhizobial proteins specifically expressed on each legume host. For instance, the induction of a hydrogenase enzyme able to recycle the hydrogen evolved by nitrogenase is known to depend on the identity of the legume host and, in collaboration with Dr. Fernandez-Pacios, we are pursuing the elucidation of structure-to-function relationships in R. leguminosarum host-dependent hydrogenase-related proteins acting as enzyme subunits, chaperones, scaffolding- and oxygen-protective proteins. On the plant side, we are determining the host-dependent profile of Nodule-specific peptides (NCR antimicrobial peptides) produced by the plant and sent to the bacteroid. Results obtained indicate the existence of additional levels of plant- dependent control of bacterial behaviour.
Effect of a mutation affecting Bradyrhizobium sp. T3SS on symbiotic performance
We are also interested in the role of protein secretion systems in rhizobia. Similarly to many bacterial pathogens, rhizobia are able to inject proteins, called effectors, into the plant cells by means of different protein secretion systems such as type III (T3SS), structurally related to bacterial flagella, and the recently described type VI (T6SS), similar to the tail spike of the T4 phage.Analysis of specific mutants in T3SS and T6SS present in some of the rhizobia isolated by our research group has revealed the relevant role of secretion systems on the establishment of effective symbiosis and on the definition of host range.
Other aspects of our studies are related to earlier steps of the symbiotic interaction, when the bacteria are located outside of the plant. At these stages, the ability to provide a coordinate response of the whole bacterial population is a key aspect of bacterial adaptation to rhizosphere conditions. Bacteria are able to detect high cell densities, and also to modify the expression pattern of the cell in response to it, through a process known as “quorum sensing”based on the accumulation of chemical signals known as autoinducers. The analysis of mutants affected on each of the major quorum sensing systems in R. leguminosarum systems is allowing us to determine the relevance of cell-to cell communication in this rhizobial species.

Effect of the deletion of an Rlv quorum sensing system on symbiotic performance on pea plants

2) Biodiversity and symbiotic performance of native microflora nodulating wild legumes in Western Mediterraneum.

Analysis of new symbiotic combinations based on poorly known endemic legumes might provide new applications for the Rhizobium- legume symbiosis. Lupinus (lupines) embraces a very diverse group of legumes including plants with highly protein-rich seeds, and their symbiosis are the subject of research projects carried out in collaboration with the group of Dr. Juan Imperial at CBGP. Like other legumes, lupines exhibit dinitrogen-fixing capacity through its association with soil rhizobia, resulting in plants with a great value for human and animal feeding and for improving degraded soils or soils with a problematic fertilization.



In contrast to most Lupinus spp., which preferentially thrives in acid soils, Lupinus mariae-josephae grows only in alkaline-lime soils. Bacteria isolated from root nodules of this unique lupine species are being genetically and symbiotically studied with particular emphasis given to their taxonomy and evolution.

Also, in collaboration with research groups from Argelia and Tunisia we are working on the characterization of diazotrophic symbiosis of wild, legume shrubs (i.e. Retama raetam and different lupin species), native in Northern Africa, that play a key function in the reduction of soil degradation and in the prevention of desert progression. The singular root systems of these plants are ideal for dune stabilization, for the restoration and conservation of ecosystems in arid areas, and in the extension of vegetable cover to desert regions. These applied objectives are combined with more basic research on the genomics of these endosymbiotic bacteria.



Representative Publications

Msaddak, A; Rejili, M; Durán, D; Rey, L; Palacios, JM; Imperial, J; Ruiz-Argüeso, T; Mars, M. "Definition of two new symbiovars, sv. lupini and sv. mediterranense, within the genera Bradyrhizobium and Phyllobacterium efficiently nodulating Lupinus micranthus in Tunisia". Systematic and Applied Microbiology. DOI: 10.1016/j.syapm.2018.04.004".

Ahnia, H; Bourebaba, Y; Durán, D; Boulila, F; Palacios, JM; Rey, L; Ruiz-Argüeso, T; Boulila, A; Imperial, J. 2018. "Bradyrhizobium algeriense sp. nov., a novel species isolated from effective nodules of Retama sphaerocarpa from Northeastern Algeria". Systematic and Applied Microbiology. DOI: 10.1016/j.syapm.2018.03.004".

Rodrigue, A; Albareda, M; Mandrand-Berthelot, MA; Palacios, J. 2017. "Nickel in Microbial Physiology - From Single Proteins to Complex Trafficking Systems: Nickel Import/Export", p. 237-258. In D. Zamble, M. Rowińska-Żyrek, and H. Kozlowski (eds.), The Biological Chemistry of Nickel. Royal Society of Chemistry. DOI: 10.1039/9781788010580-00237".

Sánchez-Cañizares, C; Jorrín, B; Durán, D; Nadendla, S; Albareda, M; Rubio-Sanz, L; Lanza, M; González-Guerrero, M; Prieto, R; Brito, B; Giglio, M; Rey, L; Ruiz-Argüeso, T; Palacios, J; Imperial, J. 2018. "Genomic diversity in the endosymbiotic bacterium Rhizobium leguminosarum". Genes. DOI: 10.3390/genes9020060".

Rubio-Sanz, L; Brito, B; Palacios, J. 2018. "Analysis of metal tolerance in Rhizobium leguminosarum strains isolated from an ultramafic soil". FEMS Microbiology Letters. DOI: 10.1093/femsle/fny010".

Durán, D; Imperial, J; Palacios, J; Ruiz-Argüeso, T; Göttfert, M; Zehner, S; Rey, L. "Characterization of a novel MIIA domain-containing protein (MdcE) in Bradyrhizobium spp". FEMS Microbiology Letters. DOI: 10.1093/femsle/fnx276".

Msaddak, A; Rejili, M; Duran, D; Rey, L; Imperial, J; Palacios, J; Ruiz-Argueso, T; Mars, M. 2017. "Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils". FEMS Microbiology Ecology. DOI: 10.1093/femsec/fix068".

Msaddak, A; Durán, D; Rejili, M; Mars, M; Ruiz-Argüeso, T; Imperial, J; Palacios, J; Rey, L. 2017. "Diverse bacteria affiliated with the genera Microvirga, Phyllobacterium and Bradyrhizobium nodulate Lupinus micranthus growing in soils of Northern Tunisia". Applied and Environmental Microbiology. DOI: 10.1128/aem.02820-16".

Bourebaba, Y; Durán, D; Boulila, F; Ahnia, H; Boulila, A; Temprano, F; Palacios, JM; Imperial, J; Ruiz-Argüeso, T; Rey, L. 2016. "Diversity of Bradyrhizobium strains nodulating Lupinus micranthus on both sides of the Western Mediterranean: Algeria and Spain". Systematic and Applied Microbiology. DOI: 10.1016/j.syapm.2016.04.006".

Baginsky, C; Brito, B; Scherson, R; Pertuzé, R; Seguel, O; Cañete, A; Araneda, C; Johnson, WE. 2015. "Genetic diversity of Rhizobium from nodulating beans grown in a variety of Mediterranean climate soils of Chile". Archives of Microbiology. DOI: 10.1007/s00203-014-1067-y".

Albareda, M; Rodrigue, A; Brito, B; Ruiz-Argueso, T; Imperial, J; Mandrand-Berthelot, M-A; Palacios, J. 2015. "Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake". Metallomics. DOI: 10.1039/C4MT00298A".

Tellez-Rio, A; García-Marco, S; Navas, M; López-Solanilla, E; Tenorio, JL; Vallejo, A. 2015. "N2O and CH4 emissions from a fallow–wheat rotation with low N input in conservation and conventional tillage under a Mediterranean agroecosystem". Science of the Total Environment. DOI: 10.1016/j.scitotenv.2014.11.041".

Sánchez-Cañizares, C; Palacios, J. 2013. "Construction of a marker system for the evaluation of competitiveness for legume nodulation in Rhizobium strains". Journal of Microbiological Methods. DOI: S0167-7012(13)00003-1 [pii] 10.1016/j.mimet.2012.12.022".

Durán, D; Rey, L; Sánchez-Cañizares, C; Navarro, A; Imperial, J; Ruiz-Argüeso, T. 2013. "Genetic diversity of indigenous rhizobial symbionts of the Lupinus mariae-josephae endemism from alkaline-limed soils within its area of distribution in Eastern Spain". Systematic and Applied Microbiology. DOI: S0723-2020(12)00159-2 [pii] 10.1016/j.syapm.2012.10.008".

Ormeño-Orrillo, E; Servín-Garcidueñas, LE; Imperial, J; Rey, L; Ruiz-Argüeso, T; Martínez-Romero, E. 2013. "Phylogenetic evidence of the transfer of nodZ and nolL genes from Bradyrhizobium to other rhizobia". Molecular Phylogenetics and Evolution. DOI: S1055-7903(13)00099-7 [pii] 10.1016/j.ympev.2013.03.003".

Durán, D; Rey, L; Sánchez-Cañizares, C; Jorrín, B; Imperial, J; Ruiz-Argüeso, T. 2013. "Biodiversity of Slow-Growing Rhizobia: The Genus Bradyrhizobium", p. 21-46. In B. Rodelas and J. González (ed.), Beneficial Plant-microbial Interactions: Ecology and Applications. CRC Press.

Rubio-Sanz, L; Prieto, RI; Imperial, J; Palacios, JM; Brito, B. 2013. "Functional and expression analysis of the metal-inducible dmeRF system from Rhizobium leguminosarum bv. viciae". Applied and Environmental Microbiology. DOI: AEM.01954-13 [pii] 10.1128/AEM.01954-13".

Albareda, M.; Manyani, H.; Imperial, J.; Brito, B.; Ruiz-Argueso, T.; Bock, A.; Palacios, J.M. 2012. Dual role of HupF in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum. BMC Microbiology 12:256.

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