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Mechanisms of adaptation of bacteria to the rhizospheric environment. Characterization of bacterial consortia for agricultural and environmental technologies (RIZOSFERA-UAM)

Specialized Group:

Rafael Rivilla and Marta Martín

Biology Department, Faculty of Sciences, Autonomous University of Madrid

rafael.rivilla@uam.es; m.martin@uam.es

Group photo. From left to right Paula Sansegundo Lobato, Álvaro Gómez Luengo, Esther Blanco Romero, Miguel Redondo. Grandson, David Durán, Ignacio Fernández Puente, Marta Martín, Daniel Garrido Sanz and Rafael Rivilla

 

The Rizosfera UAM group is interested in the knowledge of the molecular mechanisms that promote the competition and persistence of bacteria in a complex and changing ecological niche such as the rhizosphere of plants. We use as model bacteria Pseudomonas fluorescens F113, which in addition to promoting plant growth, produces a broad spectrum antifungal effective against phytopathogenic fungi. We have also used this rhizobacteria previously in PCB bioremediation technologies. We have worked on the regulation of phase variation and mobility as the main characters involved in the competitive colonization of the rhizosphere. We observed that during the root colonization process, hypermobile phase variants that express two flagellar apparatus were selected; a typical one of Pseudomonas and another cryptic that does not appear in laboratory cultures and that is more similar to the flagellum of Azotobacter. These hypermobile phase variants displace the wild stock in competitive rhizosphere colonization experiments (Martínez-Granero et al., 2006; Barahona et al., 2016). By dissecting the signal transduction mechanisms that regulate movement in P. fluorescens F113, we have constructed multiple hypermobile mutants that are more competitive than the wild line. The performance of biological control tests with these mutants showed that competitiveness and persistence improve the antifungal qualities of the strain in tests carried out with pathogenic strawberry and tomato fungi (Navazo et al., 2009; Barahona et al., 2011). Our most recent research focuses on the regulation of adaptive responses to environmental changes carried out by the transcriptional regulators AmrZ and FleQ. The transcriptomic analyzes performed with the mutants in amrZ and fleQ under both laboratory culture conditions and, during the process of colonization of the rhizosphere and chromatin immunoprecipitation assays that allow the analysis of AmrZ and FleQ regulons, have shown that these proteins are global transcriptional factors and that they form a node of regulation central in the signaling responses that occur when there are environmental changes (Figure 1). Both proteins repress each other and antagonistically regulate the formation of exopolysaccharides, movement capacity, biofilm formation, regulation of type VI secretion systems, and iron and di-cGMP homeostasis (Martínez-Granero et al. ., 2014; Muriel et al., 2017; Blanco-Romero et al., 2018, Muriel et al., 2019).

Figure 1. FleQ and AmrZ form a central node in the regulation of P. fluorescens F113 responses to environmental changes. Blanco Romero et al., Scientific Reports 2018 8: 13145. © The Authors 2018 http://creativecommons.org/licenses/by/4.0/.

Likewise, we have phylogenetically analyzed the Complex of species of P. fluorescens, to which the model strain F113 belongs. This complex has a high genomic and genetic diversity. The analysis in silico of the complete genomes deposited in the databases has allowed us to group all the strains of this Complex into 8 phylogenetic groups that present specific characteristics. Regarding its possible applications in agrobiotechnology, the phylogenetic groups that accumulate a greater number of characteristics that promote plant growth are: P. corrugata (including F113) protecting grams and P. chlororaphis. On the other hand, and regarding its applications in environmental technologies, the group of greatest interest for the degradation of pollutants is P. jessenii (Garrido-Sanz et al., 2016).

Regarding the transfer of knowledge and applications of soil bacteria in environmental technologies, the analysis of the Fluorescens Complex has allowed us to determine group-specific sequences and we have designed a PCR strategy, which allows us to assign any isolate to one of the 8 subgroups (Garrido-Sanz et al., 2017). Also, we have isolated 2 bacterial consortia for the decontamination of PCBs and Diesel, in rhizoremediation systems. Metagenomic analysis has allowed us to characterize these consortia and elucidate the role that each member plays in the degradation of the pollutant (Garrido-Sanz et al., 2018; Garrido-Sanz et al., 2019). Based on this type of analysis, we are also collaborating with companies in the agrobiotechnology sector, characterizing consortiums to be used as agricultural inoculants to promote plant growth.

 

Bibliography

Barahona E, Navazo A, Garrido-Sanz D, Muriel C, Martínez-Granero F, Redondo-Nieto N, Martín M and Rivilla R. (2016) Pseudomonas fluorescens F113 can produce a second flagelar apparatus, which is important for plant root colonization. Front Microbiol 7:1471

Barahona E, Navazo A, Martínez-Granero F, Zea-Bonilla T, Pérez-Jiménez RM, Martín M and Rivilla R. (2011) Pseudomonas fluorescens F113 mutant with enhanced competitive colonization ability and improved biocontrol activity against fungal root pathogens. Appl Environ Microbiol. 77:5412-9

Blanco-Romero E, Redondo-Nieto M, Martínez-Granero F, Garrido-Sanz D, Ramos-González MI, Martín M and Rivilla R. (2018) Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440. Sci Rep. 8(1):13145.

Garrido-Sanz D, Arrebola E, Martínez-Granero F, García-Méndez S, Muriel C, Blanco-Romero E, Martín M, Rivilla R, Redondo-Nieto M. (2017) Classification of isolates from the Pseudomonas fluorescens Complex into phylogenomic groups based in group-specific markers. Front Microbiol. 8:413

Garrido-Sanz D, Manzano J, Martín M, Redondo-Nieto M, Rivilla R. (2018) Metagenomic analysis of a biphenyl-degrading soil bacterial consortium reveals the metabolic roles of specific populations. Front Microbiol. 9:232.

Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M. (2016) Genomic and genetic diversity within the Pseudomonas fluorescens Complex. PLoS One. 11(2):e0150183.

Garrido-Sanz D, Redondo-Nieto M, Guirado M, Pindado Jiménez O, Millán R, Martin M, Rivilla R. (2019) Metagenomic insights into the bacterial functions of a Diesel-degrading consortium for the rhizoremediation of Diesel-polluted soil. Genes (Basel). 10(6)456

Martínez-Granero F, Redondo-Nieto R, Vesga P, Martín M and Rivilla R. (2014) AmrZ is a global transcriptional regulator implicated in iron uptake and environmental adaption in Pseudomonas fluorescens F113. BMC Genomics. 26;15:237

Martínez-Granero F, Rivilla R and Martín M. (2006) Rhizosphere selection of highly motile phenotypic variants of Pseudomonas fluorescens with enhanced competitive colonization ability. Appl Environ Microbiol. 72(5):3429-34.

Muriel C, Arrebola E, Redondo-Nieto M, Martínez-Granero F, Jalvo B, Pfeilmeier S, Blanco-Romero E, Baena I, Malone JG, Rivilla R and Martín M. (2017) AmrZ is a major determinant of c-di-GMP levels in Pseudomonas fluorescens F113. Sci Rep. 8(1):1979.

Muriel C, Blanco-Romero E, Trampari E, Arrebola E, Durán D, Redondo-Nieto M, Malone JG, Martín M and Rivilla R. (2019) The diguanylate cyclase AdrA regulates flagellar biosynthesis in Pseudomonas fluorescens F113 through SadB. Sci Rep. 9(1):8096.

Navazo A, Barahona E, Redondo-Nieto M, Martínez-Granero F, Rivilla R and Martín M. (2009) Three independent signalling pathways repress motility in Pseudomonas fluorescens F113. Microbial Biotech. Vol 2 Issue 4: 489-498

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