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    • 专利摘要:
    Bacterial strain Pseudomonas palmensis BBB001, microorganism from the group of Gram bacteria, genus Pseudomonas, stimulating the adaptive metabolism of plants against abiotic stress and improving plant nutrition in iron and other nutrients. This strain, isolated from the rhizosphere of Nicotiana glauca, has been characterized from a morphological, biochemical and genetic point of view through total sequencing of its genome, identifying itself as a new species, reducing oxidative stress in plants, inducing greater production and an improvement in its adaptation to abiotic stress conditions, for example, due to lack of water or high salinity, so it can be used, alone or in combination with other strains, in order to increase the fitness of plants in plant species of agronomic food interest. On the other hand, since it is capable of improving the nutrition of iron, phosphorus and potassium, it also has application as a biofertilizer, both in organic and conventional agriculture. (Machine-translation by Google Translate, not legally binding)
    公开号:ES2811673A1
    申请号:ES202031185
    申请日:2020-11-26
    公开日:2021-03-12
    发明作者:Albanchez Enrique Gutierrez；Trueba Ignacio Horche；Garcia Jose Antonio Lucas；Solano Beatriz Ramos；Manero Francisco Javier Gutierrez
    申请人:Biobab R&d S L；
    IPC主号:
    专利说明:

    [0002] Pseudomonas palmensis BBB001 stimulating the adaptive metabolism of plants against abiotic stress and improving mineral nutrition
    [0004] The present invention refers to the bacterial strain Pseudomonas palmensis (BBB001 internal laboratory code), as a new species of the genus Pseudomonas, for use in the treatment of plants in order to improve adaptation to abiotic stress, reducing oxidative stress of such that it increases growth and production. In addition, it is capable of producing siderophores, improving the iron nutrition of plants, reversing the symptoms of iron deficiency, and stimulating the mobilization of other nutrients such as phosphorus and potassium, which is why it is also of interest as a biofertilizer for organic farming. and conventional.
    [0006] This strain has been deposited for patent purposes in the Spanish Collection of Type Cultures of the University of Valencia (CECT), where it has been assigned the number 30222.
    [0008] SCOPE
    [0010] The invention falls within the field of agri-food biotechnology, specifically within plant growth regulating bacteria, since the aforementioned bacterial strain can serve as a basis for the preparation of different types of stimulant products of the adaptive metabolism of plants. These products will improve the adaptation of plants to different abiotic stress conditions such as water deficit or excess soil salinity.
    [0012] And also within the field of organic biofertilizers, since the strain can be used to improve the nutrition of the plant in general and more specifically, the absorption of iron in soils, especially with basic pH, both in any bacterial formulation and with bacterial metabolites. obtained under certain conditions.
    [0014] Furthermore, since it is a strain belonging to a new species, following the terminology used for the indexing of bacteria in Bergey's "Determinant Bacteriology Manual", March 2001 edition, together with the genomic analysis performed, the invention can be classified as one of the bacterial species of the genus Pseudomonas .
    [0015] STATE OF THE ART
    [0017] The mechanisms of action of plant growth-promoting bacteria can be summarized into two types: direct, when the bacteria or their metabolites alter the metabolism of the plant (hormonal activity, stimulation of adaptive mechanisms), and indirect, when they synthesize compounds that they facilitate the uptake or mobilization of nutrients or prevent the growth of pathogenic microorganisms on the plant, without altering its metabolism. In the case of this patent, both are of interest. The plant has a secondary, highly inducible metabolism, related to the adaptation of the plant to adverse situations that it has to face during its life.
    [0019] The genus Pseudomonas is common among soil bacteria. Following the taxonomy of the Bergey's Manual, March 2001 edition, this bacterium falls within the Bacteria Domain, Phylum Proteobacteria, Class gamma proteobacteria, Order Pseudomonadales, Family Pseudomonaceae. The genus Pseudomonas is very common in the edaphic system, and has been repeatedly described as a protective bacterium against different plant diseases. Some bacteria in this group produce yellow-green fluorescent pigments that are easily soluble in water. Among other functions, these pigments act as siderophores (molecules capable of capturing iron from the medium for the metabolism of the microorganism). In addition, they have great metabolic versatility due to a large number of plasmids that contain inducible operons for the synthesis of specific enzymes that allow the compounds present in the medium to be catabolized. The presence of Pseudomonas sp. in the rhizosphere of different plants, it beneficially affects their physiology, indicating that their selection by the plant at the rhizospheric level is very possible. The effects of this strain on the physiology of different plants indicate that the plant selects them for its benefit.
    [0021] There are numerous references in the literature relating to compositions and formulations containing strains of the genus Pseudomonas , alone or in combination with other organisms to stimulate and improve plant growth, or that serve as a basis for the formulation of phytosanitary products, protectors against pathogens or for preserve the good growth of the crops, some of which have been patented, case of the European patents with publication numbers in Spain ES2707807-T3, 2019-04-05, New fluorescent Pseudomonas of the species Pseudomonas azotoformans for the stimulation of the emergence and growth of plants, and ES2624788-T3, 2017-07-17, Biological culture of a strain of the species Pseudomonas graminis and use of said culture as an antagonist for the biological control of pathogenic bacteria; or the national patent ES2572746-B1, 2016 09-21, for Procedure for obtaining a composition promoting plant growth comprising Pseudomonas putida and its uses.
    [0023] In the case of the present patent application, new technologies have allowed the determination of a new species, Pseudomonas palmensis BBB001, based on its unique genetic characteristics, which differentiate it from other Pseudomonas strains when the BBB001 genome is compared with the 254 genomes. complete and available Pseudomonas.
    [0025] The parameters that make it possible to identify a new species are one of the following: i) mean nucleotide identity (ANI) and mean amino acid identity (AAI), the limit values for defining a new species being less than 95%; ii) DNA-DNA digital hybridization (dDDH), with values below 70%; iii) Guanine-cytosine content (G + C), values above 1%; iv) correlation index of frequencies of tetranucleotide use (TETRA), with values below 0.99; v) multilocus sequence analysis (MLSA), with values below 97%.
    [0027] When comparing the BBB001 genome with the 254 available genomes, Pseudomonas alkylphenolica is the closest species according to the ANI and AAI values were 83.39% and 85.11%, respectively, both below 95%, the DNA-DNA digital hybridization values (dDDH) 27.10%, below 70% and guanine-cytosine content (G + C) 3.43%, above 1%. The values of the correlation index of the frequencies of use of tetranucleotides (TETRA) against the most similar species in this analysis, Pseudomonas sp.NZ CP024478.1 (strain HLS-6), was 0.983, below 0.99. On the other hand, in the phylogenetic analysis and delimitation of species based on the multilocus sequence analysis (MLSA) of the selected genes (16S rRNA, gyrB, rpoB rpoD), the highest estimate of similarity is 91.52% with respect to Pseudomonas japónica , which is the most similar species in this analysis; values below 97% indicate that it is a new species. The phylogeny of single nucleotide polymorphisms (SNPs) in the set of genes shared by all Pseudomonas genomes (core genome), revealed that its core genome consists of 585 gene families, representing only 0.05% of the total content of gene families of this group, a value that reinforces its identity as a new species. And finally, the phylogeny based on the presence or absence of homologous gene families in the pan-genome, yields very similar results to those obtained based on the analysis of SNPs. Tables 2 and 3 of the embodiment of the invention section show all the results of similarity between the new species and those most similar to it.
    [0028] Therefore, based on the polyphasic approach, a new species has been described for which the name of Pseudomonas palmensis sp. nov (CECT Deposit No. 030222). The physiological characteristics and the genetic analysis of this strain allow it to be unequivocally identified, differentiating it from other species of the genus Pseudomonas .
    [0030] The Pseudomonas palmensis strain is characterized by its beneficial effects on plants: it induces the metabolism involved in the elimination of free radicals produced in stress situations, improving the adaptation of the plant to these conditions through a mechanism of redox metabolism homeostasis and an increase of the water potential under these conditions, a clear indicator of the capacity of this strain to induce a water balance, resulting in a greater capacity of the plant to resist water stress conditions. On the other hand, it is capable of improving the iron nutrition of plants, also improving their growth.
    [0032] Being a new species, there are no Pseudomonas palmensis patents on any of the reported effects. With regard to the genus Pseudomonas, there are several publications that describe their ability to produce siderophores and modulate the metabolism involved in oxidative stress (Bar-Ness et. Al., 1991, Journal Iron nutrition and interactions in plants, 271-281; Weger et. al., 1988, DOI: 10.1128 / jb.170.10.4693-4698.1988; Ghosh et. al., 2018, DOI: https://doi.org/10.1007/s13213-018-1366-7; Vives-Peris et. al., 2018, DOI: https://doi.org/10.1007/s00299-018-2328-z). Regarding the strains of Pseudomonas that show the greatest similarity with the new species proposed based on the criteria set forth above, which are P.alkylphenolica, P.japonica or Pseudomonas sp.NZ CP024478.1 (strain HLS-6), there is no patent or publication on these species in the field of application of the present invention. There is some information on P.japonica related to the degradation of industrial oil ( Pseudomonas japonica sp. Nov., A novel species that assimilates straight chain alkylphenols. JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY 2008 54; 1 Strain Number cited in this paper: TISTR 1526) and with the ability to prevent the adhesion of mollusks to any surface (WO2014149324A1), but not related to the agri-food field to which the present invention refers.
    [0034] THE INVENTION
    [0036] The object of the invention that is described here and that, in view of the prior state of the art, is understood to meet the conditions of novelty and inventive step necessary to be able to be worthy of the patent right, is the isolation and characterization of the bacterial strain Pseudomonas palmensis BBB001 (CECT 30222), which is a microorganism of the group of Gram-bacteria, genus Pseudomonas, with the ability to stimulate the adaptive metabolism to abiotic stress of plants, reducing oxidative stress by inducing the metabolism involved in the elimination of free radicals produced in stressful situations, improving the adaptation of the plant to these conditions through the homeostasis of redox metabolism, in such a way that growth and production are stimulated, in addition to being applied by the mobilization of nutrients, especially for iron nutrition.
    [0038] The physiological characteristics and genetic analysis of this strain, with a genome sequenced in accordance with the WIPO ST.25 standard that is included at the end of this specification, allow it to be unequivocally identified, differentiating it from other species of the genus Pseudomonas .
    [0040] In a bacteria screening carried out in the rhizosphere of Nicotiana glauca , a strain belonging to the genus Pseudomonas was isolated whose genetic analysis did not allow it to be placed in any of the known species of this genus.
    [0042] Once isolated, a characterization of the repertoire of unique genes of Pseudomonas BBB001 was carried out. In the comparative analysis of the 254 complete genomes, the BPGA program identified a total of 489 genes present exclusively in Pseudomonas BBB001, of which 41 genes were associated with a specific subsystem. Among the 41 unique genes of Pseudomonas BBB001, those related to iron uptake and metabolism, and those related to the synthesis of amino acids and derivatives, stand out due to their abundance. These 41 genes corresponding to SEQ ID NO: 1 to 41 of the sequence list, have the capacity to encode formulations for the production of substances or compounds on an industrial scale, and can be used for heterologous expression in obtaining products containing material. biological strain.
    [0044] After its characterization, various tests were carried out to reveal biochemical activities that indicate its potential capacity to induce adaptive metabolism, reducing oxidative stress and promoting plant growth, on the one hand, and on the other, its ability to improve nutrition. iron. These were, production of auxins, degradation of 1-aminocyclopropane-1-carboxylate, solubilization of phosphate and production of siderophores and chitinases, resulting positive for the production of auxins and siderophores in vitro. The BIOLOG Eco profile indicates that it is capable of degrading the tricarboxylic acids malic, hydroxybutyric and glucosamic acid, and the degradation of 1P glucose, cellobiose, lactose and N-acetylglucosamine stand out among the sugars. As nitrogen sources, it uses putrescine, phenylethylamine, serine and glycol-L-glutamic acid.
    [0046] So far, consistent experiences have been carried out in the direct inoculation of Pseudomonas palmensis in a model plant ( Arabidopsis thaliana) where it has characterized the metabolic profile of enzymes related to the control of oxidative stress and redox balance of the plant and the modification of photosynthetic parameters. related to fluorescence as an indicator of the potential for stimulating plant growth and production, and also of the health status of the plant as a result of the effects on the plant's redox balance.
    [0048] Likewise, direct inoculations have been carried out on blackberry plants ( Rubus sp. Var Lochness), growing in production greenhouses. The total accumulated production has been determined, and the metabolic profile of enzymes related to the control of oxidative stress in blackberry leaves has been determined, at two moments of the cycle (flowering and full production), making two applications per month, during the 6 months of the production cycle.
    [0050] These two experiments carried out in different plant species show that the bacterium is capable of modulating the metabolism involved in the adaptation of the plant to abiotic stress, controlling oxidative stress by increasing the capacity to eliminate oxygen free radicals (ROS) by: 1) an increase in the activities of ROS scavenging enzymes, superoxide dismutase (SOD) or catalase (CAT), and 2) an increase in the dissipation of excess photosynthetic energy responsible for the generation of free radicals ROS (non photochemical quenching, NPQ) under normal conditions.
    [0052] Another experiment has been carried out to demonstrate the ability to stimulate adaptive metabolism under salinity stress conditions in tomato plants. The strain induces a substantive improvement in the water potential with respect to the control, slightly increasing the content of proline, a compatible osmolyte. The increase in water potential under these conditions is a clear indicator of the ability of this strain to induce a water balance, resulting in a greater capacity of the plant to resist conditions of salinity or water stress.
    [0053] In another experiment carried out in olive trees in production in an intensive and irrigated system, an experiment was carried out with BBB001 to evaluate the ability to increase production under normal irrigation conditions and with a 25% reduction in irrigation. In a sampling prior to harvest, we have found an increase of more than 40% in the average fresh weight of the fruits with respect to its control under standard irrigation conditions, and with water reduction. On the other hand, the weight of the fruits of the plants treated with BBB001 at the radical level reached the same values in both irrigation regimes.
    [0055] On the other hand, iron deficiency chlorosis reversal experiments have been carried out in tomato plants. These experiments have been carried out by direct inoculation of Pseudomonas palmensis in tomato plants in which an iron deficiency had been induced and the substrate had been adjusted to basic pH to ensure the insolubilization of Fe. Likewise, the grown strain has been tested. in a specific medium for the production of siderophores (modified succinate medium), with the strain, and we also tested only the metabolic liquid. Similar results have been found with all treatments, highlighting the effect on the improvement of the iron, phosphorus and potassium content, the improvement of photosynthesis, an increase in photosynthetic pigments and, therefore, an improvement in growth (weight gain dry).
    [0057] The aforementioned experiments on the use of Pseudomonas palmensis BBB001 with the capacity to stimulate the metabolism of adaptation to abiotic stress in plants, reducing oxidative stress, by increasing the activity of enzymes related to ROS scavenging , in such a way that it is stimulated growth and production, in addition to having application as a biofertilizer because it stimulates the mobilization of nutrients, specifically the nutrition of iron, phosphorus and potassium, are set out at the end of this report, within the embodiment section.
    [0059] Ultimately, the aim pursued with this invention and which constitutes the technical advantage provided with it, is to have a bacterium (biostimulant / biofertilizer) that improves the ability to stimulate the plants' abiotic stress adaptation metabolism, reducing oxidative stress, in such a way that growth and production are stimulated. On the other hand, it has application as a biofertilizer because it stimulates the mobilization of nutrients, specifically the nutrition of iron, phosphorus and potassium, bringing said bacteria or any of its parts into contact with the plant by any available means, improving the effect with certain bacterial species.
    [0060] Consequently, the present patent application claims the use of the strain Pseudomonas palmensis BBB001, or any bacterial molecule, fraction or formulation derived from it, or of the metabolites of the culture broth of the strain, in any proportion, for its application in any type of plant species, in order to increase the adaptability of plants to any condition of abiotic stress, for example in salinity conditions, increasing production, as well as to improve mineral nutrition in iron, phosphorus and potassium from plants.
    [0062] Said use of Pseudomonas palmensis BBB001 may be as part of any preparation with the strain, either individually or in combination with other bacterial species or organisms, and by any available means that puts the bacteria in contact with the seed, the root or aerial system. of the plants.
    [0064] In particular, the use of Pseudomonas palmensis BBB001 is suitable in combination with Pseudomonas fluorescens CECT 9015, or as part of any preparation with this other strain, to improve the response to salt stress; and also in combination with Arthrobacter oxydans Code CECT 30231, to improve mineral nutrition in iron, nitrogen, phosphorus and potassium, both in organic and conventional agriculture.
    [0066] FORM OF REALIZATION.-
    [0068] The strain of the genus Pseudomonas described here was isolated by studying the rhizosphere of natural populations of Nicotiana glauca in a transect on the island of Las Palmas de Gran Canaria (Canary Islands). This plant species ( Nicotiana glauca) was selected for being from the Solanaceae family, for having an active secondary metabolism and for having been a good source of microorganisms with biological activity of interest in agriculture.
    [0070] The rhizosphere samplings for the isolation of the bacterial strain were carried out in natural populations of Nicotiana glauca in December 2017. As a result of this sampling, 450 strains were collected, among which Pseudomonas palmensis (BBB001, internal laboratory code) was found. The isolation of said strain was carried out on nutrient agar (PCA).
    [0072] In the laboratory, this microorganism is maintained with a high survival rate in 20% glycerol in nutrient broth (Pronadisa) at -80 ° C or in 15% glycerol in water at 20 ° C and are easily recovered in the culture medium used for isolation both in solid phase and in liquid phase at 28 ° C.
    [0074] I. Morphological, biochemical and genetic characteristics of Pseudomonas palmensis BBB001.-
    [0076] For the characterization of the strain, different phenotypic characters were considered, which are detailed in this report: (i) morphology of the colonies (ii) morphology of the cells, (iii) metabolic profile, iv) Comparative analysis of the genome of the strain Pseudomonas BBB001 and the available complete genomes of the genus Pseudomonas.
    [0078] Table 1 specifies the morphology of the colonies at 24 h of incubation at 28 ° in agar for standard methods (PCA).
    [0080] TABLE 1
    [0082]
    [0085] Growing in liquid medium (Pronadisa Nutritive Broth) the color of the medium changes to yellow from the exponential phase of growth to the stationary phase of growth.
    [0087] The morphological characters of Pseudomonas palmensis BBB001 at 24 h of incubation at 28 ° in agar for standard methods (PCA) correspond to a Gram negative bacillus.
    [0089] Once isolated and characterized, with internal reference code BBB001, various tests were carried out to reveal the potential of this bacterium. These were, production of auxins, degradation of 1-aminocyclopropane-1-carboxylate, solubilization of phosphate and production of siderophores and chitinases, resulting positive for the production of siderophores.
    [0092] The metabolic profile (BIOLOG Eco, www.biolog.com/products-portfolio-overview/microbialcommunity-analysis-with-ecoplates/) indicates that it is capable of degrading the acids: malic tricarboxylic, hydroxybutyric and glucosamic acid, and the degradation of glucose 1 P, cellobiose, lactose and N-acetylglucosamine stand out among the sugars. As nitrogen sources, it uses putrescine, phenylethylamine, serine and glycol-L-glutamic acid.
    [0094] To investigate the phylogenetic relationship of the strain Pseudomonas palmensis BBB001 with respect to the other species of the genus Pseudomonas and define its taxonomic assignment, its complete genome was compared with the 254 Pseudomonas genomes that are available and complete in the databases. Three main strategies were used, according to the following defining criteria of a new species of bacteria:
    [0096] 1. Estimates of the degree of similarity between genomes: mean nucleotide identity (ANI), mean amino acid identity (AAI), DNA-DNA hybridization in silica or dDDH (digital DNA-DNA hybridization), difference in guanine-cytosine content (G + C) and frequency of use of tetranucleotides (TETRA):
    [0098] • The ANI and AAI values represent a robust measure of the evolutionary distance between two genomes; when these values are less than 95%, it is assumed that it is a new species. It has been empirically verified that ANI and AAI values of 95-96% are equivalent to a DDH (DNA-DNA hybridization) value of 70%, another parameter commonly used to delimit prokaryotic species (eg, Konstantinidis and Tiedje 2005, PNAS 102: 2567- 2572; Richter and Rosselló-Mora 2009, PNAS 106: 19126-19131; Kim et al. 2014, International Journal of Systematic and Evolutionary Microbiology 64: 346-351).
    [0099] • Differences in G + C content within the same species are generally not greater than 1%; Meier-Koltho et al. 2014, International Journal of Systematic and Evolutionary Microbiology 64: 352-356).
    [0100] • The dDDH index has shown a greater correlation with traditional DDH values (Auch et al. 2010, Standards in Genomic Sciences 2: 1). For this reason, it is considered that dDDH values higher than 70% are indicative that the compared genomes belong to the same species.
    [0101] • The TETRA values between the Pseudomonas BBB001 genome and the 26 most related genomes. The genomes of closely related strains will predictably show similar frequencies of use of tetranucleotides, with correlation indices (TETRA) equal to or greater than 0.99, therefore, TETRA values lower than 0.99 are indicators of a new species (Teeling et al. 2004, Environmental Microbiology 6: 938947; Richter and Rosselló-Mora 2009, PNAS 106: 19126-19131).
    [0103] 2. Phylogenetic analysis and species delimitation based on multilocus sequence analysis (MLSA: multilocus sequence analysis):
    [0105] • The sequencing of the 16S ribosomal gene (16S rRNA) is the basic tool in current bacterial species classification systems. Generally, it is accepted that two different species will present similarity values for the 16S rRNA gene lower than 98.65-99% (Kim et al. 2014, International Journal of Systematic and Evolutionary Microbiology 64: 346-351). However, in many cases, the 16S rRNA gene can offer limited resolving power. On the one hand, this gene may have a low discrimination capacity between closely related species. On the other hand, some species may show very similar 16S rRNA sequences (<99%), despite being clearly different based on DDH values (Ash et al. 1991, International Journal of Systematic and Evolutionary Microbiology 41: 343 -346; Rosselló-Mora and Amann 2001, FEMS Microbiology Reviews 25: 39-67). In the specific case of the genus Pseudomonas, Mulet et al. Have recommended the analysis of three additional genes (gyrB, rpoB and rpoD) to delimit species, identify new strains, or resolve the phylogenetic relationships within this group (Mulet et al. 2012a, Systematic and Applied Microbiology 35: 455-464; Mulet et al. 2012b, Systematic and Applied Microbiology 35: 145-149; Sánchez et al. 2014, Systematic and Applied Microbiology 37: 89-94). Mulet et al. Established a mean similarity of 97% as a criterion for the delimitation of species based on the MLSA of these four genes within the genus Pseudomonas (Mulet et al. 2010, Environmental Microbiology 12: 1513-1530).
    [0107] 3. Phylogenetic analysis at the complete genome level, based on the identification of variants (single nucleotide polymorphisms, SNPs) in the conserved fraction of the genome (core genome) and on the presence / absence of genes in the pan-genome:
    [0109] • Phylogeny of SNPs (single nucleotide polymorphism) in the set of genes shared by all Pseudomonas genomes ( core genome), and phylogeny based on the presence or absence of homologous gene families in the pan- genome. Advances in the sequencing and comparison of bacterial genomes have revealed an unexpected variability in the gene content of the different species of the same genus, and even of the different strains of the same species. The genomes of Escheríchia coli strains, for example, share only 40% of their genes (Rasko et al. 2008, Journal of Bacteriology 190: 6881-6893). This has led to formulate the concept of core genome or basic genome, to define the set of genes shared by all bacterial species of a certain group. Genes that are absent in one or more members of the group, and therefore not part of the core genome , are called accessory genes. Finally, the complete gene repertoire (that is, the sum of the core genome and accessory genes) has been called the pan-genome.
    [0111] Finally, as a result obtained from the analysis of the Pseudomonas pan-genome, the repertoire of unique genes present in the Pseudomonas strain BBB001 was characterized.
    [0113] 1. Estimates of the degree of similarity between genomes.-
    [0115] 1.1. Average nucleotide identity (ANI) and average amino acid identity (AAI) parameters:
    [0117] The first stage of this analysis consists of the comparison at the nucleotide and amino acid level of the Pseudomonas BBB001 genome with respect to all the complete genomes available in the RefSeq database (NCBI Reference Sequence database) for the genus Pseudomonas .
    [0119] The estimates of the nucleotide identity indices (ANI) were calculated with the OAU.jar program.
    [0121] For the comparison of the amino acid content (AAI) the tool CompareM v0.0.23 (https://github.com/dparks1134/CompareM) was used. This tool identifies homologous genes and calculates the identity between them.
    [0123] 1.2. DNA-DNA hybridization in silica (dDDH) and G + C content:
    [0126] Based on the results of the previous section, the 26 genomes located in the fourth quartile of the distribution of ANI values (ie, predictably, those most closely related to Pseudomonas BBB001) were selected to calculate intergenomic distances and dDDH indices. , using the web server GGDC (Genome-to-Genome Distance Calculator. This server also calculates the difference in the G + C content of the analyzed genomes.
    [0128] 1.3. Tetranucleotide Use Frequencies (TETRA):
    [0130] The JSpecies software (Richter and Rossello-Mora 2009, PNAS 106: 19126-19131) was used to calculate the differences in tetranucleotide use profiles between the Pseudomonas BBB001 genome and the 26 most related genomes.
    [0132] 2. Phylogenetic analysis and species delimitation based on multilocus sequence analysis (MLSA: multilocus sequence analysis) .-
    [0134] In the multilocus analysis, also carried out in the subset of 26 genomes, the four recommended housekeeping genes were included for the delimitation of species in the genus Pseudomonas: 16S, gyrB, rpoD and rpoB (eg, Mulet et al. 2012a, Systematic and Applied Microbiology 35: 455-464).
    [0136] -16S: A homemade bash script pipeline was used to extract the multiple copies of this gene in each of the complete genomes analyzed. These copies were collapsed into a consensus in which each variable position was represented as an ambiguity.
    [0138] -gyrB, rpoD and rpoB: The gyrB, rpoD and rpoB genes were extracted from the entire genomes in question by mapping against reference using BWA 0.7.12 (Li and Durbin 2010, Bioinformatics 26: 589-595).
    [0140] Furthermore, in order to be able to compare the resulting phylogeny with that obtained by Mulet et al. When investigating the phylogenetic position of Pseudomonas alkylphenolica (Mulet et al. 2015, International Journal of Systematic and Evolutionary Microbiology 65: 4013-4018), the sequences from 13 other species or strains used in that work, without published complete genomes.
    [0141] For each of the aforementioned genes, an alignment of all the sequences was performed using the Mafft v7.310 program (Katoh et al. 2002, Nucleic Acids Research 30: 3059-3066). In each of the 4 alignments, those regions that were ambiguous (i.e. regions absent in some sequences and / or misaligned) were eliminated.
    [0143] Finally, the 4 genes were concatenated and the nucleotide substitution models that best fit each of them were estimated using PartitionFinder 2 (Lanfear et al. 2012, Molecular Biology and Evolution 29: 1695-1701). To obtain the phylogenetic tree, MrBayes v3.2 was used (Ronquist et al. 2012, Systematic Biology 61: 539-542).
    [0145] A study of the similarity of these 4 genes between Pseudomonas BBB001 and the rest of the species or strains was also carried out, using a Biopython module called DistanceCalculator. In the case of the 16S gene, being of multiple copy, the mean of the similarity obtained for each copy was calculated.
    [0147] 3. Phylogenetic analysis based on the sequences of complete genomes.-
    [0149] The BPGA software (Chaudhari et al. 2016, Scientific Reports 6: 24373) was used to perform homology clustering of the annotated genes in the 253 complete genomes of Pseudomonas and in Pseudomonas BBB001. The grouping threshold was 50% homology, thus grouping together homologous genes and also genes that may belong to the same family. BPGA identifies the gene families shared by all the analyzed genomes (core genome), the accessory genes and, in addition, the unique functions, that is, genes that have not been grouped into any of the clusters created.
    [0151] 3.1. Phylogeny of SNPs (single nucleotide polymorphisms) present in core genes:
    [0153] First, a homemade pipeline of bash scripts was designed to extract the nucleotide sequences associated with the genes identified as core genome by BPGA.
    [0155] The genetic distance of these sequences was analyzed using DistanceCalculator and an alignment was generated for each of the core genes using Mafft v7.310 (Katoh et al. 2002, Nucleic Acids Research 30: 3059-3066). Finally, the information on the content of gaps in the generated alignments was extracted to identify poor quality alignments.
    [0158] For the study of SNPs, it is necessary to ensure that all the extracted positions are homologous positions, so those genes that included sequences with a distance greater than 50% and that also included a gap content greater than 10% of the sequence length.
    [0160] Geneious v10.2.2 (Kearse et al. 2012, Bioinformatics 28: 1647-1649) was used to eliminate the positions where more than 10% of the sequences had a gap and, finally, to extract the SNPs in PHYLIP format.
    [0162] The RAxML v8.2.9 software (Stamatakis 2014, Bioinformatics 30: 1312-1313) was used to generate the maximum likelihood phylogenetic tree of all the concatenated SNPs. The support of each node was calculated by performing 1000 bootstrap replicas.
    [0164] 3.2 Phylogeny of the matrix presence / absence of genes or gene families in the pangenome:
    [0166] The gene presence / absence matrix produced by BPGA was used to reconstruct a maximum likelihood phylogenetic tree using IQTREE (Chernomor et al. 2016, Systematic Biology 65: 997-1008). The support of each node was calculated by performing 1000 bootstrap replicas.
    [0168] 4. Characterization of the repertoire of unique genes of Pseudomonas BBB001.-
    [0170] To determine whether the unique functions identified had not been previously described, a local database of the nr (nonredundant) protein database available in the NCBI / EMBL / DDBJ database collection was created to perform a search for you are using the BLAST + 2.6.0 program (Camacho et al. 2008, BMC Bioinformatics 10: 421).
    [0172] A homemade pipeline of scripts written in bash language was used to extract the relevant information from the first correspondence obtained in the search carried out. Exclusive genes are presented in attached file.
    [0174] 5. Discussion of results.-
    [0177] The results obtained when comparing our strain with 254 Pseudomonas genomes and that have allowed it to be resolved as a new species, Pseudomonas palmensis BBB001, are indicated below; all values are the result of comparison with the most similar species available. Thus its unique genetic characteristics are: with respect to Pseudomonas alkylphenolica, ANI and AAI values of 83.39% and 85.11%, respectively (table 2), the estimated values of dDDH of 27.10%, content in G + C, which shows a difference 3.43% (table 2). Likewise, it presents TETRA values of 0.983, compared to the most similar species in this analysis Pseudomonas sp.NZ CP024478.1 (strain HLS-6) (table 2).
    [0179] Table 2 shows the results of the estimates of the degree of similarity between genomes. For each genome, its length (in base pairs, bp), the number of annotated genes, and the values of ANI, AAI, dDDH, intergenomic distance, difference in G + C content and TETRA index estimated in the comparison with the genome of Pseudomonas BBB001. In column 1, after the species name, the RefSeq genome accession number is indicated.
    [0181] TABLE 2
    [0184]
    [0187] The estimates of similarity in the MLSA analysis for the 16S rRNA gene (sequence deposited in Genebank MW009702) yielded values between 98.52% and 99.42%, close to or above the threshold value to be included in the same species, however, the Similarity values for the other three genes included in the MLSA are, however, considerably lower <97% (91.52%, with respect to Pseudomonas japónica, the most similar species in this analysis, Table 3) established by Mulet and
    [0190] collaborators for the delimitation of species based on the MLSA of these four genes within the genus Pseudomonas.
    [0191] Table 3 shows the percentage of similarity for each of the four genes included in the MLSA and the mean similarity calculated for the four genes together.
    [0192] TABLE 3
    [0193]
    [0196]
    [0199] Phylogeny of SNPs in the set of genes shared by all Pseudomonas genomes (core genome). The comparison of the 254 complete genomes available for the genus Pseudomonas and the genome of Pseudomonas BBB001, carried out with the BPGA software, revealed that its core genome consists of 585 gene families, representing only 0.05% of the total content of gene families of this group. The vast majority of the families that make up the core genome are associated with functions of ribosome translation and biogenesis, or of amino acid metabolism and transport.
    [0201] After extracting the orthologous genes (275 genes) from the group of families of the core genome, a total of 164,394 polymorphic positions (single nucleotide polymorphisms, SNPs) were identified in the 254 genomes. Based on the SNPs, five large well-differentiated groups are obtained, which generally agree with the phylogeny of the genus Pseudomonas presented in Gomila et al. 2015 (Frontiers in Microbiology 6: 214):
    [0203] • Group of P. aeruginosa, P. denitrificans, P. knackmussii and P. citronellolis. (102 genomes)
    [0204] • Group of P. stutzeri, to which P. balearica also belongs. ( 11 genomes)
    [0205] • Group of P. syringae, in which P. amygdali , P.
    [0206] savastanoi , P. viridiava and P. cichorii . (22 genomes)
    [0207] • Group of P. fluorescens, which includes other species such as P. mandelii, P.
    [0208] koreensisis, P. brassicacearum, P. protegens or P. fragi. (57 genomes) • Group of P. putida, within which is found Pseudomonas BBB001. (43 genomes)
    [0209] • Other groups: (19 genomes)
    [0211] The P. putida group includes a total of 43 of the 254 genomes analyzed complete and available in databases. In addition to all the genomes belonging to P. putida, this group includes other species such as P. monteilii or P. parafulva. Consistent with the MLSA results, Pseudomonas BBB001 forms a statistically well supported subgroup with the species P. alkylphenolica and Pseudomonas sp. NZ CP024478.1 (strain HLS-6). Within this subgroup is not possible to make a direct comparison with the results of the MLSA, as the species P. japonica and P. vranovensis not
    [0214] they have complete published genomes and are therefore not included in the core genome analysis. However, although the MLSA phylogeny did not allow to resolve the phylogenetic position of Pseudomonas BBB001 with respect to the other species, the SNPs phylogeny provided higher resolution, recovering Pseudomonas BBB001 as the basal lineage of this subgroup (that is, Pseudomonas BBB001 was the first to be separated from P. alkylphenolica and Pseudomonas sp. strain HLS-6).
    [0216] Phylogeny based on the presence or absence of homologous gene families in the pangenome. Comparative analysis of the 254 genomes revealed the presence of a total of 65,137 accessory gene families in the pan-genome. The information on the presence or absence of genes in each genome was transformed into a binary matrix.
    [0218] In general, the phylogeny obtained from the information on the presence / absence of genes in the pan-genome was similar to that obtained based on the analysis of SNPs, although some significant difference was observed. For example, the group of P. stutzeri, which according to the phylogeny of SNPs is closer to the group of P. putida than P. aeruginosa, appears as the basal group, the most divergent of all those analyzed, based on its content of accessory genes.
    [0220] In the pan-genome phylogeny, Pseudomonas BBB001 is also part of the P. putida group, constituting a well differentiated subgroup together with P. alkylphenolica and Pseudomonas sp. NZ CP024478.1 (strain HLS-6). In this case, contrary to the phylogeny of SNPs, the analysis establishes, with a significant supporting value, a closer relationship between Pseudomonas BBB001 and Pseudomonas sp. (strain HLS-6). It is therefore likely that the accessory gene repertoire of Pseudomonas BBB001 is more similar to that of Pseudomonas sp. (strain HLS-6) than that of P. alkylphenolica.
    [0222] II. Evidence of Pseudomonas palmensis as a stimulant of the adaptive metabolism of plants against abiotic stress and an improver of iron nutrition. -
    [0224] 1st. Direct inoculation experiment of Pseudomonas palmensis in a model plant ( Arabidopsis thaliana). An experiment carried out in an experimentation chamber under controlled conditions of light, humidity and temperature on a total of 42 plants and a N = 3, with a random block model - a cell suspension of the strain was inoculated into pregerminated A. thaliana seedlings to the 2 and 5 weeks from germination. At 6 weeks measured the fluorescence photosynthetic parameters (F0, Fv / Fm, PSII, NPQ), the plants were harvested, and the enzymatic activities related to ROS scavenging (SOD, APX, CAT), and the glutathion Ascorbate cycle were weighed and analyzed. (dehydroascorbate reductase - DHR, monodehydroascorbate reductase-MDHR, glutathione reductase-GR). A significant increase in the capacity to dissipate energy (Non photochemical quenching-NPQ) was observed and the metabolic profile of enzymes related to the control of oxidative stress consists of a significant increase in catalase (CAT) and glutathione reductase (GR) activity, and a decrease in APX activity. A fresh weight gain was recorded.
    [0226] 2nd. Direct inoculation experiment of Pseudomonas palmensis in blackberry ( Rubus var. Lochness) in production greenhouses. Experiment carried out in real conditions of field production on a total of 120 plants and n = 3, with an experimental model of random blocks. Cell suspensions of the strain were applied at the root level during the 6 months of the production cycle, twice a month from October to March. The total production was collected and two sampling times were determined, full flowering and fruiting. At each moment the fluorescence photosynthetic parameters (F0, Fv / Fm, PSII, NPQ) were measured and leaves were taken, where the photosynthetic pigments and the enzymatic activities related to ROS scavenging (SOD, APX, CAT) were analyzed. and Ascorbate-glutathione cycle (dehydroascorbate reductase-DHR, monodehydroascorbate reductase-MDHR, glutathione reductase-GR); The antioxidant potential (ability to inhibit the oxidation of B-carotene) and the levels of malondialdehyde-MDA, indicator of the oxidative state of the cell, were assessed. A significant increase in the capacity to dissipate energy (Non photochemical quenching-NPQ) and a decrease in chlorophyll B were observed at both sampling times; the metabolic profile of enzymes related to the control of oxidative stress consists of a significant increase in superoxide dismutase (SOD) and monodehydroascorbate reductase (MDHA) activity, and a decrease in ascorbate peroxidase (APX) activity, associated with an improvement in the antioxidant potential and a level of malondialdehyde slightly lower than the control in fruiting. There was an increase in fruit production.
    [0228] 3rd. Adaptive metabolism stimulation experiment in tomato salinity conditions (var Casillas). This experiment was carried out in a greenhouse under controlled conditions of light, humidity and temperature on a total of 336 plants, 4 treatments, 3R per treatment, n = 28, organized in random blocks. Tomato seeds were germinated in pots, making 3 applications with a bacterial suspension at 2, 4 and 6 weeks from germination; A 500 mM NaCI solution was applied in the irrigation for a week, normal irrigation was maintained for another week, after which the water potential was measured with a Scholander camera and the dry weight of the root, aerial part and height was determined. . A significant decrease in height and air weight, an increase in water potential and an increase in proline, an osmolyte related to resistance to water stress, were observed. In this experiment the combination of P. palmensis with another pseudomonas P. fluorescens CECT9015 was also tested. It was observed that the combination of both produced significant increases in root height and dry weight, as well as an increase in water potential and a significant increase in proline, this effect being synergistic according to Colby (http://www.jstor.org / stable / 4041058) as strain CECT9015 individually was not responsible for these increases.
    [0230] 4th. An experiment was carried out in an irrigated superintensive olive tree, reducing irrigation by 25% over usual (eliminating one irrigation out of every 4). Pseudomonas strain BBB001 was tested in radical application. Applications were made every 15 days from April to September (12 applications). The number of plants in the trial was 20 per treatment (3) plus the control, with the two irrigation regimes, (100% water and 75% water). The follow-up sampling (September) prior to harvest indicated that the strain BBB001 applied at the root level caused an increase in fresh weight in olives of 44.52% over the control with water (mean weight of 20 fruits, n = 3), and 45.96% over the control with water reduction, reaching the same weight for olives treated with BBB001 in the two irrigation regimes.
    [0232] 5th. Iron chlorosis reversal experiment in tomato plants (var. Casillas). Experiment carried out in a greenhouse under controlled conditions of light, humidity and temperature on a total of 216 plants, 9 treatments, 24 plants per treatment organized in 3 replications, following an experimental model of random blocks. The substrate was kept at basic pH with 5mM sodium bicarbonate buffer throughout the experiment. The seeds were germinated in substrate pots, watering with Hoagland's solution without iron once a week, for 8 weeks, until chlorosis appeared. Since the chlorosis appeared, they began to irrigate with Hoagland with Fe, providing the Fe in insoluble form (Cl3Fe), maintaining a control with a complete Hoagland solution with soluble Fe; 3 doses of bacteria were applied with a difference of 4 days between applications. At 2 weeks, the chlorosis had reversed, the fluorescence photosynthetic parameters (F0, Fv / Fm, PSII, NPQ) were measured and the plants were harvested. Dry weight, photosynthetic pigments, and foliar nutrient analysis were analyzed. I know
    [0235] observed an increase in Fo, Fv / Fm and ePSR, and a decrease in energy dissipation (NPQ), together with an increase in photosynthetic pigments (chlorophyll a, b and carotenes) indicating an improvement in the fitness of the plant. The nutrient analysis indicated an increase in the iron concentration of 25%, as well as an improvement in the zinc content, and an increase of 8.46% and 1.3% in the analysis of the absorption of phosphorus and potassium. , respectively.
    [0237] In this same experiment, were tested 1) P.palmensis grown in nutrient broth (results given above), and 2) P. palmensis grown in medium siderophore production, 3) bacterial metabolites contained in the culture medium responsible mobilization Insoluble Fe (siderophores medium). In general, the results were similar for dry weight and pigments, with P. palmensis always standing out. All these treatments were also tested, combined with an auxin-producing strain of the species Arthrobacter oxydans Code CECT. In general, the results were similar for dry weight and pigments, with P. palmensis alone always standing out; However, the combination of P. palmensis with Arthrobacter oxydans Code CECT had a synergistic effect according to Colby (http://www.jstor.org/stable/4041058) on Fe absorption, increasing Fe content by 36.4% with respect to to the control and effect of each strain individually. Likewise, an increase of 1.5%, 9.7% and 9.5% was observed in the analysis of the absorption of nitrogen, phosphorus and potassium.
    [0239] INDUSTRIAL APPLICATION. -
    [0241] Given the above- mentioned properties of Pseudomonas palmensis BBB001 as a stimulator of adaptive metabolism to abiotic stress, improving the oxidative balance of the plant, modulating the activity of enzymes related to ROS scavenging and due to its ability to mobilize nutrients, specifically iron, nitrogen, phosphorus and potassium, this bacterial strain has a specific application in the agri-food, chemical and pharmaceutical industry, as it can be used as part of any preparation (individually or in combination with other microorganisms) and making them come into contact (the strain or any part of it) with the seed, the root or aerial system of the plants by any available means, in any plant species, or in any form of in vitro culture, to increase the adaptability of the strain to abiotic stress conditions and improve mineral nutrition, specifically iron, nitrogen, phosphorus and potassium.
    权利要求:
    Claims (13)
    [1]
    1. Bacterial strain Pseudomonas palmensis BBB001 (CECT deposit number 30222), microorganism of the group of Gram-bacteria, genus Pseudomonas, characterized by comprising a nucleotide sequence corresponding to SEQ ID NO: 1 to 41, where one or more of These 41 unique genes characteristic of the isolated strain encode formulations for the production of substances or compounds on an industrial scale.
    [2]
    2. Bacterial strain Pseudomonas palmensis BBB001 (CECT 30222), according to claim 1, characterized by its ability to stimulate adaptive metabolism to abiotic stress in plant species, modulating the oxidative response by inducing the metabolism involved in the elimination of free radicals produced in the stress situation, improving growth and plant production.
    [3]
    3. Bacterial strain Pseudomonas palmensis BBB001 (CECT 30222), according to claim 2, characterized by its ability to increase the activity of ROS scavenging enzymes in plant species.
    [4]
    4. Bacterial strain Pseudomonas palmensis BBB001 (CECT 30222), according to claim 2, characterized by its ability to increase the dissipation of excess photosynthetic energy responsible for the generation of ROS free radicals (NPQ) in plant species.
    [5]
    5. Bacterial strain Pseudomonas palmensis BBB001 (CECT 30222), according to claim 1, characterized by its ability to stimulate the absorption of iron, phosphorus and potassium, improving mineral nutrition.
    [6]
    6. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any molecule or bacterial formulation derived from it, or of the metabolites of the culture broth of the strain, in any proportion, according to claims 1 and 2, for its application in any type of agricultural or forest cultivation, in order to improve the adaptation of the plant to any condition of abiotic stress.
    [7]
    7. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any molecule or bacterial formulation derived from it, or of the metabolites of the culture broth of the strain,
    two
    in any proportion, according to claims 1 and 2, for its application in any plant species under salinity conditions.
    [8]
    8. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any of its parts, according to claims 1 and 2, for its application in any plant species, in order to improve the response to stress, increasing production.
    [9]
    9. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any bacterial molecule or formulation derived from it, or of the metabolites of the culture broth of the strain, in any proportion, according to claims 1 and 5, for its application in any species of plants to improve mineral nutrition, in iron, phosphorus and potassium.
    [10]
    10. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any bacterial molecule or formulation derived from it, according to claims 1 to 7, forming part of any preparation, either individually or in combination with other organisms, and by any available means that put the bacteria in contact with the seed, the root or aerial system of the plants.
    [11]
    11. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any bacterial molecule or formulation derived from it, according to claim 10, in combination with Pseudomonas fluorescens (CECT 9015), or as part of any preparation with Pseudomonas fluorescens (CECT 9015), to improve the response to saline stress.
    [12]
    12. Use of Pseudomonas palmensis BBB001 (CECT 30222), or any bacterial molecule or formulation derived from it, according to claim 10, in combination with Arthrobacter oxydans (CECT 30231), or as part of any preparation with Arthrobacter oxydans (CECT 30231, to improve mineral nutrition in iron, nitrogen, phosphorus and potassium, both in organic and conventional agriculture.
    [13]
    13. Use of specific genes of Pseudomonas palmensis BBB001 (CECT 30222), according to claim 1, for heterologous expression to obtain products containing biological matter of the strain.
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