Comparative genomics of the genus Pseudomonas reveals host- and environment-specific evolution

[EN]Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances

Metagenomic analysis of the evolution of microbial communities in foods subjected to refrigeration and in conditions of absence of cold

La cadena del frío constituye un elemento clave en seguridad alimentaria, pues la mayoría de los microorganismos detienen su crecimiento a bajas temperaturas. Se han desarrollado técnicas, basadas en la secuenciación masiva, que analizan las poblaciones bacterianas de una muestra mediante secuenciación de un fragmento del gen ribosómico 16S, permitiendo la caracterización microbiana de alimentos./nEl objetivo del presente estudio consistió en la identificación y cuantificación de bacterias sobre alimentos refrigerados y sin refrigerar utilizando secuenciación masiva del ADNr16S, para describir el rol del mantenimiento de la cadena del frío sobre la evolución de comunidades microbianas en alimentos./nAsí, se secuenció el ADN extraído de muestras de pollo, espinacas, queso fresco y yogurt, a los 2 y 4 días. Las Unidades de Operación Taxonómica (Operational Taxonomic Units: OTUs) obtenidas se compararon con bases de datos de secuencias de organismos (NCBI). Además, se realizó el cultivo de microorganismos de las muestras en el momento de su compra./nDe forma general se observó un aumento de la cantidad y diversidad de bacterias en las muestras sin refrigerar, confirmando que la cadena del frío retrasa el desarrollo de microorganismos en los alimentos, aumentando la vida útil de los mismos. Además, el estudio demuestra la eficacia de la secuenciación masiva del ADNr16S para estudiar el efecto de la temperatura en el desarrollo de comunidades bacterianas sobre los alimentos.The cold chain is a key element in food safety since most microorganisms stop their growth at low temperatures. Techniques that analyse the bacterial populations of a sample by sequencing a fragment of the 16S ribosomal gene, allowing the microbial characterization of foods have been developed./nThe objective of the present study was to identify and quantify bacteria on refrigerated and uncooled foods using massive sequencing of rDNA16S, to describe the role of maintenance of the cold chain on the evolution of microbial communities in food./nThus, the DNA extracted from the samples was sequenced at 2d and 4d. The OTUs obtained were compared with those of the databases and identified. The culture of microorganisms of the samples was carried out at 0d./nIn general, an increase in the amount and diversity of bacteria was observed in the uncooled samples, confirming that the cold chain delays the development of microorganisms in foods, increasing the shelf life of them. In addition, the study demonstrates the efficacy of the massive sequencing of rDNA16S to study the effect of temperature on the development of bacterial communities on food

Bacterial fertilizers based on rhizobium laguerreae and bacillus halotolerans enhance cichorium endivia L. phenolic compound and mineral contents and plant development

[EN] Today there is an urgent need to find new ways to satisfy the current and growing food demand and to maintain crop protection and food safety. One of the most promising changes is the replacement of chemical fertilizers with biofertilizers, which include plant root-associated beneficial bacteria. This work describes and shows the use of B. halotolerans SCCPVE07 and R. laguerreae PEPV40 strains as efficient biofertilizers for escarole crops, horticultural species that are widely cultivated. An in silico genome study was performed where coding genes related to plant growth promoting (PGP) mechanisms or different enzymes implicated in the metabolism of phenolic compounds were identified. An efficient bacterial root colonization process was also analyzed through fluorescence microscopy. SCCPVE07 and PEPV40 promote plant development under normal conditions and saline stress. Moreover, inoculated escarole plants showed not only an increase in potassium, iron and magnesium content but also a significant improvement in protocatechuic acid, caffeic acid or kaempferol 3-O-glucuronide plant content. Our results show for the first time the beneficial effects in plant development and the food quality of escarole crops and highlight a potential and hopeful change in the current agricultural system even under saline stress, one of the major non-biological stresses.[ES] Hoy en día existe una necesidad urgente de encontrar nuevas formas de satisfacer la actual y creciente demanda de alimentos y mantener la protección de los cultivos y la seguridad alimentaria. Uno de los cambios más prometedores es la de los fertilizantes químicos por biofertilizantes, que incluyen bacterias beneficiosas asociadas a las raíces de las plantas. Este trabajo describe y muestra el uso de las cepas B. halotolerans SCCPVE07 y R. laguerreae PEPV40 como biofertilizantes eficientes para los cultivos de escarola, especies hortícolas ampliamente cultivadas. Se realizó un estudio genómico in silico en el que se codificaron genes relacionados con los mecanismos de promoción del crecimiento vegetal (PGP) o con diferentes enzimas implicadas en el metabolismo de compuestos fenólicos. También se analizó el proceso de colonización bacteriana de las raíces mediante microscopía de fluorescencia. SCCPVE07 y PEPV40 promueven el desarrollo de la planta en condiciones normales y estrés salino. Además, las plantas de escarola inoculadas mostraron no sólo un aumento en el contenido de potasio, hierro y magnesio, sino también una mejora significativa en el contenido de ácido protocatechuico, ácido cafeico o kaempferol 3-O-glucurónido. Nuestros resultados muestran por primera vez los efectos beneficiosos en desarrollo de la planta y la calidad alimentaria de los cultivos de escarola y ponen de manifiesto un cambio potencial y esperanzador en el sistema agrícola actual, incluso bajo estrés salino, uno de los principales estreses no biológicos. Traducción realizada con la versión gratuita del traductor www.DeepL.com/Translato

Phylogenomic analyses of the genus Pseudomonas lead to the rearrangement of several species and the definition of new genera

[EN]Pseudomonas represents a very important bacterial genus that inhabits many environments and plays either prejudicial or beneficial roles for higher hosts. However, there are many Pseudomonas species which are too divergent to the rest of the genus. This may interfere in the correct development of biological and ecological studies in which Pseudomonas are involved. Thus, we aimed to study the correct taxonomic placement of Pseudomonas species. Based on the study of their genomes and some evolutionary-based methodologies, we suggest the description of three new genera (Denitrificimonas, Parapseudomonas and Neopseudomonas) and many reclassifications of species previously included in Pseudomonas

Farmaconciencia. Realización de un programa de concienciación sobre el uso imprudente de medicamentos en oficinas de farmacia con alumnos de prácticas tuteladas de la facultad de farmacia: resistencia a los antibióticos

Memoria ID-204. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2019-2020

Plants Probiotics as a Tool to Produce Highly Functional Fruits: The Case of Phyllobacterium and Vitamin C in Strawberries

10 páginas, 1 tabla, 1 figuraThe increasing interest in the preservation of the environment and the health of consumers is changing production methods and food consumption habits. Functional foods are increasingly demanded by consumers because they contain bioactive compounds involved in health protection. In this sense biofertilization using plant probiotics is a reliable alternative to the use of chemical fertilizers, but there are few studies about the effects of plant probiotics on the yield of functional fruits and, especially, on the content of bioactive compounds. In the present work we reported that a strain of genus Phyllobacterium able to produce biofilms and to colonize strawberry roots is able to increase the yield and quality of strawberry plants. In addition, the fruits from plants inoculated with this strain have significantly higher content in vitamin C, one of the most interesting bioactive compounds in strawberries. Therefore the use of selected plant probiotics benefits the environment and human health without agronomical losses, allowing the production of highly functional foods.This work was granted by “Junta de Castilla y León” (Regional Government, Grant SA183A11-2) and MINECO (Central Government, Grant AGL2011-29227). Paula García-Fraile is recipient of a postdoctoral researcher contract from Academy of Sciences of the Czech Republic. José David Flores-Félix was supported by a fellowship of Salamanca University. Marta Marcos García was supported by a fellowship of Fundación Miguel Casado San José. Luís R. Silva is grateful to the financial support from the European Union (FEDER funds through COMPETE) and National Funds (FCT, Fundação para a Ciência e Tecnologia) through project Pest-C/EQB/LA0006/2013 and from the European Union (FEDER funds) under the framework of QREN through Project NORTE-07-0124-FEDER- 000069.Peer reviewe

Serratia strains isolated from the rhizosphere of raulí ( Nothofagus alpina ) in volcanic soils harbour PGPR mechanisms and promote raulí plantlet growth

[EN] Raulí is one of the most emblematic tree species of the Chilean temperate forests. Due to the high quality wood, this tree has been used for furniture and handicrafts manufacturing, which has positioned raulí as one of the most important commercial timber species in Chile. Currently, the international market demands sustainable production system for forest production, more specifically in plantlets production. In this regard, plant growthpromoting rhizobacteria (PGPR) inoculants may enhance the growth and survival of plantlets in nurseries, which means an increase in the effectiveness of replanting operations. Therefore, the aim of the present study was to isolate, characterize and screen rhizosphere-associated bacteria with PGPR potential, isolated from raulí that growth in volcanic soils in southern Chile. A total of 1,261 bacterial strains were isolated from different volcanic soils. Out of 1,261 isolates, 100 were selected based on their high levels of indole acetic acid (IAA) production. These isolates were then subjected to screening for 1-aminocyclopropane-1-carboxylic acid deaminase activity, and their ability to fix nitrogen was determined. From the 100 selected isolates, 7 were chosen for producing the highest amount of IAA to continue with genetic characterization based on their 16S rRNA gene sequences. These 7 isolates were characterized as members of the Serratia genus and were used to develop multi-strain inoculant mixtures. Later, a nursery study followed to determine the effect of inoculation with the Serratia strains on the growth of RA88 raulí clone plantlets. The nursery experiment demonstrated that Serratia strains have the potential to increase the root collar diameter, height, relative chlorophyll content, biomass and nitrogen content of raulí plantlets. The study concluded, that Serratia strains have the potential to be used as biofertilizers to increase plant growth in nursery conditions

MALDI-TOF Mass Spectrometry Is a Fast and Reliable Platform for Identification and Ecological Studies of Species from Family Rhizobiaceae

Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies

Selection of the root endophyte Pseudomonas brassicacearum CDVBN10 as plant growth promoter for Brassica napus L. crops

[EN]Rapeseed (Brassica napus L.) is an important crop worldwide, due to its multiple uses, such as a human food, animal feed and a bioenergetic crop. Traditionally, its cultivation is based on the use of chemical fertilizers, known to lead to several negative e ects on human health and the environment. Plant growth-promoting bacteria may be used to reduce the need for chemical fertilizers, but e cient bacteria in controlled conditions frequently fail when applied to the fields. Bacterial endophytes, protected from the rhizospheric competitors and extreme environmental conditions, could overcome those problems and successfully promote the crops under field conditions. Here, we present a screening process among rapeseed bacterial endophytes to search for an e cient bacterial strain, which could be developed as an inoculant to biofertilize rapeseed crops. Based on in vitro, in planta, and in silico tests, we selected the strain Pseudomonas brassicacearum CDVBN10 as a promising candidate; this strain produces siderophores, solubilizes P, synthesizes cellulose and promotes plant height in 5 and 15 days-post-inoculation seedlings. The inoculation of strain CDVBN10 in a field trial with no addition of fertilizers showed significant improvements in pod numbers, pod dry weight and shoot dry weight. In addition, metagenome analysis of root endophytic bacterial communities of plants from this field trial indicated no alteration of the plant root bacterial microbiome; considering that the root microbiome plays an important role in plant fitness and development, we suggest this maintenance of the plant and its bacterial microbiome homeostasis as a positive result. Thus, Pseudomonas brassicacearum CDVBN10 seems to be a good biofertilizer to improve canola crops with no addition of chemical fertilizers; this the first study in which a plant growth-promoting (PGP) inoculant specifically designed for rapeseed crops significantly improves this crop’s yields in field conditions

Diseño de contenidos inclusivos y remodelación de una asignatura para una docencia “sin barreras”

Memoria ID2022-208 Ayudas de la Universidad de Salamanca para la innovación docente, curso 2022-2023