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

Diseño y creación de artículos digitales e infografías interactivas para la enseñanza y el aprendizaje virtual y presencial de la microbiología

Memoria ID-148. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2020-2021

Impartición de contenidos de microbiología mediante el desarrollo de exposiciones interactivas y podcast específicos para la inclusión educativa de alumnos con discapacidad visual

Memoria ID2022-218 Ayudas de la Universidad de Salamanca para la innovación docente, curso 2022-2023

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

Bacteria belonging to pseudomonas typographi sp. Nov. from the bark beetle ips typographus have genomic potential to aid in the host ecology

22 páginas, 6 tablas, 5 figurasEuropean Bark Beetle Ips typographus is a secondary pest that affects dead and weakened spruce trees (Picea genus). Under certain environmental conditions, it has massive outbreaks, resulting in the attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits yet to be discovered. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. A polyphasic taxonomical approach showed that they belong to a new species for which the name Pseudomonas typographi sp nov. is proposed. Genome sequences show their potential to hydrolyze wood compounds and synthesize several vitamins; screening for enzymes production was verified using PNP substrates. Assays in Petri dishes confirmed cellulose and xylan hydrolysis. Moreover, the genomes harbor genes encoding chitinases and gene clusters involved in the synthesis of secondary metabolites with antimicrobial potential. In vitro tests confirmed the capability of the three P. typographi strains to inhibit several Ips beetles’ pathogenic fungi. Altogether, these results suggest that P. typographi aids I. typographi nutrition and resistance to fungal pathogensThis research was funded by Czech Science Foundation (GACR), grant number GACR-Senior 19-09072S. Researchers also thank the Excellence Unit of the Spanish-Portuguese Institute for Agricultural Research (CIALE) (CLU-2018-04) for the provision of research facilitiesPeer reviewe

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

19 páginas, 7 figurasPseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxaThis work was funded by the Regional Government of Castile and Leon, Escalera de Excelencia CLU-2018-04, co-funded by the P.O. FEDER of Castilla y León 2014–2020. ZSS and EPA received grants from the Regional Government of Castile and Leon.Peer reviewe

Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products

12 páginas, 4 figurasMicrobes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.Z.S.S. and E.P.A. received grants from the Regional Government of Castile and Leon. Also, this work was supported by the Regional Government of Castile and Leon (Escalera de Excelencia CLU-2018-04) and co-funded by the Operational Program of the European Regional Development Fund for Castile and Leon 2014–2020.Peer reviewe

Design and application of microbial biofertilizers

Soil beneficial microbes, especially plant growth promoting microorganisms (bacteria and fungi), are susceptible to be used in microbial-based bioformulations. These products, which can also be referred as biofertilizers, have been studied for several decades and their benefits for the environment and agro-systems versus chemically synthetized products are sufficiently demonstrated. Here, we describe the key stages that a biofertilizer product goes through in the bioformulation processes, from the lab to the field, with special emphasis in the strain(s) selection, viability, competence, and stability. Moreover, we focus on carrier materials, their nature, and their roles to help the active microorganism to survive and persist under stress conditions, such as drought, pathogens, and soil degradation. Finally, we reviewed the current state of legislation and bioformulation marketing in several world regions. Overall, with this chapter we intend to enumerate the steps in the formulation of a successful biofertilizer and to further discuss key stages and handicaps in the process of production, registration, and safe application in the fields.Peer reviewe

A guide for the analysis of plant microbial communities through high-throughput sequencing methods

Plant microbiome research allows an understanding of microbial functions and their ecology. This knowledge can be applied to develop efficient biofertilizers based on the most relevant taxa or functions of the microbiome. Nowadays, the advance of high-throughput sequencing methods have enabled us to get sequences from (meta)genomes, (meta)transcriptomes, and marker genes from complete microbial communities. To reach this goal, several programs allow the decoding of many features of the plant microbiome, such as its taxonomic composition and its functions. However, the analysis of this kind of data is not so easy and requires some expertise in bioinformatics. Here we aim to provide a brief introduction to the analysis of high-throughput sequencing data to help researchers be immersed in these methodologies. We include key steps and common workflows in plant microbiome research, including many examples of bioinformatic tools and databases, and mention their inherent biases. We hope this chapter allows researchers that are not used to utilizing next-generation sequencing to be started with these methods easily.Peer reviewe

New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host

14 páginas, 6 figurasIps typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here, we aim to deep into the ecological functions and taxonomical composition of I. typographus associated bacteria.This research was cofounded by Czech Science Foundation (GAČR), grant number GAČR-Senior 19-09072 S and the Regional Government of Castile and Leon (Escalera de Excelencia CLU-2018-04), co-funded by the Operational Program of the European Regional Development Fund for Castile and Leon 2014–2020. E.P.-A. received a grant co-financed by the Regional Government of Castille and Leon and the FEDER funds. Z.S-S also received a grant co-financed by the European NextGenerationEU, Spanish “Plan de Recuperación, Transformación y Resiliencia”, Spanish Ministry of Universities, and University of Salamanca (“Ayudas para la recualificación del sistema universitario español 2021–2022”)Peer reviewe