Proportions of taxa belonging to the gut core microbiome change throughout the life cycle and season of the bark beetle Ips typographus.

The European spruce bark beetle, Ips typographus, is a serious pest of spruce forests in Europe, and its invasion and development inside spruce tissues are facilitated by microorganisms. We investigated the core gut bacterial and fungal microbiomes of I. typographus throughout its life cycle in spring and summer generations. We used cultivation techniques and molecular identification in combination with DNA and RNA metabarcoding. Our results revealed that communities differ throughout their life cycle and across generations in proportion of dominantly associated microbes, rather than changes in species composition. The bacteriome consisted mostly of the phylum Gammaproteobacteria, with the most common orders and genera being Enterobacteriales (Erwinia and Serratia), Pseudomonadales (Pseudomonas), and Xanthomonadales. The fungal microbiome was dominated by yeasts (Saccharomycetes-Wickerhamomyces, Kuraishia, and Nakazawaea), followed by Sordariomycetes (Ophiostoma bicolor and Endoconidiophora polonica). We did not observe any structure ensuring long-term persistence of microbiota on any part of the gut epithelium, suggesting that microbial cells are more likely to pass through the beetle's gut with chyme. The most abundant taxa in the beetle's gut were also identified as dominant in intact spruce phloem. Therefore, we propose that these taxa are acquired from the environment rather than specifically vectored between generations.

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

BACKGROUND: Ips 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. RESULTS: We assessed the metabolic potential of a collection of isolates obtained from different life stages of I. typographus beetles. All strains showed the capacity to hydrolyse one or more complex polysaccharides into simpler molecules, which may provide an additional carbon source to its host. Also, 83.9% of the strains isolated showed antagonistic effect against one or more entomopathogenic fungi, which could assist the beetle in its fight against this pathogenic threat. Using culture-dependent and -independent techniques, we present a taxonomical analysis of the bacteriome associated with the I. typographus beetle during its different life stages. We have observed an evolution of its bacteriome, which is diverse at the larval phase, substantially diminished in pupae, greater in the teneral adult phase, and similar to that of the larval stage in mature adults. Our results suggest that taxa belonging to the Erwiniaceae family, and the Pseudoxanthomonas and Pseudomonas genera, as well as an undescribed genus within the Enterobactereaceae family, are part of the core microbiome and may perform vital roles in maintaining beetle fitness. CONCLUSION: Our results indicate that isolates within the bacteriome of I. typographus beetle have the metabolic potential to increase beetle fitness by proving additional and assimilable carbon sources for the beetle, and by antagonizing fungi entomopathogens. Furthermore, we observed that isolates from adult beetles are more likely to have these capacities but those obtained from larvae showed strongest antifungal activity. Our taxonomical analysis showed that Erwinia typographi, Pseudomonas bohemica, and Pseudomonas typographi species along with Pseudoxanthomonas genus, and putative new taxa belonging to the Erwiniaceae and Enterobacterales group are repeatedly present within the bacteriome of I. typographus beetles, indicating that these species might be part of the core microbiome. In addition to Pseudomonas and Erwinia group, Staphylococcus, Acinetobacter, Curtobacterium, Streptomyces, and Bacillus genera seem to also have interesting metabolic capacities but are present in a lower frequency. Future studies involving bacterial-insect interactions or analysing other potential roles would provide more insights into the bacteriome capacity to be beneficial to the beetle.

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

Microbes 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.

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera.

Pseudomonas 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 taxa.

Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology.

European 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 pathogens.