Littérature scientifique sur le sujet « Exo-metabolome »

Fusarium kuroshium is the fungal symbiont associated with the ambrosia beetle Euwallacea kuroshio, a plague complex that attacks avocado, among other hosts, causing a disease named Fusarium dieback (FD). However, the contribution of F. kuroshium to the establishment of this disease remains unknown. To advance the understanding of F. kuroshium pathogenicity, we profiled its exo-metabolome through metabolomics tools based on accurate mass spectrometry. We found that F. kuroshium can produce several key metabolites with phytotoxicity properties and other compounds with unknown functions. Among the metabolites identified in the fungal exo-metabolome, fusaric acid (FA) was further studied due to its phytotoxicity and relevance as a virulence factor. We tested both FA and organic extracts from F. kuroshium at various dilutions in avocado foliar tissue and found that they caused necrosis and chlorosis, resembling symptoms similar to those observed in FD. This study reports for first-time insights regarding F. kuroshium associated with its virulence, which could lead to the potential development of diagnostic and management tools of FD disease and provides a basis for understanding the interaction of F. kuroshium with its host plants.

The control and development of plant growth promoters is a key factor for the agro-nomy industry in its economic performance. Different genera of bacteria are widely used as natural biostimulants with the aim of enhancing nutrition efficiency, abiotic stress tolerance and/or crop quality traits, regardless of their nutrients content. However, the complete exo-metabolome of the bacteria responsible for the biostimulant effect is still unknown and needs to be investigated. Three bacteria with different biostimulant effects were studied by untargeted metabolomics in order to describe the metabolites responsible for this effect. The pentose phosphate pathway, tryptophan metabolism, zeatin biosynthesis, vitamin B6 metabolism and amino acid metabolism were the highlighted pathways related to bacteria biostimulant activity. These results are related to the plant hormones biosynthesis pathway for auxins and zeatins biosynthesis. Fourteen metabolites were identified as biomarkers of the biostimulant activity. The results suggest a greater relevance of auxins than cytokinin pathways due the importance of the precursors identified. The results show a clear trend of using indole-3-pyruvate and 3-Indoleglycolaldehyde pathways to produce auxins by bacteria. The results demonstrate for the first time that 4-Pyridoxic acid, the fructosamines N-(1-Deoxy-1-fructosyl)phenylalanine and N-(1-Deoxy-1-fructosyl)isoleucine and the tripeptides diprotin A and B are metabolites related to biostimulant capabilities. This study shows how untargeted metabolomic approaches can be useful tools to investigate the bacteria exo-metabolomes related to biostimulant effects.

Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

The interactions occurring in the phycosphere between algae and bacteria are of different kinds and may influence the growth of microalgae. In the past few years, the growing interest on microalgal industrial and biotechnological applications hijacked the attention of the scientific community on the study of microalgae-bacteria interactions. A deeper knowledge of the composition of the microbiota associated to microalgae and on the mechanisms ruling microalgae-bacteria interactions may improve the current mass-culture techniques and enhance the productivity. Tetraselmis suecica is a green marine alga with several biotechnological applications. It is mainly used for aquaculture and cosmetic applications and for the production of bioactive compounds. Nevertheless, still little is known about the microbiota associated to T. suecica and its effect on the microalga growth, In this thesis the bacterial community associated with T. suecica (strain F&M M33) cultures, grown in different conditions, was described through a metagenomic approach, to evaluate the presence of a stably associated bacterial community. NGS metagenetic analysis were performed on four T. suecica cultures, derived from the same original culture but separated for years, and kept under different growing conditions. Despite the different characteristics of the cultures (seasons and cultures size), a “core” bacterial community was identified, accounting for the large part of the total bacterial community. Among the “core” OTUs it was possible to identify 7 different genera and at least 13 different families. However the relative abundance of the taxa forming the “core” community varied strongly, indicating that growing conditions and/or external contaminations influence the relative abundance of these microorganisms. Moreover, the isolation of strains belonging to the “core” community opened an interesting chance to evaluate the effects of these bacteria on T. suecica growth. The understanding of which molecules are involved in the interactions is a fundamental part in the study of microalgal-bacteria interaction. The associated bacterial population, release several compounds which may act as microalgal growth promoting features (MPG) affecting different aspects of microalgae such the composition in terms of lipids, pigments or cell dimensions. However, to date only few studies have phenotypically characterized bacteria associated with microalgae for the selection of microalgal growth-promoting bacteria. Therefore, in this thesis 200 bacterial strains were isolated from different cultures of Tetraselmis suecica, identified through 16S rDNA sequencing and phenotypically characterized for MPG traits. 46 strains were been identified as producers of MPG compounds: either indol-3-acetic acid (IAA) and/or siderophores. 22 isolates were tested in co-cultures with the axenic microalga to their effects on T. suecica growth: 4 of them showed a positive effect on microalgal growth. In particular two strains: Vitellibacter sp. and Sphyngopyxis flavimaris were able to enhance considerably the growth of T. suecica, in the condition tested. To deepen the knowledge of the molecules involved in the interactions, the supernatants T. suecica cultures, axenic and in co-culture with Vitellibacter sp. or Sphyngopyxis flavimaris, were analyzed with a non-targeted metabolomics approach. The characterization of the exo-metabolome of T. suecica, was described for the first time. It was possible to identify culture-characteristics compounds and several compounds involved in the metabolism of vitamins. It was observed that Sphyngopyxis flavimaris produce IAA also in co-culture conditions.