Littérature scientifique sur le sujet « Caballeronia »

Abstract Many interspecific interactions are shaped by coevolution. Transmission mode is thought to influence opportunities for coevolution within symbiotic interactions. Vertical transmission maintains partner fidelity, increasing opportunities for coevolution, but horizontal transmission may disrupt partner fidelity, potentially reducing opportunities for coevolution. Despite these predictions, the role of coevolution in the maintenance of horizontally transmitted symbioses is unclear. Leveraging a tractable insect–bacteria symbiosis, we tested for signatures of pairwise coevolution by assessing patterns of host–symbiont specialization. If pairwise coevolution defines the interaction, we expected to observe evidence of reciprocal specialization between hosts and their local symbionts. We found no evidence for local adaptation between sympatric lineages of Anasa tristis squash bugs and Caballeronia spp. symbionts across their native geographic range. We also found no evidence for specialization between three co-localized Anasa host species and their native Caballeronia symbionts. Our results demonstrate generalist dynamics underlie the interaction between Anasa insect hosts and their Caballeronia symbionts. We predict that selection from multiple host species may favor generalist symbiont traits through diffuse coevolution. Alternatively, selection for generalist traits may be a consequence of selection by hosts for fixed cooperative symbiont traits without coevolution.

Acid sulfate soils contain sulfide minerals that have adverse environmental effects because they can lead to acidic drainage and prevent the establishment of vegetation. The current study examined the effect of a novel method for the restoration of these soils and the promotion of germination and plant growth. Thus, we isolated two strains of phosphate solubilizing bacteria, Methylobacterium sp. PS and Caballeronia sp. EK, characterized their properties, and examined their effects in promoting the growth of tomato plants (Lycopersicon esculentum L.) in acid sulfate soil. Compared with untreated control soil, treatment of acid sulfate soils with these bacterial strains led to increased seed germination, growth of plants with more leaves, and plants with greater levels of total-adenosine tri-phosphate (tATP). Relative to the untreated control soil, the addition of Caballeronia sp. EK led to a 60% increase in seed germination after 52 days, growth of plants with more than 3 times as many leaves, and a 45.2% increase in tATP after 50 days. This strain has potential for use as a plant biofertilizer that promotes vegetation growth in acid sulfate soils by improving the absorption of phosphorous.

Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. Methods Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. Results All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.

The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h−1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20–28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation.

Dongcai is loved for its delicious flavor and nutritional value. The microorganisms in Dongcai play a vital role in their flavor, quality, and safety, and the microbial communities of Dongcai vary greatly from region to region. However, it remains unknown what the predominant microorganisms are in different traditional Dongcai and how they affect its flavor. The objective of this study is to explore the microbial diversity of traditional fermented Dongcai in three representative Chinese regions (Tianjin, Sichuan, and Guangzhou) and further assess their microbial functions. The microbial diversity of fermented Dongcai in Guangdong has the lowest diversity compared to fermented Dongcai in Sichuan, which has the highest. The distribution of the main genera of fermented Dongcai varies from region to region, but Carnimonas, Staphylococcus, Pseudomonas, Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, and Rhodococcus are the dominant genera in common. In addition, halophilic bacteria (HAB, i.e., Halomonas Bacillus, Virgibacillus, etc.) and lactic acid bacteria (LAB, i.e., Weissella and Lactobacillus) are also highly abundant. Of these, Burkholderia-Caballeronia-Paraburkholderia, Rhodococcus, Sphingomonas, Ralstonia, and Chromohalobacter are dominant in the Sichuan samples. In the Tianjin samples, Lactobacillus, Weissella, Virgibacillus, Enterobacter, Klebsiella, and Pseudomonas are the most abundant. Predictions of microbial metabolic function reveal that carbohydrates, amino acids, polyketides, lipids, and other secondary metabolites are abundantly available for biosynthesis. In addition, the different flavors of the three types of Dongcai may be due to the fact that the abundance of HAB and LAB shows a significant positive correlation with the amounts of important metabolites (e.g., salt, acid, amino nitrogen, and sugar). These results contribute to our understanding of the link between the distinctive flavors of different types of Dongcai and the microorganisms they contain and will also provide a reference for the relationship between microbial communities and flavor substances in semi-fermented pickles.

A plant auxin hormone indole-3-acetic acid (IAA) can be assimilated by bacteria as an energy and carbon source, although no degradation has been reported for indole-3-propionic acid and indole-3-butyric acid. While significant efforts have been made to decipher the Iac (indole-3-acetic acid catabolism)-mediated IAA degradation pathway, a lot of questions remain regarding the mechanisms of individual reactions, involvement of specific Iac proteins, and the overall reaction scheme. This work was aimed at providing new experimental evidence regarding the biodegradation of IAA and its derivatives. Here, it was shown that Caballeronia glathei strain DSM50014 possesses a full iac gene cluster and is able to use IAA as a sole source of carbon and energy. Next, IacE was shown to be responsible for the conversion of 2-oxoindole-3-acetic acid (Ox-IAA) intermediate into the central intermediate 3-hydroxy-2-oxindole-3-acetic acid (DOAA) without the requirement for IacB. During this reaction, the oxygen atom incorporated into Ox-IAA was derived from water. Finally, IacA and IacE were shown to convert a wide range of indole derivatives, including indole-3-propionic acid and indole-3-butyric acid, into corresponding DOAA homologs. This work provides novel insights into Iac-mediated IAA degradation and demonstrates the versatility and substrate scope of IacA and IacE enzymes.

La stabilité évolutive des relations hôte-microbe est cruciale pour la symbiose. La transmission verticale des symbiotes microbiens des parents à la progéniture est bien établie, mais l'acquisition environnementale par transmission horizontale de symbiotes nécessite des adaptations spécifiques. Les insectes de l'infra-ordre Pentatomomorpha disposent d'un mécanisme efficace pour l'acquisition de leur symbiote à partir du sol. Ces insectes possèdent une architecture intestinale distinctive contenant une région postérieure, appelée M4, composée de centaines de cryptes, constituant une niche spécifique pour abriter des symbiotes intestinaux bénéfiques. Les Coreoidea sélectionnent spécifiquement des bactéries Caballeronia. Ma thèse explore la spécificité de cette association et les mécanismes bactériens sous-jacents. Trois espèces de Coreoidea (Riptortus pedestris, Leptoglossus occidentalis, Coreus marginatus) montrent une préférence pour des sous-clades spécifiques de Caballeronia, influencée par la compétition interspécifique. La région M4 est dominée par une seule espèce bactérienne, suggérant une forte pression de sélection. La spécificité de la souche est alignée avec un avantage en termes de fitness reproductif. Des criblages génétiques ont révélé des fonctions cruciales pour la colonisation des cryptes, notamment le chimiotactisme, la résistance aux peptides antimicrobiens et de la capacité à utiliser des sources de carbone néoglucogéniques, la taurine et l'inositol, suggérant que l'hôte fournit ce type de métabolites comme nutriments aux symbiotes. Ces découvertes démontrent que malgré une grande diversité microbienne environnementale, les insectes sélectionnent des symbiotes spécifiques grâce à des mécanismes multifactoriels
The evolutionary stability of host-microbe relationships is crucial for symbiosis. Vertical transmission of microbial symbionts from parents to offspring is well established, but environmental acquisition through horizontal transmission of symbionts requires specific adaptations. Insects of the infraorder Pentatomomorpha have an effective mechanism for acquiring their symbionts from the soil. These insects possess a distinctive intestinal architecture with a posterior region called M4, composed of hundreds of crypts that provide a specific niche for harboring beneficial gut symbionts. Coreoidea specifically select Caballeronia bacteria. My thesis explores the specificity of this association and the underlying bacterial mechanisms. Three species of Coreoidea (Riptortus pedestris, Leptoglossus occidentalis, Coreus marginatus) show a preference for specific subclades of Caballeronia, influenced by interspecific competition. The M4 region is dominated by a single bacterial species, suggesting strong selective pressure. Strain specificity is aligned with a reproductive fitness advantage. Genetic screenings revealed crucial functions for crypt colonization, including chemotaxis, resistance to antimicrobial peptides, and the ability to utilize neoglucogenic carbon sources such as taurine and inositol, suggesting that the host provides these metabolites as nutrients to the symbionts. These findings demonstrate that despite high environmental microbial diversity, insects select specific symbionts through multifactorial mechanisms

Les bactéries du sol sont adaptées pour survivre dans ce milieu et pour faire face à divers organismes y vivant, comme d'autres bactéries, champignons, plantes et insectes. Pour mieux connaitre ces adaptations et comprendre si ces adaptations se chevauchent ou sont spécifiques à chacun de ces modes de vie, j'ai utilisé l'approche dites « Transposon sequencing » (Tn-seq) pour identifier les gènes essentiels et conditionnellement essentiels dans deux bactéries du sol bien connues, Caballeronia insecticola et Sinorhizobium meliloti. J'ai utilisé des cribles Tn-seq réalisés dans les milieux naturels des microbes (in situ), combinés à des expériences in vitro. La sélection des conditions in vitro a été guidée par des analyses transcriptomiques, des études physiologiques, la génétique, la génomique et des analyses biochimiques, ainsi que par les expériences Tn-seq in situ. Ces conditions in vitro consistent en plusieurs facteurs de stress (comme des peptides antimicrobiens ou AMP) ou de conditions nutritionnelles (panel de sources de carbone, d'azote et de soufre) et physiologiques (motilité et chimiotaxie) que les microbes rencontrent dans leurs milieux naturels. Ces conditions in vitro simplifiées décomposent les conditions naturelles en composants uniques et facilitent ainsi l'interprétation des cribles Tn-seq in situ. C. insecticola est une bactérie polyvalente qui établit des interactions spécifiques avec des insectes, des plantes, des champignons et d'autres bactéries. J'ai analysé quatre modes de vie différents de C. insecticola avec l'approche Tn-seq : le sol, la rhizosphère des plants de soja, l'organe symbiotique intestinal de l'insecte Riptortus pedestris et la surface des hyphes des champignons Cunninghamella. Pour les interactions bactéries-bactéries, je me suis concentré sur la compétition entre la souche de rhizobium S. meliloti et la souche productrice de toxines Rhizobium sp. Pop5, car cette interaction est bien caractérisée et repose sur la production du AMP phazolicine par la souche Pop5.Au total, 34 cribles chez C. insecticola et 4 cribles chez S. meliloti ont été réalisés et analysés, ce qui a permis de découvrir des phénotypes pour 1 162 gènes de C. insecticola et 264 gènes de S. meliloti. Chez C. insecticola, le génome essentiel, c'est-à-dire l'ensemble des gènes qui ne peuvent être supprimés et qui sont donc indispensables à la vie bactérienne, a été défini. Il est constitué de 498 gènes, avec des gènes codant des fonctions cellulaires attendues, comme la transcription, la traduction, la production d'énergie, la biosynthèse de l'enveloppe cellulaire et le cycle cellulaire, ou des gènes moins attendus comme ceux impliqués dans la modification spécifique de la partie lipidique A du lipopolysaccharide avec des groupes 4-amino-4-désoxy-L arabinose. Les résultats des différents cribles ont été vérifiés en utilisant des mutants d'insertion ou de délétion de C. insecticola et S. meliloti et en caractérisant leur phénotype dans les conditions in situ et in vitro appropriées. Au total, 23 mutants de C. insecticola et 8 mutants de S. meliloti ont été phénotypés. Dans chaque cas, le phénotypage de ces mutants a confirmé les données Tn-seq, illustrant la robustesse et le potentiel de la méthode.Parmi les fonctions bactériennes cruciales dans tous les milieux naturels, tant chez C. insecticola que chez S. meliloti, figure l'enveloppe bactérienne, ce qui suggère qu'elle constitue un bouclier contre les agressions environnementales, comme les AMPs fréquemment produits par d'autres organismes. La motilité bactérienne et la chimiotaxie chez C. insecticola sont cruciales dans l'interaction avec les insectes et dans le sol, lorsque les bactéries circulent sur les hyphes fongiques. Enfin, chaque milieu impose des contraintes métaboliques spécifiques aux bactéries. Ces travaux ont mis en évidence des adaptations à la fois généralistes et spécifiques à l'environnement chez les bactéries du sol
Soil bacteria are adapted to survive in their abiotic soil environment as well as to cope with different organisms, including other bacteria, fungi, plants and insects with which they share that environment. With the objective to contribute to the understanding of these adaptations and to answer the question if adaptations are overlapping or unique for each of these lifestyles, I used the transposon-sequencing (Tn-seq) approach to identify essential and conditionally fitness genes in two well-studied soil bacteria, Caballeronia insecticola and Sinorhizobium meliloti. The experimental strategy consisted in the use of Tn-seq screens performed in the natural, in situ environments of the microbes combined with multiple in vitro experiments in synthetic environments. The selection of these in vitro conditions was informed by available transcriptome analyses, physiological studies, genetics, genomics and biochemical analyses as well as the in situ Tn-seq experiments themselves. The selected in vitro conditions were a variety of stressors (e.g. antimicrobial peptides or AMPs) or nutritional (e.g. a panel of carbon, nitrogen and sulphur sources) and physiological (e.g. motility and chemotaxis) conditions that the microbes encounter in their natural environments. These simplified synthetic conditions decompose the complexity of natural conditions in single components and facilitate thereby the interpretation of the in situ Tn-seq screens.C. insecticola is a versatile bacterium establishing specific interactions with insects, plants, fungi and other bacteria. I analyzed four different lifestyles of C. insecticola with the Tn-seq approach: soil, the rhizosphere of soybean plants, the gut symbiotic organ of the insect Riptortus pedestris and the surface of the hyphae of Cunninghamella fungi. For bacteria-bacteria interactions, I focused on the competition of the rhizobium strain S. meliloti with the toxin producing strain Rhizobium sp. Pop5 because this interaction is well characterized and based on the production of the AMP phazolicin by the strain Pop5.In total, 34 screens in C. insecticola and 4 screens in S. meliloti were performed and analysed, resulting in the discovery of phenotypes for 1162 C. insecticola genes and 264 S. meliloti genes. In C. insecticola, the essential genome, i.e. the set of genes that cannot be removed and that are therefore indispensable to support bacterial life, was precisely defined. I found that it is constituted of 498 genes, including the genes encoding the expected cellular functions, like transcription, translation, energy production, cell envelope biosynthesis and cell cycle, but also less expected genes like those involved in the specific modification of the lipid A moiety of lipopolysaccharide with 4-amino-4-deoxy-L arabinose groups. Results of the different Tn-seq screens were verified by independent experiments, using insertion or deletion mutants of C. insecticola and S. meliloti in selected genes and characterization of the phenotype of these mutants in the relevant environmental and in vitro conditions. In total, 23 mutants in C. insecticola and 8 mutants in S. meliloti were phenotyped. In each case, the phenotyping of these mutants confirmed the Tn-seq data, illustrating the robustness and potential of the method.Among the crucial bacterial functions in all natural environments, in both C. insecticola and S. meliloti, is the bacterial envelope, suggesting that it constitutes a shield, fending of environmental stresses, in particular AMPs frequently produced by other organisms. Bacterial motility and chemotaxis in C. insecticola are particularly important in the interaction with insects but also in the soil, when bacteria hitchhike on fungal hyphae. Finally, each environment imposes specific metabolic constraints on the bacteria. Together, this work highlighted both generalist and environment-specific adaptations in soil bacteria