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In the agroecosystem, plant crops are the primary trophic producer that can be consumed/parasitized by a plethora of organisms, including viruses, bacteria, fungi, nematodes and many herbivore insects. On one hand, plants support these organisms as food resources; on the other hand, plants defend themselves against those consumers by employing constitutive and induced defenses. Both features might be involved in plant-mediated indirect interactions when multiple pests share the same host plant. It means that the presence of one pest might have an indirect effect on another plant through the modification of some plant host features (nutritional quality or defense). During my Ph.D. study, I assessed the modulating factors (both abiotic and biotic factors) that might affect the plant-mediated indirect interactions, and also investigated the influences of such indirect interactions at long term and on a tri-trophic system, and finally analyzed the underlying phytochemical mechanisms by mechabolomics analyses. Firstly, sublethal effects of beta-cypermethrin, a pyrethroid pesticide as the abiotic factor, were assessed on the interspecific interactions between the specialist aphid Aphis glycines, and the generalist aphid Aulacorthum solani on soybeans. Sublethal concentration (LC5) of beta-cypermethrin accelerated the interspecific competition between the two species of aphids. Induced susceptibility of soybean plants to one species of aphids caused by the other species would be significantly impaired by the exposure to sublethal beta-cypermethrin.Secondly, various pest species abundance and feeding strategies, i.e. the piercing-sucking aphid, the chewing caterpillar, the plant fungus and the root-knot nematode, were introduced on tomato plants, Solanum lycopersicum to evaluate the plant-mediated indirect interactions among these pests. In the results, insect performances, i.e. the number of aphid individuals and development rate of caterpillar larva, were correlated to the abundance of indirect interactions whether pests attacked tomato plants sequentially or simultaneously. When pests attacked tomato plants at the same time, insect performances were positively correlated to the abundance of indirect interactions. Nevertheless, when pests infested tomato plants in sequence, the insect performances were negatively correlated to the abundance of indirect interactions. However, such a correlation was not detected with the pathogenic organisms (fungi and nematodes). Thirdly, the population dynamic of aphid M. euphorbiae was also monitored under a tri-trophic system. We found that the aphid population, involved in the above-belowground interactions, slowed down in both the short term and long term via reduced survival of nymph aphids and facilitating induction of winged aphids. Furthermore, parasitism efficiency of the natural enemy Aphidius ervi to aphids and tomato yields were also reduced by such above-belowground interactions. Lastly, following an untargeted metabolomic approach, we detected many significant chemical variations between non-infested and infested plants, disregarding the pest infestation. Most of them are probably induced by the presence of nematodes, the only belowground pest. On the opposite, we did not observe many chemical differences in roots metabolome when we compared the different types of infestation, meaning that the presence of nematodes probably lead the metabolomic signal in infested roots, disregarding the presence of other pests aboveground. All the studies may contribute to a comprehensive understanding of the diverse interactions among plants, pesticides, various pests, and natural enemies, and optimizing the integrated pest management in the agroecosystem.; Les plantes, en tant que producteurs primaires, peuvent être consommées/attaquées par de nombreux organismes, notamment des virus, des pathogènes, des insectes herbivores ou encore des nématodes phytophages. D'une part, les plantes sont une ressource alimentaire principale pour ces organismes ; d'autre part, les plantes peuvent se défendre contre ces consommateurs en mobilisant des défenses constitutives et/ou induites. En cas de défenses induites suite à l’attaque d’un ravageur, des interactions indirectes médiées par la plante peuvent apparaitre entre ce ravageur et d’autres ravageurs partageant le même hôte i.e. la présence d’un ravageur va provoquer des modifications au niveau de la plante qui peuvent à leur tour impacter les autres ravageurs présents sur la même plante. Tout d’abord, les effets sublétaux de la bêta-cyperméthrine, un pesticide de type pyréthrinoïdes, ont été évalués sur les interactions interspécifiques entre le puceron spécialiste Aphis glycines et le puceron généraliste Aulacorthum solani sur soja. La concentration sublétale (LC5) de bêta-cyperméthrine accélère la compétition interspécifique entre les deux espèces de pucerons. La sensibilité des plants de soja aux pucerons induite par une pré-infestation d’une autre espèce de puceron pourrait ainsi être considérablement réduite par une exposition préalable à la bêta-cyperméthrine sublétaux. Dans un deuxième temps, nous nous sommes intéressés aux facteurs biotiques susceptibles de moduler les interactions indirectes. Dans ce cadre, divers ravageurs, à savoir le puceron, la chenille, le phytopathogène et le nématode, ont été introduits et suivis sur des plants de tomate, Solanum lycopersicum. La performance des ravageurs arthropodes, (e.g. le nombre d'individus de pucerons et le taux de développement des larves de lépidoptères) était corrélée au nombre d’interactions indirectes (i.e. au nombre d’espèces de ravageurs partageant le même hôte), que les ravageurs attaquent les plants de tomate séquentiellement ou simultanément. En effet, lorsque les ravageurs étaient mis en présence d’un plant de tomate de manière simultanée, la performance des insectes était positivement corrélée au nombre d’interactions indirectes. A l’inverse, lorsque les ravageurs étaient mis en présence de plants de tomate de façon séquentielle, la performance des insectes ravageurs était négativement corrélée à l'abondance des interactions indirectes. Enfin, aucune corrélation n'a pas été détectée pour les pathogènes, champignons et nématodes. D’autre part, nous avons pu mettre en évidence que la présence de nématodes et d’oïdium réduisait à court-terme i.e. à l’échelle d’une génération l’abondance de pucerons sur un plant de tomate attaqués par ces trois ravageurs. Nous avons voulu tester cette interaction indirecte sur du long-terme i.e. à l’échelle d’un suivi de la dynamique de populations des pucerons. De plus, nous avons ajouté à cette expérimentation des parasitoïdes du puceron afin de voir l’impact de ces interactions indirectes sur le troisième niveau trophique. La population de pucerons impliquée dans les interactions indirectes testées a été réduite à court et à long terme parce-que la survie des nymphes diminuait. De plus, le nombre de pucerons ailés a augmenté. Enfin, le taux de parasitisme de l’ennemi naturel Aphidius ervi. Ainsi, ce travail démontre la présence d’interactions indirectes fortes entre les différents ravageurs partageant une même plante hôte et ces interactions sont susceptibles d’être modulées par de nombreux facteurs comme le nombre ou encore la diversité des ravageurs. De plus, elles sont susceptibles de modifier le service de biocontrôle rendu par les auxiliaires des cultures ainsi que le rendement de la culture. Il est donc nécessaire de comprendre et prendre en compte ces interactions indirectes dans le cadre d’attaques multiples pour adopter les stratégies IPM les plus adéquates.

In this study, we developed a rapid, specific, and sensitive loop-mediated isothermal amplification technique combined with a lateral flow dipstick (LAMP-LFD) method to detect Salmonella targeting the siiA gene in powdered infant formula (PIF). The specificity of the detection method (LAMP-LFD) approached 100% using 21 Salmonella and 31 non-Salmonella bacterial strains. This detection method exhibited high sensitivity limits for pure cultures at 3.7 cfu/mL and in PIF at 2.2 cfu/g without enrichment. To evaluate the applicability of the LAMP-LFD method, we detected 60 positive PIF samples and 20 negative PIF samples. The results showed that the method of LAMP-LFD had a high diagnostic specificity of 100% for detection of Salmonella in PIF. To reduce incidence of LAMP contamination, we applied propidium monoazide (PMA) to eliminate carryover contamination of LAMP. At the same time, we found that PMA does not affect observation of LFD for measurement of LAMP signal. The results verified that the method of LAMP-LFD targeting the siiA gene is rapid, accurate, and sensitive for Salmonella detection in PIF, and that PMA shows great potential to be widely used to eliminate the amplicon contamination risk generated by the highly sensitive LAMP reaction in the detection process.

Due to the lack of electricity and thermostatic instruments in certain settings for convenient detection of Cronobacter species in powdered infant formula (PIF), a novel investigation was conducted to establish an electricity-free visual detection system for rapid detection of Cronobacter species in PIF. This system included a portable electricity-free heater that could use the exothermic reaction of calcium oxide and water and 3 kinds of phase change materials to supply 3 constant temperatures for immunomagnetic separation, DNA extraction, and loop-mediated isothermal amplification assay. Meanwhile, the amplified reaction combined with hydroxynaphthol blue could achieve rapid visual detection. Primers designed based on the 16S-23S ribosomal RNA internal transcribed spacer were used in loop-mediated isothermal amplification to specifically monitor Cronobacter species, and the detection limit can reach 4.2 × 102 cfu/g in PIF by an electricity-free heater in 2 h 30 min. Moreover, 2 h of pre-enrichment was necessary when the level of the PIF samples with Cronobacter spp. was 100 cfu/g. The stability of the system was evaluated in ambient temperature at 4°C, 25°C, and 37°C. The results suggested that the electricity-free heater can maintain 3 constant temperatures to support different processes. Therefore, this amplification and visual system is applicable for use in many fields for rapid and specific detection of Cronobacter species in PIF.

We show that capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) generates very large numbers of peptide and protein identifications (IDs) by combining four technologies: a separation capillary coated to generate very low electroosmosis, an electrokinetically-pumped sheath-flow nanoelectrospray interface to produce high-sensitivity ionization, an Orbitrap Fusion Lumos Tribrid platform to provide high-speed analysis, and use of an advanced peak determination (APD) algorithm to take advantage of the mass spectrometer’s data acquisition speed. The use of the APD algorithm resulted in two-times more identification than the Standard Peak Algorithm. We also investigated the effect of the isolation window, injection time, and loading amount. Optimization of these parameters produced over 27,000 peptide identifications and nearly 4,400 protein group identifications from 220 ng of K562 cell digest in a single 120 min run, which is 2.7 times the number of IDs in the previous state of the art produced by CZE-ESI-MS/MS.