Within the EGI team (Ecology and Genetics of Insects) of the UMR IGEPP (Institute of Genetics, Environment and Plant Protection), we are developing research aimed at developing agroecological approaches to crop protection that are less dependent on the use of synthetic pesticides. Our work focuses on the identification of action levers to increase the efficiency of regulation of crop pests by their natural predators. For many years, we have been developing studies on the communities of generalist beneficials naturally present in agricultural environments (spiders, carabid beetles and staphylinidae,…). Carabid beetles form a very abundant and diversified group with a very diversified diet including numerous organisms harmful to crops (insects and molluscs, weed seeds,…). As such, they are major players in the provision of the ecosystem service of pest control in temperate agricultural environments. In practice, recommendations are based on the existence of a positive relationship between abundance and diversity of beneficials, on the one hand, and intensity of biological control of pests, on the other. However, the biodiversity-service relationship remains largely conjectural and is not always verified in practice. Our hypothesis is that the inability of this conjecture to account for reality stems from the fact that it ignores the complexity of the network of interactions, particularly the food web, that links the communities of beneficials and pests, and more broadly all the organisms that frequent the crops. Thus, an increase in the abundance and/or diversity of beneficials could sometimes result, for example, in a generalization of intraguild predation (predation of predators on other predators) leading to a reduction of the predation pressure on phytophagous pests and thus of the pest control service. In order to better describe and understand these phenomena, we have undertaken large-scale studies of the food web structure linking arthropods in agricultural environments with a particular focus on carabid beetles. Indeed, due to the difficulty of observation, the diet of these organisms remains poorly known. However, the development of high-throughput sequencing and molecular barcoding approaches opens new perspectives to address this issue.
The internship proposed here is part of a project to describe the diets of a community of carabid beetle species captured in wheat fields (ANR NGB project). The DNA of the consumed resources, present in the stomach contents of individuals belonging to several species, has been amplified with different pairs of universal primers, and the amplification products have been sequenced. The work will consist in analyzing the results of sequencing products obtained with primers chosen to amplify plant DNA. It will include two steps:
– The first step will consist in the constitution of a reference database of sequences for all the higher plants listed in the INPN database. The international databases will be queried and the available sequences will be grouped in this reference database. The final database will be analyzed, in particular to identify its level of completeness and the degree of coverage of the different plant families, in order to be able to detect all types of plants (seeds or other tissues) consumed by carabids.
– The second step will be to compare the sequences acquired during the project with this reference database in order to identify the plant species whose DNA is present in the stomach contents of carabid beetles, and finally to reconstitute the plant part of the carabid beetle’s diet in agricultural environments.
Place of training and supervision.
The internship will take place in the IGEPP premises at INRAe du Rheu. It will be supervised by Elsa Canard (CR INRAe) and Manuel Plantegenest (Pr Agrocampus ouest). It will be carried out in collaboration with Sebastian Ortiz-Martinez (post-doc) and Ambre Sacco-Martret de Préville (PhD student) who is carrying out their research work in the framework of the NGB project.
Period and conditions of the internship.
The internship will take place during the fall-winter 2021/22 period for a minimum duration of 4 months (it could be up to 6 months if starting earlier in the summer). An internship allowance under normal conditions is provided (approximately 600 euros per month). The expected level is at least bachelor degree, or more.