PhD Research Project: Dynamics, function and influence of gut microbiome in pesticides resistance

Background
The development of insecticide resistance is a worldwide concern and elucidating the underlying mechanisms is critical for effective crop protection and human health. However, it is challenging to identify resistance mechanisms because they occur over evolutionary time. A further challenge is that resistance can occur via direct organism response (metabolic, physiological, and target-site changes) or via the gut microbiome. Increasing evidence suggests that the gut microbiome can both promote pesticide resistance in pests 1 and help non-target species to defend themselves from pesticides2,3. However, despite these recent advances, many fundamental questions about the dynamics, function and influence of microbiomes remain unresolved. Answering these questions require integrative approaches.

This project will elucidate mechanisms of insecticides resistance using a multiomics approach on a massively multigenerational system. The outcome of the project will enable a deep understanding of the spatiotemporal nature of resistance.

Generally, insect pests are not suitable for cross-generational studies, having complex life cycles. Moreover, the link between resistant phenotypes and the underlying molecular mechanisms is difficult to establish in these species because they cannot be easily manipulated in the laboratory. Here, we propose to use the invertebrate model specie Daphnia to uncover the mechanisms of insecticide resistance. This species has a life cycle that provides unique advantages over insects. Yet, being an arthropod it shares a large proportion of genes and their functions with insects. Daphnia alternates sexual and asexual reproduction. Dormant stages are the endpoint of sexual reproduction and are preserved in lake sediment creating and archive of living fossils spanning decades or even centuries. These dormant stages can be revived and maintained in the laboratory via clonal reproduction. The properties of Daphnia provide the unique opportunity to identify plastic and genetic mechanisms of response to pesticides through evolutionary time. Moreover, recent studies revealed the key role of the gut microbes in Daphnia resistance to toxins, revealing that microbiome transplant can increase resistance of susceptible strains.

The objectives of the proposed research are:
Objective 1: To study mechanisms of insecticide resistance using the model species Daphnia. Genomics, transcriptomics of the jost and metagenomics of gut microbiota will be investigated in resistant and susceptible genotypes in presence and absence of insecticides.
Objective 2. To uncover mechanisms of insecticide resistance underlying resistant phenotypes. An integrative analysis of multiomics data will be conducted using advanced computational tools and biostatistic approaches.
Objective 3. To investigate the evolution of insecticide resistance over evolutionary time by studying mechanisms of pesticide resistance in strains resurrected from different times of the last century. Historical and modern phenotypes will be studied in the same settings to uncover the evolution of resistance.
Objective 4. To investigate how to induce resistance via microbiome transplant. The microbiome of resistant strains will be transplanted in susceptible strains and their resistance to insecticides quantified via phenotypic and molecular essays.

Expected outcome
The multiomics and microbiota analysis of resistant and susceptible strains will allow us to uncover the mechanisms of insecticide resistance. The study of these mechanisms across multiple generations will allow us to understand the scale and speed of evolutionary changes leading to pesticide resistance.

References

1 Xia, X. et al. Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.). Front Microbiol 9, 25, doi:10.3389/fmicb.2018.00025 (2018).
2 Pietri, J. E. & Liang, D. The Links Between Insect Symbionts and Insecticide Resistance: Causal Relationships and Physiological Tradeoffs Annals of the Entomological Society of America 111, 92-97 (2018).
3 Almeida, L. G., Moraes, L. A., Trigo, J. R., Omoto, C. & Consoli, F. L. The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation. PLoS One 12, e0174754, doi:10.1371/journal.pone.0174754 (2017).
4 Macke, E., Callens, M., De Meester, L. & Decaestecker, E. Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. Nat Commun 8, 1608, doi:10.1038/s41467-017-01714-x (2017).