Interspecies Interactions Between the Nematode Pristionchus pacificus and Bacterial Food Sources

Abstract

The past few decades biological research has turned its attention towards the interspecies interactions taking place between multicellular organisms and their associated microbial communities. The focus has been placed mainly on symbiotic prokaryotes and their ability to modulate their host’s physiological traits and responses, with the most representative example belonging to the field of human gut microbiome research. While currently popular, these interactions consist only a fraction of the inter- and intra-species relationships within a given niche. Ecological communities are often represented as complex networks, in an attempt to illustrate the multifaceted interplay present as well as the communication between the interacting partners that may determine their evolutionary trajectories and influence their adaptation. The study of such systems depends on the ability to establish simple but representative proxies. Nematodes, such as Pristionchus pacificus, and their diverse environment possess an array of properties that deem them an excellent choice to study interspecies interactions. During the last years, we have gathered important information regarding the effect of bacterial diets on P. pacificus’ behavior along with the worm’s impact on the associated bacterial communities. My work aims to broaden the scope of the questions and hypotheses formed, from specific genes or traits to entire regulatory networks as well as outline the importance of the information harnessed from the bacteria itself. To this end, I initially reconstructed the phylogeny and identified the metabolic potential of a subset of bacteria isolated from Pristionchus- associated environments in previous studies. This strategy allowed me to uncover the variation of the predicted metabolic potential across the phylogeny, detect genus- specific metabolic signatures in the bacterial strains and associate them with nematode traits from previous works. Furthermore, I identified environmentally responsive regulatory networks in P. pacificus through the implementation of a gene co-expression network constructed with transcriptomic profiles of the nematode and almost half of the sequenced bacterial strains as a dietary source. Lastly, I combined the collected data both from the bacteria and the nematode in a bipartite network and revealed the bacterial metabolic pathways with the strongest effect on the worm’s regulatory networks. Overall, my work explores the interspecies interactions between P. pacificus and bacterial food sources and offers novel insights on a larger scale.