Insight into the genomic architecture of a South African entomopathogenic nematode and its associated bacterial symbiont

Abstract

Nematoda is one of the most prolific and biologically-diverse of all animal phyla, with species adopting lifestyles ranging from free-living to parasitic. Among the diversity of parasitic nematodes lies a specialized group known as entomopathogenic nematodes that features the ability to rapidly kill insect hosts facilitated through a mutualist association with insect pathogenic bacteria. South Africa offers a range of undisturbed habitats that plays host to a great diversity of plant and insect species. Therein lies an opportunity for the recovery of novel entomopathogenic nematode species with a greater tolerance towards local environments and insects, which could potentially be exploited for biological control. In this study, a small-scale survey was conducted in the Gauteng province of South Africa in 2014, which led to the isolation of a new steinernematid, Steinernema sp. HBG28 and its associated bacterial symbiont, Xenorhabdus khoisanae strain MCB. It was found that phase I and phase II variants of X. khoisanae strain MCB featured the ability to swarm on solid agar. This is the first report of swarming behaviour observed in Xenorhabdus bacteria undergoing phenotypic variation. Genomic sequencing was performed on X. khoisanae strain MCB, revealing a genome of 4,6 Mbp in length with 3,869 protein- coding genes, of which, fourteen genes were specifically implicated in flagellar motility. Comparative genomic analyses with other Xenorhabdus spp. indicated the presence of these flagellar motility genes, with the exception of two chemotaxis genes found only in X. khoisanae (cheA and cheY), suggesting that these genes may be necessary in bacterial swarming during phase variation. Additionally, a draft genome assembly of Steinernema sp. HBG28 was produced, which was 97 Mbp in length and consisted of 35,869 predicted protein-coding genes, 1,281 tRNAs and 43 rRNAs. Further genomic characterization of Steinernema sp. HBG28 confirmed its mutual role iii in insect pathogenicity along with its bacterial symbiont. This study was unique as it represented the first genomic characterization of a new Steinernema entomopathogenic nematode species and its associated bacterial symbiont in South Africa. Furthermore, this study paves the way for further research into the biological mechanisms involved in host-parasite and host-symbiont interactions.