The rapidly emerging technique of environmental DNA (eDNA) sequencing is revolutionizing the study of biodiversity and the tracking of ecosystem transformations. eDNA analysis utilizes the DNA shed by organisms into their environment and provides insight into the presence of species while leaving ecosystems undisturbed. This method holds great promise for a variety of applications, including environmental monitoring, biodiversity assessment, soil analysis and beyond. Current eDNA sequencing methods allow the identification of both bacterial and eukaryotic species in aquatic, soil and other sample types. The potential of eDNA sequencing is an indispensable tool for biomonitoring and conservation. eDNA analysis requires trace amounts of DNA per species within a given sample, with no prior knowledge of species identity or relative abundance, and is sensitive enough to detect thousands of species simultaneously in a given sample.

Representative publications:

I. Pathiraja, D., Cho, J., Kim, J. and Choi, I.G., 2023. Metabarcoding of eDNA for tracking the floral and geographical origins of bee honey. Food Research International, 164, p.112413.

II. Pathiraja, D., Wee, J., Cho, K. and Choi, I.G., 2022. Soil environment reshapes microbiota of laboratory-maintained Collembola during host development. Environmental microbiome, 17(1), p.16.

Marine heterotrophic bacteria (MHB) are the primary degraders of marine ecosystems and encode a diverse repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of various algal cell wall polysaccharides. A comprehensive survey of the genomic content of MHB revealed that CAZymes dedicated to the depolymerization of algal cell wall polysaccharides are clustered in genomic regions known as polysaccharide utilization loci (PULs). My research focuses on the metabolism of red algal polysaccharides (agar, carrageenan, and porphyran) in MHB. Next generation sequencing (NGS)-based genomic and transcriptomic approaches are used for the discovery of PULs in novel marine bacterial isolates and metagenomic approaches for marine environmental samples. Functional characterization of novel CAZymes identified in marine PULs will lead to the elucidation of red algal polysaccharide metabolism in marine ecosystems.

Representative publications:

I. Pathiraja, D., Christiansen, L., Park, B., Schultz-Johansen, M., Bang, G., Stougaard, P. and Choi, I.G., 2021. A novel auxiliary agarolytic pathway expands metabolic versatility in the agar-degrading marine bacterium Colwellia echini A3T. Applied and environmental microbiology, 87(12), pp.e00230-21.

II. Christiansen, L., Pathiraja, D., Bech, P.K., Schultz-Johansen, M., Hennessy, R., Teze, D., Choi, I.G. and Stougaard, P., 2020. A multifunctional polysaccharide utilization gene cluster in Colwellia echini encodes enzymes for the complete degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan. MSphere, 5(1), pp.10-1128.

Marine algal biomass is a sustainable feedstock for the production of value-added products using microbial metabolic chassis. However, key algal cell wall polysaccharides are recalcitrant to conventional bacterial metabolic chassis and cannot be assimilated. Marine heterotrophic bacteria have the intrinsic ability to degrade algal cell wall polysaccharides, but robust genetic manipulation tools are not well developed. Synthetic biology integrates several scientific disciplines, including molecular biology, biochemistry, genetics, systems biology and bioinformatics, to create new or redesign existing biological systems. Therefore, synthetic biology approaches are widely used to engineer non-model organisms as metabolic chassis for consolidated biological processes. The design-build-test-learn (DBTL) cycle in synthetic biology is used to design, construct and optimize the bacterial chassis.Engineered marine bacterial metabolic chassis can be used for direct bioconversion of marine algal feedstocks into value-added chemicals.

Representative publications:

I. Pathiraja, D., Park, B., Kim, B., Stougaard, P. and Choi, I.G., 2023. Constructing Marine Bacterial Metabolic Chassis for Potential Biorefinery of Red Algal Biomass and Agaropectin Wastes. ACS Synthetic Biology.