Sujan Khadka

Email: sujan.khadka@ntnu.no

Affiliation: Department of Biotechnology and Food Science, NTNU , Trondheim, Norway

Presentation:

In 2012, I began my journey into the world of biology. I’ve always wanted to learn more about the biology of microbes, so I enrolled in a four-year B.Sc. program in Microbiology at Tribhuvan University (TU) in Nepal. During my B.Sc., I had a great opportunity to learn about various facets of microbiology and to see the unseen, microbes. Throughout my studies, my inclination had always been more towards understanding how microbes interact with the biotic and abiotic components of the environment. I have accomplished a two-year M.Sc. from Central China Normal University, China, where I learned about aquatic microorganisms and their role in the biodegradation of environmental pollutants and aquaculture systems.

Following my MSc, I worked as a research student at the Nepal Academy of Science and Technology (NAST), where I studied the microbial quality of wastewater and aquaculture farm water. I’ve seen how harmful bacteria, combined with rising drug resistance, affect fish and humans. This sparked my interest in understanding the relationship between waterborne microorganisms and the microbes found in fish.

ESR3: Examine interactions between microbes in water (planktonic and particle-associated) and fish by microbiome analyses

Fish is the most important single source of high-quality protein for humans, accounting for 17% of all animal protein consumed by the world’s population, and demand is growing in tandem with population growth (Thilsted et al., 2014). Both caught fisheries and aquaculture output contribute considerably to fulfilling the expanding global demand for fish, but the aquaculture industry has been a key contributor and has developed far faster than the captured fisheries industries in the previous two decades (Boyd et al., 2022). Recirculating aquaculture system (RAS) has been a convenient way to fulfil fish demand in several parts of the globe. However, reports from some of the world’s leading fish producing countries, fish mortality has increased in recent days, with the harmful microbe-fish interaction being one of the possible determinants for mortality. Therefore, microbial management of the rearing environment is of utmost importance to improve and increase the fish’s health and survival.

My PhD research focuses on bacterial management in RAS and consists of three studies. The goal of the first study is to evaluate to which extent the biofilter-biofilm communities influence the microbiomes of the fish and the water in the RAS. To test this, we will collect biofilm carriers with known distinct biofilter communities from two distinct commercial RAS, operate the two identical RAS for one month with different biofilm carriers in biofilters, and then swap the biofilters between the facilities. The second study will investigate how the water quality, biofilter function, fish mucosal health, and the microbiomes in the biofilter, water and fish (skin, gut and gills) are affected by increasing salinity during “smoltification”. The experiment will be carried out under two distinct levels of particle loads and will be designed to determine the influence of salinity and particle load on the mucosal microbiomes of the salmon. The third study includes the uptake rates of bacteria in the gut of the yolk-sac fry of salmon and the effect of the size of bacterial aggregates on this uptake rate. Overall, this project will primarily employ the PCR and 16S rDNA Illumina next-generation sequencing (NGS) technique to study the associated microbial communities residing in different environments. In addition, the communities’ similarities and dissimilarities will be examined using bioinformatics and statistical tools.

The overall aims of this PhD project are: 1) to exhibit the concept that variation of biofilter-biofilm communities can impact the composition of microbiota in rearing water and fish, 2) to display the idea that changes in the level of salinity and particle load can affect the composition of the mucosal microbiomes of the salmon, 3) to demonstrate that the size of the bacterial aggregates affects the bacterial uptake rates in the gut of yolk-sac fry of salmon, 4) to recommend the microbial management practices in the RAS by adjusting the ways to select and promote the beneficial fish-microbe interaction