We welcome PhD research fellow Trong Thuc Nguyen to DeepSeaQuence!
My name is Thuc, and I have just started as a PhD research fellow at the University of Bergen and the DeepSeaQuence project. I grew up in Vietnam and got my bachelor’s degree in biotechnology there. In 2018, I came to Europe for the first time to study the Erasmus Mundus Master in Marine environment and resources (MER). With my master’s programme, I had the chance to study in several European countries, starting at Southampton (United Kingdom), the Basque Country (Spain), and Liege (Belgium). I completed my master’s thesis in the UK at the Centre for environment, fisheries, and aquaculture science (Cefas), working on developing a high-throughput assay for identification of Vibrio species. My research interests are applied microbiology and biotechnology.
My PhD project aims to investigate the diversity of biosynthetic gene clusters and antimicrobial peptides in Arctic deep-sea hydrothermal vent microbiomes. With -omic technologies, the goal is to investigate those metabolic interactions inside the deep-sea microbial communities, search for novel biological compounds that can be applied in biotechnology, and infer the potential ecological roles of such compounds.
Eavesdropping on deep sea biofilms through transcriptomics
Lab work for the DeepSeaQuence project is underway, and our first goal is to establish a transcriptomics-workflow for samples recovered from the deep sea. Transcriptomics (or RNA-sequencing) gives us unique snapshots of all the genes that the microbial communities living at hydrothermal vents were actively using at the moment that we sampled them – for example genes that help them to use volcanic gasses as energy sources, to break down organic matter, or to defend themselves against competing microbes. RNA molecules are very fragile, so we have to work carefully and find an optimal protocol that allows us to recover as much RNA from our frozen samples, copy it into DNA and sequence it without losing too much along the way. We are excited to soon get a glimpse into the private life of these communities that hide at the seafloor in total darkness!
DeepSeaQuence on its way!
DeepSeaQuence has officially started! The project was kicked off by joining the Center for Deep Sea Research (CDeepSea) to the Arctic mid-Ocean Ridge. Sampling was conducted at different hydrothermal vent sites.
Majestic structures and dense biofilms at Ægir’s Kilde
The microbiomes at deep-sea hydrothermal vent sites are fueled by the energy from the hydrothermal fluids, and thus, primary production is independent of photosynthesis. This is also the case for Ægir’s vent microbiome surrounding the chimneys at both focused-flow as well as diffuse-flow, emitting either white or shimmering hot fluids.
Blade coring and biofilm sampling at Seven Sisters Vent Field
On the other hand, the Seven Sisters vent field (~130 meters depth), at the southern part of the Arctic mid-Ocean Ridge, is situated in the epipelagic zone on top of a flat-top volcano. The microbiomes at this vent field could to a larger extent be influenced by photosynthesis and a larger organic input.