Better together – Workshop on DNA analyses
Date of publication: Oct 4, 2022

Microbes play a vital role in our restoration efforts – they might induce larval settlement in corals, protect against toxic sulfide build-up in the sediment of seagrass, or mediate oxidative stress in kelps resulting from heat waves. Knowledge of the microbial communities in, on and around these key-stone organisms is therefore essential to increase restoration success. This requires tools that allow us to reliably and efficiently characterize these communities. Since RESTORESEAS is a big consortium of different scientific teams we need to characterize them in a comparable way. Therefore, scientists from the Center of Marine Sciences (CCMAR) of the University of Algarve, the Natural History Museum of Vienna (NHMW) and University of Amsterdam (UVA) came together in the University of Ghent (UGENT) in Belgium, to discuss our approaches and develop an analysis pipeline that everybody can use.

Preparation of our samples and sequencing with Oxford Nanopore Technology.

These included wet-lab approaches to extract and amplify DNA from samples of our organisms of interest, and prepare them for sequencing by adding barcodes and adapters. The latter is called library preparation and was followed by sequencing via the Oxford Nanopore Technology (ONT) MinION. Through ONT sequencing, a wealth of microbial genetic information is rapidly generated and even genome reconstruction is possible. These approaches have become increasingly accessible in the recent past for in-house sequencing. To identify which microbes are present in our sample and how abundant they are, we further analyzed the sequence data obtained through different bioinformatical tools that are open-source and free for everyone to use. For this UGENT has established a sequencing and bioinformatics pipeline to get reliable and robust results.

Martin talking about the scientific infrastructure at the NHMW.

We further exchanged ideas on different projects and wondered about the best way to isolate and grow microorganisms and screen our bacterial collections for their functions. We talked about new and exciting approaches on how to investigate the effects of microorganisms on their host and the environment.

Moreover, we initiated platforms to share our future culturing and screening results, but also share our bioinformatic analysis pipeline so everybody can have reproducible results with audited code of our members. Sharing our ideas and exchanging results makes a uniform approach possible and will establish to synergistically analyze diverse ecosystems.

We are lucky to have these innovative minds with vast scientific backgrounds. This type of interaction and exchange of expertise is rare and valuable in the scientific landscape and we are especially proud that RESTORESEAS enables us to advance our skills in this regard.

The RESTORESEAS team focusing on the interactions between microbes and their host

Written by Christian Pruckner, NHMW