5th Biofilm Workshop - Omic approaches in Biofilm research: advances in ecology and ecotoxicology

In mid September FRAM hosted the 5th Biofilm workshop at Kristineberg Marine Research and Innovation Centre in Fiskebäckskil at the Swedish westcoast. The workshop provided a platform to generate a deeper understanding of the current omics approaches applied in environmental biofilm research, including meta-genomics, -transcriptomics, -proteomics and -metabolomics, to predict and assess effects from environmental stressors, in the context of global change.

The workshop included lectures, poster presentations and discussion meetings. It was a meeting place for professionals and students to be updated on state-of-the art of important omic approaches, discussing main research priorities in the field for the next few years, and continue or initiate collaborations between research groups in the field.

Eight invited speakers gave a cutting-edge perspective on methods currently available for omic approaches on biofilms research to improve our understanding of microbial diversity, microbial processes, species interactions and their link with ecosystem functioning and ecosystem services, when faced with different environmental stressors (e.g. pollutants, ocean acidification, salinity, elevated temperature, etc. The lectures gave the background to the discussions that followed on the applicability of the methods to answer specific questions and how to apply them in different experimental setups. The workshop was chaired by Natàlia Corcoll.

The workshop was the fifth Biofilm workshop in a series that are arranged every second year to strength the collaborations between research groups, with the ambition of increasing the impact of research on biofilms ecology and ecotoxicology on aquatic biofilms in marine and freshwater ecosystems at European-wide scale but also globally. Previous workshops were held in Germany (2010), Switzerland (2012), France (2014) and Spain (2016). Next workshop (2020) will be celebrated in Switzerland and hosted by the Aquatic Biofilms group at EAWAG.

Finally, 28 participants from 8 different countries, and 16 different organizations joined the workshop at Kristineberg.

Watch a short video about the workshop to hear some views about the workshop, on YouTube. 
 

 List of keynotes by invited speakers;

• Metabarcoding and metagenomics in periphyton biofilms for ecotoxicology - Natàlia Corcoll, Dept. of Biological and Environmental Sciences, University of Gothenburg, Sweden.
• Diatoms metabarcoding to monitor freshwater ecosystems - Agnès Bouchez, INRA-UMR CARRTEL, Thonon, France.
• Poorly known fungi in natural and engineered biofilms - Christian Wurzbacher, Technical University of Munich, Germany.
• Microbial interactions exposed - Genomic shortcuts to understand microbial communities - Stefan Bertilsson, Uppsala University and Swedish University of Agricultural Sciences, Sweden.
• Metagenomics of the Baltic Sea: Links between the environment and the (meta)genome - Anders Andersson, KTH Royal Institute of Technology in Stockholm, Sweden.
• Metatranscriptomics for the Ecology and Function of Environmental and Engineered Biofilms - Mark Dopson, Centre for Ecology and Evolution in Microbial model Systems, Linnaeus University, Sweden.
• Metaproteomics, trends and opportunities to read-across in environmental assessment - Susana Cristobal, Dept. of Clinical and Experimental Medicine Cell Biology, Linköping University, Sweden.
• Potential and challenges of community metabolomics in ecotoxicological assessment - Mechthild Schmitt-Jansen, Dept. Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research - UFZ, Germany.

 In addition, several posters were presented and generated interesting discussions.

• Anchoring of aquatic biofilm metabolomics to ecological responses - Stefan Lips, Helmholtz-Centre for Environmental Research - UFZ, Germany.
• Diversity of Bacillus species in Mangrove Ecosystem of Miani Hor, Balochistan Coastline-Pakistan - Syed Rehmat Ullah Shah, University of Agriculture, Lasbela, Pakistan.
• Ecotoxicogenomics as a tool to assess multiple-stress responses in fluvial systems - Helena Guasch, University of Girona, Spain.
• High-throughput 16S rRNA gene sequencing reveals interactions between multiple stressors on river biofilms under controlled conditions - Ferran Romero Blanch, Catalan Institute for Water Research, Spain.
• How can temperature modulate herbicides impact on the freshwater diatoms Gomphonema gracile and Nitzschia palea? - Floriane Demailly, National Research Institute of Science and Technology for Environment and Agriculture, France.
• Implementing OMICs responses in risk assessment processing - Floriane Larras, Helmholtz-Centre for Environmental Research - UFZ, Germany.
• Micropollutant biotransformation potential of natural stream biofilms - Werner Leonardo Desiante, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Switzerland.
• Striking Against Bacterial Slime on Medical Device Surfaces: Characterization of Mycobacterium chimaera Biofilms on Medical Device Materials - Jayaleka Amarsinghe, Winchester Engineering and Analytical Center, USA.
• The nectar-microbial loop in Manuka plants: microbial composition and its effect on biological interactions - Jorge Bresciano, Massey University, Palmerston North, New Zeeland.

Thanks!

The organizing committee would like to thank all participants for actively contributing to an inspiring workshop. All shared their knowledge and engaged in the discussions with their special competences. One specific outcome of the workshop was that we agreed to draft a manuscript on the topic to address the status in the field of omics and biofilm research and challenges ahead.

The workshop was a co-arrangement with the University of Gothenburg via the FRAM Centre and the NICE programme. Financial support were received from the Swedish Research council (VR) and the Swedish research council for sustainable development (Formas).

Natàlia Corcoll, Åsa Arrhenius, Thomas Backhaus
Organizing committee from Dept. of Biological and Environmental Sciences, University of Gothenburg, Sweden