Chercheurs, médiateurs et musées universitaires : une relation à (dé)construire, des pratiques à systématiser

peer reviewedRendez-vous annuel de la culture scientifique et technologique en Wallonie et à Bruxelles, le Printemps des Sciences rassemble des partenaires issus du monde de l’enseignement supérieur et du secteur culturel. Lors de l’édition 2018, une équipe de chercheurs a proposé l’activité « Histoire contée : étudions les cyanobactéries de l'Antarctique ! » qui s’est déroulée au sein d’une exposition temporaire présentant le patrimoine universitaire scientifique liégeois. Cette expérience d’une collaboration fructueuse entre des chercheurs, des médiateurs et la commissaire de l’exposition a permis de poser les bases d’une réflexion plus large sur les relations qui peuvent exister entre ces différents partenaires. Cette communication (i) proposera une analyse diagnostique de l’expérience décrite ci-dessus et élargira la réflexion aux autres collaborations existantes dans les musées universitaires associés à l’ULiège ; (ii) interrogera la coexistence de temporalités et de réalités spécifiques pour chaque acteur concerné (iii) appréciera les freins et les opportunités des collaborations entre chercheurs et musées universitaires scientifiques (dans ce cas), selon des considérations pratiques relevées sur le terrain. Ces axes ouvrent notamment les interrogations suivantes : « est-il indispensable de présenter la recherche actuelle dans un musée de sciences ? Qui sont les chercheurs investis pour y (re)présenter cette recherche ?* » ; « comment la médiation est-elle réalisée ? » ; « la présence physique du chercheur est-elle un atout, voire une nécessité ? » ; « faut-il capitaliser sur des événements ponctuels pour valoriser la recherche ? » ; « quelles relations potentielles les chercheurs pourraient-ils développer avec les médiateurs du musée ? » ; « pourquoi les chercheurs devraient aujourd’hui choisir le musée comme vecteur de diffusion ? » et enfin, « en quoi la démonstration de la recherche actuelle au sein du musée universitaire peut-elle susciter des vocations auprès du jeune public ? ». Loin de chercher à épuiser ces questionnements, notre communication tentera de les nourrir pour envisager l’étendue de la complexité du sujet. * Interrogation notamment traitée via un sondage réalisé auprès des chercheurs de l’ULiège.4. Quality educatio

Past cyanobacteria biodiversity in herbarium collections: a time travel to a lost world?

A pilot study of the cyanobacterial diversity in ten herbarium samples from the Smithsonian Institution (Washington DC, USA) was carried out. The samples had been collected between 1897 and 1964 in Antarctica, Alaska, Yellowstone Park and Austrian and American glaciers. The V3-V4 portion of the 16S rRNA gene was sequenced by multiplex 454 pyrosequencing and data was analyzed using the bioinformatic pipeline of Pessi et al. (2016). We obtained 131 OTUs (threshold of 97.5% 16S rRNA similarity), of which 74 were very closely related to existing sequences in public databases. Moreover, the diversity patterns were different between samples, ruling out an homogenization due to contaminations during the handling of herbarium samples since their collection and in our laboratory. The older specimen (1898) came from a pool at 46°C in Yellowstone Park with dominant sequences of Stigonema and Leptolyngbya, that are known from these biotopes. For the Antarctic samples taken in 1948-9 from Ross Island, in 1940 from Deception Island and in 1964 from Victoria Land, the DNA could be amplified in all cases and 55 OTUs were detected. Sequences of Nostoc sp., Microcoleus sp., Phormidesmis priestleyi, Leptolyngbya sp., and Timaviella sp. were retrieved. An Alaskan river specimen from 1949 yielded mostly Nostoc sequences, as could be expected from the herbarium label. This study gives access to the cyanobacterial community composition in a period where anthropogenic and climatic pressures were still low in the remote polar regions. We will assess if it is possible to detect changes in biogeographic patterns or shifts of genotypes towards more generalist ones.HERBA: Herbaria for the preservation of cyanobacterial diversity and biogeography studies : past and futur

A Summer of Cyanobacterial Blooms in Belgian Waterbodies: Microcystin Quantification and Molecular Characterizations

In the context of increasing occurrences of toxic cyanobacterial blooms worldwide, their monitoring in Belgium is currently performed by regional environmental agencies (in two of three regions) using different protocols and is restricted to some selected recreational ponds and lakes. Therefore, a global assessment based on the comparison of existing datasets is not possible. For this study, 79 water samples from a monitoring of five lakes in Wallonia and occasional blooms in Flanders and Brussels, including a canal, were analyzed. A Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) method allowed to detect and quantify eight microcystin congeners. The mcyE gene was detected using PCR, while dominant cyanobacterial species were identified using 16S RNA amplification and direct sequencing. The cyanobacterial diversity for two water samples was characterized with amplicon sequencing. Microcystins were detected above limit of quantification (LOQ) in 68 water samples, and the World Health Organization (WHO) recommended guideline value for microcystins in recreational water (24 µg L−1) was surpassed in 18 samples. The microcystin concentrations ranged from 0.11 µg L−1 to 2798.81 µg L−1 total microcystin. For 45 samples, the dominance of the genera Microcystis sp., Dolichospermum sp., Aphanizomenon sp., Cyanobium/Synechococcus sp., Planktothrix sp., Romeria sp., Cyanodictyon sp., and Phormidium sp. was shown. Moreover, the mcyE gene was detected in 75.71% of all the water samples

Drivers of the terrestrial cyanobacterial community composition in the Sør Rondane Mountains, East Antarctica

The sparse ice-free regions of Antarctica harbor diverse microbial communities that can vary significantly between regions and micro-climatic conditions. The factors responsible for the diversity and community structure in inland nunataks of East Antarctica are still poorly understood. During the BELSPO MICROBIAN project, three sampling campaigns took place in the Sør Rondane Mountains during the austral summers of 2018, 2019 and 2020, resulting in more than 100 samples ranging from different types of barren bedrock to substrates covered by biofilms and well-developed biological soil crusts including lichens, mosses, microalgae and/or cyanobacteria. Cyanobacterial diversity was assessed by amplicon sequencing targeting the V3-V4 variable region of the 16S rRNA gene with cyanobacteria-specific primers using the Illumina MiSeq platform (2x300 bp). The recently developed CyanoSeq database was used for the taxonomic affiliation of the OTUs (99% similarity threshold). Whilst favorable habitats, such as sheltered spots in rocky areas, enhance the development of different kinds of cyanobacterial crusts, cyanobacteria were present even in the most extreme ones. Granitic soils were dominated by very diverse cyanobacterial crusts, mostly composed by filamentous cyanobacteria of the Leptolynbyaceae, Oculatellaceae and Microcoleaceae families, and by Nostocaceae. Most abundant OTUs on gneiss bedrock were from the Cyanothecaceae and Microcoleaceae. In contrast, marble soils were dominated almost exclusively by the Chroococcidiopsaceae family. Moraine samples from very dry areas were mainly characterized by members of the Gomontiellaceae family whereas moraine samples taken close to a lake were rich in filamentous taxa as well, mostly belonging to the Leptolynbyaceae, Oculatellaceae and Gomontiellaceae families. Next to bedrock type, other abiotic variables such as pH, NO3 and TOC were especially important drivers of the community composition in each sampled site.MICROBIAN15. Life on lan

MICROBIAN : Microbial diversity in the Sør Rondane Mountains in a context of climate change

The Sør Rondane Mountains (SRM) represent a c. 900 km² large mountain range, encompassing a large range of terrestrial habitats differing in geology and soil characteristics, exposure time and microclimatic conditions. The objectives of the BelSPO project MICROBIAN are to (i) use a combination of remote sensing (Digital Elevation Model) and close-range field observation techniques to map physical habitat characteristics and the presence/extent of biological crust communities in the region of the Princess Elisabeth Station Antarctica (PEA), (ii) generate a comprehensive inventory of the taxonomic and functional diversity of microbial communities in these habitats by amplicon sequencing of the 16S and 18S rRNA genes and metagenomics, (iii) use mesocosm field experiments (Open Top Chambers and snow fences) to mimic the possible effects of future climate change on the taxonomic diversity of these microbial ecosystems, and (iv) conduct field experiments to inform policy-makers in view of decision making regarding environmental protection and prevention measures to reduce the introduction and spread of non-native species and to avoid cross-contamination between sites. The proposed research will provide a proof of concept to use high resolution satellite images for identifying regions of particular biological interest in East Antarctica and more broadly make a significant contribution to understanding Antarctic terrestrial microbial ecology.MICROBIA

The science-policy link in practice: how to propose an Antarctic Specially Protected Area (ASPA)?

The BelSPO projects ANTAR-IMPACT, BELDIVA and MICROBIAN and literature data concerning the biodiversity in the inland biotopes of the Western Sør Rondane Mountains (Dronning Maud Land) indicated a very rich and unique terrestrial biodiversity on the nunataks in the surroundings of Princess Elisabeth Station, including biofilms and Biological Soil Crusts. However, there is potential for negative impacts due to visits and (human) disturbances, mainly driven by the presence of infrastructures in the vicinity. Therefore, the involved scientists initiated the process of creating an ASPA in collaboration with the relevant ministries (Foreign Affairs, Environment and Science Policy). The first step was the submission of a Working Paper (WP42) at CEP XX (2017) with a Preliminary assessment of the values to be protected, using the template of Appendix 4 to the CEP XX report. Other countries scrutinized the document and raised useful comments and questions. The Information Paper (IP42) submitted at CEP XXI (2018) contained the answers to these questions. The next step was the writing of a Management Plan, based on a Guide that includes all the elements to describe (annex to Resolution 2 (2011)). Several versions were discussed, also with the station operator. The WP15 was finally presented to CEP XXIV that forwarded it to the Subsidiary Group on Management Plan, where it will be further improved during the intersessional period. The process was a learning experience for the scientists, from creating the maps to developing management options, and lastly communicating the importance of the area to policy- and decision-makers.MICROBIAN15. Life on lan

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox, a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). This public toolbox is designed for researchers without a specific training in bioinformatics (launched by a single command line). Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. All the workflows are based on Singularity containers and Nextflow to increase reproducibility. The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales (Cyanobacteria). This study is published at https://doi.org/10.1093/gigascience/giad022GENER

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

peer reviewed[en] BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales

Histoire évolutive du mulot sylvestre (Apodemus sylvaticus) dans la région paléarctique, avec un accent sur la colonisation des îles Orcades et de l'Islande

To improve our knowledge concerning the hypothesis of northern refugia during the last glaciation for European species, we have focused our study on the evolutionary history of the wood mouse (Apodemus sylvaticus) throughout its Palearctic distribution. In addition, we also studied the wood mice populations from Orkney Islands and Iceland in order to understand their ways of colonization in the Atlantic islands. We used different molecular markers (cytb mitochondrial gene and a mitochondrial pseudogene). A geometric morphometric analysis using a morphological marker (mandible) was also used. This work highlights the potential existence of new wood mice lineages in Western Europe. These would be genetically differentiated, probably due to a geographical separation of an ancestral population in different refugia situated in the Iberian Peninsula during the last glacial maximum. Morphological differences also exist between the wood mice lineages. However, the study did not bring any evidence concerning the existence of Nordic refugia for this species. Concerning the insular populations, our results seem to show that populations from Orkney Islands and Iceland are genetically close to the Great Britain populations. They would have been introduced in these islands by Vikings or by earlier human populations. Additional sampling in Western Europe and in the Atlantic islands will clarify the origins of these populations