Microbial cultures are crucial in expanding our understanding of the ecology, biochemical functioning and the evolutionary relations among Bacteria, Archaea and unicellular Eukaryota. This user story describes how we used the microbial Antarctic Resource System (mARS), hosted at biodiversity.aq, to communicate the existence of dedicated Antarctic culture collections and their content to the wider scientific community.
“For the public culture collection BCCM/ULC, it is very important to be referenced in GBIF as our strains represent a portion of biodiversity that can be ordered and used in research, and our mission is to be useful for society. However, it is not always easy to be visible for the potentially interested scientists. We benefited from a considerable help of the dedicated mARS members to format our data and are very thankful!” - dr. Annick Wilmotte, promotor of BCCM/ULC.
The BCCM/ULC Cyanobacteria Collection is a small and dedicated public collection, currently containing one of the largest collections of documented (sub)polar cyanobacteria worldwide. The collection is hosted by the Centre for Protein Engineering (University of Liège).
Microbial biodiversity is of fundamental importance to ecosystem functioning. To gain insights into the hidden world of microbes, culturing techniques still hold an important place in many research strategies, as they allow to perform experiments with particular organisms in isolation. For example, the use of cultures enables researchers to test substrates and waste products of strains, look at their enzyme expression rate in response to an environmental stimulus with mRNA sequencing, study interactions with other organisms, or infer their phylogenetic placement in the the tree of life using by comparing DNA sequences.
Especially Antarctic microbes have long interested scientists for their ability to thrive in the extreme cold, dry and saline environments that are common on the continent. The peculiar geographic location of Antarctica, isolated by the Southern Ocean and Circum Antarctic polar vortex winds, also created the conditions for the evolution of unique microbial diversity, while it significantly limited the presence (and thus impact) of humans. This is reflected in the relative high number of endemic taxa, with evidence indicating that at least some of these lineages trace their occupation of the frozen continent back to the early stages of the breakup of Gondwana.
However, obtaining living material from the last true wilderness on Earth is not straightforward, and most Antarctic microbes are slow growing, with very specific nutrient and culture requirements. Therefore, several dedicated culture collections exist, that maintain living specimen collected over the last two decades. This allows continuity in experiments (i.e. they can be repeated with the same strains), or facilitates comparison with new specimen in a research field that is in continuous flux driven by rapidly evolving technologies.
We used the framework of the microbial Antarctic Resource System (mARS) to create additional visibility for two culture collections, being the BCCM/ULC public Cyanobacteria Collection, supported by the Belgian Science Policy Office (Belspo) and hosted at the University of Liège, and the MNA-CIBAN Bacterial Collection of the Italian National Antarctic Museum.
In close collaboration with the hosting institutions, we used a standardized approach to compile a dataset with all the available information on each individual culture in the collection. This way, mARS helps to preserve data and connect researchers to the existing wealth of microbial resources that can be effectively browsed to identify any strain of interest. In addition, the data resources also serve as a reference for the occurrence of specific microbial species, which is relatively rare at a species or population level for prokaryotes.
The mARS data portal archives microbial datasets that are geo-referenced and annotated with metadata and environmental measurements. While mARS is generally aimed at amplicon or metagenome/metatranscriptome sequencing, the use of global standards for data archiving, such as DarwinCore (DwC) and Minimum Information about any (x) Sequence (MIxS), enables the portal to be sufficiently flexible to easily handle and organize the data and metadata of the microbial culture collections.
The approach we took was to view each strain as an ecological occurrence linked to a DNA sequence. As such, strains could be characterized by a sampling moment, a geographic location and any number of measured environmental parameters associated with the original source material that was collected in situ. Like this, the culture collections could be archived as microbial sequence datasets on mARS, as well as biodiversity occurrence datasets on GBIF.
The biodiversity.aq website is one of the Belgian federal contributions to the LifeWatch ERIC. This is a long lasting project that is coordinated by the Royal Belgian Institute of Natural Sciences (RBINS) and aims to function as an Antarctic thematic LifeWatch virtual laboratory. Its implementation by the Belgian Biodiversity Platform (BBPf) ascertains that biodiversity.aq can take advantage of the relevant experience of the Belgian GBIF node.
The microbial Antarctic Resource System (mARS) is an online data portal, supported by the Scientific Committee on Antarctic Research (SCAR) and RBINS. The main focus of mARS is to archive and document microbial sequencing data collected within the geographic jurisdiction of the Antarctic Treaty (1959), and to make this freely available for the global scientific community.
E-mail mARS: Maxime Sweetlove and Anton Van de Putte
E-mail BCCM/ULC Cyanobacteria Collection: BCCM.ULC@ulg.ac.be
mARS: http://mars.biodiversity.aq
BCCM/ULC Cyanobacteria Collection: http://bccm.belspo.be/about-us/bccm-ulc
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