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Scientists and the public increasingly recognize global biodiversity threats as a critical challenge. Molecular sequencing technologies can be instrumental in developing strategies to protect and restore biodiversity. But how can we bring together molecular sequence and biodiversity infrastructures to prevent further decline in biodiversity? 

Here, Robert Waterhouse and Jerry Lanfear share highlights from their latest Opinion Article, which examines how the ELIXIR initiative works towards improving the integration of molecular data into the broader landscape of biodiversity infrastructure. 

Biodiversity research is a vast field. It spans different scales—from studying a single species to whole ecosystems or even global patterns. It also encompasses many taxonomic groups such as megafauna, species of insects, and fungi. 

Biodiversity is critical for the health of our planet. Human activities are causing unprecedented biodiversity declines threatening the ecosystem upon which our society depends. To protect and restore biodiversity, we first need to understand it. That’s what makes biodiversity research, across all its dimensions, so important. 

The role of molecular sequencing technologies in biodiversity research 

Molecular sequencing technologies are becoming more and more common in biodiversity research. A key reason is that such technologies can overcome taxonomic biases often resulting from traditional methods. For example, humans prefer to record species that are easy to find and identify, such as birds and large insects.  

Molecular technologies can detect the full range of biodiversity. In practice, this means the sequencing of DNA or RNA from biological samples is becoming a standard and essential part of many field studies. As a result, the routine production of molecular sequence data derives from those samples. 

Such technologies also have high throughput. In fact, individual field experiments can generate high volumes of diverse sequence data. 

Informing the understanding of biodiversity 

Molecular technologies are a critical part of the toolkit needed to enhance the understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline.  

There are three fundamental DNA-based technologies that can help improve our understanding of how life on earth functions and responds to environmental pressures:  

1. Genome sequencing: This technology provides a complete DNA sequence for an organism.  A high-quality genome generates valuable insights into an organism’s taxonomic relationship with other species. It can also serve as a foundation for other DNA-based research.  For instance, it enables the identification of genes and other features of the genome and the formation of a ‘’map’’ of the full genetic code that creates each organism. 
2. DNA barcoding: This method uses short, specific sequences of DNA to distinguish species, aiming to build the inventory of life on Earth and provide a basis for global species monitoring. It can be applied as a high throughput screening tool to identify large numbers of known organisms. 
3. Metagenomics: This approach is very common across microbial studies. Metagenomics has enabled the discovery of previously unknown species from an environmental sample (e.g. sea water). It is deployed as a high throughput method for species identification, discovery and/or environmental monitoring. 

Integrating molecular data into the wider landscape of biodiversity research infrastructures 

Molecular sequencing initiatives are producing reference catalogues of genetic and genomic biodiversity. Such catalogues need to be connected to biodiversity research infrastructures that are aggregating knowledge from scientific collections, human-made observations, and literature.  

Community initiatives need to be proactive rather than reactive. In our research, we propose actions to overcome current and future challenges and ensure that sequencing data can deliver their full potential in support of biodiversity research. 

Leading the future of biodiversity research 

Our Opinion Article is a first step towards identifying areas that require proactive community input to develop solutions that will deliver enhanced integration across the many dimensions of biodiversity research. While data collection and production are generally researcher-driven and supported by research-focused funding bodies, data management and so-called “data stewardship” are just as important. However, they are often overlooked or insufficiently considered.  

It is essential to consider how we can, as a community, ensure the longer-term utility of data being generated through short-term research projects. This will require concerted efforts to demonstrate the importance of supporting infrastructures that provide scientists with the means to take advantage of integrated biodiversity data to address critical research questions. 

The role of ELIXIR 

ELIXIR has a key role to play as a forum to bring together active partners in the field. As a research infrastructure, the organization develops services and technical solutions that help coordinate life sciences resources across Europe. 

As a starting point, the ELIXIR portfolio of biodiversity informatics services and resources highlights existing infrastructures and aims to stimulate improved integration. Training and knowledge transfer, driven by the ELIXIR Training Platform, brings researchers together. This is key to building the community needed to define short and longer-term goals.  

Moreover, the ELIXIR Tools ecosystem helps researchers find, register, and benchmark software tools, and promotes best practices for their development. The ELIXIR Research Data Management Kit also offers guidance on life sciences data management practices applicable to metadata in biodiversity-related research.  

Beyond the technical activities, a vital part of achieving longer-term aims is ensuring strong collaborations with initiatives that span the biodiversity field. ELIXIR is engaged with other key players such as GBIF, DiSSCo, CETAF, ENVRI, COL, BLR and OBIS, in part through the BiICKL and BGE projects, funded by the European Commission, as well as with networks such as the alliance for biodiversity knowledge.   

such as GBIF, DiSSCo, CETAF, ENVRI, COL, BLR and OBIS, in part through the BiICKL and BGE projects, funded by the European Commission, as well as with networks such as the alliance for biodiversity knowledge.   

Implications for sustainability and food security 

The sustainability of ecosystem services and food security is one area where the improved integration of molecular data into the wider landscape of biodiversity research infrastructures will have major implications.  

Agriculture, forestry, and fishery industries often rely on a limited number of species that make up most “services”. Understanding and being able to monitor how species and communities of species respond to the dramatic planetary changes that characterize the Anthropocene will be critical to the development of realistic plans for global food security.  

Plus, many of the services that ELIXIR develops to support biodiversity research can be applied to these other areas (and vice versa). There is great scope for synergies and benefits by aligning and coordinating across these different areas, which is a core part of ELIXIR’s mission. 

Next steps 

We have recently started to formalize our ELIXIR Biodiversity-focused efforts, through the formation of an ELIXIR Biodiversity Community. This is a key step as it will cement relationships internally within ELIXIR and create a strong platform for engagement and collaboration with other infrastructures. 

Read the full Opinion Article today on F1000Research or explore our ELIXIR Gateway to discover more research projects and outputs from or funded by ELIXIR.