Relaunch of the NEMOte BARCODing Website
We are pleased to announce the relaunching of the NEMOte BARCODing website.
This will be the home of research news relating to the project “NEMOte BARCODing: Advancing monitoring of Baltic benthic ecosystems”, a research project lead by Francisco Nascimento, Department of Ecology, Environment and Plant Science, Stockholm University. The project aims at improving environmental monitoring techniques using DNA methods, and focusing on the inclusion of smaller animals, meiofauna, and especially Nematode worms in monitoring programs. NEMOte BARCODing have been ongoing since 2019 and a lot of interesting results and data have been gathered. These will now be reported, among other places here at the NEMOte BARCODing website. The project is coming to an end this year, but we hope it will spark and inspire further research and interest both among researchers, students and the public. Below follows a brief summary of the project and what has been done so far:
Monitoring biodiversity changes is critical to understand how ecosystems respond to disturbance. This is dependent on effective methods to assess biodiversity and ecological status of ecosystems. Such methods are particularly valuable for habitats under severe pressure like the Baltic Sea soft-sediments. Monitoring programs for benthic ecosystems focus on macrofauna, animals larger than 1 mm, for the evaluation of ecosystem health. In the Baltic Sea where there are very few macrofauna species this type of monitoring could run into problems of distinguishing between impact levels. The inclusion of smaller organisms could enable a more fine-grained analysis and possibly reduce monitoring costs. Nematodes are the most abundant and diverse group on the seafloor, and is almost exclusively in the meiofauna size range, and their ubiquity would lend them well for inclusion in monitoring programs. However, for smaller organisms such as nematodes, traditional methods of determining species visually are very time consuming and requires detailed species knowledge. Newer techniques such as metabarcoding, a DNA-method that identifies a species based on is "barcode" (A barcode is a segment of DNA from an organism that enables its identification), could however make their inclusion feasible. This project tries to develop and enable the application of these methods to nematodes in the Baltic Sea, both for monitoring of the Baltic in particular, and for application in other regions. To achieve this project had three main parts where specific goals where set for each, but the parts are also intertwined and interdependent. As such large parts of the field and laboratory work within the project related to all parts. Samples have been taken yearly to from monitoring stations across the Baltic as a part of the Swedish monitoring programs. These samples were also collected from before the start of the project, in total samples from 71 monitoring stations from the year 2015 to 2023 have been collected for use in this research project. A lot of additional field and laboratory work have also been carried out and the time has come to share the results of NEMOte BARCODing project with the wider public. The different parts of the project were:
Improving DNA barcode reference libraries for Baltic Sea nematodes.
The first part of this project aimed at improving DNA barcode reference libraries for Baltic Sea nematodes. For it to be possible to identify a species by its barcode, a reference barcode from that species must be present in a reference library. This part of the project aimed at improving these by uploading DNA barcodes from known species of nematodes to the larger DNA reference libraries. Within the project 40 reference barcodes have been uploaded, enabling the use of these in research projects and monitoring programs using metabarcoding.
Quantifying abundances biomass of meiofauna species from sequencing read counts
This second part of the project tried to develop methods to quantify the abundance, the number, and biomass, the mass, of meiofauna species from the data gotten by sequencing the DNA of those species. The data gotten from sequencing, DNA-methods, only gives a relative value of the occurrence of the different species, and these relative values align more with the proportional mass of the species and not the number of individuals. These relative values could also be skewed by factors that differ between species, such as the number of rRNA gene copies, and biases in the DNA-methods. The calculation of actual abundance and biomass from sequencing data would enable more precise and accurate use of meiofauna data, which would ease and improve the use of this type of data in both monitoring and research. The experiments to achieve this part of the project is still ongoing, and updates on the results will be published here.
Improving management tools to assess the status of aphotic Baltic benthic ecosystems
In monitoring the use of indices is common to summaries multiple factors into one value to determine monitoring and management outcomes. In the Baltic Sea the index BQI (Benthic quality index) is commonly used in Swedish monitoring programs. With the addition of nematodes into indices like BQI a more fine-grained value could be given of heavily impacted sites or sites that for other reasons have few macrofauna species. This inclusion requires innovation, the finetuning and weighting of different variables, as well as validation and benchmarking against the original formulation of the index. In essence this inclusion will be the creation of a sub index to a parent index like BQI. But if done right the newly developed index will both enable more detailed analysis as well as comparability with historical monitoring results. A number of ways of integrating nematode metabarcoding data into BQI are now being explored within the scope of this project. Soon one or several of these new index formulas will be presented and introduced here on the website along with tools for their use.
Wrapping up
In addition to these parts, the project has aimed at a broader improvement of DNA-method application on benthic communities, both for research and monitoring. The use of metabarcoding techniques even on larger animals could be cost saving in regions where species identification of these animals is very time consuming. Metabarcoding methods have thus also been applied to macrofauna communities to benchmark these DNA-methods to traditional visual methods of identification and quantification.
This project is coming to and end this year and this website have been developed to communicate the results of the project. The website is now launched and will soon contain more updates. During this period after launch the site might undergo some slightly design changes and page additions. During this time the website will also publish updates on the findings of the project so far, these updates can be found under the “News” section. The website will then publish regular updates on the further findings of the project. As this project comes to an end, we ask ourselves what the future of DNA-methods are going to be in monitoring. We believe and hope our project will be a contributing factor for their advancement.