Metabarpark comes to an end

Dear followers of the Metabarpark project, please be aware that the project ended officially in November 2017. We have waited to make this post so that some papers with results could appear and a new project is up and running.

We are proud of the success of the Metabarpark project. We could develop novel metabarcoding methods for the assessment of benthic communities on hard substrata. These methods were applied to representative communities of the two National Parks studied, and a bewildering biodiversity was uncovered. We also proved the adequacy of metabarcoding to detect the less evident impacts (on meio- and micro-organisms) of the presence of invasive seaweeds in sublittoral communities in both Parks.

We are happy to announce that our activity will continue in the framework of a new project funded by the Ministry of Science, the PopCOmics project. In this new project, we seek to continue the development of molecular tools as applied to ecological and conservation issues.

Thanks for having followed this project! Please bookmark the webpage of PopCOmics http://popcomicsproject.blogspot.com/ and watch out for interesting news.

The Metabarpark team

Results from Metabarpark published!

The paper with the main results of the Metabarpark project has been published in the international journal PeerJ. It is open access and freely accesible at:

https://peerj.com/articles/4705/

It took us a while to get it published, but we hope that the scientific community will appreciate these results and the new application of metabarcoding techniques to natural benthic communities.

The article is dedicated to Alex Macía, owner of the Cíes Diving club, who provided logistics in the Atlantic Islands, and who recently died while following his passion for diving.

The supplementary material of the article includes the updated MOTU tables that summarize the biodiversity found in the two National Parks during our samplings.

Venn diagrams showing the number of different taxa recovered with 18S (blue) or COI (red) at different taxonomic ranks.

Results of the study of invasive algae published in Marine Pollution Bulletin

We are happy to report that the results concerning the invaded vs non-invaded communities sampled in 2015 have now been published in the international journal Marine Pollution Bulletin (MPB 127: 54-66, 2018).

Elsevier kindly provides a 50 days free access (starting 21 Dec) to this article at https://authors.elsevier.com/a/1WG02,ashmKxI
After this period you will need a subscription to be able to download it

In this paper we report on the effect that invasive algae have at the community level, targeting mainly the smaller size components (small macrobenthos and meiobenthos), using the 18S and the COI genes and the fractionation procedure and bioinformatic pipeline developed in our project. Here goes the abstract:

We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

Images of the communities analysed, with (left) and without (right) invasive algae. A,B: Cc (Caulerpa cylindracea) communities. C,D: Ll (Lophocladia lallemandii) communities. E,F: Aa (Asparagopsis armata) communities. Pictures: (A) from Eneko Aspillaga; (B,F) from the authors; (C,D) from Pol Capdevila; (E) from Enric Ballesteros

Results from Metabarpark samplings published in PeerJ Preprints

While the article is being peer-reviewed, we have published the manuscript in Pre-print format in the repository PeerJ Preprints, where it is freely available at https://peerj.com/preprints/3429/



METABARCODING LITTORAL HARD-BOTTOM COMMUNITIES: UNEXPECTED DIVERSITY AND DATABASE GAPS REVEALED BY TWO MOLECULAR MARKERS

Wangensteen OS, Palacín C, Guardiola M, Turon X (2017) PeerJ Preprints 5:e3429v1



We report in this manuscript the astonishing diversity found in communities from Islas Cies and Cabrera. We address several technical aspects, compare the two genes studied (18S and COI), and perform ecological analyses. Here goes the abstract:



We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities. The new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

Percent of MOTUs found for the main categories of organisms in the three fractions (A, B, C) studied with 18S (left) and COI (right) in all communities studied

Metabarpark at the Pint of Science festival in Blanes

The Pint of Science festival aims to deliver interesting talks on the latest science research in an accessible format to the public – mainly across bars and pubs (preferably with a pint of beer in hands). It is an International festival being held annually over three days at the same time in hundreds of cities across the world. Blanes, the host city of the CEAB, has participated for the first time in this year’s Pint of Science festival. The scientists of the CEAB gave nine talks three evenings (15-17 May 2017).

Xavier Turon participated in the first day of the festival, presenting the opening talk at a nice bar (Casal la Cooperativa) on the topic: Biodiversity 2.0: genetics and computers to study the living organisms. His talk introduced the topic of the ongoing sixth extinction caused by human pressures, and how computer science and genetics can help mitigating these effects. In particular, how we should complete biodiversity inventories as a first step towards conservation. The examples presented drew mainly from results obtained in Metabarpark.

It was an enjoyable and challenging experience to try to explain in lay terms some complex analysis we do in our research. The audience was very interested and asked many relevant questions after the talk.

The banner of the festival in Blanes

Metabarpark at the meeting "Developing new genetic tools for bioassessment of aquatic ecosystems in Europe"

Metabarpark was present at the meeting on metabarcoding held in Essen (Germany) in March 7th-9th 2017. This was the kick-off conference of the European Union COST action DNAqua-Net (http://dnaqua.net/).

This project aims at integrating a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices and metrics for routine application for biodiversity assessments and biomonitoring of European water bodies. It also envisages training and dissemination activities. The objectives of Metabarpark are fully compatible with the goals of DNAqua-Net and we wanted to be counted in and contribute.

Xavier Turon is one of the Spanish members of DNAqua-Net and attended this conference, where ca. 200 researchers gathered together to present results, discuss hot topics, and delineate the way forward for achieving a wide acceptance by management bodies of genetic methods for biodiversity assessment in the European context.

Xavier presented the communication "Under the canopy: community-wide effects of invasive algae in marine protected areas revealed by metabarcoding", by Xavier Turon, Owen Wangensteen, Emma Cebrian and Creu Palacín. In this contribution the main results concerning the effects of three invasive algae (Caulerpa cylindracea and Lophocladia lallemandii in Cabrera, and Asparagopsis armata in the Atlantic) on the benthic communities were exposed. We have also drafted and sent a manuscript for publication with these results. This contribution is also the first result of the collaboration between the National Park projects Metabarpark and Corclim.

The logo of DNAqua-Net

A heatmap representation of the samples of communities with and without Asparagopsis armata from Cíes Islands, separated by invasion status (green: non-invaded, red: invaded) and fraction (blue: macrobenthos; turquoise: meiobenthos)

Metabarpark at the meeting "Jornadas de Investigación en la Red de Parques Nacionales 2016”

On October, 18 to 20, 2016 the meeting “Jornadas de Investigación en la Red de Parques Nacionales 2016” was held in the National Park of Tablas de Daimiel in Ciudad Real. This meeting gathered together staff from the OAPN central services, from the different National Parks, members of the Scientific Committee of the OAPN, and researchers that are developing projects in the National Park Network. The results of 13 projects corresponding to the 2013 call were presented in public talks, and there were also technical talks about programs currently underway in the Parks Network.

Xavier Turon gave a talk about the Metabarpark project, presenting the main findings and highlighting the potential of the genetic information for mid- and long- term biomonitoring of the communities.

This meeting has been a very good occasion for sharing experiences and discussing with colleagues and Park managers. Among the attendants were the staff from the Atlantic Islands Park (Pepín, Mercedes, Vicente), and many other acquaintances. It was such a pleasure to meet them all! I cannot resist mentioning also the fine gastronomy we enjoyed and the nice visit to the Tablas de Daimiel National Park that we did.

Family foto of the attendants to the meeting