CHALLENGEN comes to an end

By Xavier Turon and Marta Pascual

Dear followers of the ChallenGen project, we must announce that the project ended officially the 31^st December 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 very happy about the success of the ChallenGen project and the advances made in the three main objectives, along with our participation in dissemination and outreach activities and student formation.

We have an impressive list of ca. 50 papers, which is on a par with other projects with much (and we mean real much) more budget available.

These results are level with the output in form of meeting presentations, divulgation activities and media appearance. The team has been keen in reaching both the specialized audiences and the general public.

We also emphasize that 5 PhD theses have been completed or initiated within the project, and 18 MSc theses and 12 Bachelor theses have been presented, always with the highest marks.

We want to congratulate the team of the project for the important results obtained. 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. Please bookmark the webpage of PopCOmics http://popcomicsproject.blogspot.com/ and watch out for interesting news.

ChallenGen is over, long live PopCOmics!

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

by Xavier Turon

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: Wangensteen OS, Cebrian E, Palacín C, Turon X. 2018. Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding. Marine Pollution Bulletin, 127:54-66.

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 macrofauna and meiofauna), 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 metabarcoding communities from the National Parks published in PeerJ Preprints

by Xavier Turon

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 Wangensteen OS, Palacín C, Guardiola M, Turon X. 2017. Metabarcoding litoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers. 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 studied with 18S (left) and COI (right) in all communities.