Monday, December 21, 2015

Video contest winners!

by Maria Casso

Last week, on December 17th, was the award ceremony of the I Video Contest Comas i Solà organised by the UB. I participated in this contest with a video about my research.

There were three categories: "the best video", "the most watched video on youtube", "the most original video". I am very proud to say that my video resulted to be the winner in the category "most original video"! During the ceremony, we could saw the three videos.

Thanks to the UB Divulga for organising the contest. I hope next year it will be more participants and even more quality. I think it is a nice way to divulge science and research!

Friday, November 27, 2015

Seminar: DNA Metabarcoding

by Maria Casso

Yesterday, Xavier Turon and Owen Wangensteen participated at the seminar "DNA Metabarcoding", organised by the Biodiversity Research Institute (IRBio). DNA metabarcoding is a method to assess biodiversity which combines DNA based identification and next generation sequencing, and it can have several applications. The aim of the seminar was to show the potencial and limitations of the method.

The first lecture was Xavier's and it was an introduction about the impediments of taxonomy and how can metabarcoding methods contribute to assess biodiversity. After him, Owen talked about the specific case of metabarcoding of hard bottom marine communities. He also explained the few but critical stages of the pipeline were there isn't a consensus among scientists. It is really awesome to watch live how a new method is developing and be part of it.

The seminar took place at the School of Biology (UB). Many researchers and students attended, and some interesting questions came out. It was dense but also clarifying and motivating.

Wednesday, November 18, 2015

Sea stars, Sampling & Sun

by Maria Casso

Yesterday we went to Sant Feliu de Guíxols, a locality situated on the Costa Brava. We sampled some sea stars by scuba diving, from surface to 20m depth.

We were very lucky because the day was sunny and the sea was oddly calm. It is a beautiful spot, but usually, at this time of year is very difficult to find such good weather conditions. Moreover, the water was warmer than we expected (18ºC at 12m and 16ºC at 20m depth).

Friday, November 6, 2015

Lectures at the Course “New Technologies applied to the control and monitoring of invasive species”

by Xavier Turon

In October, 19 to 23, the National Parks Autonomous Agency (OAPN) organised a course on new technologies applied to the study of invasive species in Vigo (Galicia). This course was attended by staff, technicians, and rangers of the National Parks in Spain.

I was invited to give a lecture about “Genetic tools and invasive species”. It was an enjoyable experience, with interested audience that posed clever questions... and of course it was an occasion to enjoy good shellfish “mariscada” typical of Galicia’s gastronomy.

The Cíes Islands, part of the National Park of the Atlantic Islands in whose facilities the course was given. The ChallenGen project, in collaboration with the Metabarpark project, has been working on the benthic communities of these Islands.

Thursday, November 5, 2015

New paper published: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Getting sediment samples from a multicorer device.
by Xavier Turon

Another article with results from the ChallenGen Project is now published:

Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X. 2015. Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons. PLoS One 10(10): e0139633. doi:10.1371/journal.pone.0139633

This is our first paper about the metabarcoding of marine communities. In this article we focus on deep-sea sedimentary communities. Samples were collected during the DOSMARES and INDEMARES projects from canyons and adjacent areas in the Catalan and Balearic Islands coasts.

This is the abstract of the article:

Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100-2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.

Multidimensional Scaling (MDS) plots showing the differentiation found between the zones studied (BC, Blanes Canyon; OS, Blanes Open Slope; CC, Cap de Creus Canyon; MC, ;Menorca Canal; ST, Serra de Tramuntana Slope).

Wednesday, November 4, 2015

Monitoring invasive ascidians at Ebro Delta

A nice view of the bivalve culture area.
by Maria Casso

Today we went to the Ebro Delta, for monitoring the invasive ascidians at the oyster and mussel culture structures. After a week of stormy days, we had a sunny and calm monitoring day.

We want to thank the Institute of Food and Agricultural Research and Technology (IRTA) for providing the boat and skipper and collaborate in this monitoring.

Víctor Ordóñez writting down the observations.
Maria Casso and Jose Luís Costa (IRTA).

Saturday, October 31, 2015

Video: Alien Species VS. Genomics
by Maria Casso

The University of Barcelona (UB) organises for the first time a short film contest that allows researchers describing the scientific studies they develop to the general public.

I decided to participate in this contest as I'm a PhD student at the UB.

You can watch it here.

I hope you like it!

Tuesday, October 13, 2015

Population genetics with R

by Maria Casso

Visit at the Centre de Restautació i Interpretació Paleontològica (CRIP).
Last week, I participated in a very interesting course: Exploratory Methods for Population Genetics Using R, organized by Transmitting Science. The course took place in Hostalets de Pierola (Barcelona), from 5th to 9th October. We learnt about some interesting R packages from their very authors, Dr. Emmanuel Paradis and Dr. Thibaut Jombart, who are excellent teachers.

It was intense but also fun as I had the opportunity to play with my own data with the new R packages, with the support and advice of the teachers. Moreover, it was very interesting to meet people working on similar data type than me so with similar problems, as we could discuss about it and maybe found some solutions.

Thanks to the organization, the teachers and the participants!

3rd ChallenGen meeting!

The 2nd October, we had a meeting in Blanes, with most of the members of the group. Besides the updates from everyone, we could discuss about some methods to analyse GBS data, and listen to an interesting seminar about metabarcoding by Owen Wangensteen.

Monday, September 14, 2015

New article of ChallenGen accepted!

by Xavier Turon

Another article including results from ChallenGen has been accepted for publication in Frontiers in Microbiology. The title of the paper is “Temporal stability of bacterial symbionts in a temperate ascidian” by López-Legentil S, Turon X, Espluga R, Erwin PM.

This article is the result of collaborative work between the projects ChallenGen and MarSymbiOmics (CTM2013-43287). The goal of MarSymbiOmics is the study of symbioses of invertebrates from a molecular perspective. It is only natural that we coordinate efforts… We are more focused on the genetics of the host, while the MarSymbiOmics team is interested in the genetics of the microbiome.

A colony of Didemnum fulgens in the monitoring site at L’Escala (Catalan coast, NW Mediterranean).
In this particular study we have monitored the population of an ascidian species, Didemnum fulgens, over an annual cycle. Its pattern of growth and reproduction has been published a while ago (López-Legentil S, Erwin PM, Velasco M, Turon X. 2013. Growing or reproducing in a temperate sea: optimization of resource allocation in a colonial ascidian, Invertebrate Biology 132:69-80).

Now we publish the results of the temporal changes in microbiome composition of that same population using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses based on the16S rRNA gene. The overall bacterial community in D. fulgens had a distinct signature from the surrounding seawater and was stable over time and across seasonal fluctuations in temperature. Bacterial symbionts were also observed in the inner tunic of larvae of D. fulgens. Our results suggest that, as seen for sponges and corals, some species of ascidians host stable and unique bacterial communities that are at least partially inherited by their progeny by vertical transmission.

Soon available in Open Access!!!

Monday, August 31, 2015

The importance of being barcoded

by Owen S. Wangensteen

When, back in 2003, Canadian biologist Paul Hebert proposed the creation of a public database of short sequences aimed at identifying biological specimens by means of just these small sequences (DNA-barcodes), he did not find the unanimous response anyone would expect nowadays. Detractors were many and they actually made a lot of scientific noise. In fact, as Laurence Packer once pointed, scientific papers published from 2004 to 2007 criticizing and opposing DNA-barcoding were more numerous (and had more citations) than papers written by the first “barcoders” who embraced the idea. Then, a miracle occurred: as the public databases grew, DNA-barcoding started to prove its utility in a myriad of forms. From long-disputed basic taxonomy issues to medico-legal forensics, passing through river ecology, agricultural sciences, control of disease outbreaks, food security or biodiversity conservation, all took advantage of DNA-barcoding in ways only a few would have dreamt of some years before.

The reticences were mainly based in some false concerns and a few ancestral fears. Morphological taxonomists argued that no small-sequence could replace their meticulous, morphological observations and thorough interpretations, while internally fearing to lose their jobs. Geneticists argued that genomes were way too complex to be reduced to just a three-hundred base-pairs sequence. Ecologists thought that molecular methods were too expensive and beyond their field of expertise. All of them were basically wrong.

DNA-barcoding does not plan (and is never going) to replace taxonomists. At its best, DNA-barcoding is meant to replace traditional identification keys (which were probably bound to disappear anyway!). Identification keys are usually a nightmare even for expert taxonomists and are completely useless for specious groups including thousands or tens of thousands of species. DNA-barcoding will only facilitate the work of taxonomists, which are still needed (in fact, more needed than ever) for identifying problematic specimens. Given the estimations for the global number of species and the current description rate of new species, we will need taxonomists, at least, for the next 500 years, or probably much longer. This is more than most scientists working in other areas of knowledge could bet.

It is true that genomes of non-model organisms are large, complex, gigantic monsters waiting to be tamed. But the fact is that all you need for unambiguously identify the species where a specimen belongs is a fragment of just a few hundreds base-pairs of a highly variable genomic region (in most cases, just 200 base-pairs will do!). Mitochondrial DNA (and, specifically, the cytochrome oxidase I gene, COI) has proven its power to achieve this task in many groups of organisms (including animals; other genes are most used for green plants or fungi). If you need your sequences just for identification purposes, all you need is to sequence but 200 base-pairs of COI. Fast and easy.

And unexpensive. Sequencing costs have done nothing but plummeting over the last three decades and they are predicted to keep decreasing in a month-to-month basis. Astounding sequencing technologies that grew up under the big umbrella of Human Genome Project have already arrived to average-sized laboratories. Nowadays, DNA-barcoding of an unknown specimen is something that a freshman biology student could perform during his/her first lab course. Costs and complexity are no longer valid excuses.

I recently understood the pivotal importance of barcoding (i.e. the urgent need for getting the sequences from as many different species as you can and depositing them in a public database as soon as possible) when I started analyzing the data we got from bulk-sequencing environmental samples collected in shallow marine hard-bottom communities of selected marine reserves in Spain. This kind of research is crucial to understand how marine communities are changing (and they are changing indeed, probably at a faster pace than we use to think). We need to sample these communities and characterize them as soon as possible, if we want to be able to detect any changes in the near future, before it's too late. The sensible way to do this is by metabarcoding them. That is: get the sample inside a bag, blend it with a kitchen blender, extract the DNA of every organism present in the mixture, use this DNA to amplify a useful genetic marker (COI is the usual choice), and then try to match the millions of sequences you get to the current contents of public barcoding databases, in order to identify the organisms that are present in your samples (and probably their abundances, but that's another story I will be writing some other day). The first steps of this procedure proved to be surprisingly easy. Notably, it is the last identification step which is currently limiting the utility of this technique. We have literally millions of different COI sequences, representing all the biodiversity hidden in our samples, but we are able to identify (give a species name) just a small percentage of these sequences. Marine barcoding databases are not as developed as terrestrial ones. Small and microscopic organisms are much more underrepresented in the databases than big, macroscopic ones. A surprisingly high percentage of marine diversity is yet unknown, even for shallow ecosystems in the Mediterranean or temperate Atlantic European shores, which have been extensively studied by marine biologists, at least since Aristotle.

If we want to begin to understand the biodiversity changes which are happening now in our beloved marine ecosystems, we really need to undertake the titanic task of sequencing the DNA-barcodes of as many marine species as possible, and release the data to our public databases. I am confident that metabarcoding will become the main tool of marine ecologists in the next few years. We need to extract its full power as soon as possible by expanding our databases and filling the main gaps. This is no task for an individual or a small group of people. Given the overwhelmingly high number of different marine species, this is a task for several hundreds of marine taxonomists, working across the World, identifying species in their different groups of expertise, sequencing data, curating taxonomies, releasing data, and waiting for no bigger reward on these data release but contributing to help other marine biologists in building the greatest and most useful marine taxonomy enterprise of all time.

As Harry Truman once said, it is amazing what you can accomplish if you do not care who gets the credit.

Comparing DNA-barcoding vs environmental-DNA metabarcoding approaches to biodiversity monitoring. In DNA-barcoding, a single individual is analyzed, whereas metabarcoding can analyze whole communities by using the power of next-generation sequencing technologies.

Hebert et al. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270, 313–321. doi: 10.1098/rspb.2002.2218

Thursday, August 27, 2015

The opening of the New Suez Canal

by Enrique Macpherson

The New Suez Canal was opened on August 6th 2015. The ecological impact can be catastrophic...

In September 2014, one month after the enlargement of the Suez Canal was announced, eighteen scientists published an article in the journal Biological Invasions highlighting the threat of invasive species and calling the expansion “ominous.” The article asked for compliance with United Nations treaties that have jurisdiction over environmental issues in the Mediterranean, and to which Egypt is a signatory.

Lophocladia lallemanii is an invasive red algae species from the Indo-Pacific, present in the Mediterranean Sea. It completely overgrows macroalgal communities and seagrass Posidonia oceanica meadows.

By December, two hundred concerned scientists from twenty-five countries, began a letter writing campaign to environmental groups asking for help approaching authorities to request an environmental risk assessment of the Canal expansion. We wrote, “We recognize that global trade and shipping are vital to society, however, the existing international agreements also recognize the urgent need for sustainable practices that minimize unwanted impacts and long term consequences.”

A single Member of the European Parliament, Ricardo Serrão Santos of Portugal, introduced a statement about the canal on the floor of the Parliament. He said, "I would like to draw your attention to the enlargement of the Suez Canal. This process will increase marine pollution, including more alien species. The expected impact goes far beyond the proposing country and will have implications across the Mediterranean Sea, as indeed has the actual Suez Canal. For this reason I call for a proper environmental impact study that is holistic, comprehensive, deep, international and, more important, consequential." No further action was taken by the Parliament.

Siganus sp. are voraceous herbivorous fishes.
Of the dozens of environmental groups who received the letter, only the International Union for Conservation of Nature (IUCN) responded. They wrote to the Directorate-General of the European Commission suggesting mitigation measures and offering technical assistance. “Effective solutions do exist, for example the creation of an environmental barrier to biological invasions using naturally occurring highly saline Bitter Lakes (these lakes reduced the introduction of Red Sea species into the Mediterranean for many decades).” By February, the letter authored by the concerned scientists collected five hundred signatures from forty countries. Still, the international community remained mute.

No response ever came from any group charged with environmental oversight of the Mediterranean. No environmental risk assessment was ever performed. This willful myopia by the bodies whose mission is to protect the sea is putting the Mediterranean at grave risk.

"Especies invasoras: El regalo tóxico de Egipto al Mediterráneo", El Mundo, Ciencia, 21 Aug 2015.
"Ecological worries about Suez Canal extension", BBC, Science in action, 13 Aug 1025.
"Suez, così cambierà la fauna del mare", La Stampa, Opinioni, 7 Aug 2015.
"Raddoppio di Suez, per le specie tropicali sarà un’autostrada per il Mediterraneo", Il Secolo XIX, Mondo, 7 Aug 2015.
"توسيع قناة السويس يوسِّع غزو الكائنات البحرية للبحر المتوسط"
Nature Middle East, 7 Aug 2015.
"Ecologists fear new Suez Canal plays ‘Russian roulette’ with the Mediterranean", Science News, 7 Aug 2015.
"L’expansion du canal de Suez a des effets négatifs sur la diversité biologique de la Méditerranée", Libération, 6 Aug 2015.
"Ecologists concerned over Suez expansion impacts", DW, 6 Aug 2015.
Fish News EU, 5 Aug 2015.
"Enlargement of the Suez Canal: The number of ships is increasing, the number of invasive species too;", Bloom Association, 5 Aug 2015.
"Muschel-Migration im Mittelmeer", Universität Wien, Medienportal, 4 Aug 2015.
"Silence on the Suez", Huffington Post, Science, 8 May 2015.
"Suez Expansion, effects unknown", Nature, News in focus, 1 Jan 2015.
"La invasión que viene de Suez" La Vanguardia, Tendencias, 30 Nov 2014.
"Under the ships in the Suez Canal", The New York Times, Opinion Pages, 12 Nov 2014.

Galil BS, F Boero, ML Campbell, JT Carlton, E Cook, S Fraschetti, S Gollasch, CL Hewitt, A Jelmert, E Macpherson, A Marchini, C McKenzie, D Minchin, A Occhipinti-Ambrogi, H Ojaveer, S Olenin, S Piraino, GM Ruiz. 2015. ‘Double trouble’: the expansion of the Suez Canal and marine bioinvasions in the Mediterranean Sea. Biological Invasions 17: 973-976.

Galil BS, F Boero, ML Campbell, JT Carlton, E Cook, S Fraschetti, S Gollasch, CL Hewitt, A Jelmert, E Macpherson, A Marchini, C McKenzie, D Minchin, A Occhipinti-Ambrogi, H Ojaveer, S Olenin, S Piraino, GM Ruiz. 2015. The Enlargement of the Suez Canal and Introduction of Non‐Indigenous Species to the Mediterranean Sea. Limnology and Oceanography Bulletin 24: 41-43.

Monday, August 10, 2015

ChallenGen at the 6th International Barcode of Life Conference (Guelph, Canada)

ChallenGen Project will be present in the 6th International Barcode of Life Conference that will be held at Guelph (Canada), next August 18th - 21st 2015. Our postdoc researcher Owen S. Wangensteen will be presenting our most recent developments of metabarcoding pipelines to study the biodiversity of marine hard-bottom communities with a level of detail never seen before.

Monday, July 20, 2015

ChallenGen at the 8​th International Tunicate Meeting (Aomori, Japan, 13­-17 July, 2015)

by Xavier Turon

Ascidians (Halocynthia roretzi) exhibited at the meeting venue... Can you believe that Japanese people eat them and consider them a delicacy?... I tried, between us, it is disgusting for my western taste.
The International Tunicate Meeting was held this year in Japan. I attended it and presented an oral communication about “Utility of the metabarcoding approach for the determination of tunicate in environmental DNA samples” (with Owen, Cruz, Magdalena, and Iosune Uriz).

I was happy to present in the first morning of the meeting, and could thus relax for the rest of the sessions. The meeting was very interesting, particularly the final discussion about the correct names of the species in the complex C​iona intestinalis.​ It seems that the species whose genome we sequenced, whose development has been studied all over the world, one of the best investigated invertebrate species, should be called C​iona robusta! ​I was called in as an expert taxonomist (an endangered species, btw) and had my saying on it, not to the likings of everyone, to be honest. I guess the controversy will continue for some time.

I also took advantage of my trip to sample D​idemnum vexillum​ in its native area. Dr. Gretchen Lambert was kind enough to give me some samples from the South collected during a pre­meeting course. I could collect myself in the Aomori Marine Station thanks to the help of Dr. Gaku Kumano. Overall, it was an enjoyable trip and experience.

Friday, July 17, 2015

New paper published: Corridors for aliens but not for natives: effects of marine urban sprawl at a regional scale

"Marine urban sprawl creates corridors for invasives

It is well established that corridors can, in certain cases, help spread non-native species in terrestrial ecosystems. In a new study by Airoldi et al., the authors expand on this theme with a look at the spread of non-native species at a regional scale. This study compares artificial marine infrastructure (ex. harbors, dikes, piers, breakwaters, etc.) and natural reefs. Their extensive look at 500 kilometers of shoreline in the North Adriatic Sea provides clues as to how marine corridors contribute to the spread of native and non-native species alike."

Read more here.

Paper Reference: Airoldi, L., X. Turon, S. Perkol-Finkel, and M. Rius. 2015. Corridors for aliens but not for natives: effects of marine urban sprawl at a regional scale. Diversity and Distributions 21: 755-768.

Tuesday, June 23, 2015

New paper published: Applications of next generation sequencing to the study of biological invasions

"Genomics holds the key to understanding ecological and evolutionary processes
Scientists call for a gap between genomics and invasion biology to be bridged

Scientists at the University of Southampton think that Next-Generation Sequencing (NGS) of invasive organisms holds the key to furthering our understanding of ecological and evolutionary processes."

Read more at the University of Southampton website.

Paper Reference: Rius M, Bourne S, Hornsby HG, Chapman MA. 2015. Applications of next generation sequencing to the study of biological invasions. Current Zoology 61: 488–504

Monday, June 8, 2015

Xavier Turon visits Marc Rius at Southampton

by Xavier turon

Xavier Turon at the entrance hall of NOC with the figurehead of the HMS Challenger. No less!
I have performed a research stay with Marc Rius at the National Oceanography Center of Southampton (NOC), invited by the University of Southampton where Marc is associate professor, from 25th May to 6th ­June.

We have been working on ongoing research about the validity of commonly used primers for barcoding genes in the group of ascidians, as part of our efforts to develop efficient metabarcoding markers for invertebrates. The results of this stay will be expanded to other groups and published.

We also sampled marinas in the Southampton area looking for Didemnum vexillum, and could get a couple of good populations from the area. It was a pleasure to share these two productive weeks with Marc and his students... and of course with his family as well.

Tuesday, May 19, 2015

After Pints and Science

Yesterday, the Cara B was full! Many different people came and some did interesting questions. The afternoon was funny, educative and inspiring.

...And the speakers had a beer for free thanks to the Pint of Science Festival Team!

Monday, May 4, 2015

ChallenGen at Pint of Science!

Pint of Science Festival arrives in Barcelona from 18th to 20th May. Xavier Turon and Maria Casso will participate in this edition for the first time speaking about diversity and climate change with a beer in their hand. These are main subjects of the ChallenGen Project and we are pleased to present it and share our knowledge to the general public. Thanks a lot to the Pint of Science Barcelona Organization for inviting us to participate in this event!

We will be at Cara B bar on Monday 18th, from 8pm. Everybody will be more than welcomed!

Monday, March 23, 2015

In the beginning...

This is the starting point of the blog of ChallenGen Project, a project funded by the Spanish Ministry of Economy and Competitiveness which aims at shedding light on some hot topics involving the application of genetic and genomic tools to marine ecology. Project ChallenGen is structured into three broad research lines, representing current challenges for marine ecologists:

1. To tackle and mitigate the problem of introduced species.
2. To develop new tools for biodiversity assessment.
3. To predict foreseeable changes in a scenario of increasing temperature.