Detailed Schedule

Sunday 8th

18:00h Ice breaker

Welcome: Josep Lluís Pelegrí Director of the Institut de Ciències del Mar (CSIC), Spain

Monday 9th – Populations, Community and Functional Ecology

8:30h Welcome to the VI Ramon Margalef Summer Colloquia, Javier del Campo and Ramiro Logares, Institut de Ciències del Mar (CSIC), Spain

Who was Ramon Margalef? Cèlia Marrasé, Institut de Ciències del Mar (CSIC), Spain

9:00h   Silvia G. Acinas
Revealing keystone ocean prokaryotic genomes
Institut de Ciències del Mar (CSIC), Spain
Prokaryotes are a relevant component of the ocean’s food networks; they are responsible for 30% of the primary production (fixing CO2) and most of the respiration of the ocean and are key players in all marine biogeochemical cycles. They account for 1029 cells in the global ocean representing a major player of the microbial world, yet only a few thousands of species of marine prokaryotes has been described to date despite that recent estimations claim about 1011 prokaryotes species in our planet. To fully understand which are the ecologically key microorganisms in the ocean, a combination of different approaches is needed to fully cover the whole spectrum of microbial diversity targeting both, the highly abundant and rare microbial taxa. To that end, microbial metagenomics are crucial to enable to reconstruct microbial genomes, what it is called Metagenomic-Assembled Genomes (MAGs). In parallel, single cell genomes through the analyses of Single Amplified Genomes (SAGs) is an alternative approach to target ecologically relevant and uncultured abundant individual genomes without cultivation. Using these approaches we are conducting the reconstruction of thousands of microbial genomes from two unexplored marine ecosystems: the polar Artic and the bathypelagic deep ocean, to investigate the ecology, function and evolution of the uncultured marine prokaryotes.

11:00h Marta Pascual
Population connectivity and adaptation in marine eukaryotes
Universitat de Barcelona, Spain
Population genetic structure and adaptation are key mechanisms to understand species distribution and ecosystems functioning. Massive sequencing is revolutionizing population studies and can now be applied even to non-model species from a wide array of taxonomic groups. How many management units are in a basin? Which is the degree of connectivity between marine areas? What is the effect of oceanographic discontinuities on geneflow? Are there loci responsible for local adaptation? How can an organism change and adapt through its lifetime? The accuracy in answering these old questions may rely on the type and number of genetic markers being assayed. I will discuss some of these issues using high-throughput sequencing techniques and marine species lacking reference genomes as case studies.

— Lunch Break —

14:00h Salvador Almagro-Moreno
Evolutionary approaches to understand Vibrionaceae niche colonization
University of Central Florida, USA
The propensity of prokaryotes to exchange genetic material and responsiveness to environmental fluctuations make them a captivating group in which to study evolution and niche colonization. My talk will focus on the ability of several members of the family Vibrionaceae to colonize the diverse set of niches they inhabit. I will discuss how environmental factors affect their colonization patterns, which genetic traits are prerequisites in colonizing a new niche, and what are their ecological relationships with other members of their natural environment. I will address these questions using a mix of genomics, phylogenetics, ecology and molecular biology.

15:30h Student presentations

Tuesday 10th – Ecosystem ecology

Ocean ‘omics: A large scale multidisciplinary analysis path to study marine micro-organisms
Genoscope, CEA, France

Marine planktonic organisms are (yet) poorly understood key players of several planet scale major biogeochemical loops (carbon, oxygen, nitrogen) and are also at the basis of the whole oceanic food chain. To which extend will environmental changes affect them ? Can we try to predict the consequences on human activities ? We will use the Tara Oceans project as playground to illustrate how can a multidisciplinary approach, from genomics to imaging via oceanography and computing, try to assess these questions.

11:00h Marta Goberna
Microbial diversity, evolutionary legacies and the functioning of terrestrial ecosystems
Centre d’Investigacions sobre Desertificació (UV-CSIC), Spain
Which are the mechanisms that assemble biological communities and how the diversity of biological communities contributes to the functioning of ecosystems are central topics in ecology. We address both questions focusing on soil microbial communities, which are stunningly diverse components of terrestrial ecosystems that deliver essential services including organic matter decomposition and nutrient cycling. By using metagenomics, we reconstruct microbial phylogenies, predict functional traits and perform network analyses. We combine taxonomic, phylogenetic and functional approaches to better understand the links between above- and belowground communities, their resistance and resilience to ecological disturbance and how their evolutionary legacies impact key ecosystem functions.

— Lunch Break —

14:00h Jed Fuhrman
Marine microbial ecological and biogeochemical processes: integration of classic and omics approaches
University of Southern California, USA
Around 1980 we learned marine bacteria process ~25% of global productivity via the “microbial loop.” Since then we have learned of the importance of viruses, diverse abundant non-“extremophile” archaea, picoplanktonic photoautotrophs, mixotrophs, ubiquitous rhodopsins, surprising dynamics, etc. ‘Omics has provided the ability to analyze the compositions and activities of natural populations directly. I’ll briefly summarize historic discoveries and discuss recent work in my lab including results on seasonality and predictability of microbial populations, surprisingly rapid community changes and parasitism during and after the spring bloom, interactions among bacteria, archaea, viruses, and protists, and the importance of microdiversity.

15:30h Discussions

Wednesday 11th – Evolutionary Ecology and Co-evolution

9:00h   Naiara Rodríguez-Ezpeleta
Making sense of omics data for making ecologically informed marine ecosystem and resource management decisions
AZTI, Spain
Recent advances in the application of omics techniques to underexplored environments and/or to the study of non-model organisms have led to a paradigm shift in the field of marine ecosystem and resource management. Major changes have arisen from the application of metabarcoding to the study of macrofauna, and from the application of population genomics to the study of organisms for which no prior genomic information is available. Yet, before these techniques can be routinely applied to monitor marine ecosystems and resources, and thus be used for taking management decisions, they need to be benchmarked, calibrated and standardized. I will present several case studies on the application of omics for marine management that illustrate the promises and challenges of this fast-moving field.

11:00h Esther Garcés
Shaping marine microbial food webs: the role of marine parasites
Institut de Ciències del Mar (CSIC), Spain
Parasitism is the most common interaction between predators and prey and has evolved to encompass nearly all branches of the tree of life. In marine ecosystems, parasitism recently emerged as a significant agent in the top-down control of phytoplankton blooms. My research focuses on simple ecological questions about parasites during blooms of their microalgal hosts: which species are you? where are you coming from? how abundant are you? which interactions do you have with the community components?, and so on. The ultimate goal is to understand the role of parasites in the coastal ecosystem and the use of -omics techniques are clearly changing several paradigms in this field of ecology and evolution.f

12:30h Purificación López-García
Inferring metabolic function and interactions from metagenomes of complex microbial communities
Ecologie, Systématique et Evolution, Université Paris-Sud-CNRS, France
Sequencing the genomes of microbial communities from different environments can both inform about dominant metabolic functions in particular ecosystems and serve as basis to reconstruct genome scaffolds for particular lineages of organisms. While these approaches have been largely applied to marine plankton, soils or, lately, animal microbiomes, they have been less applied to other kinds of ecosystems. I will summarize recent work we have been doing on calcifying and non-calcifying phototrophic microbial mats. These are diverse and complex microbial communities, often encompassing highly divergent lineages, where a vast array of microbial metabolisms occurs in association with redox gradients. I will discuss about the importance of particular core metabolic functions across redox gradients in these systems and comment about the potential implications for past microbial ecosystems.

— Lunch Break —

17:00h Visit the Barcelona Supercomputing Center (BSC):

Proud to be a data parasite: extracting knowledge from publicly available metagenomic datasets
The European Bioinformatics Institute, UK
Metagenomics is a rapidly expanding research field and new datasets are being produced at an accelerating pace. For example, the EBI Metagenomics resource now houses over 120,000 publicly available datasets from a wide range of environments. Here, we describe ways in which knowledge can be extracted from this wealth of data, from comparison of datasets across different projects, to combining data from billions of sequences to provide comprehensive overviews of microbial community composition and function. What knowledge can we already extract from the public datasets, what are we missing, and how should this guide future research?

— Gala dinner —

Thursday 12th – Quantitative and Theoretical Ecology

9:00h  Sergio Vallina
Ecological evolution (eco-evo) modelling and comparative genomics: mind the gap
Instituto Español de Oceanografia, Spain
Modelling ecological evolution of species traits is a challenging goal for numerical ecologists. There is currently the view that there is a lot of hidden potential from genomics data to help models in this quest. However, ecological models and genomics data “need and provide” very different kind of information. Metaphorically speaking, they belong to different scientific universes even if they try to answer similar ecological questions. That means that there is large * gap * between the information that ecological models need and the information that genomics data may be able to provide. By definition a model is a crude simplified version of reality, which means that they do not model “explicitly” many of the processes that take place during ecological dynamics. This implies that some of these non-explicitly resolved processes need to be parameterized by making strong assumptions. Others are just left behind as if they would not exist at all, which is a stronger assumption. For example, ecological models do not provide equations explicitly linking genes to functions. The temperature optima of a species is a trait that depends on enzymatic processes being coded in genes being expressed. However, species traits (e.g. temperature optima) are included in the models as a “parameter values” that need to be known in advance. Using eco-evo these parameters (or trait values) can change in time through trait-diffusion, but the model will not solve explicitly the mutations of the organisms’ genomes — it will just try simulate its effect on the communities being modelled. Ideally we would like to obtain information on the model parameter values from genomics data — But how? Can we really do that today? I would argue that this gap between ecological models and genomics data is currently too large (unfortunately), and it is still unknown how we will be able to close it in the near future. Yet, merging eco-evo with genomics data is clearly the way forward in numerical ecology. Put Your Seat Belt On.

11:00h Damien Eveillard
Investigating microbial ecosystems: a computational journey from co-occurrence to metabolic networks
Université de Nantes, France
Ecosystems are today analyzed by emphasizing their genomic composition. However, understanding interactions within communities to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. Such a task must be achieved by dedicated computational approaches inspired by Systems Biology. First, we will present a network analysis of the global ocean to improve understandings of a biological process. Second, we will describe how to integrate heterogeneous omics knowledge to emphasize functional units at the community level. Finally, we will illustrate a quantitative modeling that considers genome-scale knowledge to predict community behaviors.

— Lunch Break —

14:00h Santiago F. Elena 1,2,3
Experimental host-range expansion in a plant RNA virus: an interplay between viral fitness and regulation of host’s transcriptome
1Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, València, Spain
2Instituto de Biología Integrativa y de Sistemas (I2SysBio), CSIC-UV, Paterna, València, Spain
3Santa Fe Institute, Santa Fe, New Mexico, USA

Experimental evolution offers a testing ground for evolutionary hypotheses. The evolution of generalist and specialist pathogen strains, a process that is in the basis of viral emergence, is of particular interest.
We are exploring the extent in which host genetic variability for susceptibility to infection influences the degree of virus local adaptation. Experiments resulted in higher viral fitness on the local host, though some hosts selected for costless generalists. We compared the transcriptomes of plants infected with ancestral or evolved viruses and found that generalists manipulate similar sets of genes across host genotypes while specialists do not so.

15:30h Discussions

Friday 13th – Wrap-up

9:00h Student presentations

— Lunch Break —

14:00h Round table

Carles Pedrós-Alió, National Center for Biotechnology (CSIC), Spain
Marta Estrada, Institut de Ciències del Mar (CSIC), Spain
Iñaki Ruiz-Trillo, Institut de Biologia Evolutiva (UPF-CSIC), Spain