Institut Méditerranéen d’Océanologie

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lundi 1er février 2016


Emmanuel Boss (School of Marine Sciences, University of Maine) animera lundi 1er février 2016, à 13h, dans l’amphithéâtre Oceanomed un séminaire intitulé : "Ecological and physical processes underlying phytoplankton blooms ".

Abstract
Bottom up constraints (light, nutrients) have been used to explain phytoplankton dynamics for years, largely due to the fact that data on top-down constraints are not available on the same scales. In this talk I revisit the bottom-up explanations for some vernal blooms and show evidence of them not being consistent with year-around in-situ data collected with profiling floats and observations from iron fertilized blooms. I will then address where in the theoretical ecological framework lies the problem and further use simple models to study the dynamics of phytoplankton in the upper ocean. I will conclude with a discussion of the limitation of current modeling approaches and data availability for understanding phytoplankton dynamics.

Jeudi 11 février 2016

Pascal SIMONET animera le jeudi 11 février 2016, à 13h, dans l’amphithéâtre Oceanomed un séminaire intitulé : "Soil metagenomics. Potential and pitfalls ".

Abstract
Bacteria cultivability imitation can be circumvented by modern alternative approaches including metagenomics or single cell genomics. Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes. Recommended reading : Jacquiod S, Demanèche S, Delmont TO, Ausec L, Dunon V, Franqueville L, Mandic-Mulec I, Springael D, Vogel TM and Simonet P. 2014. Genetic screening of a fosmid metagenomic soil library using radio-labeled oligonucleotide probes. J. Biotechnol. 190 : 18-29. doi : 10.1016/j.jbiotec.2014.03.036. Nesme J, Cécillon S, Delmont TO, Monier J-M, Vogel T.M and Simonet P. 2014. Large scale metagenomic-based study of antibiotic resistance in the environment. Current Biol. 24 : 1096-1100.

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