Browsing by Author "Magalhães, Catarina"
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- Exploration of the types of rarity in the Arctic Ocean from the perspective of multiple methodologiesPublication . Pascoal, Francisco; Costa, Rodrigo; Assmy, Philipp; Duarte, Pedro; Magalhães, CatarinaThe Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.
- The link between the ecology of the prokaryotic rare biosphere and its biotechnological potentialPublication . Pascoal, Francisco; Magalhães, Catarina; Costa, RodrigoCurrent research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.
- The ocean sampling day consortiumPublication . Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Jones, Scott; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Caçador, Isabel; ten Hoopen, Petra; Canning-Clode, João; Aguirre-Macedo, Ma L.; Bobrova, Oleksandra; Vezzi, Alessandro; Marteinsson, Viggo; Collin, Rachel; Reynisson, Eyjolfur; Loureiro, Clara M.; Luna, Gian M.; Quero, Grazia M.; Löscher, Carolin R.; Kremp, Anke; Amaral, Valentina; DeLorenzo, Marie E.; Yoshida, Takashi; Øvreås, Lise; Wang, Shiao; Fuhrman, Jed A.; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ogata, Hiroyuki; Conan, Pascal; Todorova, Nadezhda; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Nyhus, Paul A. F.; Yakimov, Michael M.; Santana, Rafael; Baltar, Federico; Bodrossy, Levente; Ingleton, Tim; Van De Kamp, Jodie; Frampton, Dion M.; Ostrowski, Martin; Van Ruth, Paul; Karamfilov, Ventzislav; Malthouse, Paul; Bizsel, Kemal C.; Claus, Simon; Deneudt, Klaas; Pedrotti, Maria L.; Munnik, Kate; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Rodriguez-Ezpeleta, Naiara; Kotoulas, Georgios; Berteaux-Lecellier, Veronique; Cochrane, Guy; Wecker, Patricia; Cariou, Thierry; Cancio, I.; Lauro, Federico M.; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Iriberri, Juan; Zaid, El H.; Golyshin, Peter N.; Boukhatem, Noureddine; L’Haridon, Stephane; Martin, Patrick; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Gasol, Josep M.; Jensen, Rachelle M.; Gerdts, Gunnar; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; Jude-Lemeilleur, Florence; De Pascale, Fabio; Bente, Edvardsen; Schiavon, Riccardo; dos Santos, Antonina; Moncheva, Snejana; Villar, Emilie; Pesant, Stéphane; Cataletto, Bruno; Malfatti, Francesca; Polymenakou, Paraskevi; Edirisinghe, Ranjith; Sonnenschein, Eva C.; Silveira, Jorge A. H.; Barbier, Michele; Karlsen, Hans E.; Dzhembekova, Nina; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut C.; Bresnan, Eileen; Johnson, Zackary; Ramos, Sandra; Sinigalliano, Christopher D.; Siam, Rania; Gidley, Maribeth L.; Biancalana, Florencia; Zingone, Adriana; O’Gara, Fergal; Danovaro, Roberto; Tsiamis, George; Clark, M. S.; Costa, Ana C.; El Bour, Monia; Martins, Ana M.; Magalhães, Catarina; Collins, R. E.; Poulton, Nicole; Ducluzeau, Anne-Lise; Abdallah, Rehab Z.; Jackson, Stephen; Martinez, Jonathan; Costello, Mark J.; Amaral-Zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Glöckner, Frank O.Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.