Fuhrman Jed A.

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Fuhrman
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Jed A.
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The ocean sampling day consortium

2015-06-19 , Kopf, Anna , Bicak, Mesude , Kottmann, Renzo , Schnetzer, Julia , Kostadinov, Ivaylo , Lehmann, Katja , Fernandez-Guerra, Antonio , Jeanthon, Christian , Rahav, Eyal , Ullrich, Matthias S. , Wichels, Antje , Gerdts, Gunnar , Polymenakou, Paraskevi , Kotoulas, Georgios , Siam, Rania , Abdallah, Rehab Z. , Sonnenschein, Eva C. , Cariou, Thierry , O’Gara, Fergal , Jackson, Stephen , Orlic, Sandi , Steinke, Michael , Busch, Julia , Duarte, Bernardo , Caçador, Isabel , Canning-Clode, Joao , Bobrova, Oleksandra , Marteinsson, Viggo , Reynisson, Eyjolfur , Loureiro, Clara Magalhaes , Luna, Gian Marco , Quero, Grazia Marina , Loscher, Carolin R. , Kremp, Anke , DeLorenzo, Marie E. , Øvreås, Lise , Tolman, Jennifer , LaRoche, Julie , Penna, Antonella , Frischer, Marc , Davis, Timothy , Katherine, Barker , Meyer, Christopher P. , Ramos, Sandra , Magalhaes, Catarina , Jude-Lemeilleur, Florence , Aguirre-Macedo, Ma Leopoldina , Wang, Shiao , Poulton, Nicole , Jones, Scott , Collin, Rachel , Fuhrman, Jed A. , Conan, Pascal , Alonso, Cecilia , Stambler, Noga , Goodwin, Kelly , Yakimov, Michail M. , Baltar, Federico , Bodrossy, Levente , Van De Kamp, Jodie , Frampton, Dion M. F. , Ostrowski, Martin , Van Ruth, Paul , Malthouse, Paul , Claus, Simon , Deneudt, Klaas , Mortelmans, Jonas , Pitois, Sophie , Wallom, David , Salter, Ian , Costa, Rodrigo , Schroeder, Declan C. , Kandil, Mahrous M. , Amaral, Valentina , Biancalana, Florencia , Santana, Rafael , Pedrotti, Maria Luiza , Yoshida, Takashi , Ogata, Hiroyuki , Ingleton, Timothy , Munnik, Kate , Rodriguez-Ezpeleta, Naiara , Berteaux-Lecellier, Veronique , Wecker, Patricia , Cancio, Ibon , Vaulot, Daniel , Bienhold, Christina , Ghazal, Hassan , Chaouni, Bouchra , Essayeh, Soumya , Ettamimi, Sara , Zaid, El Houcine , Boukhatem, Noureddine , Bouali, Abderrahim , Chahboune, Rajaa , Barrijal, Said , Timinouni, Mohammed , El Otmani, Fatima , Bennani, Mohamed , Mea, Marianna , Todorova, Nadezhda , Karamfilov, Ventzislav , ten Hoopen, Petra , Cochrane, Guy R. , L’Haridon, Stephane , Bizsel, Kemal Can , Vezzi, Alessandro , Lauro, Federico M. , Martin, Patrick , Jensen, Rachelle M. , Hinks, Jamie , Gebbels, Susan , Rosselli, Riccardo , De Pascale, Fabio , Schiavon, Riccardo , dos Santos, Antonina , Villar, Emilie , Pesant, Stephane , Cataletto, Bruno , Malfatti, Francesca , Edirisinghe, Ranjith , Herrera Silveira, Jorge A. , Barbier, Michele , Turk, Valentina , Tinta, Tinkara , Fuller, Wayne J. , Salihoglu, Ilkay , Serakinci, Nedime , Ergoren, Mahmut Cerkez , Bresnan, Eileen , Iriberri, Juan , Fronth Nyhus, Paul Anders , Bente, Edvardsen , Karlsen, Hans Erik , Golyshin, Peter N. , Gasol, Josep M. , Moncheva, Snejana , Dzhembekova, Nina , Johnson, Zackary , Sinigalliano, Christopher D. , Gidley, Maribeth Louise , Zingone, Adriana , Danovaro, Roberto , Tsiamis, Georgios , Clark, Melody S. , Costa, Ana Cristina , El Bour, Monia , Martins, Ana M. , Collins, R. Eric , Ducluzeau, Anne-Lise , Martinez, Jonathan , Costello, Mark J. , Amaral-Zettler, Linda A. , Gilbert, Jack A. , Davies, Neil , Field, Dawn , Glockner, Frank Oliver

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.

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Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys

2015-12-22 , Walters, William , Hyde, Embriette R. , Berg-Lyons, Donna , Ackermann, Gail , Humphrey, Greg , Parada, Alma , Gilbert, Jack A. , Jansson, Janet K. , Caporaso, J. Gregory , Fuhrman, Jed A. , Apprill, Amy , Knight, Rob

Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.

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