Gasol Josep M.

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Gasol
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Josep M.
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Towards a better understanding of microbial carbon flux in the sea

2008-09-18 , Gasol, Josep M. , Pinhassi, Jarone , Alonso-Saez, Laura , Ducklow, Hugh W. , Herndl, Gerhard J. , Koblizek, Michal , Labrenz, Matthias , Luo, Ya-Wei , Moran, Xose Anxelu G. , Reinthaler, Thomas , Simon, Meinhard

We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.

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Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA

2010-12-30 , Pommier, Thomas , Neal, Phillip R. , Gasol, Josep M. , Coll, Montserrat , Acinas, Silvia G. , Pedros-Alio, Carlos

Due to analytical limitations, patterns of richness and evenness of microbes are scarce in the current literature. The newest and powerful pyrosequencing technology may solve this issue by sampling thousands of sequences from the same community. We conducted a study of diversity along a horizontal transect (ca. 120 km) and a depth profile (surface to bottom at ca. 2000 m) in the northwestern Mediterranean Sea, using this technology on the V6 region of the 16S rDNA gene and analyzed patterns of richness and evenness of marine free-living bacterial communities. A total of 201605 tag sequences were obtained from the 10 samples considered and clustered according to their similarity in 1200 operational taxonomic units (OTUs) per sample on average. We found a parallel decrease in richness and evenness from coast to offshore and from bottom to surface. We also observed a predominance of a few OTUs in each sample, while ca. 50% of all OTUs were found as singletons, which indicated that the community structures differed dramatically between sites despite the relative proximity and the physical connectivity between the samples. Despite these differences, using the 300 most abundant OTUs only was sufficient to obtain the same clustering of samples as with the complete dataset. Finally, both richness and evenness were negatively correlated with bacterial biomass and heterotrophic production.

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Coherent patterns in bacterial growth, growth efficiency, and leucine metabolism along a northeastern Pacific inshore-offshore transect

2011-01 , del Giorgio, Paul A. , Condon, Robert H. , Bouvier, Thierry , Longnecker, Krista , Bouvier, Corinne , Sherr, Evelyn B. , Gasol, Josep M.

We investigated the patterns in bacterial growth, production, respiration, growth efficiency (BGE), and bacterial leucine respiration and C-to-leucine yield (i.e., conversion factor [CF]) along a transect off the coast of Oregon. Plankton respiration along the transect averaged 1.15 ± 0.16 mg C L-1 h-1, peaking in the coastal upwelling region. The respiration in the filtered fraction, which was dominated by bacterial biomass, accounted for 79% of the total respiration. The different approaches that we used converged to an average BGE of 13% ± 1%, with peaks of over 20% in the more productive coastal areas and values declining to below 5% toward the oligotrophic gyre waters. There was overall coherence between the various aspects of bacterial C metabolism: communities with low BGE also tended to have low growth rates and high leucine-to-thymidine incorporation ratios. The patterns in BGE were mirrored at the single compound level, and in the most oligotrophic sites, bacteria tended to quickly respire a large fraction (20-75%) of the leucine that was taken up and had the lowest C-to-leucine yield, suggesting that the patterns in bulk BGE and growth also apply to individual substrates. Bacterial growth was a function of both C consumption and BGE; these two aspects of bacterial C metabolism do not necessarily covary, and they are regulated differently. The patterns in C consumption, growth, BGE, and leucine metabolism all reflect the basic physiological response of bacteria to energy limitation due to high maintenance costs associated with life in oligotrophy.

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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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Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency

2015-11-13 , Sebastian, Marta , Smith, Alastair , Gonzalez, Jose M. , Fredricks, Helen F. , Van Mooy, Benjamin A. S. , Koblizek, Michal , Brandsma, Joost , Koster, Grielof , Mestre, Mireia , Mostajir, Behzad , Pitta, Paraskevi , Postle, Anthony D. , Sanchez, Pablo , Gasol, Josep M. , Scanlan, David J. , Chen, Yin

Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.

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Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

2020-03-12 , Chen, Michael L. , Becraft, Eric D. , Pachiadaki, Maria G. , Brown, Julia M. , Jarett, Jessica K. , Gasol, Josep M. , Ravin, Nikolai V. , Moser, Duane P. , Nunoura, Takuro , Herndl, Gerhard J. , Woyke, Tanja , Stepanauskas, Ramunas

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

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