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Publications

2024

  • Lee K.S., Landry Z., Athar A., Alcolombri U., Pramoj Na Ayutthaya P., Berry D., de Bettignies P., Cheng J.X., Csucs G., Cui L., Deckert V., Dieing T., Dionne J., Doskocil O., D’Souza G., García-Timermans C., Gierlinger N., Goda K., Hatzenpichler R., Henshaw R.J., Huang W.E., Iermak I, Ivleva N.P., Kneipp J., Kubryk P., Küsel K., Lee T.K., Lee S.S., Ma B., Martínez-Pérez C., Matousek P., Meckenstock R.U., Min W., Mojzeš P., Müller O., Kumar W., Nielsen P.H., Notingher I, Palatinszky M., Pereira F.C., Pezzotti G., Pilat Z., Plesinger F., Popp J., Probst A.J., Riva A., Saleh A.A.E., Samek O., Sapers H.M., Schubert O.T., Stubbusch A.K.M., Tadesse L.F., Taylor G.T., Wagner M., Wang J., Yin H., Yue Y., Zenobi R., Zini J., Sarkans U. and Stocker R.  MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data, Nature Microbiology. doi:10.1038/s41564-024-01656-3.(2024)

2023

  • Lars Behrendt*, Uria Alcolombri*, Jonathan E Hunter*, Steven Smriga, Tracy Mincer, Daniel P Lowenstein, Yutaka Yawata, Francois Peaudecerf, Vicente Fernandez, Helen F Fredricks, Henrik Almblad, Joe J Harrison, Roman Stocker, Benjamin AS Van Mooy. Microbial metabolic specificity controls pelagic lipid export efficiency. bioRxiv. 2023.12. 08.570822 (2023).

  • Estelle E Clerc, Jean-Baptiste Raina, Johannes M Keegstra, Zachary Landry, Sammy Pontrelli, Uria Alcolombri, Bennett S Lambert, Valerio Anelli, Flora Vincent, Marta Masdeu-Navarro, Andreas Sichert, Frédéric De Schaetzen, Uwe Sauer, Rafel Simó, Jan-Hendrik Hehemann, Assaf Vardi, Justin R Seymour, Roman Stocker. Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nature Communications. 14, 8080 (2023).

  • Nissan Alon, Alcolombri Uria, Peleg Nadav, Galili Nir, Jimenez-Martinez Joaquin, Molnar Peter, Holzner Markus. Global warming accelerates soil heterotrophic respiration. Nature Communications. 14, 1, 3452 (2023).

  • Słomka Jonasz, Alcolombri Uria, Carrara Francesco, Foffi Riccardo, Peaudecerf François J, Zbinden Matti, Stocker Roman. Encounter rates prime interactions between microorganisms. Interface Focus. 13, 2, 20220059 (2023).

  • Clifton Ben E, Alcolombri Uria, Jackson Colin J, Laurino Paola. Ultrahigh-affinity transport proteins from ubiquitous marine bacteria reveal mechanisms and global patterns of nutrient uptake. bioRxiv. (2023).

2022

  • Norris Noele, Alcolombri Uria, Keegstra Johannes M, Yawata Yutaka, Menolascina Filippo, Frazzoli Emilio, Levine Naomi M, Fernandez Vicente I, Stocker Roman. Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake. Biophysical Journal. 121, 11, 2046-2059 (2022).

  • Nguyen Trang TH, Zakem Emily J, Ebrahimi Ali, Schwartzman Julia, Caglar Tolga, Amarnath Kapil, Alcolombri Uria, Peaudecerf François J, Hwa Terence, Stocker Roman. Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. Nature Communications. 13, 1, 1657 (2022).

  • Alcolombri Uria, Pioli Roberto, Stocker Roman, Berry David. Single-cell stable isotope probing in microbial ecology. ISME Communications. 2, 1, 55 (2022).

  • de Schaetzen Frédéric, Fan Mingzhen, Alcolombri Uria, Peaudecerf François J, Drissner David, Loessner Martin J, Stocker Roman, Schuppler Markus. Random encounters and amoeba locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii. Proceedings of the National Academy of Sciences. 119, 32, e2122659119 (2022).

2021

  • Lee Kang Soo, Pereira Fátima C, Palatinszky Márton, Behrendt Lars, Alcolombri Uria, Berry David, Wagner Michael, Stocker Roman. Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions. Nature Protocols. 16, 2, 634-676 (2021).

  • Graff van Creveld Shiri, Ben-Dor Shifra, Mizrachi Avia, Alcolombri Uria, Hopes Amanda, Mock Thomas, Rosenwasser Shilo, Vardi Assaf, . Biochemical characterization of a novel redox-regulated metacaspase in a marine diatom. Frontiers in Microbiology. 2578 (2021).

  • Alcolombri Uria, Peaudecerf François J, Fernandez Vicente I, Behrendt Lars, Lee Kang Soo, Stocker Roman. Sinking enhances the degradation of organic particles by marine bacteria. Nature Geoscience. 14, 10, 775-780 (2021).

  • Shemi Adva, Alcolombri Uria, Schatz Daniella, Farstey Viviana, Vincent Flora, Rotkopf Ron, Ben-Dor Shifra, Frada Miguel J, Tawfik Dan S, Vardi Assaf. Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean. Nature microbiology. 6, 11, 1357-1366 (2021).

  • Hunter Jonathan E, Fredricks Helen F, Behrendt Lars, Alcolombri Uria, Bent Shavonna M, Stocker Roman, Van Mooy Benjamin AS. Using high-sensitivity lipidomics to assess microscale heterogeneity in oceanic sinking particles and single phytoplankton cells. Environmental Science & Technology. 55, 22, 15456-15465 (2021).

2020

  • Słomka Jonasz, Alcolombri Uria, Secchi Eleonora, Stocker Roman, Fernandez Vicente I. Encounter rates between bacteria and small sinking particles. New Journal of Physics. 22, 4, 43016 (2020).

  • Nissan Alon, Alcolombri Uria, de Schaetzen Frédéric, Berkowitz Brian, Jimenez-Martinez Joaquin. Reactive transport with fluid–solid interactions in dual-porosity media. ACS Es&T Water. 1, 2, 259-268 (2020).

2018

  • Lei Lei, Cherukuri Kesava Phaneendra, Alcolombri Uria, Meltzer Diana, Tawfik Dan S. The dimethylsulfoniopropionate (DMSP) lyase and lyase-like cupin family consists of bona fide DMSP lyases as well as other enzymes with unknown function. Biochemistry. 57, 24, 3364-3377 (2018).

  • Lei Lei, Alcolombri Uria, Tawfik Dan S. Biochemical profiling of DMSP Lyases. Methods in enzymology. 605, 269-289 (2018).

  • van Creveld Graff Shiri, Ben-Dor Shifra, Mizrachi Avia, Alcolombri Uria, Hopes Amanda, Mock Thomas, Rosenwasser Shilo, Vardi Assaf. A redox-regulated type III metacaspase controls cell death in a marine diatom. bioRxiv. 444109 (2018).

2017

  • Alcolombri Uria, Lei Lei, Meltzer Diana, Vardi Assaf, Tawfik Dan S. Assigning the algal source of dimethylsulfide using a selective lyase inhibitor. ACS chemical biology. 12, 1, 41-46 (2017).

  • Lei Lei, Alcolombri Uria, Tawfik Dan S. DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function. bioRxiv. 161257 (2017).

  • Lei Lei, Cherukuri Kesava Phaneendra, Meltzer Diana, Alcolombri Uria, Tawfik, Dan S. Native or promiscuous? Analyzing putative dimethylsulfoniopropionate lyases using a substrate proofing approach. bioRxiv. 168930 (2017).

2015

  • Alcolombri Uria, Ben-Dor Shifra, Feldmesser Ester, Levin Yishai, Tawfik Dan S, Vardi Assaf. Identification of the algal dimethyl sulfide–releasing enzyme: A missing link in the marine sulfur cycle. Science. 348, 6242, 1466-1469 (2015).

2014

  • Alcolombri Uria, Elias Mikael, Vardi Assaf, Tawfik Dan S. Ambiguous evidence for assigning DddQ as a dimethylsulfoniopropionate lyase and oceanic dimethylsulfide producer. Proceedings of the National Academy of Sciences. 111, 20, E2078-E2079 (2014).

  • Alcolombri Uria, Laurino Paola, Lara-Astiaso Pedro, Vardi Assaf, Tawfik Dan S. DddD is a CoA-transferase/lyase producing dimethyl sulfide in the marine environment. Biochemistry. 53, 34, 5473-5475 (2014).

2011

  • Alcolombri Uria, Elias Mikael, Tawfik Dan S. Directed evolution of sulfotransferases and paraoxonases by ancestral libraries. Journal of molecular biology. 411, 4, 837-853 (2011).

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