Article
Microbiology
Vanessa Joglar, Xose Anton Alvarez-Salgado, Ana Gago-Martinez, Jose M. Leao, Clara Perez-Martinez, Benjamin Pontiller, Daniel Lundin, Jarone Pinhassi, Emilio Fernandez, Eva Teira
Summary: The study found that in the waters off the northwest Iberian Peninsula, the concentration of cobalamin B12 is very low, mainly concentrated in the subsurface Eastern North Atlantic Central Water. B12 concentration is not a predictive factor for phytoplankton biomass or production, while prokaryote production is the best predictor for primary production. Eukaryote community composition is more closely correlated with prokaryote community composition, indicating that biotic interactions play a significant role in regulating microbial communities.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani Garapati, Steven J. Marygold, Vitor Trovisco, Gil Dos Santos, Kathleen Falls, Christopher Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodriguez-Lopez, Marcio L. Acencio, Martin Kuiper, Astrid Laegreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus Chibucos, Michelle Giglio, Suvarna Nadendla, James Munro, Rebecca Jackson, Margaret J. Duesbury, Noemi Del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert Daniel Finn, Alexander Lawson Mitchell, Neil David Rawlings, Lorna Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jurg Bahler, Elizabeth R. Bolton, Jeffery L. De Pons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek A. Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea Auchincloss, Kristian Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria J. Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Sandra Orchard, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos N. Chan, Christian Grove, Raymond Y. N. Lee, Hans-Michael Muller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser
Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan Da Silva, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leyla Garcia Castro, Penelope Garmiri, George Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair Mac-Dougall, Fabio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodriguez Lopez, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea Auchincloss, Kristian Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard de Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang
Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Karin Holmfeldt, Emelie Nilsson, Domenico Simone, Margarita Lopez-Fernandez, Xiaofen Wu, Ino de Bruijn, Daniel Lundin, Anders F. Andersson, Stefan Bertilsson, Mark Dopson
Summary: Investigating the deep terrestrial virosphere reveals unique viral communities associated with Firmicutes and Patescibacteria, impacting ecological dynamics through viral predation and nutrient recycling. The presence of 'kill-the-winner' oscillations and 'boom and burst' cycles suggest complex interactions within deep groundwater ecosystems.
COMMUNICATIONS BIOLOGY
(2021)
Article
Microbiology
Matthias Hoetzinger, Emelie Nilsson, Rahaf Arabi, Christofer M. G. Osbeck, Benjamin Pontiller, Geoffrey Hutinet, Oliver W. Bayfield, Sachia Traving, Veljo Kisand, Daniel Lundin, Jarone Pinhassi, Mathias Middelboe, Karin Holmfeldt
Summary: This study isolated novel phage genera and species during a Baltic Sea mesocosm experiment, some of which were found to contain gene sets potentially coding for the synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Additionally, phages isolated from a Rheinheimera strain showed high genetic similarity to previously isolated genotypes, pointing to genomic consistency in this population. The investigated phages were mainly detected after a phytoplankton bloom peak in the mesocosm experiment, indicating a potential influence on the succession of heterotrophic bacteria associated with phytoplankton blooms in the Baltic Proper during summer months.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Limnology
Eric Capo, Elias Broman, Stefano Bonaglia, Andrea G. Bravo, Stefan Bertilsson, Anne L. Soerensen, Jarone Pinhassi, Daniel Lundin, Moritz Buck, Per O. J. Hall, Francisco J. A. Nascimento, Erik Bjorn
Summary: The expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in sediments, promoting the expansion of Hg methylators whose metabolism and biology have not yet been characterized.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Tobias Fietze, Piotr Wilk, Florian Kabinger, Saber Anoosheh, Anders Hofer, Daniel Lundin, Christian G. Feiler, Manfred S. Weiss, Christoph Loderer
Summary: Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides and their activity depends on the formation of catalytic dimers. This study discovered a novel domain in class II RNRs that is responsible for the formation of catalytic dimers. This domain, called the HUG domain, acts as an interlock to maintain the integrity and functionality of the dimer even at low enzyme and/or effector concentrations.
Article
Ecology
Benjamin Pontiller, Sandra Martinez-Garcia, Vanessa Joglar, Dennis Amnebrink, Clara Perez-Martinez, Jose M. Gonzalez, Daniel Lundin, Emilio Fernandez, Eva Teira, Jarone Pinhassi
Summary: Coastal upwelling zones are important areas of oceanic productivity. Bacteria play a vital role in the remineralization of dissolved organic matter (DOM) produced by phytoplankton, but the molecular processes involved in the regulation of phytoplankton-derived DOM turnover by bacterial taxa are not well understood. This study used metatranscriptome analysis to compare the gene expression of bacterioplankton in the Northwest Iberian upwelling system. The results showed that different bacterial taxa had specific transcriptional responses during different phases of phytoplankton bloom development, decay, and senescence. The study also highlighted the importance of gene systems involved in the degradation and uptake of carbohydrates and nitrogen-rich compounds in shaping the fate of organic matter in these upwelling-driven ecosystems.
Article
Environmental Sciences
Maria Vila-Costa, Daniel Lundin, Emilio O. Casamayor, Sandra N. Meijer, Pilar Fernandez, Jordi Dachs
Summary: This study demonstrates the significance of microbial degradation in the environmental fate of PAHs in high altitude deep lakes, as shown by the presence of PAH degrading genes and the accurate prediction of PAH concentrations in sediment when degradation is included in the model.
ENVIRONMENTAL POLLUTION
(2022)
Article
Biochemical Research Methods
Maria Prager, Daniel Lundin, Fredrik Ronquist, Anders F. Andersson
Summary: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
BMC BIOINFORMATICS
(2023)
Article
Microbiology
Anabella Aguilera, Javier Alegria Zufia, Laura Bas Conn, Leandra Gurlit, Sylwia Sliwinska-Wilczewska, Gracjana Budzalek, Daniel Lundin, Jarone Pinhassi, Catherine Legrand, Hanna Farnelid
Summary: Cluster 5 picocyanobacteria play a significant role in primary productivity in aquatic ecosystems. This study characterized 17 novel estuarine picocyanobacterial strains and found that they exhibit different growth adaptability and tolerance under various environmental conditions. This new knowledge is important for understanding and evaluating productivity in current and future ecosystems.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Hanna M. Bensch, Daniel Lundin, Conny Tolf, Jonas Waldenstrom, Markus Zottl
Summary: In social species, gut microbiome similarity among group members is mainly explained by shared environmental effects rather than host relatedness. This was shown through a cross-foster experiment conducted on Damaraland mole-rats under controlled laboratory conditions, using 16S amplicon sequencing to analyze gut microbiome composition. These findings, in conjunction with studies in wild animal populations, suggest that environmental factors have a stronger influence on gut microbiome composition similarity than host genetics among conspecifics.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Hugo Lebrette, Vivek Srinivas, Juliane John, Oskar Aurelius, Rohit Kumar, Daniel Lundin, Aaron S. Brewster, Asmit Bhowmick, Abhishek Sirohiwal, In-Sik Kim, Sheraz Gul, Cindy Pham, Kyle D. Sutherlin, Philipp Simon, Agata Butryn, Pierre Aller, Allen M. Orville, Franklin D. Fuller, Roberto Alonso-Mori, Alexander Batyuk, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Ville R. I. Kaila, Britt-Marie Sjoberg, Jan Kern, Katarina Roos, Martin Hogbom
Summary: This study presents a high-resolution room temperature structure of the class Ie R2 protein radical in RNR, revealing conformational reorganization and restructuring of the hydrogen bond network. These findings help explain radical handling and transfer mechanisms in RNR and have implications for radical transfer in proteins more generally.
Article
Microbiology
Hanna M. M. Bensch, Conny Tolf, Jonas Waldenstrom, Daniel Lundin, Markus Zottl
Summary: In mammals, the gut microbiota plays a vital role in their health. Recent research has shown that captive animal populations often have different gut microbiota diversity and composition compared to wild populations. This study compares the gut bacterial microbiota of wild and captive Damaraland mole-rats and reveals significant changes in the gut microbiota composition between the two groups.
Article
Environmental Sciences
Eva Hogfors-Ronnholm, Daniel Lundin, Diego Brambilla, Stephan Christel, Margarita Lopez-Fernandez, Tom Lillhonga, Sten Engblom, Peter Osterholm, Mark Dopson
Summary: This study revealed distinct microbial communities and activities in various stages of acid sulfate soils, with Gallionella and Sulfuricella dominating the community during the conversion process.
COMMUNICATIONS EARTH & ENVIRONMENT
(2022)
