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3. Are bacteria claustrophobic? The problem of micrometric spatial confinement for the culture of micro-organisms

Author

Molinaro, Céline, Da Cunha, Violette, Gorlas, Aurore, Iv, François, Gallais, Laurent, Catchpole, Ryan, Forterre, Patrick, and Baffou, Guillaume

Subjects
Physics - Biological Physics, Condensed Matter - Soft Condensed Matter
Abstract

Culturing cells confined in microscale geometries has been reported in many studies this last decade, in particular following the development of microfluidic-based applications and lab-on-a-chip devices. Such studies usually examine growth of Escherichia coli. In this article, we show that E. coli may be a poor model and that spatial confinement can severely prevent the growth of many micro-organisms. By studying different bacteria and confinement geometries, we determine that the growth inhibition observed for some bacteria results from fast dioxygen depletion, inherent to spatial confinement, and not to any depletion of nutriments. This article unravels the physical origin of confinement problems in cell culture, highlighting the importance of oxygen depletion, and paves the way for the effective culture of bacteria in confined geometries by demonstrating enhanced cell growth in confined geometries in the proximity of air bubbles., Comment: 6 pages, 4 figures

Published
2020

7. Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Author

Mizuno, Carolina M, Guyomar, Charlotte, Roux, Simon, Lavigne, Régis, Rodriguez-Valera, Francisco, Sullivan, Matthew B, Gillet, Reynald, Forterre, Patrick, and Krupovic, Mart

Subjects
Vaccine Related, Prevention, Biodefense, Genetics, Infectious Diseases, 2.2 Factors relating to physical environment, Infection, MD Multidisciplinary
Abstract

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.

Published
2019

16. Halovirus genomes are homogeneous across continents

Author

Roux, Simon, Enault, Francois, Ravet, Viviane, Colombet, Jonathan, Bettarel, Yvan, Auguet, Jean-Christophe, Bouvier, Thierry, Lucas-Staat, Soizick, Vellet, Agnès, Prangishvili, David, Forterre, Patrick, Debroas, Didier, and Sime-Ngando, Telesphore

Subjects
Biotechnology, Genetics, Infection, Australia, Caudovirales, Chromosome Mapping, Genetic Variation, Genome, Viral, Metagenomics, Ponds, Salinity, Senegal, Spain, Evolutionary Biology, Microbiology
Abstract

Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.

Published
2016

17. Analysis of metagenomic data reveals common features of halophilic viral communities across continents.

Author

Roux, Simon, Enault, Francois, Ravet, Viviane, Colombet, Jonathan, Bettarel, Yvan, Auguet, Jean-Christophe, Bouvier, Thierry, Lucas-Staat, Soizick, Vellet, Agnès, Prangishvili, David, Forterre, Patrick, Debroas, Didier, and Sime-Ngando, Telesphore

Subjects
Caudovirales, Chromosome Mapping, Genome, Viral, Senegal, Australia, Spain, Salinity, Genetic Variation, Metagenomics, Ponds, Genome, Viral, Microbiology, Evolutionary Biology
Abstract

Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.

Published
2016

21. The Tree of Life

Author

Gaia, Morgan, Da Cunha, Violette, Forterre, Patrick, and Rampelotto, Pabulo H., Series Editor

Published
2018
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26. Une histoire subjective des recherches sur les archées en France

Author

Forterre, Patrick

Subjects
LUCA, ADN, Archee, DNA topoisomerases, France, institut pasteur, virus, microbiologie, hyperthermophiles, reverse gyrase, Archaea
Abstract

Les archées représentent l’un des trois domaines du vivant, au côté des bactéries et des eucaryotes. Très tôt après leur découverte, en 1977, l’auteur a entrepris l’étude de ces microorganismes. Il décrit la découverte dans son équipe à Orsay de nouvelles familles d’enzymes impliquées dans la modification des super-hélices d’ADN. L’une de ces enzymes, la reverse gyrase, est essentielle à la vie à très haute température, une autre, l’ADN topoisomérase VI « chez les archées », a permis d’identifier une protéine clef impliquée dans la diversification de notre matériel génétique. Archaea represent one of the three domains of life, alongside bacteria and eukaryotes. Very soon after their discovery, in 1977, the author undertook the study of these microorganisms. He describes the discovery in his team at Orsay of new families of enzymes involved in the modification of DNA superhelices. One of these enzymes, reverse gyrase, is essential for life at very high temperatures, another, DNA topoisomerase VI "in the archaea", has identified a key protein involved in the diversification of our genetic material

Published
2023

27. Glossaire

Author

Rossignol, Jean-Michel, Abergel, Chantal, Capy, Pierre, Claverie, Jean-Michel, Vienne, Dominique de, Ehrhart, Jean-Claude, Forterre, Patrick, Feunteun, Jean, and Nicolas, Jean-François

Subjects
biologie, biology, Glossaire, Glossary
Abstract

A Activation de la transcription Induction de la transcription* d’un gène* (cf. Répression). La régulation de la transcription peut avoir lieu : en cis. C’est un effet positionnel dû à l’insertion à proximité du gène d’une séquence (cf. Cis Regulatory Element) capable d’augmenter sa transcription (promoteur-activateur). en trans. Dans ce cas c’est un facteur protéique qui intervient directement sur la machinerie de transcription du gène (transactivateur). Activation d’un proto-oncogène en on...

Published
2023

33. Glossary. Glossary of Biology Words

Author

Rossignol, Jean-Michel, primary, Abergel, Chantal, additional, Capy, Pierre, additional, Claverie, Jean-Michel, additional, Vienne, Dominique de, additional, Ehrhart, Jean-Claude, additional, Forterre, Patrick, additional, Feunteun, Jean, additional, and Nicolas, Jean-François, additional

Published
2022
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39. The emergence, spread and vanishing of a French SARS‐CoV‐2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule

Author

Colson, Philippe, primary, Gautret, Philippe, additional, Delerce, Jeremy, additional, Chaudet, Hervé, additional, Pontarotti, Pierre, additional, Forterre, Patrick, additional, Tola, Raphael, additional, Bedotto, Marielle, additional, Delorme, Léa, additional, Bader, Wahiba, additional, Levasseur, Anthony, additional, Lagier, Jean‐Christophe, additional, Million, Matthieu, additional, Yahi, Nouara, additional, Fantini, Jacques, additional, La Scola, Bernard, additional, Fournier, Pierre‐Edouard, additional, and Raoult, Didier, additional

Published
2022
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40. Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island

Author

Antranikian, Garabed, Suleiman, Marcel, Schäfers, Christian, Adams, Michael W. W., Bartolucci, Simonetta, Blamey, Jenny M., Birkeland, Nils-Kåre, Bonch-Osmolovskaya, Elizaveta, da Costa, Milton S., Cowan, Don, Danson, Michael, Forterre, Patrick, Kelly, Robert, Ishino, Yoshizumi, Littlechild, Jennifer, Moracci, Marco, Noll, Kenneth, Oshima, Tairo, Robb, Frank, Rossi, Mosè, Santos, Helena, Schönheit, Peter, Sterner, Reinhard, Thauer, Rudolf, Thomm, Michael, Wiegel, Jürgen, and Stetter, Karl Otto

Published
2017
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49. Ancient Fossil Record and Early Evolution (ca. 3.8 to 0.5 Ga)

Author

López-García, Purificación, Moreira, David, Douzery, Emmanuel, Forterre, Patrick, Van Zuilen, Mark, Claeys, Philippe, Prieur, Daniel, Gargaud, Muriel, editor, Claeys, Philippe, editor, López-García, Purificación, editor, Martin, Hervé, editor, Montmerle, Thierry, editor, Pascal, Robert, editor, and Reisse, Jacques, editor

Published
2006
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50. Prebiotic Chemistry — Biochemistry — Emergence of Life (4.4-2 Ga)

Author

Pascal, Robert, Boiteau, Laurent, Forterre, Patrick, Gargaud, Muriel, Lazcano, Antonio, López-García, Purificación, Moreira, David, Maurel, Marie-Christine, Peretó, Juli, Prieur, Daniel, Reisse, Jacques, Gargaud, Muriel, editor, Claeys, Philippe, editor, López-García, Purificación, editor, Martin, Hervé, editor, Montmerle, Thierry, editor, Pascal, Robert, editor, and Reisse, Jacques, editor

Published
2006
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