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6 results on '"Jean Francois Humbert"'

1. Diversity, spatial distribution and activity of fungi in freshwater ecosystems

Author

Cécile Lepère, Isabelle Domaizon, Jean-Francois Humbert, Ludwig Jardillier, Mylène Hugoni, and Didier Debroas

Subjects
Fungi, Freshwaters, Meta-analysis, Diversity, Medicine, Biology (General), QH301-705.5
Abstract

High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.

Published
2019
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2. Bacterial communities associated with four cyanobacterial genera display structural and functional differences: Evidence from an experimental approach

Author

Lin Zhu, Anouk Zancarini, Imen Louati, Silvia de Cesare, Charlotte Duval, Kevin Tambosco, Cecile Bernard, Didier DEBROAS, Lirong Song, Julie Leloup, and Jean-Francois Humbert

Subjects
Cyanobacteria, pyrosequencing, Bacterial communities, Cultures, Natural samples, Functional and structural diversity, Microbiology, QR1-502
Abstract

To overcome the limitations associated with studying the interactions between bacterial communities (BCs) and cyanobacteria in natural environments, we compared the structural and functional diversities of the BCs associated with fifteen non-axenic cyanobacterial strains in culture and two natural BCs sampled during cyanobacterial blooms. No significant differences in richness and diversity were found between the natural and cultivated BCs, although some of the cyanobacterial strains had been isolated 11 years earlier. Moreover, these BCs shared some similar characteristics, such as a very low abundance of Actinobacteria, but they display significant differences at the OTU level. Overall, our findings suggest that BCs associated with cyanobacteria in culture are good models to better understand the interactions between heterotrophic bacteria and cyanobacteria. Additionally, BCs associated with heterocystous cyanobacterial strains cultivated in Z8X culture medium without nitrate (Aphanizomenon-Dolichospermum) demonstrated significant differences compared to BCs associated with non-heterocystous strains cultivated in Z8 culture medium (Planktothrix-Microcystis) in terms of their composition and their ability to utilize different carbon sources, suggesting the potential influence of cyanobacterial metabolism and/or culture media on associated BCs. Finally, half of the dominant operational taxonomic units (OTUs) in these BCs were specifically associated with cyanobacteria or other phytoplankton, whereas the remaining OTUs were generally associated with ecosystems containing high Organic Matter (OM) content, such as sludge or intestines.

Published
2016
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3. New Biomonitoring Approaches based on Next Generation Sequencing : a Test for Freshwater Diatom Communities

Author

Lenaïg Kermarrec, Frédéric Rimet, Alain Franc, Philippe Chaumeil, Jean Francois Humbert, Agnès Bouchez, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Ghent University [Belgium] (UGENT). National Botanic Garden of Belgium, Ghent, BEL., École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
comparaison de séquences, diatomées, eau douce, évaluation de la qualité, qualité environnementale, [SDV]Life Sciences [q-bio], outil moléculaire, [SDE]Environmental Sciences, marquage génétique, identification moléculaire, ComputingMilieux_MISCELLANEOUS, rivière
Abstract

International audience

Published
2012

4. Assessment of the impact of tebuconazol (fungicide) on lake and stream bacterial communities using a 16S rRNA pyrosequencing method

Author

Noemie Pascault, Joan Artigas, Simon Roux, Remy Tadonleke Dzatchou, Alexandra ter Halle, Gilles Mailhot, Stéphane Pesce, Jean Francois Humbert, Didier Debroas, Agnès Bouchez, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Photochimie moléculaire et macromoléculaire (PMM), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Labo/service de l'auteur, Ville service., Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut de Chimie du CNRS (INC), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
lac Léman, freshwater ecosystems, [SDV]Life Sciences [q-bio], TBZ, ARN 16S, planktonic bacterial communities, communauté bactérienne, lac d'aiguebelette, pyroséquençage, tebuconazol, benthic bacterial communities, [SDE]Environmental Sciences, pollution, perialpine lakes, pesticide
Abstract

International audience; The pollution of lakes and rivers by the agricultural use of pesticides is a growing problem worldwide. As these substances have complex effects on ecosystems, we need to improve our understanding of their fate and their impact on biological communities. With this in mind, we carried out experimental study of the responses of planktonic bacterial communities from lakes and benthic bacterial communities from streams to the fungicide tebuconazol, and of its degradation by these different communities. For each type of ecosystem, communities were collected from pristine environments (Lake Aiguebelette and the upstream segment of the river Morcille, France) and pre-exposed environments (Lake Léman and the downstream segment of the river Morcille, France in which tebuconazol was found). The experiments were carried out in 20L microcosms in which communities from each of the four environments were either not Exposed (control), or exposed to a low (2μg/L) or high (20μg/L) concentration of the fungicide, in order to simulate the contamination levels encountered in aquatic ecosystems. Results obtained after three weeks of incubation showed that 60 to 70% of the initial concentration of tebuconazol had been degraded in the stream microcosms, whereas only minor degradation had occurred in the lake microcosms (15-20%). The fungicide had no significant impact on benthic bacterial abundance, although the proportion of dead bacteria increased. The changes observed in planktonic bacterial abundance and dead bacteria were transient and depended on previous exposure. To complete these findings, the bacterial diversity is characterizing by pyrosequencing of the gene coding for 16S rRNA. This high-throughput sequencing technology provides a deep inventory of the diversity in microbial communities. All the resulting findings will be discussed with regard to the fungicide history of the different communities studied, and to the rate at which these communities degrade the fungicide

Published
2011

5. Efficiency of 3 genetic markers to determine the composition of a diatom assemblage using next generation sequencing

Author

Lenaïg Kermarrec, Frédéric Rimet, Alain Franc, Philippe Chaumeil, Jean Francois Humbert, Agnès Bouchez, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), University of Adelaide. Adélaide, AUS., École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
comparaison de séquences, protiste, diatomées, eau douce, évaluation de la qualité, qualité environnementale, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, marquage génétique, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2011

6. Comparative effects of the quality and quantity of light and temperature on the growth of Planktothrix agardhii and P. rubescens

Author

Laura Oberhaus, Jean-François Briand, Christophe Leboulanger, Stéphan JACQUET, Jean Francois Humbert, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Ponts et chaussées, Université de Toulon (UTLN), Université Montpellier 2 - Sciences et Techniques (UM2), and Institut Pasteur [Paris]

Subjects
PLANKTOTHRIX RUBESCENS, PLANKTHOTHRIX AGARDHII, growth, [SDV]Life Sciences [q-bio], temperature, light, Planktothrix rubescens, competition, cyanobacteria, Planktothrix agardhii, ComputingMilieux_MISCELLANEOUS
Abstract

The effects of temperature, light intensity, and quality on the growth of the cyanobacteria Planktothrix agardhii (Gomont) Anag. et Komarek and P. rubescens (Gomont) Anag. et Komarek were assessed in batch cultures. The relative competitiveness of the green-pigmented P. agardhii and the red-pigmented P. rubescens was evaluated in separate and mixed cultures, under different light intensities and qualities (green, red, and white), and at two different temperatures, chosen as representative of the natural conditions favoring the respective blooms of each species. In monocultures, the P. rubescens strain appeared to be particularly well adapted to low intensities of green light and displayed a strong photoinhibition under high irradiance levels. The P. agardhii strain appeared less specialized with regard to light quality and also less sensitive to photoinhibition at higher irradiances. In competition experiments, temperature (15 degrees C vs. 25 degrees C) was the most important parameter in determining relative fitness of the species and competitive success. At 15 degrees C, P. rubescens appeared to be much more competitive than P. agardhii, while P. agardhii was more competitive at 25 degrees C. Under low irradiance, however, the pigmentation of these strains was of primary importance in determining the outcomes of the competition experiments. On the basis of our experimental results and on field observations, we propose that the successful growth leading to the proliferation of these two differently pigmented strains may largely depend on the combined conditions of light and temperature. The two strains, being genetically close relatives, could therefore be considered as two ecotypes that are adapted to different light and temperature environments. Competition experiments showed that the combination of these parameters largely controls the success of one strain in comparison to the other.

Published
2007

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