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1. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast)

Author

Alison Gallet, Eric Kouamé Yao, Pierre Foucault, Cécile Bernard, Catherine Quiblier, Jean-François Humbert, Julien Kalpy Coulibaly, Marc Troussellier, Benjamin Marie, and Sébastien Duperron

Subjects
Hemichromis, Tilapia, Sarotherodon, Chrysichthys, Cichlidae fish, Claroteidae, Microbiology, QR1-502
Abstract

Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.

Published
2022
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2. Impacts of nutrient loading and fish grazing on the phytoplankton community and cyanotoxin production in a shallow tropical lake: Results from mesocosm experiments

Author

Mathias K. Ahoutou, Eric Kouamé Yao, Rosine Y. Djeha, Mamadou Kone, Kevin Tambosco, Charlotte Duval, Sahima Hamlaoui, Cécile Bernard, Marc Bouvy, Benjamin Marie, Bernard Montuelle, Marc Troussellier, Felix K. Konan, Julien Kalpy Coulibaly, Mireille Dosso, Jean‐François Humbert, and Catherine Quiblier

Subjects
biomanipulation, eutrophication, freshwater lagoon, Ivory Coast, mesocosm experiment, phytoplankton, Microbiology, QR1-502
Abstract

Abstract Given the increasing eutrophication of water bodies in Africa due to increasing anthropogenic pressures, data are needed to better understand the responses of phytoplankton communities to these changes in tropical lakes. These ecosystems are used by local human populations for multiple purposes, including fish and drinking water production, potentially exposing these populations to health threats if, for example, an increase in toxic cyanobacterial blooms is associated with increasing eutrophication. To test the short‐term response of the phytoplankton community to the addition of nutrients (phosphorus and nitrogen, alone or in combination) and Nile tilapia, we developed an in situ mesocosm experiment in a freshwater lagoon located near Abidjan (Ivory Coast). We found that phytoplankton growth (estimated by chlorophyll‐a quantification) was highly stimulated when both nitrogen and phosphorus were added, while there was no clear evidence for such colimitation by these two nutrients when considering their concentrations in the lagoon. Phytoplankton growth was accompanied by significant changes in the diversity and composition of this community and did not lead to an increase in the proportions of cyanobacteria. However, the addition of fish to some mesocosms resulted in a drastic decrease in phytoplankton biomass and a dominance of chlorophytes in this community. Finally, these experiments showed that the addition of nitrogen, alone or combined with phosphorus, stimulated microcystin production by cyanobacteria. In addition, no evidence of microcystin accumulation in the fish was found. Taken together, these data allow us to discuss strategies for controlling cyanobacterial blooms in this tropical ecosystem.

Published
2022
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3. Characterization of Potential Threats from Cyanobacterial Toxins in Lake Victoria Embayments and during Water Treatment

Author

Mark Olokotum, Jean-François Humbert, Catherine Quiblier, William Okello, Ronald Semyalo, Marc Troussellier, Benjamin Marie, Kathrin Baumann, Rainer Kurmayer, and Cécile Bernard

Subjects
drinking water, rapid sand filtration, recreational areas, exposure routes, Microcystis, Dolichospermum, Medicine
Abstract

Africa’s water needs are often supported by eutrophic water bodies dominated by cyanobacteria posing health threats to riparian populations from cyanotoxins, and Lake Victoria is no exception. In two embayments of the lake (Murchison Bay and Napoleon Gulf), cyanobacterial surveys were conducted to characterize the dynamics of cyanotoxins in lake water and water treatment plants. Forty-six cyanobacterial taxa were recorded, and out of these, fourteen were considered potentially toxigenic (i.e., from the genera Dolichospermum, Microcystis, Oscillatoria, Pseudanabaena and Raphidiopsis). A higher concentration (ranging from 5 to 10 µg MC-LR equiv. L−1) of microcystins (MC) was detected in Murchison Bay compared to Napoleon Gulf, with a declining gradient from the inshore (max. 15 µg MC-LR equiv. L−1) to the open lake. In Murchison Bay, an increase in Microcystis sp. biovolume and MC was observed over the last two decades. Despite high cell densities of toxigenic Microcystis and high MC concentrations, the water treatment plant in Murchison Bay efficiently removed the cyanobacterial biomass, intracellular and dissolved MC to below the lifetime guideline value for exposure via drinking water (−1). Thus, the potential health threats stem from the consumption of untreated water and recreational activities along the shores of the lake embayments. MC concentrations were predicted from Microcystis cell numbers regulated by environmental factors, such as solar radiation, wind speed in the N–S direction and turbidity. Thus, an early warning through microscopical counting of Microcystis cell numbers is proposed to better manage health risks from toxigenic cyanobacteria in Lake Victoria.

Published
2022
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4. Assessment of some key indicators of the ecological status of an African freshwater lagoon (Lagoon Aghien, Ivory Coast).

Author

Mathias Koffi Ahoutou, Rosine Yao Djeha, Eric Kouamé Yao, Catherine Quiblier, Julie Niamen-Ebrottié, Sahima Hamlaoui, Kevin Tambosco, Jean-Louis Perrin, Marc Troussellier, Cécile Bernard, Luc Seguis, Marc Bouvy, Jacques Pédron, Felix Koffi Konan, Jean-François Humbert, and Julien Kalpy Coulibaly

Subjects
Medicine, Science
Abstract

The supply of drinking water is a vital challenge for the people who live on the African continent, as this continent is experiencing strong demographic growth and therefore increasing water demands. To meet these needs, surface water resources are becoming increasingly mobilized because underground resources are not always available or have already been overexploited. This situation is the case in the region of Abidjan in the Ivory Coast, where the drinking water deficit is a growing problem and it is therefore necessary to mobilize new water resources to ensure the supply of drinking water. Among the potential resources, local managers have identified a freshwater lagoon, Lagoon Aghien, That is in close proximity to the city of Abidjan. With the aim of enhancing knowledge on the ecological functioning of the lagoon and contributing to the assessment of its ability to provide drinking water, several physical and chemical parameters of the water and the phytoplankton community of the lagoon were monitored for 17 months (December 2016-April 2018) at six sampling stations. Our findings show that the lagoon is eutrophic, as evidenced by the high concentrations of total phosphorus (>140 μg L-1), nitrogen (1.36 mg L-1) and average chlorophyll-a (26 to 167 μg L-1) concentrations. The phytoplankton community in the lagoon is dominated by genera typical of eutrophic environments including mixotrophic genera such as Peridinium and by cyanobacteria such as Cylindrospermopsis/Raphidiopsis, Microcystis and Dolichospermum that can potentially produce cyanotoxins. The two rainfall peaks that occur in June and October appeared to be major events in terms of nutrient flows entering the lagoon, and the dynamics of these flows are complex. Significant differences were also found in the nutrient concentrations and to a lesser extent in the phytoplankton communities among the different stations, especially during the rainfall peaks. Overall, these results reveal that the quality of the lagoon's water is already severely degraded, and this degradation could increase in future years due to increasing urbanization in the watershed. These results therefore raise questions about the potential use of the lagoon as a source of drinking water if measures are not taken very quickly to protect this lagoon from increasing eutrophication and other pollution sources.

Published
2021
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5. Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France

Author

Anouk Zancarini, Isidora Echenique-Subiabre, Didier Debroas, Najwa Taïb, Catherine Quiblier, and Jean-François Humbert

Subjects
Medicine, Science
Abstract

Abstract Epilithic river biofilms are complex matrix-enclosed communities harboring a great diversity of prokaryotic and eukaryotic microorganisms. Interactions between these communities and the relative impacts of environmental factors on their compositions are poorly understood. In this study, we assessed the spatio-temporal variation in the diversity and composition of bacterial and microeukaryotic communities within biofilms in a French river. Significant changes were found in the composition of these microbial communities over the sampling period and between the upstream and downstream stations. In addition, the beta diversity of the bacterial community tended to decrease along the river, mostly as a result of turnover. These changes could be caused by the different water temperatures and geological and hydrological river contexts at the sampling sites (from karst landscape to river plain). Finally, our network analysis showed multiple correlations among dominant OTUs. Among them, negative correlations between Rhodobacteraceae and two other dominant groups of photosynthetic microorganisms (cyanobacteria and diatoms) were particularly interesting, which raises the question of what environmental factors trigger the changes occurring in benthic microbial photosynthetic communities.

Published
2017
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6. Can participatory approaches strengthen the monitoring of cyanobacterial blooms in developing countries? Results from a pilot study conducted in the Lagoon Aghien (Ivory Coast).

Author

Veronica Mitroi, Kouadio Chrislain Ahi, Pierre-Yves Bulot, Fulbert Tra, José-Frédéric Deroubaix, Mathias Koffi Ahoutou, Catherine Quiblier, Mariatou Koné, Julien Coulibaly Kalpy, and Jean-François Humbert

Subjects
Medicine, Science
Abstract

Monitoring of cyanobacteria in freshwater ecosystems is a complex task, which is time consuming and expensive due to the chaotic population dynamics and highly heterogeneous distribution of cyanobacteria populations in water bodies. The financial cost constitutes a strong limitation for the implementation of long-term monitoring programs in developing countries, particularly in Africa. The work presented here was performed in the framework of an international project addressing the sustainable monitoring and management of surface water resources used for the production of drinking water in three African countries. We tested the potential of a citizen approach for monitoring cyanobacterial blooms, which are a growing threat to the drinking water supply. This pilot study was designed, implemented and evaluated in close interaction with the Pasteur Institute of the Ivory Coast and with the populations of three villages located on the shoreline of a freshwater lagoon located near Abidjan city. Based on the use of a smartphone application, the citizens of the three villages were invited to report water color changes, as these changes could reflect cyanobacteria proliferations. A two-year experimentation period has shown that it is possible to mobilize the local populations to monitor cyanobacterial blooms. The data collected by citizens were consistent with the data obtained by a classical monitoring of cyanobacteria performed over seven months, but it appeared that new approaches were needed to validate the citizen data. This participatory approach also provided great improvements to the understanding and awareness of local populations regarding water quality and cyanobacterial bloom issues. Finally, we discuss some of the difficulties and limitations of our participatory monitoring approach that should be considered by further implementations. Despite these difficulties, our work suggests that citizen monitoring is a promising approach that may complement the classical approach to sustainable monitoring of cyanobacteria in developing countries.

Published
2020
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8. Assessment of cyanotoxins in water and fish in an African freshwater lagoon (Lagoon Aghien, Ivory Coast) and the application of WHO guidelines

Author

Eric Kouamé Yao, Mathias Koffi Ahoutou, Mark Olokotum, Sahima Hamlaoui, Emilie Lance, Benjamin Marie, Cecile Bernard, Rosine Yao Djeha, Catherine Quiblier, Jean-François Humbert, and Julien Kalpy Coulibaly

Abstract

In comparison with northern countries, limited data are available on the occurrence and potential toxicity of cyanobacterial blooms in lakes and ponds in Sub-Saharan countries. With the aim of enhancing our knowledge on cyanobacteria and their toxins in Africa, we performed a 17-month monitoring of a freshwater ecosystem, Lagoon Aghien (Ivory Coast), which is used for multiple practices by riverine populations and for drinking water production in Abidjan city. The richness and diversity of the cyanobacterial community were high and displayed few variations during the entire survey. The monthly average abundances ranged from 4.1x104 cell mL− 1 to 1.8x105 cell mL− 1, with higher abundances recorded during the dry seasons. Among the five cyanotoxin families analyzed, only microcystins (MC) were detected with concentrations ranging from 0 to 0.364 µg L− 1 in phytoplankton cells, from 32 to 1,092 µg kg− 1 fresh weight of fish intestines and from 33 to 383 µg kg− 1 in fish livers. Even if the MC concentrations in water and fish are low, usually below the thresholds defined in WHO guidelines, these data raise the issue of the relevance of these WHO guidelines for Sub-Saharan Africa, where local populations are exposed throughout the year to these toxins in multiple ways.

Published
2023
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9. Porrentruy, Bibliothèque cantonale jurassienne, MP 4-1 : Excerpts from the Annals of the Collège de Porrentruy

Author

Voisard, François-Humbert

Abstract

This volume contains “année après année tout ce qui s’est passé de remarquable dans cet établissement [the Collège de Porrentruy] depuis 1588 à 1771” (p. 1). So reads the title page of this paper manuscript, which moreover provides information on its provenance. Property of the Jesuit priest Voisard (1749-1818), at his death the manuscript was bequeathed to Henri Joliat (1803-1859), who deposited it in 1856 in the library of the Collège de Porrentruy. The text begins in 1588 with the establishment of the Collège directed by the Jesuits; this volume concludes in 1661. The years that follow are treated in a second volume, MP 4-2. These excerpts from the annals are probably the French translation and summary of the volume in Latin in the Jura Cantonal Library (A2597)., Online Since: 2022-12-14

Published
2023
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11. Porrentruy, Bibliothèque cantonale jurassienne, MP 10 / A3269 : Abrégé de l’histoire des évêques de Basle depuis l’établissement de l’Evêché jusqu’à nos jours composé par le P. Voisard 1781

Author

Vautrey, Louis and Voisard, François-Humbert

Abstract

According to the preface (pp. 5-8), the Jesuit François-Humbert Voisard (1749-1818) wrote the Abrégé as the first history in French of the bishops of Basel and dedicated it to his students. Entirely focused on the ecclesiastical history of Basel and Porrentruy, the text’s structure reveals its pedagogic nature: a short question introduces each chapter, and the text that immediately follows provides a more or less lengthy reply to the question. According to Gustave Amweg’s Bibliographie du Jura bernois, Voisard’s Abrégé survives in five copies and has not been published to this day. This manuscript has been corrected, annotated, and ends with an index of the bishops and the clerical institutions of the Basel episcopacy (pp. 459-460). Ownership notes inscribed on the front pastedown document its provenance: “Ce livre appartient à Henri Joliat, étudiant en rhétorique. Porrentruy, le 3 mai 1819 / Et / Schwartzlin Père / et /à l’abbé Vautrey à qui il a été remis par M. l’abbé Marquis en 1813”., Online Since: 2022-12-14

Published
2023
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12. Porrentruy, Bibliothèque cantonale jurassienne, MP 11 / A3269 : Abrégé de l’histoire des évêques de Basle depuis l’établissement de l’Evêché jusqu’en 1781 par le P. Voisard professeur au collège de Porrentruy

Author

Quiquerez, Jean-Georges, Voisard, François-Humbert, and Quiquerez, Auguste

Abstract

One of the five copies of the Abrégé de l’histoire des évêques de Bâle by the Jesuit, François-Humbert Voisard (1749-1818), a history textbook organized according to questions and responses and dating from 1781. Except for the address of the dedication, the preface of this volume uses nearly the same terms as those in a second copy in the Bibliothèque cantonale jurassienne (MP 10 / A 3269). It differs, however, in lacking annotation and correction. In addition, the copy is incomplete, since it stops suddenly at the beginning of the fourth part, dedicated to the bishops of Basel and of Porrentruy (p. 360). Before coming to the library of the Collège de Porrentruy in 1842, the manuscript belonged to a certain Quiquerez (back pastedown), probably Jean-Georges, mayor and notary of Porrentruy, and then to his son, Auguste (1801-1882), a Jurassien engineer, historian, archeologist, and geologist, as indicated by his ex-libris (p. V1)., Online Since: 2022-12-14

Published
2023
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15. Unusual cohabitation and competition between Planktothrix rubescens and Microcystis sp. (cyanobacteria) in a subtropical reservoir (Hammam Debagh) located in Algeria.

Author

Fatma Zohra Guellati, Hassen Touati, Kevin Tambosco, Catherine Quiblier, Jean-François Humbert, and Mourad Bensouilah

Subjects
Medicine, Science
Abstract

Succession in bloom-forming cyanobacteria belonging to distant functional groups in freshwater ecosystems is currently an undescribed phenomenon. However in the Hammam Debagh reservoir (Algeria), P. rubescens and Microcystis sp. co-occur and sometimes proliferate. With the aim of identifying the main factors and processes involved in this unusual cohabitation, water samples were collected monthly from February 2013 to June 2015 at the subsurface at four sampling stations and along the entire water column at one sampling station. In addition, the composition of the cyanobacterial communities was estimated by Illumina sequencing of a 16S rRNA gene fragment from samples collected over one year (October 2013-November 2014). This molecular approach showed that the Hammam Debagh reservoir displays high species richness (89 species) but very low diversity due to the high dominance of Microcystis in this community. Furthermore, it appears that Planktothrix rubescens and Microcystis sp. coexisted (from September to January) but proliferated alternately (Spring 2015 for P. rubescens and Spring 2014 and Autumn 2014/2015 for Microcystis). The main factors and processes explaining these changes in bloom-forming species seem to be related to the variation in the depth of the lake during the mixing period and to the water temperatures during the winter prior to the bloom season in spring.

Published
2017
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16. Spatial and Temporal Variability in the Development and Potential Toxicity of Phormidium Biofilms in the Tarn River, France

Author

Isidora Echenique-Subiabre, Maxime Tenon, Jean-François Humbert, and Catherine Quiblier

Subjects
river biofilms, benthic cyanobacteria, biofilm development, anatoxins, mass spectrometry, model II regression, coefficient of determination, Medicine
Abstract

Proliferation of Phormidium biofilms in rivers is becoming a worldwide sanitation problem for humans and animals, due to the ability of these bacteria to produce anatoxins. To better understand the environmental conditions that favor the development of Phormidium biofilms and the production of anatoxins, we monitored the formation of these biofilms and their toxins for two years in the Tarn River, biofilms from which are known to have caused the deaths of multiple dogs. As previously observed in New Zealand, Phormidium biofilm development occurred in riffle areas. The coverage of these biofilms at the bottom of the river exhibited strong spatial and temporal variations, but was positively correlated with water temperature and depth. Anatoxin-a was detected in less than 50% of the biofilms. The concentrations of these toxins in the biofilms exhibited high spatiotemporal variability, with the highest concentrations being recorded at the end of the summer period at the upstream sampling sites. These findings suggest that the maturity of the biofilms, combined with the local environmental conditions, have an impact on the production of anatoxin, making risk assessment for these benthic proliferations challenging.

Published
2018
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17. Reporting on the degradation of aquatic environments. The role of knowledge in the implementation of policies for the protection of water resources in sub-Saharan Africa

Author

Veronica Mitroi, José Frédéric Deroubaix, Youssoupha Tall, Ahi Kouaido Chrislain, Jean-François Humbert, Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Eau Environnement et Systèmes Urbains (LEESU), École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Félix Houphouët-Boigny (UFHB), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), and Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
politique de l'eau, représentations de l’eau, Geography, Planning and Development, Afrique de l’Ouest, sciences participatives, gestion des ressources naturelles, Dégradation de l'environnement, U70 - Sciences humaines et sociales, Conservation de l'eau, savoirs experts, expert knowledge, West Africa, dégradation des milieux aquatiques, observatoire de milieu, P10 - Ressources en eau et leur gestion, local representations, environment observatory, Global and Planetary Change, [SHS.SOCIO]Humanities and Social Sciences/Sociology, production de savoirs, knowledge production, [SDE.ES]Environmental Sciences/Environmental and Society, environment quality, Urban Studies, Milieu aquatique, degradation of aquatic environments, Gestion des connaissances, P01 - Conservation de la nature et ressources foncières, Ressource en eau
Abstract

International audience; This article examines the role that the production of knowledge on the ecological state of aquatic ecosystems plays in the implementation of policies for protecting these environments, used for water supply. Based on interdisciplinary research carried out in two sub-Saharan countries (Côte d'Ivoire and Senegal) by a team of sociologists and ecologists, the article shows how expert knowledge of environmental quality assessment interacts with the local actors, existing management structures and with local representations of these environments. Through this interdisciplinary approach, we question the difficulties of integrating a diversity of points of view on water resources. We highlight the obstacles, uncertainties and controversies linked with the production of expertise and its integration into existing management systems. More specifically, we describe the main challenges for institutionalizing long-term monitoring of the water resources (Aquatic Ecosystems Observatories). We also discuss the possibilities and the interest for integrating expert and local knowledge for co-constructing a shared diagnosis.; Cet article questionne le rôle de la production des savoirs sur l’état écologique des milieux dans la gestion et la mise en oeuvre de politiques de surveillance et de protection des ressources en eau utilisées pour la production d’eau potable en Afrique subsaharienne. Sur la base d’une recherche interdisciplinaire réalisée en Côte d’Ivoire et au Sénégal par une équipe comprenant des sociologues et des écologues, l’article montre comment des savoirs experts d’évaluation de la qualité des milieux interagissent avec les jeux d’acteurs, les structures de gestion existantes et les représentations locales de ces mêmes milieux. Nous interrogeons à travers cette approche interdisciplinaire les difficultés d’articulation de la diversité de points de vue sur les ressources en eau, ainsi que les freins, les incertitudes et controverses autour de la production de savoirs et de leur intégration dans des dispositifs de gestion. Nous analysons plus particulièrement les principaux défis pour la mise en place des suivis de l’état écologique des milieux aquatiques, ainsi que les possibles contributions des savoirs experts et locaux à la co-construction d’un diagnostic partagé.

Published
2022
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18. What urban lakes and ponds quality is about? Conciliating water quality and ecological indicators with users’ perceptions and expectations about urban lakes and ponds quality in urban areas

Author

Veronica Mitroi, Veronique Maleval, José-Frédéric Deroubaix, Brigitte Vinçon-Leite, Jean-François Humbert, Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Capital Environnemental (GEOLAB-CE), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Dynamiques Géoenvironnementales Actuelles (GEOLAB-DGA), Laboratoire Eau Environnement et Systèmes Urbains (LEESU), École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by the French National Research Agency under Grant ANR-10-CEPL-0010. We thank all the project members and partners who contributed to the data collection and analysis: Centre National de la Recherche Scientifique, Sorbonne universite, University of Limoges, University Paris-Sud, Museum National d'Histoire Naturelle de Paris, Ecole des Ponts Paris'Tech., and ANR-10-CEPL-0010,PULSE,Lacs périurbains, société et environnement(2010)

Subjects
ecological status, territorial management, Urban lakes and ponds, ecological indicators, P01 - Conservation de la nature et ressources foncières, [SHS.GEO]Humanities and Social Sciences/Geography, P10 - Ressources en eau et leur gestion, Management, Monitoring, Policy and Law, water quality public perceptions, ecosystem services
Abstract

International audience; Urban lakes and ponds (L&Ps) provide numerous ecological and social services for local populations living in urban areas. Their monitoring and management are mostly based on water quality and ecological indicators and poorly consider public preferences and expectancies related to these artificial ecosystems. Even fewer studies bring together expert indicators and public expectations to inform management objectives for urban lakes. Based on an interdisciplinary study, this paper compares an expert assessment of the ecological quality of three urban L&Ps located in the Ile-de-France area with the public perception of these lakes. This approach permits us to explore the compatibilities and incongruences between the various ways in which scientists, managers and urban users assess urban L&P quality. Based on these data, we discuss how it could be possible to define management objectives that integrate quality indicators and expect these objectives to be used in a territorial approach that might allow to obtain a better adequacy between social users' expectations and the ecological status of these L&Ps.; Les lacs et étangs urbains (L&P) fournissent de nombreux services écologiques et sociaux aux populations locales vivant dans les zones urbaines. Leur suivi et leur gestion sont majoritairement basés sur la qualité de l'eau et des indicateurs écologiques mais tiennent peu compte des préférences et des attentes du public vis-à-vis de ces écosystèmes artificiels. Peu d'études réunissent des indicateurs d'experts et les attentes du public pour éclairer les objectifs de gestion des lacs urbains. Sur la base d'une étude interdisciplinaire, cet article met en regard l'expertise de la qualité écologique de trois L&P urbains situés en Ile-de-France avec la perception publique de ces lacs. Cette approche nous permet d'explorer les compatibilités et les incongruences entre les différentes façons dont les scientifiques, les gestionnaires et les usagers urbains évaluent la qualité des L&P urbains. Sur la base de ces données, nous discutons comment il pourrait être possible de définir des objectifs de gestion intégrant des indicateurs de qualité et attendons que ces objectifs soient utilisés dans une approche territoriale qui pourrait permettre d'obtenir une meilleure adéquation entre les attentes des usagers sociaux et l'état écologique des L&P.

Published
2022
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20. Choisir de lutter contre certaines pollutions plutôt que d’autres

Author

YOUSSOUPHA TALL, José-Frédéric Deroubaix, Ibrahima Dia, Mitroï, Veronica, Tidiane Ndoye, Sylvain Landry Faye, and Jean François Humbert

Subjects
Pollution de l'eau, Sociology and Political Science, H02 - Pesticides, Dégradation de l'environnement, Pollution par l'agriculture, Pollution, U70 - Sciences humaines et sociales, Education, History and Philosophy of Science, Toxicité des pesticides, Anthropology, Eutrophisation, P10 - Ressources en eau et leur gestion, Ressource en eau, P02 - Pollution
Abstract

L'ensemble des activités en lien avec l'eau du lac de Guiers au Sénégal a potentiellement des conséquences importantes sur son état écologique. Cet article part du constat que la pollution par les pesticides concentre l'essentiel des débats et des actions entreprises tandis que l'enrichissement en nutriments des eaux du lac (représentant un risque d'eutrophisation) n'est un problème que rarement évoqué. Ce constat conduit les auteurs à s'interroger sur les facteurs sociopolitiques qui conduisent à " l'invisibilisation " de certaines causes de dégradation des milieux aquatiques. En nous appuyant sur une enquête de terrain auprès des gestionnaires et usagers du lac, nous montrons les concurrences entre les différents services administratifs qui conduisent à diverses formes de segmentation des causes de dégradation et à la sélection de l'une d'entre elles. Nous montrons ensuite comment cette formalisation du problème est diffusée et renforcée par la mise en oeuvre de bonnes pratiques agricoles, essentiellement centrées sur la question des produits phytosanitaires et relayées par des acteurs territoriaux. Cette analyse de la construction institutionnelle de l'ignorance est enfin complétée par une étude des représentations que les usagers se font de la dégradation de leur lac, permettant d'identifier les dynamiques sociales, les conflits et les jeux de pouvoir autour de l'appropriation de l'espace et de l'accès à l'eau, qui conduisent à l'invisibilisation du problème de l'eutrophisation.

Published
2021
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21. Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus.

Author

Imen Louati, Noémie Pascault, Didier Debroas, Cécile Bernard, Jean-François Humbert, and Julie Leloup

Subjects
Medicine, Science
Abstract

The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing) and Microcystis (colonial and non-N2 fixing) that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.

Published
2015
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22. Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

Author

Noémie Pascault, Cécile Bernard, Jacques Pédron, Valentin Loux, Julie Leloup, Jean-François Humbert, Véronique Martin, Olivier Rué, Jennifer Tambosco, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility (MIGALE), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-11-JSV7-0014,PHYCOCYANO,Relation fonctionnelle Cyanobactéries/Bactéries : Dynamique de la phycosphère et recyclage interne de l'azote(2011)

Subjects
Cyanobacteria, Microcystis, natural conditions, metabolisms of cyanobacteria, Microcystis sp, 03 medical and health sciences, Nutrient, Botany, Microbiome, Phosphate metabolism, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Microbiota, Functional redundancy, cyanosphere, Nutrients, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Lakes, chemotrophic bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bloom, Bacteria
Abstract

International audience; Specific interactions have been highlighted betweencyanobacteria and chemotrophic bacteria within thecyanosphere, suggesting that nutrients recycling couldbe optimized by cyanobacteria/bacteria exchanges. Inorder to determine the respective metabolic roles ofthe cyanobacterial and bacterial consortia (micro-biome), a day–night metatranscriptomic analysis wasperformed onDolichospermumsp. (N2-fixer) andMicro-cystissp. (non N2-fixer) natural blooms occurringsuccessively within a Frenchperi-urban lake. The taxo-nomical and functional analysis of the metatran-scriptoms have highlighted specific association ofbacteria within the cyanosphere, driven by the cyano-bacteria identity, without strongly modifying the func-tional composition of the microbiomes, suggestingfunctional redundancy within the cyanosphere. More-over, the functional composition of these active com-munities was driven by the living mode. During the twosuccessive bloom events, it appeared that NH4+(newlyfixed and/or allochthonous) was preferentially trans-formed into amino acids for the both the microbiomeand the cyanobacteria, while phosphate metabolismwas enhanced, suggesting that due to a high cellulargrowth, P limitation might take place within the cyano-sphere consortium.

Published
2021
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23. High nutrient loading and climatic parameters influence the dominance and dissimilarity of toxigenic cyanobacteria in northern bays of Lake Victoria

Author

Ronald Semyalo, Mark Olokotum, Arthur Escalas, Jean-François Humbert, Marc Troussellier, Sahima Hamlaoui, Cécile Bernard, William Okello, Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Murchison meteorite, Bays and gulfs, Beta diversity, 010501 environmental sciences, Aquatic Science, Lake Victoria, Cyanobacteria, 01 natural sciences, Phytoplankton, Dominance (ecology), 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Diversity, Ecology, 010604 marine biology & hydrobiology, Eutrophication, Lake Victoria, Cyanobacteria, Phytoplankton, Diversity, Bays and gulfs, 15. Life on land, Eutrophication, 13. Climate action, [SDE]Environmental Sciences, Environmental science, Alpha diversity, Species richness, Bay
Abstract

International audience; utrophication of Lake Victoria led to changes in its phytoplankton communities. However, different levels of eutrophication exist in the open lake and the bays, and between embayments. This study utilized spatial and temporal sampling of Napoleon Gulf and Murchison Bay, exhibiting different trophic conditions. Over one year, we investigated phytoplankton biomass, richness, diversity and dissimilarity, and related the dynamics of the dominant species to the limnological and climatic conditions. The results confirmed that Napoleon Gulf and Murchison Bay showed large differences in eutrophication status, with lower nutrient concentrations in Napoleon Gulf than in Murchison Bay, where a strong gradient was observed from inshore to offshore areas. These nutrient dynamics resulted in a 4 to 10 fold higher chlorophyll-a in Murchison Bay than in Napoleon Gulf. From the embayments, 135 phytoplankton taxa were recorded with no significant differences in alpha diversity. However, high dissimilarity in community structure was observed in beta diversity, mostly due to a turnover among the dominant toxigenic species. Thus, from a similar species pool, there was a shift in the dominant toxigenic cyanobacteria from Microcystis flos-aquae and M. aeruginosa in Murchison Bay, Dolichospermum circinale and Planktolyngbya circumcreta in Napoleon Gulf to D. circinale in the offshore stations. These cyanobacteria are toxigenic taxa with known health hazards. Using partial least square models, we showed that both climatic variables (e.g. wind, solar radiation) and levels of inorganic dissolved nutrients (e.g. SRP, NO3-, and NH4+) are the main drivers of differences and dominance in cyanobacteria communities in northern Lake Victoria.

Published
2021
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24. Assessment of some key indicators of the ecological status of an African freshwater lagoon (Lagoon Aghien, Ivory Coast)

Author

Jacques Pédron, Catherine Quiblier, Luc Séguis, Marc Bouvy, Julien Kalpy Coulibaly, Kevin Tambosco, Felix Koffi Konan, Rosine Yao Djeha, Marc Troussellier, Eric Kouamé Yao, Mathias Koffi Ahoutou, Jean-François Humbert, Julie Niamen-Ebrottié, Sahima Hamlaoui, Jean-Louis Perrin, Cécile Bernard, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Jean Lorougnon Guédé (UJloG ), Université Nangui Abrogoua (UNA), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Nangui Abrogoua, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Physiology, Marine and Aquatic Sciences, Water Columns, Fresh Water, Plant Science, 010501 environmental sciences, Oceanography, Plant Tropisms, 01 natural sciences, Geographical locations, Nutrient, Water column, Natural Resources, Plant Growth and Development, Multidisciplinary, Ecology, biology, Eukaryota, Côte d'Ivoire, Plants, Plankton, Pollution, 6. Clean water, Plant Physiology, [SDE]Environmental Sciences, Water Resources, Medicine, Seasons, Research Article, Lagoons, Watershed, Algae, Science, Cyanobacteria, Tropism, Spatio-Temporal Analysis, Phytoplankton, Animals, 14. Life underwater, Phototropism, 0105 earth and related environmental sciences, Bacteria, Chlorophyll A, 010604 marine biology & hydrobiology, Cylindrospermopsis, Ecology and Environmental Sciences, Water Pollution, Organisms, Biology and Life Sciences, Nutrients, Bodies of Water, 15. Life on land, biology.organism_classification, Invertebrates, Water resources, Lakes, Cote d'Ivoire, 13. Climate action, Africa, Earth Sciences, Environmental science, Water quality, People and places, Eutrophication, Zoology, Organism Development, Developmental Biology
Abstract

The supply of drinking water is a vital challenge for the people who live on the African continent, as this continent is experiencing strong demographic growth and therefore increasing water demands. To meet these needs, surface water resources are becoming increasingly mobilized because underground resources are not always available or have already been overexploited. This situation is the case in the region of Abidjan in the Ivory Coast, where the drinking water deficit is a growing problem and it is therefore necessary to mobilize new water resources to ensure the supply of drinking water. Among the potential resources, local managers have identified a freshwater lagoon, Lagoon Aghien, That is in close proximity to the city of Abidjan. With the aim of enhancing knowledge on the ecological functioning of the lagoon and contributing to the assessment of its ability to provide drinking water, several physical and chemical parameters of the water and the phytoplankton community of the lagoon were monitored for 17 months (December 2016-April 2018) at six sampling stations. Our findings show that the lagoon is eutrophic, as evidenced by the high concentrations of total phosphorus (>140 μg L-1), nitrogen (1.36 mg L-1) and average chlorophyll-a (26 to 167 μg L-1) concentrations. The phytoplankton community in the lagoon is dominated by genera typical of eutrophic environments including mixotrophic genera such as Peridinium and by cyanobacteria such as Cylindrospermopsis/Raphidiopsis, Microcystis and Dolichospermum that can potentially produce cyanotoxins. The two rainfall peaks that occur in June and October appeared to be major events in terms of nutrient flows entering the lagoon, and the dynamics of these flows are complex. Significant differences were also found in the nutrient concentrations and to a lesser extent in the phytoplankton communities among the different stations, especially during the rainfall peaks. Overall, these results reveal that the quality of the lagoon’s water is already severely degraded, and this degradation could increase in future years due to increasing urbanization in the watershed. These results therefore raise questions about the potential use of the lagoon as a source of drinking water if measures are not taken very quickly to protect this lagoon from increasing eutrophication and other pollution sources.

Published
2021
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25. A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.

Author

Jean-François Humbert, Valérie Barbe, Amel Latifi, Muriel Gugger, Alexandra Calteau, Therese Coursin, Aurélie Lajus, Vanina Castelli, Sophie Oztas, Gaëlle Samson, Cyrille Longin, Claudine Medigue, and Nicole Tandeau de Marsac

Subjects
Medicine, Science
Abstract

Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.

Published
2013
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26. Comment on 'Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances'

Author

Jean-François Humbert, Dirk Maes, Pierre-André Cornillon, Laurence Gaume, Jean-Marc Bonmatin, Marion Desquilbet, Hans Van Dyck, Manuela Grippa, Régis Céréghino, David Goulson, Toulouse School of Economics (TSE-R), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Sussex, ANR-16-IDEX-0006 (Investissements d’Avenir program), Agence Nationale de la Recherche, ANR-17-EURE-0010,CHESS,Toulouse Graduate School défis en économie et sciences sociales quantitatives(2017), ANR-16-IDEX-0006,MUSE,MUSE(2016), ANR-15-CE21-0006,IDAE,Institutionnalisations des agroécologies(2015), ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), Toulouse School of Economics (TSE), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, KARLI, Mélanie, Toulouse Graduate School défis en économie et sciences sociales quantitatives - - CHESS2017 - ANR-17-EURE-0010 - EURE - VALID, MUSE - - MUSE2016 - ANR-16-IDEX-0006 - IDEX - VALID, and Institutionnalisations des agroécologies - - IDAE2015 - ANR-15-CE21-0006 - AAPG2015 - VALID

Subjects
0106 biological sciences, 0303 health sciences, Multidisciplinary, Insecta, Ecology, MEDLINE, Ecological data, Fresh Water, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Geography, Fresh water, Meta-analysis, Animals, Humans, B- ECONOMIE ET FINANCE, Data selection, 030304 developmental biology, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

Van Klink et al . (Reports, 24 April 2020, p. 417) argue for a more nuanced view of insect decline, and of human responsibility for this decline, than previously suggested. However, shortcomings in data selection and methodology raise questions about their conclusions on trends and drivers. We call for more rigorous methodology to be applied in meta-analyses of ecological data.

Published
2020
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27. Can participatory approaches strengthen the monitoring of cyanobacterial blooms in developing countries? Results from a pilot study conducted in the Lagoon Aghien (Ivory Coast)

Author

Julien Coulibaly Kalpy, Mariatou Koné, Jean-François Humbert, Kouadio Chrislain Ahi, Mathias Koffi Ahoutou, Fulbert Tra, Catherine Quiblier, Pierre-Yves Bulot, José-Frédéric Deroubaix, Veronica Mitroi, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Félix Houphouët-Boigny (UFHB), Laboratoire Interdisciplinaire Sciences, Innovations, Sociétés (LISIS), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Gustave Eiffel, Laboratoire Eau Environnement et Systèmes Urbains (LEESU), École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Pasteur de Côte d'Ivoire, Réseau International des Instituts Pasteur (RIIP), Université Jean Lorougnon Guédé (UJloG ), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université de Paris (UP), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Paris Cité (UPCité)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Participatory monitoring, Water supply, Distribution (economics), Marine and Aquatic Sciences, Social Sciences, Pilot Projects, 01 natural sciences, Freshwater ecosystem, Social Geography, Water Quality, education.field_of_study, Multidisciplinary, Geography, Eukaryota, Plants, Pollution, 6. Clean water, Work (electrical), Research Design, Medicine, Engineering and Technology, Research Article, Lagoons, Environmental Monitoring, Algae, Science, Population, Equipment, Cyanobacteria, Research and Analysis Methods, Human Geography, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Water Supply, 14. Life underwater, education, Environmental planning, Developing Countries, 0105 earth and related environmental sciences, Communication Equipment, Bacteria, business.industry, 010604 marine biology & hydrobiology, Ecology and Environmental Sciences, Water Pollution, Organisms, Biology and Life Sciences, Citizen journalism, Pilot Studies, Bodies of Water, [SDE.ES]Environmental Sciences/Environmental and Society, Lakes, Cote d'Ivoire, 13. Climate action, Earth Sciences, Water quality, Cell Phones, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract

International audience; Monitoring of cyanobacteria in freshwater ecosystems is a complex task, which is time consuming and expensive due to the chaotic population dynamics and highly heterogeneous distribution of cyanobacteria populations in water bodies. The financial cost constitutes a strong limitation for the implementation of long-term monitoring programs in developing countries, particularly in Africa. The work presented here was performed in the framework of an international project addressing the sustainable monitoring and management of surface water resources used for the production of drinking water in three African countries. We tested the potential of a citizen approach for monitoring cyanobacterial blooms, which are a growing threat to the drinking water supply. This pilot study was designed, implemented and evaluated in close interaction with the Pasteur Institute of the Ivory Coast and with the populations of three villages located on the shoreline of a freshwater lagoon located near Abidjan city. Based on the use of a smartphone application, the citizens of the three villages were invited to report water color changes, as these changes could reflect cyanobacteria proliferations. A two-year experimentation period has shown that it is possible to mobilize the local populations to monitor cyanobacterial blooms. The data collected by citizens were consistent with the data obtained by a classical monitoring of cyanobacteria performed over seven months, but it appeared that new approaches were needed to validate the citizen data. This participatory approach also provided great improvements to the understanding and awareness of local populations regarding water quality and cyanobacterial bloom issues. Finally, we discuss some of the difficulties and limitations of our participatory monitoring approach that should be considered by further implementations. Despite these difficulties, our work suggests that citizen monitoring is a promising approach that may complement the classical approach to sustainable monitoring of cyanobacteria in developing countries.

Published
2020
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28. Birnessite: A New Oxidant for Green Rust Formation

Author

François Humbert, Pierrick Durand, Romain Coustel, Amira Doggaz, Christian Ruby, Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Cristallographie, Résonance Magnétique et Modélisations (CRM2), and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
layered double hydroxide, Birnessite, LDH, oxidation, Kinetics, Inorganic chemistry, chemistry.chemical_element, 02 engineering and technology, Manganese, 010501 environmental sciences, engineering.material, Fougèrite, 01 natural sciences, Ferromanganese, lcsh:Technology, Article, chemistry.chemical_compound, iron, Mössbauer spectroscopy, [CHIM]Chemical Sciences, General Materials Science, lcsh:Microscopy, 0105 earth and related environmental sciences, lcsh:QC120-168.85, lcsh:QH201-278.5, Chemistry, lcsh:T, Spinel, 021001 nanoscience & nanotechnology, 6. Clean water, fougerite, lcsh:TA1-2040, [SDE]Environmental Sciences, engineering, manganese, Hydroxide, lcsh:Descriptive and experimental mechanics, lcsh:Electrical engineering. Electronics. Nuclear engineering, 0210 nano-technology, lcsh:Engineering (General). Civil engineering (General), lcsh:TK1-9971
Abstract

Iron and manganese are ubiquitous in the natural environment. FeII-FeIII layered double hydroxide, commonly called green rust (GR), and MnIII-MnIV birnessite (Bir) are also well known to be reactive solid compounds. Therefore, studying the chemical interactions between Fe and Mn species could contribute to understanding the interactions between their respective biogeochemical cycles. Moreover, ferromanganese solid compounds are potentially interesting materials for water treatment. Here, a {Fe(OH)2, FeIIaq} mixture was oxidized by Bir in sulphated aqueous media in the presence or absence of dissolved O2. In oxic conditions for an initial FeII/OH&minus, ratio of 0.6, a single GR phase was obtained in a first step, the oxidation kinetics being faster than without Bir. In a second step, GR was oxidised into various final products, mainly in a spinel structure. A partial substitution of Fe by Mn species was suspected in both GR and the spinel. In anoxic condition, GR was also observed but other by-products were concomitantly formed. All the oxidation products were characterized by XRD, XPS, and M&ouml, ssbauer spectroscopy. Hence, oxidation of FeII species by Bir can be considered as a new chemical pathway for producing ferromanganese spinels. Furthermore, these results suggest that Bir may participate in the formation of GR minerals.

Published
2020
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30. Evidence of the cost of the production of microcystins by Microcystis aeruginosa under differing light and nitrate environmental conditions.

Author

Enora Briand, Myriam Bormans, Catherine Quiblier, Marie-José Salençon, and Jean-François Humbert

Subjects
Medicine, Science
Abstract

The cyanobacterium Microcystis aeruginosa is known to proliferate in freshwater ecosystems and to produce microcystins. It is now well established that much of the variability of bloom toxicity is due to differences in the relative proportions of microcystin-producing and non-microcystin-producing cells in cyanobacterial populations. In an attempt to elucidate changes in their relative proportions during cyanobacterial blooms, we compared the fitness of the microcystin-producing M. aeruginosa PCC 7806 strain (WT) to that of its non-microcystin-producing mutant (MT). We investigated the effects of two light intensities and of limiting and non-limiting nitrate concentrations on the growth of these strains in monoculture and co-culture experiments. We also monitored various physiological parameters, and microcystin production by the WT strain. In monoculture experiments, no significant difference was found between the growth rates or physiological characteristics of the two strains during the exponential growth phase. In contrast, the MT strain was found to dominate the WT strain in co-culture experiments under favorable growth conditions. Moreover, we also found an increase in the growth rate of the MT strain and in the cellular MC content of the WT strain. Our findings suggest that differences in the fitness of these two strains under optimum growth conditions were attributable to the cost to microcystin-producing cells of producing microcystins, and to the putative existence of cooperation processes involving direct interactions between these strains.

Published
2012
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31. Tyre–road friction μ-estimation based on braking force distribution

Author

Deepak Paul, Simon Hegarty, Dongpu Cao, François Humbert, Efstathios Velenis, and Tamas Dobo

Subjects
0209 industrial biotechnology, Injury control, Accident prevention, Computer science, Mechanical Engineering, Work (physics), Brake control, Aerospace Engineering, Poison control, 02 engineering and technology, Vehicle dynamics, 020303 mechanical engineering & transports, 020901 industrial engineering & automation, 0203 mechanical engineering, Control theory, Distribution (differential geometry)
Abstract

In this work, we develop a rules-based µ-estimation algorithm which is independent of any tyre model and may be employed independently by brake control systems of the vehicle. The algorithm propose...

Published
2018
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32. A day in the life of microcystis aeruginosa strain PCC 7806 as revealed by a transcriptomic analysis.

Author

Cécile Straub, Philippe Quillardet, Julia Vergalli, Nicole Tandeau de Marsac, and Jean-François Humbert

Subjects
Medicine, Science
Abstract

The cyanobacterium, Microcystis aeruginosa, is able to proliferate in a wide range of freshwater ecosystems and to produce many secondary metabolites that are a threat to human and animal health. The dynamic of this production and more globally the metabolism of this species is still poorly known. A DNA microarray based on the genome of M. aeruginosa PCC 7806 was constructed and used to study the dynamics of gene expression in this cyanobacterium during the light/dark cycle, because light is a critical factor for this species, like for other photosynthetic microorganisms. This first application of transcriptomics to a Microcystis species has revealed that more than 25% of the genes displayed significant changes in their transcript abundance during the light/dark cycle and in particular during the dark/light transition. The metabolism of M. aeruginosa is compartmentalized between the light period, during which carbon uptake, photosynthesis and the reductive pentose phosphate pathway lead to the synthesis of glycogen, and the dark period, during which glycogen degradation, the oxidative pentose phosphate pathway, the TCA branched pathway and ammonium uptake promote amino acid biosynthesis. We also show that the biosynthesis of secondary metabolites, such as microcystins, aeruginosin and cyanopeptolin, occur essentially during the light period, suggesting that these metabolites may interact with the diurnal part of the central metabolism.

Published
2011
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33. A review of the socioecological causes and consequences of cyanobacterial blooms in Lake Victoria

Author

Ronald Semyalo, Bernard Montuelle, Mark Olokotum, Catherine Quiblier, Veronica Mitroi, Marc Troussellier, Jean-François Humbert, William Okello, Cécile Bernard, Makerere University [Kampala, Ouganda] (MAK), National Fisheries Resources Research Institute (NaFIRI) (NaFIRI), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Fisheries Resources Research Institue (NaFIRI), Université Paris Cité (UPCité), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), French Facility for Global Environment (Fonds Francais pour l'Environnement Mondial, FFEM), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and Université de Paris (UP)

Subjects
0106 biological sciences, Resource (biology), Watershed, Microcystis, Drainage basin, Water supply, Plant Science, 010501 environmental sciences, Aquatic Science, Cyanobacteria, 01 natural sciences, Freshwater ecosystem, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Deforestation, 14. Life underwater, Ecosystem, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, business.industry, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, Eutrophication, 6. Clean water, Lakes, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Water use
Abstract

International audience; Africa is experiencing high annual population growth in its major river basins. This growth has resulted in significant land use change and pollution pressures on the freshwater ecosystems. Among them, the Lake Victoria basin, with more than 42 million people, is a unique and vital resource that provides food and drinking water in East Africa. However, Lake Victoria (LV) has experienced a progressive eutrophication and substantial changes in the fish community leading to recurrent proliferation of water hyacinth and cyanobacteria. Based on an extensive literature review, we show that cyanobacterial biomasses and microcystin concentrations are higher in the bays and gulfs (B&Gs) than in the open lake (OL), with Microcystis and Dolichospermum as the dominant genera. These differences between the B&Gs and the OL are due to differences in their hydrological conditions and in the origins, type and quantities of nutrients. Using data from the literature, we describe the multiple ways in which the human population growth in the LV watershed is connected to the increasing occurrence of cyanobacterial blooms in the OL and B&Gs. We also described the consequences of cyanobacterial blooms on food resources and fishing and on direct water use and water supply of local populations, with their potential consequences on the human health. Finally, we discuss the actions that have been taken for the protection of LV. Although many projects have been implemented in the past years in order to improve the management of waste waters or to reduce deforestation and erosion, the huge challenge of the reduction of cyanobacterial blooms in LV by the control of eutrophication seems far from being achieved.

Published
2020
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34. Toxic benthic freshwater cyanobacterial proliferations: Challenges and solutions for enhancing knowledge and improving monitoring and mitigation

Author

Tara G. McAllister, Laura A. Reitz, Timothy W. Davis, Keith Bouma-Gregson, Yvonne Vadeboncoeur, Kaytee Pokrzywinski, Jonathan Puddick, Arthur Zastepa, Ken G. Ryan, Haywood Dail Laughinghouse, Laura T. Kelly, Catherine Quiblier, Andrew McQueen, James M. Lazorchak, Susanna A. Wood, Jean-François Humbert, Cawthron Institute, Office of informationmanagement and analysis, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agronomy department, Office of Research and Development, Te Pūnaha Matatini Centre of Research Excellence for Complex Systems, Environmental Laboratory, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université Paris Cité (UPCité), Department of Biological Sciences [Bowling Green], Bowling Green State University, School of Biological Sciences [Wellington, New Zealand], Victoria University of Wellington, Department of Biological Sciences [Dayton], Wright State University, Environment and Climate Change Canada, United States Department of Agriculture (USDA)FLA-FTL-005697Great Lakes Restoration Initiative Faculty of Science, Victoria University of Wellington 80837Royal Society of New ZealandCAW1601CSG-CAW1701National Institute of Water and Atmospheric Research Ltd, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Paris (UP)

Subjects
0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 010604 marine biology & hydrobiology, fungi, risk assessment, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 010501 environmental sciences, Aquatic Science, 01 natural sciences, 6. Clean water, Article, rivers, monitoring, cyanotoxins, 13. Climate action, Benthic zone, Environmental protection, lakes, Environmental science, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Risk assessment, 0105 earth and related environmental sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

1. This review summarises knowledge on the ecology, toxin production, and impacts of toxic freshwater benthic cyanobacterial proliferations. It documents monitoring, management, and sampling strategies, and explores mitigation options. 2. Toxic proliferations of freshwater benthic cyanobacteria (taxa that grow attached to substrates) occur in streams, rivers, lakes, and thermal and meltwater ponds, and have been reported in 19 countries. Anatoxin- and microcystin-containing mats are most commonly reported (eight and 10 countries, respectively). 3. Studies exploring factors that promote toxic benthic cyanobacterial proliferations are limited to a few species and habitats. There is a hierarchy of importance in environmental and biological factors that regulate proliferations with variables such as flow (rivers), fine sediment deposition, nutrients, associated microbes, and grazing identified as key drivers. Regulating factors differ among colonisation, expansion, and dispersal phases. 4. New -omics-based approaches are providing novel insights into the physiological attributes of benthic cyanobacteria and the role of associated microorganisms in facilitating their proliferation. 5. Proliferations are commonly comprised of both toxic and non-toxic strains, and the relative proportion of these is the key factor contributing to the overall toxin content of each mat. 6. While these events are becoming more commonly reported globally, we currently lack standardised approaches to detect, monitor, and manage this emerging health issue. To solve these critical gaps, global collaborations are needed to facilitate the rapid transfer of knowledge and promote the development of standardised techniques that can be applied to diverse habitats and species, and ultimately lead to improved management.

Published
2020
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35. Diversity, spatial distribution and activity of fungi in freshwater ecosystems

Author

Cécile Lepère, Mylène Hugoni, Ludwig Jardillier, Didier Debroas, Jean-François Humbert, Isabelle Domaizon, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), 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 Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), SENDEFO project - French ANR (National Research Agency) Contaminants-Ecosystems-Health (CES-2009), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
champignon, lcsh:Medicine, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, écosystème, Freshwater ecosystem, Microbiology, General Biochemistry, Genetics and Molecular Biology, 18S ribosomal RNA, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecosystem, 14. Life underwater, Dikarya, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, diversité, 030304 developmental biology, 0303 health sciences, Chytridiomycota, Freshwaters, Diversity, biology, Community, Ecology, 030306 microbiology, General Neuroscience, Aquatic ecosystem, lcsh:R, Fungi, General Medicine, Biodiversity, 15. Life on land, biology.organism_classification, 6. Clean water, Meta-analysis, eau douce, [SDE]Environmental Sciences, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences
Abstract

International audience; 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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36. Linking phytoplankton pigment composition and optical properties: A framework for developing remote-sensing metrics for monitoring cyanobacteria

Author

Gabriel Hmimina, Catherine Quiblier, Kevin Tambosco, Bruno J. Lemaire, Jean-François Humbert, Brigitte Vinçon-Leite, Kamel Soudani, Florence D. Hulot, Louise Audebert, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes et Interactions Toxiques, Université Paris Diderot - Paris 7 (UPD7), laboratoire Eau Environnement et Systèmes Urbains (LEESU), AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), ANR-13-ECOT-0001,OSS-CYANO,Développement d'un capteur optique et d'un système drone pour la surveillance spatiale des cyanobactéries dans les écosystèmes aquatiques continentaux(2013), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM), and ANR OSS-CYANO project, grant ANR-2013-Ecotechnologies and EcoServices (ECO-TS) of the French Agence Nationale de la Recherche

Subjects
Cyanobacteria, Chlorophyll, Environmental Engineering, [SDE.MCG]Environmental Sciences/Global Changes, 0208 environmental biotechnology, properties Optical, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, Algal bloom, Absorbance, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, indices Reflectance, Phytoplankton, Phycocyanin, Turbidity, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Absorption (electromagnetic radiation), [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Waste Management and Disposal, Ecosystem, 0105 earth and related environmental sciences, Water Science and Technology, Civil and Structural Engineering, MESH: Cyanobacteria, Cultures, Optical properties, Optical indices, Reflectance, biology, Ecological Modeling, Cyanobacteria Cultures Optical, Plankton, biology.organism_classification, Pollution, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 020801 environmental engineering, Remote Sensing Technology, Environmental science, Biological system, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Environmental Monitoring
Abstract

International audience; This study has been performed in the framework of a research program aiming to develop a low-cost aerial sensor for the monitoring of cyanobacteria in freshwater ecosystems that could be used for early detection. Several empirical and mechanistic remote-sensing tools have been already developed and tested at large scales and have proven useful in monitoring cyanobacterial blooms. However, the effectiveness of these tools for early detection is hard to assess because such work requires the detection of low concentrations of characteristic pigments amid complex ecosystems exhibiting several confounding factors (turbidity, blooms of other species, etc.). We developed a framework for performing high-throughput measurements of the absorbance and reflectance of small volumes (~= 20 mL) of controlled mixtures of phytoplankton species and studied the potential of this framework to validate remote-sensing proxies of cyanobacteria concentration. The absorption and reflectance spectra of single and multiple cultures carried a specific signal that allowed for the quantitative analysis of culture mixes. This specific signal was shown to be related to known pigment absorbance spectra. The concentrations of chlorophyll-a and -b, phycocyanin and phycoerythrin could be obtained from direct absorbance measurements and were correlated with the concentration obtained after pigment extraction (R2 ≥ 0.96 for all pigments). A systematic test of every possible two-band and three-band normalized difference between optical indices was then performed, and the coincidental correlation with chlorophyll-b (absent in cyanobacteria) was used as an indicator of non-specificity. Two-band indices were shown to suffer from non-specificity issues and could not yield strong and specific relationships with phycocyanin or phycoerythrin (maximum R2 0.8).

Published
2019
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37. Spatial and Temporal Variability in the Development and Potential Toxicity of Phormidium Biofilms in the Tarn River, France

Author

Maxime Tenon, Isidora Echenique-Subiabre, Catherine Quiblier, Jean-François Humbert, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Humbert, Jean Francois, and Quiblier, Catherine

Subjects
0106 biological sciences, 0301 basic medicine, Riffle, Health, Toxicology and Mutagenesis, lcsh:Medicine, river biofilms, Biology, Toxicology, Cyanobacteria, 01 natural sciences, Article, benthic cyanobacteria, 03 medical and health sciences, model II regression, Rivers, Water Pollutants, 14. Life underwater, mass spectrometry, biofilm development, Cyanobacteria Toxins, Ecology, 010604 marine biology & hydrobiology, lcsh:R, Biofilm, biochemical phenomena, metabolism, and nutrition, coefficient of determination, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Benthic zone, Water temperature, Biofilms, anatoxins, [SDE]Environmental Sciences, France, Potential toxicity, Environmental Monitoring, Tropanes
Abstract

International audience; Proliferation of Phormidium biofilms in rivers is becoming a worldwide sanitation problem for humans and animals, due to the ability of these bacteria to produce anatoxins. To better understand the environmental conditions that favor the development of Phormidium biofilms and the production of anatoxins, we monitored the formation of these biofilms and their toxins for two years in the Tarn River, biofilms from which are known to have caused the deaths of multiple dogs. As previously observed in New Zealand, Phormidium biofilm development occurred in riffle areas. The coverage of these biofilms at the bottom of the river exhibited strong spatial and temporal variations, but was positively correlated with water temperature and depth. Anatoxin-a was detected in less than 50% of the biofilms. The concentrations of these toxins in the biofilms exhibited high spatiotemporal variability, with the highest concentrations being recorded at the end of the summer period at the upstream sampling sites. These findings suggest that the maturity of the biofilms, combined with the local environmental conditions, have an impact on the production of anatoxin, making risk assessment for these benthic proliferations challenging.

Published
2018
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39. Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data

Author

Najwa Taib, Isabelle Domaizon, Cécile Lepère, Jean-François Humbert, Didier Debroas, Anne Oudart, Ludwig Jardillier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), 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), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), SENDEFO project - French ANR (National Research Agency) Contaminants-Ecosystems-Health, 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
0301 basic medicine, microbial eukaryotes, Bioinformatics, Applied Microbiology and Biotechnology, Microbiology, Freshwater ecosystem, Amoebozoa, 03 medical and health sciences, Monophyly, Microbial ecology, Cryptophyta, 14. Life underwater, Viridiplantae, freshwater, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS, Ecology, biology, Phylogenetic tree, Fungi, Eukaryota, bioinformatics, Plankton, biology.organism_classification, Lakes, 030104 developmental biology, metabarcoding, [SDE]Environmental Sciences, Species richness, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Stramenopiles
Abstract

International audience; Although they are widespread, diverse and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100 798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs, i.e. monophyletic groups of OTUs that are phylogenetically close). By summing the richness found in aquatic environments, we can predict the microbial eukaryotic richness to be around 200 000- 250 000 species. The molecular diversity of protists in freshwater environments is generally higher than that of the morphospecies and cultivated species catalogued in public databases. Amoebozoa, Viridiplantae, Ichthyosporea, and Cryptophyta are the most phylogenetically diverse taxa, and characterisation of these groups is still needed. A network analysis showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems. Finally, this work provides guidance for compiling metabarcoding data and identifies missing data that should be obtained to increase our knowledge on microbial eukaryote diversity.

Published
2017
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40. New Tools for the Monitoring of Cyanobacteria in Freshwater Ecosystems

Author

Jean-François Humbert and Andrea Törökné

Subjects
0106 biological sciences, Cyanobacteria, biology, Freshwater biology, Ecology, 010604 marine biology & hydrobiology, Environmental science, 010501 environmental sciences, biology.organism_classification, Bloom, 01 natural sciences, Freshwater ecosystem, 0105 earth and related environmental sciences
Published
2017
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41. Ecology of Cyanobacteria

Author

Jean-François Humbert and Jutta Fastner

Subjects
Cyanobacteria, biology, Ecology, Ecology (disciplines), 0208 environmental biotechnology, 02 engineering and technology, 010501 environmental sciences, Spatial distribution, biology.organism_classification, 01 natural sciences, 020801 environmental engineering, Environmental science, Bloom, 0105 earth and related environmental sciences
Published
2017
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43. Case Studies of Environmental Sampling, Detection, and Monitoring of Potentially Toxic Cyanobacteria

Author

Catherine Quiblier, Tomasz Jurczak, Katarzyna Izydorczyk, Isidora Echenique-Subiabre, Jutta Fastner, Mikołaj Kokociński, Kerstin Häggqvist, Mária Horecká, Antonio Quesada, Joanna Mankiewicz-Boczek, Reyhan Akçaalan, Jean-François Humbert, Tore Lindholm, and Nico Salmaso

Subjects
0301 basic medicine, Cyanobacteria, Sampling (statistics), 010501 environmental sciences, Biology, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Oceanography, Baltic sea, Environmental chemistry, Shallow lake, 0105 earth and related environmental sciences
Published
2017
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44. Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains

Author

Claire, Pancrace, Marie-Anne, Barny, Reiko, Ueoka, Alexandra, Calteau, Thibault, Scalvenzi, Jacques, Pédron, Valérie, Barbe, Joern, Piel, Jean-François, Humbert, Muriel, Gugger, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Collection des Cyanobactéries, Institut Pasteur [Paris], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut Pasteur [Paris] (IP), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut d'écologie et des sciences de l'environnement de Paris (IEES), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)

Subjects
SEQUENCE ALIGNMENT, Genome, FILAMENTOUS CYANOBACTERIA, GAS VESICLE GENES, RUBESCENS, DIVERSITY, Genetic Variation, Genomics, EVOLUTIONARY ORIGIN, SECONDARY METABOLISM, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Article, LAKE ZURICH, Oscillatoria, Microbiology, Ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], N-2 FIXATION, Genome, Bacterial, Phylogeny, NONHETEROCYSTOUS CYANOBACTERIA
Abstract

Planktothrix is a dominant cyanobacterial genus forming toxic blooms in temperate freshwater ecosystems. We sequenced the genome of planktic and non planktic Planktothrix strains to better represent this genus diversity and life style at the genomic level. Benthic and biphasic strains are rooting the Planktothrix phylogenetic tree and widely expand the pangenome of this genus. We further investigated in silico the genetic potential dedicated to gas vesicles production, nitrogen fixation as well as natural product synthesis and conducted complementary experimental tests by cell culture, microscopy and mass spectrometry. Significant differences for the investigated features could be evidenced between strains of different life styles. The benthic Planktothrix strains showed unexpected characteristics such as buoyancy, nitrogen fixation capacity and unique natural product features. In comparison with Microcystis, another dominant toxic bloom-forming genus in freshwater ecosystem, different evolutionary strategies were highlighted notably as Planktothrix exhibits an overall greater genetic diversity but a smaller genomic plasticity than Microcystis. Our results are shedding light on Planktothrix evolution, phylogeny and physiology in the frame of their diverse life styles. ISSN:2045-2322

Published
2017
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45. Basic guide to detection and monitoring of potentially toxic cyanobacteria

Author

James S. Metcalf, Jutta Fastner, Nico Salmaso, Andreas Ballot, Arnaud Catherine, Kerstin Häggqvist, Catherine Quiblier, Meriç Albay, Mária Horecká, Katarzyna Izydorczyk, Reyhan Akçaalan, Joanna Mankiewicz-Boczek, Cécile Bernard, Jiří Komárek, Jean-François Humbert, Selma Maloufi, Latife Köker, Antonio Quesada, and Claude Yéprémian

Subjects
0106 biological sciences, Cyanobacteria, Ecology, 010604 marine biology & hydrobiology, Settore BIO/07 - ECOLOGIA, Sampling design, Biological classification, 010501 environmental sciences, Biology, biology.organism_classification, 01 natural sciences, 0105 earth and related environmental sciences
Published
2017

47. Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach

Author

Lirong Song, Didier Debroas, Julie Leloup, Imen Louati, Cécile Bernard, Kevin Tambosco, Charlotte Duval, Lin Zhu, Anouk Zancarini, Silvia de Cesare, Jean-François Humbert, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Recherche pour le Développement (IRD [France-Ouest]), Centre National de la Recherche Scientifique (CNRS), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institute of Hydrobiology - State Key Laboratory of Freshwater Ecology and Biotechnology, Chinese Academy of Sciences [Changchun Branch] (CAS), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Sorbonne Université (SU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Freshwater Ecology and Biotechnology - Institute of Hydrobiology, PHYCOCYANO project in the Jeunes Chercheurs-Jeunes Chercheuses program of the French ANR (Agence Nationale de la Recherche) [ANR-11-JSV7-014-01], Hongyue Dang, Laboratoire LERMPS (LERMPS), Université de Technologie de Belfort-Montbeliard (UTBM), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie (Paris 6), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Sorbonne Universités, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Zhu, Lin, Zancarini, Anouk, Louati, Imen, Humbert, Jean Francois, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
0301 basic medicine, Microbiology (medical), Cyanobacteria, Operational taxonomic unit, bacterial communities, cyanobacteria, cultures, natural samples, functional and structural diversity, pyrosequencing, EcoPlates, [SDV]Life Sciences [q-bio], 030106 microbiology, lcsh:QR1-502, Zoology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Microbiology, lcsh:Microbiology, Actinobacteria, 03 medical and health sciences, Phytoplankton, Ecosystem, Organic matter, ComputingMilieux_MISCELLANEOUS, Original Research, chemistry.chemical_classification, biology, Ecology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, chemistry, Pyrosequencing, Species richness
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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48. Évaluation de la qualité des plans d’eau urbains et périurbains : apport des approches transdisciplinaires et régionalisées

Author

José-Frédéric Deroubaix, Brigitte Vinçon-Leite, Arnaud Catherine, Jean-François Humbert, Veronica Mitroi, Véronique Maleval, Laboratoire Dynamiques Sociales et Recomposition des Espaces (LADYSS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), laboratoire Eau Environnement et Systèmes Urbains (LEESU), AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne (UCA)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), 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), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Nanterre (UPN)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne (UCA), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), 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), Centre National de la Recherche Scientifique (CNRS)-Université Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université Paris Diderot - Paris 7 (UPD7), and Laboratoire Eau Environnement et Systèmes Urbains (LEESU)

Subjects
0208 environmental biotechnology, General Social Sciences, concertation, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, recherche transdisciplinaire, 020801 environmental engineering, lcsh:Social Sciences, lcsh:H, [SDE]Environmental Sciences, General Earth and Planetary Sciences, lcsh:Q, plans d’eau urbains et périurbains, coconstruction des indicateurs de qualité, lcsh:Science, General Agricultural and Biological Sciences, General Environmental Science
Abstract

International audience; Les plans d'eau urbains, mal connus et souvent perçus comme trop ordinaires ou artificiels, suscitent des attentes de la part des riverains, des usagers et des gestionnaires. De telles attentes qui renvoient à des lectures différentes des plans d'eau génèrent des tensions qui font de l'objectivation de leur état un enjeu cognitif fort. Cet article montre les difficultés rencontrées pour éta-blir une telle caractérisation qui soit acceptable par les diverses parties prenantes. À la suite de plusieurs articles parus dans la revue sur les enjeux de production d'indicateurs d'état du milieu (NSS 1997, 5, 2 ; 2014, 22, 1), cette contribution met en avant la nécessité de prendre en compte aussi bien les points de vue des scientifiques que ceux des gestionnaires et des usagers. Ce fai-sant, elle questionne de manière tout à fait pertinente le rôle politique de la production de connaissances sur des objets d'appa-rence anodine, faisant progresser notre compréhension de l'interface science-société, sur des questions environnementales. La Rédaction Résumé – Produire des indicateurs de qualité des écosystèmes aquatiques anthropisés tenant compte des différents usages qui leur sont associés est un défi important qui ne peut être relevé qu'à l'interface de la recherche et de l'action. Dans cette optique, les auteurs portent un regard rétrospectif sur le travail mené pendant quatre ans au sein du programme de recherche PULSE afin d'évaluer la qualité des plans d'eau en Île-de-France. Après avoir montré l'intérêt d'étudier les plans d'eau périurbains, nous présen-tons comment le projet PULSE aborde ces objets hybrides, à mi-chemin entre « infrastructure urbaine » et « milieu naturel », à travers une approche transdisciplinaire centrée sur les usages de ces espaces. Nous discutons de la diversité des savoirs, des critères de valorisation de l'état de ces écosystèmes et des actions de gestion à travers lesquels les acteurs définissent la « qualité d'un plan d'eau ». Nous montrons ensuite jusqu'à quel point la transdisciplinarité permet d'imaginer des systèmes de caractérisation inno-vants et adaptés à la spécificité régionale de ces milieux et à leurs différents usages, tout en sachant que l'évaluation de ces systèmes n'échappe cependant pas à la nécessité, tant pour les scientifiques que pour les gestionnaires, de se référer à des critères de qualité universels et normatifs.

Published
2016
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49. [François Humbert, an unknown orthopedist, initiator of cures for the 'lame']

Author

Antoine, Desseaux, Michel, Pionnier, Bernard, Guillemin, Alain Charles, Masquelet, Didier, Maynart, and François, Humbert

Subjects
Orthopedics, Scoliosis, Humans, History, 19th Century, France, History, 18th Century, Hip Dislocation, Congenital
Abstract

François Humbert (1776-1850) created in 1817 the first French orthopaedic institution, at a great turning point in orthopedics. Interested in "lame people" and "hunchbacks", he treated congenital hip dislocation and scoliosis, for about 30 years. Humbert's medical practice illustrated very well the deep transformation which occured in orthopedics at the beginning of the 19th century. As testimonies of Humbert's work, there are the books he published, his Memoirs, some buildings of his institution which have been reconverted into houses, but above all thirty-eight models of his "machines". In spite of the fact that he was the first to consider congenital hip dislocation like a curable disease, his work quickly became unknown after his death.

Published
2016

50. MOLECULAR CHARACTERIZATION OF THE DIVERSITY AND POTENTIAL TOXICITY OF CYANOBACTERIAL MATS IN TWO TROPICAL LAGOONS IN THE SOUTH PACIFIC OCEAN(1)

Author

Aurélie, Villeneuve, Dominique, Laurent, Mireille, Chinain, Muriel, Gugger, and Jean-François, Humbert

Abstract

Marine benthic cyanobacteria in tropical areas have recently been associated with several human poisoning events. To enhance the characterization of these microorganisms and their potential toxicity, benthic cyanobacterial communities were sampled in the lagoons of two islands (Raivavae and Rurutu) located in French Polynesia where human poisoning events by seafood had been reported. The morphological appearance of the mats was used to identify four types of cyanobacterial mat. By a 16S rRNA sequencing approach, it appeared that these mats were usually dominated by a restricted number of operational taxonomic units (OTUs), which were closely related to Leptolyngbya, Oscillatoria, Hydrocoleum, and Anabaena sequences, as previously reported in other tropical lagoons. Interestingly, we determined that these dominant filamentous OTUs were associated in the mats with other cyanobacteria, including unicellular species. By using a population genetic approach based on the sequencing of the internally transcribed spacer (ITS) of the rRNA operon, we found a very restricted genetic diversity in the most common OTU, which displayed a high sequence similarity with Leptolyngbya sp. In addition, there was no geographic differentiation at various spatial scales in the distribution of the different genotypes, suggesting that this species is able to spread over large distances. Finally, PCR screening of genes involved in the biosynthesis of known cyanotoxins revealed the presence of the saxitoxin gene (stxG) in two mats containing a mix of filamentous and unicellular cyanobacterial species.

Published
2016

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