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23 results on '"Jérôme Hamelin"'

1. Polyhydroxybutyrate Production from Methane and Carbon Dioxide by a Syntrophic Consortium of Methanotrophs with Oxygenic Photogranules without an External Oxygen Supply

Author

Selim Ashoor, Seong-Hoon Jun, Han Do Ko, Jinwon Lee, Jérôme Hamelin, Kim Milferstedt, and Jeong-Geol Na

Subjects
Microbiology (medical), Virology, greenhouse gas mitigation, polyhydroxybutyrate, syntrophic process, methanotrophy, oxygenic photogranules, Microbiology
Abstract

Here, a syntrophic process was developed to produce polyhydroxy-β-butyrate (PHB) from a gas stream containing CH4 and CO2 without an external oxygen supply using a combination of methanotrophs with the community of oxygenic photogranules (OPGs). The co-culture features of Methylomonas sp. DH-1 and Methylosinus trichosporium OB3b were evaluated under carbon-rich and carbon-lean conditions. The critical role of O2 in the syntrophy was confirmed through the sequencing of 16S rRNA gene fragments. Based on their carbon consumption rates and the adaptation to a poor environment, M. trichosporium OB3b with OPGs was selected for methane conversion and PHB production. Nitrogen limitation stimulated PHB accumulation in the methanotroph but hindered the growth of the syntrophic consortium. At 2.9 mM of the nitrogen source, 1.13 g/L of biomass and 83.0 mg/L of PHB could be obtained from simulated biogas. These results demonstrate that syntrophy has the potential to convert greenhouse gases into valuable products efficiently.

Published
2023
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2. Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer

Author

Nicolas Bernet, Eric Trably, Roman Moscoviz, Jérôme Hamelin, Elie Desmond-Le Quéméner, Centre International de Recherche Sur l'Eau et l'Environnement [Suez] (CIRSEE), SUEZ ENVIRONNEMENT (FRANCE), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Microbiology (medical), Electron exchange, Electrons, Biology, Microbiology, Electron Transport, 03 medical and health sciences, Electron transfer, Microbial ecology, Syntrophy, Virology, interspecies energy coupling, Electrodes, 030304 developmental biology, Mutualism (biology), 0303 health sciences, extracellular electron transfer, Bacteria, Ecology, 030306 microbiology, [SDE.IE]Environmental Sciences/Environmental Engineering, Microbiota, Infectious Diseases, ecological interactions, Fermentation, Biochemical engineering, electroactive microorganisms, Energy Metabolism, electromicrobiology, Biotechnology
Abstract

Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote competitive and even parasitic behaviour. Based on three interesting case studies identified from the literature, we also highlight that such nonmutualistic interactions could be widespread and of particular significance for the survival of pathogens or the shaping of complex microbial communities.

Published
2020
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3. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

Author

Jean Jacques Godon, Marie Léa De Almeida, Olivier Zemb, Laurent Cauquil, Jérôme Hamelin, Caroline S. Achard, Béatrice Gabinaud, Lisanne M G Verschuren, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lallemand SAS, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Topigs Norsvin Res Ctr BV, Livestock Research, Wageningen University and Research [Wageningen] (WUR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), France Génomique National, Agence Nationale pour la Recherche. Grant Number: ANR‐10‐INBS‐09, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], 16SrRNA gene, méthode de mesure, spike-in, lcsh:QR1-502, microbiome, Biotechnologies, Computational biology, Biology, Real-Time Polymerase Chain Reaction, Microbiology, lcsh:Microbiology, 16S rRNA gene, Absolute count data, Metabarcoding, Microbiome, Normalization, Spike‐in, 03 medical and health sciences, RNA, Ribosomal, 16S, Environmental Microbiology, DNA Barcoding, Taxonomic, Fokkerij & Genomica, Gene, Relative species abundance, Illumina dye sequencing, 030304 developmental biology, Gram, 0303 health sciences, communauté microbienne, Base Sequence, 030306 microbiology, Microbiota, absolute count data, High-Throughput Nucleotide Sequencing, Original Articles, Biodiversity, Sequence Analysis, DNA, 16S ribosomal RNA, DNA extraction, Hypervariable region, spike‐in, normalization, Real-time polymerase chain reaction, [SDE]Environmental Sciences, metabarcoding, Metagenome, Original Article, Metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Breeding & Genomics
Abstract

Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts., Here, we present a spike‐and‐recovery method to get quantitative estimates from 16S rRNA surveys. The method relies on adding an artificial strand of DNA to the lysis buffer before the DNA extraction and measuring its recovery either by direct sequencing or by quantitative polymerase chain reaction (qPCR). The low detection limit achieved by qPCR allows to add minute amounts of the internal standard so that the sequencing effort is focused on the unknown sequences.

Published
2020
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4. Screening and Application of Ligninolytic Microbial Consortia to Enhance Aerobic Degradation of Solid Digestate

Author

Ulysse Brémond, Aude Bertrandias, Jérôme Hamelin, Kim Milferstedt, Valérie Bru-Adan, Jean-Philippe Steyer, Nicolas Bernet, and Hélène Carrere

Subjects
Microbiology (medical), Virology, food and beverages, anaerobic digestion, biogas, solid digestate, aerobic consortia, lignin, bioaugmentation, Microbiology
Abstract

Recirculation of solid digestate through digesters has been demonstrated to be a potential simple strategy to increase continuous stirred-tank reactor biogas plant efficiency. This study extended this earlier work and investigated solid digestate post-treatment using liquid isolated ligninolytic aerobic consortia in order to increase methane recovery during the recirculation. Based on sampling in several natural environments, an enrichment and selection method was implemented using a Lab-scale Automated and Multiplexed (an)Aerobic Chemostat system to generate ligninolytic aerobic consortia. Then, obtained consortia were further cultivated under liquid form in bottles. Chitinophagia bacteria and Sordariomycetes fungi were the two dominant classes of microorganisms enriched through these steps. Finally, these consortia where mixed with the solid digestate before a short-term aerobic post-treatment. However, consortia addition did not increase the efficiency of aerobic post-treatment of solid digestate and lower methane yields were obtained in comparison to the untreated control. The main reason identified is the respiration of easily degradable fractions (e.g., sugars, proteins, amorphous cellulose) by the selected consortia. Thus, this paper highlights the difficulties of constraining microbial consortia to sole ligninolytic activities on complex feedstock, such as solid digestate, that does not only contain lignocellulosic structures.

Published
2022
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5. Examination of Gould's modified S1 (mS1) selective medium and Angle's non-selective medium for describing the diversity of Pseudomonas spp. in soil and root environments

Author

Michel Aragno, Jérôme Hamelin, Nathalie Fromin, Laurent Locatelli, Sonia Estelle Tarnawski, Microbiology laboratory, Université de Neuchâtel (UNINE), Microbiology Laborarory, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
food.ingredient, [SDE.MCG]Environmental Sciences/Global Changes, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, food, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Botany, Agar, Ribosomal DNA, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Genetic diversity, Rhizosphere, Ecology, biology, 030306 microbiology, Pseudomonas, Spacer DNA, 15. Life on land, biology.organism_classification, Pseudomonadales, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, Pseudomonadaceae, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Studies on the diversity of environmental culturable Pseudomonas populations are dependent on the isolation procedure. This procedure includes the use of selective media which may influence the recovery of strains and thus the diversity described. In this study, we assessed the use of two agar isolation media for describing the diversity of soil- and root-inhabiting Pseudomonas associated with the perennial grass Molinia coerulea. A total of 382 Pseudomonas strains were recovered on either non-selective Angle's medium, or on Gould's modified S1 (mS1) Pseudomonas-selective medium. Their diversity was assessed by restriction analysis of PCR (polymerase chain reaction)-amplified 16S-23S rDNA internal transcript spacer sequences. The comparison of mS1- and Angle-recovered populations showed that the use of mS1 selective medium led to an underestimation of both Pseudomonas counts and diversity, especially in the soil environment.

Published
2017
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6. Biofilm development during the start‐up period of anaerobic biofilm reactors: the biofilm Archaea community is highly dependent on the support material

Author

Nicolas Bernet, Jérôme Hamelin, Frédéric Habouzit, Gaëlle Santa-Catalina, Jean-P. Steyer, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
0106 biological sciences, Limiting factor, [SDV]Life Sciences [q-bio], Bioengineering, 010501 environmental sciences, Biology, Bacterial Physiological Phenomena, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Microbiology, Bioreactors, Microbial ecology, 010608 biotechnology, Environmental Microbiology, Bioreactor, Colonization, Anaerobiosis, Food science, Polymorphism, Single-Stranded Conformational, Research Articles, 0105 earth and related environmental sciences, Bacteria, Biofilm, Electrophoresis, Capillary, biology.organism_classification, Archaea, Biota, Biofilms, [SDE]Environmental Sciences, Methane, Anaerobic exercise, Biotechnology
Abstract

International audience; To evaluate the impact of the nature of the support material on its colonization by a methanogenic consortium, four substrata made of different materials: polyvinyl chloride, 2 polyethylene and polypropylene were tested during the start-up of lab-scale fixed-film reactors. The reactor performances were evaluated and compared together with the analysis of the biofilms. Biofilm growth was quantified and the structure of bacterial and archaeal communities were characterized by molecular fingerprinting profiles (capillary electrophoresis-single strand conformation polymorphism). The composition of the inoculum was shown to have a major impact on the bacterial composition of the biofilm, whatever the nature of the support material or the organic loading rate applied to the reactors during the start-up period. In contrast, the biofilm archaeal populations were independent of the inoculum used but highly dependent on the support material. Supports favouring Archaea colonization, the limiting factor in the overall process, should be preferred.

Published
2014
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7. Influence of support material properties on the potential selection of Archaea during initial adhesion of a methanogenic consortium

Author

Jérôme Hamelin, Nicolas Bernet, Frédéric Habouzit, Gaëlle Gévaudan, Jean-Philippe Steyer, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Environmental Engineering, ANAEROBIC DIGESTION, Microbial metabolism, Biomass, Bioengineering, 010501 environmental sciences, Polymerase Chain Reaction, Waste Disposal, Fluid, 01 natural sciences, Bacterial Adhesion, Water Purification, Microbiology, Species Specificity, 010608 biotechnology, Food science, MICROBIAL ADHESION, Waste Management and Disposal, Polymorphism, Single-Stranded Conformational, DNA Primers, SURFACE PROPERTIES, 0105 earth and related environmental sciences, Bacteria, biology, Renewable Energy, Sustainability and the Environment, Biofilm, Electrophoresis, Capillary, General Medicine, Adhesion, BIOLOGIE MOLECULAIRE, biology.organism_classification, Archaea, Biota, DNA Fingerprinting, 6. Clean water, Anaerobic digestion, Biofilms, COMMUNITY STRUCTURE, Waste disposal
Abstract

International audience; In anaerobic wastewater treatment systems, the complex microbial biomass including Archaea and Bacteria can be retained as a biofilm attached to solid supports . The aim of this study was to evaluate the impact of specific properties of support material on early microbial adhesion. Seven different substrata are described in terms of topography and surface energy. Adhesion of a methanogenic consortium to these substrata was tested, the adhesion was quantified as a percentage of the surface area covered and the bacterial and archaeal community structures was assessed by molecular fingerprinting profiles (CE-SSCP). As expected, the overall adhesion on the supports was influenced mainly by total surface energy. Moreover, the adhered communities were different from the parent inocula, including the Archaea/Bacteria ratio. This could have a significant impact on the start-up of anaerobic digesters for which supports favoring Archaea adhesion, responsible for the limiting reaction of the process, should be preferred.

Published
2011
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8. Spatial and temporal variations of the bacterial community in the bovine digestive tract

Author

Jérôme Hamelin, Valérie Monteils, Thierry Gidenne, Laurent Cauquil, R. J. Michelland, Laurence Fortun-Lamothe, Sylvie Combes, Asma Zened, Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut National de la Recherche Agronomique (INRA)

Subjects
DNA, Bacterial, Rumen, Microorganism, Zoology, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, Feces, 03 medical and health sciences, Microbial ecology, RNA, Ribosomal, 16S, Benzene Derivatives, medicine, Animals, Large intestine, CE-SSCP, Polymorphism, Single-Stranded Conformational, BACTERIES, PARAMETRES ENVIRONNEMENTAUX, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Bacteria, biology, 030306 microbiology, Community structure, Electrophoresis, Capillary, Biodiversity, General Medicine, biology.organism_classification, Gastrointestinal Tract, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, medicine.anatomical_structure, Cattle, Propionates, Reticulum, Biotechnology
Abstract

Aims: Improved knowledge of the bacterial community of the digestive tract is required to enhance the efficiency of digestion in herbivores. This work aimed to study spatial and temporal variations of the bacterial communities in the bovine digestive tract and their correlation with gut environmental parameters. Methods and Results: Rumen content and faeces of five cows were sampled for 3 weeks. In addition, reticulum content was sampled during the third week. Bacterial communities were assessed by studying capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. The bacterial community structure differed between the forestomach and faecal contents. The abundance of several operational taxonomic units changed from week to week. Bacterial community structure of the rumen was correlated to propionic acid and NH3–N concentrations. Conclusions: The bacterial community of the bovine digestive tract varied in space and time. Significance and Impact of the Study: The study of the bacterial communities of the digestive tract in herbivores should be widened from the rumen to the large intestine. The amplitude and origin of the temporal variation of the ruminal bacterial community need to be better understood to improve the control of the fermentative activity in herbivores.

Published
2009
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9. Structural divergence of bacterial communities from functionally similar laboratory-scale vermicomposts assessed by PCR-CE-SSCP

Author

Valérie Bru-Adan, Biswarup Sen, T.S. Chandra, Jérôme Hamelin, Jean-Jacques Godon, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Indian Institute of Technology Madras (IIT Madras), and Department of Biotechnology

Subjects
DYNAMICS, DNA, Bacterial, VERMICOMPOSTING, RDA, Biology, engineering.material, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, Soil, 03 medical and health sciences, RNA, Ribosomal, 16S, Animals, Ecosystem, Food science, CE-SSCP, Polymorphism, Single-Stranded Conformational, Soil Microbiology, 030304 developmental biology, 0303 health sciences, Bacteria, 030306 microbiology, Community structure, 16S RIBOSOMAL RNA, Electrophoresis, Capillary, General Medicine, BIOLOGIE MOLECULAIRE, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, qPCR, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Microbial population biology, Multivariate Analysis, engineering, carbon, cellulose, nitrogen, bacterium, community structure, compost, divergence, electrokinesis, gel, laboratory method, multivariate analysis, physicochemical property, polymerase chain reaction, polymorphism, RNA, bacterial gene, capillary electrophoresis, community dynamics, composting, concentration (parameters), genetic variability, microbial community, nonhuman, parameter, pH, physical chemistry, RNA fingerprinting, single strand conformation polymorphism, temperature dependence, vermicompost, Bacteria (microorganisms), Soil microbiology, Vermicompost, Biotechnology
Abstract

Aims: To evaluate bacterial community structure and dynamics in triplicate vermicomposts made from the same start-up material, along with certain physico-chemical changes. Methods and Results: The physico-chemical parameters (pH, temperature, carbon, nitrogen, soluble substances and cellulose) evolved similarly in the triplicate vermicomposts, indicating a steady function. The 16S bacterial gene abundance remained constant over time. To monitor changes in the bacterial community structure, fingerprinting based on capillary electrophoresis single-strand conformation polymorphism was employed. A rise in bacterial diversity occurred after precomposting and it remained stable during the maturation phase. However, a rapid shift in the structure of the bacterial community in the vermicompost replicates was noted at the beginning that stabilized with the process maturation. Multivariate analyses showed different patterns of bacterial community evolution in each vermicompost that did not correlate with the physico-chemical changes. Conclusions: The broad-scale functions remained similar in the triplicates, with stable bacterial abundance and diversity despite fluctuation in the community structure. Significance and Impact of the Study: This study has demonstrated that microbial fingerprinting with multivariate analysis can provide significant understanding of community structure and also clearly suggests that an ecosystem’s efficacy could be the outcome of functional redundancy whereby a number of species carry out the same function.

Published
2008
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10. How to use molecular biology tools for the study of the anaerobic digestion process?

Author

Angela Cabezas, Jérôme Hamelin, Juliana Calábria de Araújo, Diana Machado de Sousa, Amandine Galès, Cecilia Callejas, Eric Trably, Claudia Etchebehere, Antonella Marone, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Universidad ORT Uruguay, Universidade Federal de Minas Gerais, Universidad de la República, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), Funding agencies and projects ANII FSE 6437 and FCE 7062, Marie Curie Intra European Fellowship WASTE2BIOHY (FP7-MC- IEF-326974), ANR-14-CE04-0011, ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), European Project: 326974,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IEF,WASTE2BIOHY(2013), and Universidad de la República [Montevideo] (UDELAR)

Subjects
Environmental Engineering, Process (engineering), Molecular biology, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Bioreactor, Biology, Complex ecosystem, Microbial resource management, Applied Microbiology and Biotechnology, Microbiology, 12. Responsible consumption, Microbial ecology, Key point, Microbiologie, Anaerobic digestion, Function, Function (engineering), Waste Management and Disposal, media_common, WIMEK, business.industry, Pollution, 6. Clean water, Biotechnology, 13. Climate action, [SDE]Environmental Sciences, Biochemical engineering, business
Abstract

International audience; Anaerobic digestion is used with success for the treatment of solid waste, urban and industrial effluents with a concomitant energy production. The process is robust and stable, but the complexity of the microbial community involved in the process is not yet fully comprehensive. Nowadays, the study of this complex ecosystem is facilitated by the availability of different molecular tools, but it is very important to choose the adequate tool to answer specific questions. The aim of this review is to describe different molecular techniques, indicate the questions that can be addressed by each technique, enumerate their limitations and give practical advices for their use. Examples of how the molecular tools have been used to address various questions in anaerobic digestion are presented. The key point now is to apply all this information to improve anaerobic digestion. The integration of concepts of microbial-ecology, environmental-engineering, modeling and bioinformatics is currently necessary.

Published
2015
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11. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Author

David Roesti, Nathalie Fromin, S. Teyssier-Cuvelle, Jérôme Hamelin, Michel Aragno, K. Jourdain-Miserez, Pierre Rossi, François Gillet, Sonia Estelle Tarnawski, and N. Forestier

Subjects
Gel electrophoresis, 0303 health sciences, 030306 microbiology, Ecology, Visual interpretation, Data interpretation, Single band, Computational biology, Biology, Microbiology, Molecular analysis, 03 medical and health sciences, Microbial ecology, Animal ecology, Statistical analysis, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.

Published
2002
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12. Co-evolution between Frankia populations and host plants in the family Casuarinaceae and consequent patterns of global dispersal

Author

Jérôme Hamelin, Philippe Normand, Yvon Dommergues, Anne-Marie Domenach, Jeffrey O. Dawson, Pascal Simonet, René Bardin, Jeff F. Zimpfer, Paul Reddell, François Gourbière, Pilar Combarro, Elisabeth Navarro, Carole Rouvier, Yves Prin, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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
0106 biological sciences, Phylogénie, Casuarinaceae, Root nodule, [SDV]Life Sciences [q-bio], Frankia, Symbiose, Myrica, Casuarina, Plant Roots, Polymerase Chain Reaction, 01 natural sciences, Microbiology, Polymère, 03 medical and health sciences, Symbiosis, Nitrogen Fixation, RNA, Ribosomal, 16S, Actinomycetales, DNA, Ribosomal Spacer, Botany, Rosales, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Allocasuarina, biology, Host (biology), P34 - Biologie du sol, 15. Life on land, biology.organism_classification, Biological Evolution, Polymorphism, Restriction Fragment Length, 010606 plant biology & botany
Abstract

International audience; Symbioses between the root nodule-forming, nitrogen-fixing actinomycete Frankia and its angiospermous host plants are important in the nitrogen economies of numerous terrestrial ecosystems. Molecular characterization of Frankia strains using polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) analyses of the 16S rRNA-ITS gene and of the nifDnifK spacer was conducted directly on root nodules collected worldwide from Casuarina and Allocasuarina trees. In their native habitats in Australia, host species contained seven distinctive sets of Frankia in seven different molecular phylogenetic groups. Where Casuarina and Allocasuarina trees are newly planted outside Australia, they do not normally nodulate unless Frankia is introduced with the host seedling. Nodules from Casuarina trees introduced outside Australia over the last two centuries were found to contain Frankia from only one of the seven phylogenetic groups associated with the host genus Casuarina in Australia. The phylogenetic group of Frankia found in Casuarina and Allocasuarina trees introduced outside Australia is the only group that has yielded isolates in pure culture, suggesting a greater ability to survive independently of a host. Furthermore, the Frankia species in this group are able to nodulate a wider range of host species than those in the other six groups. In baiting studies, Casuarina spp. are compatible with more Frankia microsymbiont groups than Allocasuarina host spp. adapted to drier soil conditions, and C. equisetifolia has broader microsymbiont compatibility than other Casuarina spp. Some Frankia associated with the nodular rhizosphere and rhizoplan, but not with the nodular tissue, of Australian hosts were able to nodulate cosmopolitan Myrica plants that have broad microsymbiont compatibility and, hence, are a potential host of Casuarinaceae-infective Frankia outside the hosts' native range. The results are consistent with the idea that Frankia symbiotic promiscuity and ease of isolation on organic substrates, suggesting saprophytic potential, are associated with increased microsymbiont ability to disperse and adapt to diverse new environments, and that both genetics and environment determine a host's nodular microsymbiont.

Published
1999
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13. Robust estimation of microbial diversity in theory and in practice

Author

Jérôme Hamelin, Peter Neal, Joshua S. Weitz, Bart Haegeman, Jonathan Dushoff, John Moriarty, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-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 de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Department of Mathematics [Manchester] (School of Mathematics), University of Manchester [Manchester], Lancaster University, McMaster University [Hamilton, Ontario], Georgia Institute of Technology [Atlanta], French National Research Agency (ANR) [AAP215-SYSCOMM-2009], British Council, French Foreign Affairs Ministry [22732SJ], Burroughs Wellcome Fund, ANR-09-SYSC-0003,DISCO,Modélisation multi-échelles du COuplage bioDIversité Structure dans les biofilms(2009), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Modelling and Optimisation of the Dynamics of Ecosystems with MICro-organisme (MODEMIC), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Centre for Biodiversity Theory and Modelling, Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Department of Mathematics and Statistics, Department of Biology and Institute of Infectious Disease Research, and School of Biology and School of Physics

Subjects
Hill diversities, Gamma diversity, Simpson diversity, Rare species, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Biodiversity, Chao estimator, Biology, Microbiology, 03 medical and health sciences, Computer Simulation, Seawater, Quantitative Biology - Populations and Evolution, Ecology, Evolution, Behavior and Systematics, Relative abundance distribution, Soil Microbiology, 030304 developmental biology, 0303 health sciences, Bacteria, 030306 microbiology, Ecology, Populations and Evolution (q-bio.PE), Species diversity, 15. Life on land, respiratory system, Archaea, Metagenomics, FOS: Biological sciences, metagenomics, Shannon diversity, species abundance distribution, Regression Analysis, Alpha diversity, Original Article, Species richness, human activities
Abstract

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity., Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figures

Published
2013
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14. In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

Author

Philippe N. Bertin, Jérôme Hamelin, Dimitri Heintz, Christine Carapito, Corinne Casiot, Guillaume Tcherkez, Sebastien Gallien, Christine Schaeffer, Florence Goulhen-Chollet, Alain Van Dorsselaer, Françoise Gilard, Florence Arsène-Ploetze, David Halter, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Institut de Biologie des Plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche [ANR 07-BLANC-0118], French Ministry of Education and Research, and ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007)

Subjects
Metabolite, [SDV]Life Sciences [q-bio], Biology, Photosynthesis, medicine.disease_cause, Microbiology, Euglena, Mining, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, proteomics, Botany, parasitic diseases, medicine, Organic matter, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecosystem, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, 030306 microbiology, Aquatic ecosystem, fungi, Euglena mutabilis, Protist, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Metabolism, 15. Life on land, biology.organism_classification, chemistry, [SDE]Environmental Sciences, Original Article, France, Acids, primary production
Abstract

International audience; Euglena mutabilis is a photosynthetic protist found in acidic aquatic environments such as peat bogs, volcanic lakes and acid mine drainages (AMDs). Through its photosynthetic metabolism, this protist is supposed to have an important role in primary production in such oligotrophic ecosystems. Nevertheless, the exact contribution of E. mutabilis in organic matter synthesis remains unclear and no evidence of metabolite secretion by this protist has been established so far. Here we combined in situ proteo-metabolomic approaches to determine the nature of the metabolites accumulated by this protist or potentially secreted into an AMD. Our results revealed that the secreted metabolites are represented by a large number of amino acids, polyamine compounds, urea and some sugars but no fatty acids, suggesting a selective organic matter contribution in this ecosystem. Such a production may have a crucial impact on the bacterial community present on the study site, as it has been suggested previously that prokaryotes transport and recycle in situ most of the metabolites secreted by E. mutabilis. Consequently, this protist may have an indirect but important role in AMD ecosystems but also in other ecological niches often described as nitrogen-limited.

Published
2012
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15. Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge

Author

I. Taleb, Nur Hazlin Hazrin-Chong, Mike Manefield, Matthew Lee, Jérôme Hamelin, Olivier Zemb, Maria-Luisa Gutierrez-Zamora, Kirsten Coupland, ProdInra, Migration, Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], University of New South Wales [Sydney] (UNSW), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDE] Environmental Sciences, Environmental Engineering, [SDV]Life Sciences [q-bio], Stable isotope probing, Molecular Sequence Data, Stable-isotope probing, [INFO] Computer Science [cs], Microbiology, Microbial ecology, 03 medical and health sciences, chemistry.chemical_compound, Phenols, RNA, Ribosomal, 16S, [INFO]Computer Science [cs], Waste Management and Disposal, Endocrine disruptors, Phylogeny, 030304 developmental biology, Water Science and Technology, Civil and Structural Engineering, Phylotype, 0303 health sciences, Carbon Isotopes, biology, Environmental microbiology, Bacteria, Sewage, 030306 microbiology, Sequence Analysis, RNA, Ecological Modeling, Temperature, RNA, Electrophoresis, Capillary, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, Pollution, Nonylphenol, [SDV] Life Sciences [q-bio], Biodegradation, Environmental, Biochemistry, chemistry, Isotope Labeling, [SDE]Environmental Sciences, Pyrosequencing, Waste water
Abstract

International audience; Nonylphenols (NP) have estrogenic potential because of their phenolic ring, but the organisms involved in the degradation of this alkylated phenol remain unidentified. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP) and a new method based on pyrosequencing, we identified the bacteria involved in the degradation of the aromatic ring of [U-ring-13C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5 d−1. Single strand conformation polymorphism of density-separated labeled and unlabeled 16S rRNA showed significant differences and enabled selection of four representative fractions for pyrosequencing. Nineteen phylotypes showed a significant enrichment in the heavy fraction in the labeled pulse. The relative abundances of these phylotypes were combined with the RNA concentration of each fraction to yield a simple model of the distribution of each phylotype across the gradient. This model was used to estimate the percentage of labeling for each phylotype. The sequences showing the highest labeling (11%) were closely related to Afipia sp. but represented only 2 % of the RNA in the heavy fraction of the labeled pulse. The sequences representing the largest proportion of the RNA in the heavy fraction were related to Propionibacterium acnes and Frateuria aurantia, which are known to possess enzymes for phenol degradation. The model shows that despite Afipia having the highest 13C enrichment, other species encoding phenol degradation pathways are responsible for more 13C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% 13C above natural abundance.

Published
2011

16. Development and application of an enzymatic and cell flotation treatment for the recovery of viable microbial cells from environmental matrices such as anaerobic sludge

Author

Jérôme Hamelin, Gaëlle Gévaudan, Dominique Patureau, Florence Braun, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), and We gratefully acknowledge the financial support given for this research by the Agence de l'Environnement et de la Maitrise de l'Energie (ADEME) and the Institut National de la Recherche Agronomique (INRA). This work has been funded by ADEME (convention number: 0906C0008) from the Programme National de Recherche sur les Perturbateurs Endocriniens (PNRPE).

Subjects
Microbiological Techniques, Microorganism, [SDV]Life Sciences [q-bio], Colony Count, Microbial, Cellulase, Biology, Applied Microbiology and Biotechnology, cell survival, Microbiology, 03 medical and health sciences, Bacteria, Anaerobic, Microbial ecology, Methods, Environmental Microbiology, Food science, Pectinase, bacteria, 030304 developmental biology, biodiversity, 0303 health sciences, Microbial Viability, Ecology, Sewage, 030306 microbiology, microbiology, Biofilm, Archaea, DNA Fingerprinting, 6. Clean water, Enzymes, Microbial population biology, biotechnology and applied microbiology, [SDE]Environmental Sciences, biology.protein, Sewage treatment, metabolism, Food Science, Biotechnology
Abstract

Efficient dissociation of microorganisms from their aggregate matrix is required to study the microorganisms without interaction with their native environment (e.g., biofilms, flocs, granules, etc.) and to assess their community composition through the application of molecular or microscopy techniques. To this end, we combined enzymatic treatments and a cell extraction by density gradient to efficiently recover anaerobic microorganisms from urban wastewater treatment plant sludge. The enzymes employed (amylase, cellulase, DNase, and pectinase) as a pretreatment softly disintegrated the extrapolymeric substances (EPS) interlocked with the microorganisms. The potential damaging effects of the applied procedure on bacterial and archaeal communities were assessed by studying the variations in density (using quantitative PCR), diversity (using capillary electrophoresis single-strand conformation polymorphism fingerprinting [CE-SSCP]), and activity (using a standard anaerobic activity test) of the extracted microorganisms. The protocol preserved the general capacity of the microbial community to produce methane under anaerobic conditions and its diversity; particularly the archaeal community was not affected in terms of either density or structure. This cell extraction procedure from the matrix materials offers interesting perspectives for metabolic, microscopic, and molecular assays of microbial communities present in complex matrices constituted by bioaggregates or biofilms.

Published
2011
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17. Distribution of Pseudomonas populations harboring phlD or hcnAB biocontrol genes is related to depth in vineyard soils

Author

Geneviève Défago, Yvan Moënne-Loccoz, Jérôme Hamelin, Miroslav Svercel, Brion Duffy, Plant pathology Group, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Population Genetics, University of Zürich [Zürich] (UZH), Microbiology laboratory, Université de Neuchâtel (UNINE), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Agroscope Changins-Wädenswil, Swiss Federal Research Station, Plant Protection Division (ACW), Federal Department of Economic Affairs DEA, 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), University of Zurich, Svercel, M, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universität Zürich [Zürich] = University of Zurich (UZH), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), University of Zürich [Zürich] ( UZH ), Université de Neuchâtel, Laboratoire de Biotechnologie de l'Environnement [Narbonne] ( LBE ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Agroscope Changins-Wädenswil, Swiss Federal Research Station, Plant Protection Division ( ACW ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )

Subjects
Population, Soil Science, Biology, Microbiology, Vineyard, 03 medical and health sciences, chemistry.chemical_compound, 10127 Institute of Evolutionary Biology and Environmental Studies, Pseudomonas, Botany, Monoculture, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 1111 Soil Science, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Rhizosphere, education.field_of_study, Ecotype, 030306 microbiology, Diacetylphloroglucinol, 2404 Microbiology, 4-Diacetylphloroglucinol Biological control Hydrogen cyanide Monoculture Pseudomonas Soil profiles Vitis, 04 agricultural and veterinary sciences, Viti, biology.organism_classification, Horticulture, chemistry, Biological control, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Soil horizon, 2,4-Diacetylphloroglucinol, 570 Life sciences, biology, 590 Animals (Zoology), Soil profiles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Hydrogen cyanide
Abstract

International audience; The abundance and population structure of pseudomonads in soils collected from long-(1006 years) and short-(54 years) term grapevine monocultures in Switzerland were examined across five soil horizons within the 1.20e1.35 m range. Soil samples were baited with grapevine, and rhizosphere pseudomonads containing the biocontrol genes phlD (2,4-diacetylphloroglucinol synthesis) and/or hcnAB (hydrogen cyanide synthesis) were analyzed by MPN-PCR. The numbers of total, phlDþ and hcnABþ pseudomonads decreased with depth by 1.5e2 log (short-term monoculture) and 3e3.5 log (long-term monoculture). In addition, the percentages of phlDþ (except in short-term monoculture) and hcnABþ pseudomonads were also lower in deeper horizons. RFLP-profiling of phlDþ and hcnABþ pseudomonads revealed three phlD and twelve hcnAB alleles overall, but the number of alleles for both decreased in relation to depth. The only phlD allele found in deeper horizons was also found in topsoil, whereas one hcnAB allele (k) found in deeper horizons in long-term monoculture was absent in the topsoil. This suggests that certain Pseudomonas ecotypes are adapted to specific depths. Four hcnAB alleles enabled discrimination between monocultures. We conclude that soil depth is a factor selecting phlD and hcnAB genotypes, and that the allelic diversity of the two biocontrol genes decreases with depth.

Published
2010
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18. Selective microbial aerosolization in biogas demonstrated by quantitative PCR

Author

Jean-Philippe Delgenès, Nathalie Wéry, Jean-Jacques Godon, Jérôme Hamelin, Marina Moletta-Denat, Valérie Bru-Adan, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), and Centre Scientifique et Technique du Bâtiment (CSTB)

Subjects
Environmental Engineering, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Microorganism, Colony Count, Microbial, Bioengineering, 010501 environmental sciences, medicine.disease_cause, Polymerase Chain Reaction, 01 natural sciences, 7. Clean energy, complex mixtures, Microbiology, 03 medical and health sciences, Propionibacterium acnes, Biogas, AEROSOLIZATION, medicine, Anaerobiosis, Waste Management and Disposal, Aerosolization, QUANTITATIVE REAL-TIME PCR, 0105 earth and related environmental sciences, Aerosols, MICROBIAL AEROSOLS, 0303 health sciences, Bacteria, Sewage, biology, 030306 microbiology, Renewable Energy, Sustainability and the Environment, AIR, REACTION EN CHAINE PAR POLYMERASE EN TEMPS REEL, General Medicine, respiratory system, BIOLOGIE MOLECULAIRE, biology.organism_classification, Archaea, Anaerobic digestion, Microscopy, Fluorescence, Microbial population biology, Biofuels, BIOGAS, Staphylococcus, MICROBIAL DIVERSITY
Abstract

Aerosolization of Bacteria, Archaea, Synergistes, Staphylococcus spp. and Propionibacterium acnes was investigated in situ with quantitative real-time PCR of DNA isolated from sludge and biogases of anaerobic digesters. The data revealed that in biogas, Staphylococcus spp. and P. acnes were, respectively, aerosolized 30 and 220 times more and Archaea and Synergistes, respectively, 8 and 20 times less aerosolized than Bacteria. This is the first demonstration of selective microbial aerosolization for anaerobic digestors microorganisms. This study illustrates the fact that some microbial groups, such as opportunistic pathogens, are more susceptible to be aerosolized, since they use air as a dissemination vector, and that this has to be taken in account when up-grading biogas into natural gas networks.

Published
2010
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19. Specific PCR Amplification for the Genus Pseudomonas Targeting the 3′ Half of 16S rDNA and the Whole 16S–23S rDNA Spacer

Author

Sonia Estelle Tarnawski, Michel Aragno, Jérôme Hamelin, Pierre Rossi, Nathalie Fromin, Laurent Locatelli, Microbiology Laborarory, Université de Neuchâtel (UNINE), Microbiology laboratory, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
DNA, Bacterial, Sequence analysis, [SDE.MCG]Environmental Sciences/Global Changes, Sequence alignment, Biology, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, law.invention, Conserved sequence, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Species Specificity, law, Pseudomonas, RNA, Ribosomal, 16S, DNA, Ribosomal Spacer, 3' Flanking Region, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Polymerase chain reaction, DNA Primers, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, Models, Genetic, 030306 microbiology, Sequence Analysis, DNA, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, 23S, Genes, Bacterial, RNA, Ribosomal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Primer (molecular biology), Sequence Alignment, Gammaproteobacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

A PCR protocol was developed for the selective amplification of a segment of the ribosomal RNA operon in Pseudomonas strains. Two specific conserved sequences suitable for PCR priming were identified in the middle of the 16S rDNA and at the very beginning of the 23S rDNA respectively. As a result, amplified region includes the 3′ half of the 16S rDNA with the whole 16S–23S rRNA Internal Transcripted Spacer (ITS1) sequence. The specificity of the primer set was checked on sequence databases and validated on collection strains and on one hundred soil bacterial isolates. Our results showed that both collection, soil-inhabiting Pseudomonas and some Pseudomonas-related Azotobacter DNAs could be amplified. This specific PCR for the detection of Pseudomonas strains was in good agreement with colony hybridisation using a Pseudomonas-specific probe. The targeted segment is relevant for a characterisation at the species (16S rDNA) as well as at the infraspecific (ITS1) levels. This PCR-based approach offers promising potential for the characterisation of environmental Pseudomonas populations.

Published
2006
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20. Phenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses

Author

Sonia Estelle Tarnawski, Jérôme Hamelin, Michel Aragno, Nathalie Fromin, Maryline Jossi, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Microbiology Laboratory, Université de Neuchâtel (UNINE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), 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)-Ecole Nationale Supérieure de Chimie de Rennes-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-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), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
Siderophore, Perennial plant, SIDEROPHORES, [SDE.MCG]Environmental Sciences/Global Changes, Hydrogen cyanide, Soil Science, AUXIN, Biology, Rhizobacteria, Microbiology, Lolium perenne, 03 medical and health sciences, chemistry.chemical_compound, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Nitrate, FACE, PLANT GROWTH PROMOTING RHIZOBACTERIA, Botany, RELATION PLANTE-SOL, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Rhizosphere, RAY GRASS ANGLAIS, 030306 microbiology, Pseudomonas, RHIZOSPHERE COMPETENCE, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, chemistry, ROOT COLONISATION, PGPR, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, NITRATE REDUCTION, HYDROGEN CYANIDE, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

The increasing atmospheric CO 2 content (pCO 2 ) is likely to modify the ecosystem functioning including rhizosphere bacteria that are directly dependent on rhizodeposition. This may include alteration of Pseudomonas populations that display phenotypic traits in relation with plant fitness. In the present study, 1228 Pseudomonas strains were isolated from the non-rhizosphere soil, rhizosphere soil and root fractions of perennial grassland systems: Lolium perenne and Molinia coerulea . Both plants were grown under ambient (36 Pa) and elevated (60 Pa) pCO 2 in the Swiss Free Air CO 2 Enrichment (FACE) system. Pseudomonas spp. were tested for their ability to produce auxin, siderophores and hydrogen cyanide, and to dissimilate nitrate. No effect of root proximity and elevated pCO 2 was observed on the proportions of auxin producers. For L. perenne and M. coerulea , siderophore and hydrogen cyanide Pseudomonas producers were stimulated in the root fraction. In contrast lower frequencies of nitrate reducers were observed in the root fraction compared to non-rhizosphere soil. The frequencies of siderophore producers and nitrate dissimilating strains were higher, and those of hydrogen cyanide producers lower, under elevated pCO 2 for L. perenne . This alteration of the phenotypic structure of Pseudomonas guild in the root fraction is discussed in relation with the physico-biochemical modifications of the rhizosphere condition via rhizodeposition and environmental changes occurring under elevated pCO 2 .

Published
2006
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21. Nitrogen fertiliser rate affects the frequency of nitrate-dissimilating Pseudomonas spp. in the rhizosphere of Lolium perenne grown under elevated pCO2 (Swiss FACE)

Author

Sonia Estelle Tarnawski, Nathalie Fromin, L. Roussel-Delif, Michel Aragno, Elizabeth M. Baggs, Jérôme Hamelin, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Institut des Sciences Chimiques de Rennes (ISCR), 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 de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Microbiology Laboratory, Université de Neuchâtel (UNINE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-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 Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Perennial plant, N AVAILABILITY, [SDE.MCG]Environmental Sciences/Global Changes, ELEVATED ATMOSPHERIC CARBON DIOXIDE, Soil Science, chemistry.chemical_element, 010603 evolutionary biology, 01 natural sciences, Microbiology, Lolium perenne, chemistry.chemical_compound, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Nitrate, Poaceae, NITRATE DISSIMILATION, ComputingMilieux_MISCELLANEOUS, Rhizosphere, RAY GRASS ANGLAIS, biology, RHIZOSPHERE, 04 agricultural and veterinary sciences, Herbaceous plant, biology.organism_classification, Nitrogen, Agronomy, chemistry, 040103 agronomy & agriculture, Trifolium repens, 0401 agriculture, forestry, and fisheries, PSEUDOMONAS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, PERENNIAL GRASS, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

The effect of elevated pCO2 (60 Pa) on the frequency of nitrate-dissimilating Pseudomonas (NDP) was investigated in the rhizosphere of fertilised Lolium perenne swards in the Swiss Free Air Carbon dioxide Enrichment (FACE) experiment. Numbers of cultivable rootassociated Pseudomonas were greater under elevated (60 Pa) than under ambient (36 Pa) pCO2 in both high and low N-fertilised swards. For both pCO2 conditions, the NDP frequency decreased with closer root proximity to L. perenne roots in low fertilised swards. Anyway, in high N swards the NDP frequency was similar in root and soil fractions. Thus, N availability may be a major factor influencing NDP populations under elevated pCO2, most likely due to increased competition for N between plant and nitrate-dissimilating bacteria. q 2005 Elsevier Ltd. All rights reserved.

Published
2005
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22. nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass

Author

Jérôme Hamelin, Sonia Estelle Tarnawski, Nathalie Fromin, Michel Aragno, Sylvie Teyssier-Cuvelle, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Microbiology laboratory, Université de Neuchâtel (UNINE), Microbiology Laborarory, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
Perennial plant, [SDE.MCG]Environmental Sciences/Global Changes, Poaceae, Plant Roots, Microbiology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Rhizobiaceae, Phylogenetics, Nitrogen Fixation, Botany, Environmental DNA, Phylogeny, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, biology, 030306 microbiology, Genetic Variation, food and beverages, biochemical phenomena, metabolism, and nutrition, 15. Life on land, biology.organism_classification, Fixation (population genetics), Agronomy, Genes, Bacterial, bacteria, Diazotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Oxidoreductases, Soil microbiology, Bacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Rhizosphere associative dinitrogen fixation could be a valuable source of nitrogen in many nitrogen limited natural ecosystems, such as the rhizosphere of Molinia coerulea, a hemicryptophytic perennial grass naturally occurring in contrasted oligonitrophilic soils. The diversity of the dinitrogen-fixing bacteria associated with this environment was assessed by a cloning-sequencing approach on the nifH gene directly amplified from environmental DNA extracts. Seventy-seven randomly picked clones were analysed. One type of NifH sequence was dominant in both roots and surrounding soil, and represented 56% of all retrieved sequences. This cluster included previously described environmental clones and did not contain any NifH sequences similar to cultivated diazotrophs. The predominance of few NifH sequence types in the roots and the rhizosphere of Molinia coerulea indicate that the plant environment mediates a favourable niche for such dinitrogen-fixing bacteria.

Published
2002
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23. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

Author

Olivier Zemb, Caroline S. Achard, Jerome Hamelin, Marie‐Léa De Almeida, Béatrice Gabinaud, Laurent Cauquil, Lisanne M.G. Verschuren, and Jean‐Jacques Godon

Subjects
16S rRNA gene, absolute count data, metabarcoding, microbiome, normalization, spike‐in, Microbiology, QR1-502
Abstract

Abstract Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

Published
2020
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