1
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Keuschnig C, Martins JMF, Navel A, Simonet P, Larose C. Micro-fractionation shows microbial community changes in soil particles below 20 μm. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1091773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IntroductionMicro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.MethodsWe applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).ResultsOverall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.DiscussionThe observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.
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Bastian F, Melayah D, Hugoni M, Dempsey NM, Simonet P, Frenea-Robin M, Fraissinet-Tachet L. Eukaryotic Cell Capture by Amplified Magnetic in situ Hybridization Using Yeast as a Model. Front Microbiol 2021; 12:759478. [PMID: 34790184 PMCID: PMC8591292 DOI: 10.3389/fmicb.2021.759478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
A non-destructive approach based on magnetic in situ hybridization (MISH) and hybridization chain reaction (HCR) for the specific capture of eukaryotic cells has been developed. As a prerequisite, a HCR-MISH procedure initially used for tracking bacterial cells was here adapted for the first time to target eukaryotic cells using a universal eukaryotic probe, Euk-516R. Following labeling with superparamagnetic nanoparticles, cells from the model eukaryotic microorganism Saccharomyces cerevisiae were hybridized and isolated on a micro-magnet array. In addition, the eukaryotic cells were successfully targeted in an artificial mixture comprising bacterial cells, thus providing evidence that HCR-MISH is a promising technology to use for specific microeukaryote capture in complex microbial communities allowing their further morphological characterization. This new study opens great opportunities in ecological sciences, thus allowing the detection of specific cells in more complex cellular mixtures in the near future.
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Affiliation(s)
- Fabiola Bastian
- DTAMB, Université Claude Bernard Lyon 1, Bât. Gregor Mendel, Villeurbanne Cedex, France
| | - Delphine Melayah
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Nora M. Dempsey
- Université Grenoble Alpes, CNRS, Grenoble INP, Institut Néel, Grenoble, France
| | - Pascal Simonet
- Université Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, INSA Lyon, CNRS, Ampère, UMR 5005, Ecully, France
| | - Marie Frenea-Robin
- Université Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, INSA Lyon, CNRS, Ampère, UMR 5005, Ecully, France
| | - Laurence Fraissinet-Tachet
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
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Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach CF, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Plant L, Ploy MC, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel AJ, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson AS. Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environ Int 2018; 117:132-138. [PMID: 29747082 DOI: 10.1016/j.envint.2018.04.041] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/30/2018] [Accepted: 04/21/2018] [Indexed: 05/24/2023]
Abstract
There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.
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Affiliation(s)
- D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - Antoine Andremont
- INSERM, IAME, UMR 1137, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, 75018 Paris, France
| | - Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.
| | - Ana Maria de Roda Husman
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.
| | | | - Jerker Fick
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall TR1 3HD, UK.
| | - Makoto Kuroda
- National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Kristian Kvint
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | | | - Celia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.
| | - Kaare Magne Nielsen
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 0130 Oslo, Norway.
| | - Laura Plant
- Swedish Research Council, Box 1035, SE-101 38 Stockholm, Sweden.
| | | | - Carlos Segovia
- Unidad funcional de Acreditación de Institutos de Investigación Sanitaria, Instituto de Salud Carlos III, Spain.
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratory Ampère, UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Écully Cedex, France.
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.
| | - Jason Snape
- Global Environment, AstraZeneca, Cheshire SK10 4TF, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Edward Topp
- London Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Department of Biology, University of Western Ontario, London, ON N5V 4T3, Canada.
| | - Arjon J van Hengel
- Directorate Health, Directorate-General for Research and Innovation, European Commission, Brussels, Belgium.
| | - David W Verner-Jeffreys
- Cefas Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK.
| | - Marko P J Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | | | - Ann-Sofie Wernersson
- Swedish Agency for Marine and Water Management, Box 11 930, SE-404 39 Gothenburg, Sweden.
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Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S, Penuelas J. Human dissemination of genes and microorganisms in Earth's Critical Zone. Glob Chang Biol 2018; 24:1488-1499. [PMID: 29266645 DOI: 10.1111/gcb.14003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Université de Lyon, Lyon, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Steven Banwart
- Department of Geography, The University of Sheffield, Sheffield, UK
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratory Ampère, UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Écully cedex, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Steve Banwart
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Josep Penuelas
- Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Catalonia, Spain.,CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
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Hily J, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M, Vigne E, Demangeat G, Komar V, Gertz C, Marmonier A, Hemmer C, Vigneron S, Marais A, Candresse T, Simonet P, Lemaire O. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant Biotechnol J 2018; 16:208-220. [PMID: 28544449 PMCID: PMC5785345 DOI: 10.1111/pbi.12761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment. Using state of the art metagenomics, we analysed two compartments in depth, the targeted Grapevine fanleaf virus (GFLV) populations and nontargeted root-associated microbiota. Our results reveal no statistically significant differences in the genetic diversity of bacteria that can be linked to the GM trait. In addition, no novel virus or bacteria recombinants of biosafety concern can be associated with transgenic grapevine rootstocks cultivated in commercial vineyard soil under greenhouse conditions for over 6 years.
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Affiliation(s)
| | - Sandrine Demanèche
- Laboratoire Ampère (CNRS UMR5005), Environmental Microbial GenomicsÉcole Centrale de LyonUniversité de LyonEcullyFrance
| | | | - Mélanie Tannières
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
- Present address:
European Biological Control LaboratoryUSDA‐ARSCampus International de Baillarguet CS 90013 Montferrier‐Sur‐Lez34988Saint Gely‐Du‐Fesc CedexFrance
| | | | - Monique Beuve
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
| | | | | | | | - Claude Gertz
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
| | | | | | | | - Armelle Marais
- UMR 1332 Biologie du Fruit et PathologieINRAUniversité de BordeauxVillenave d'Ornon CedexFrance
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et PathologieINRAUniversité de BordeauxVillenave d'Ornon CedexFrance
| | - Pascal Simonet
- Laboratoire Ampère (CNRS UMR5005), Environmental Microbial GenomicsÉcole Centrale de LyonUniversité de LyonEcullyFrance
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8
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Blanchard LS, Monin A, Ouertani H, Touaibia L, Michel E, Buret F, Simonet P, Morris CE, Demanèche S. Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions. FEMS Microbiol Ecol 2017; 93:3778241. [PMID: 28459967 DOI: 10.1093/femsec/fix057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
To diversify their genetic material, and thereby allow adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightning-related electrical phenomena may constitute an additional gene-transfer mechanism occurring in nature. The presence in clouds of bacteria such as Pseudomonas syringae capable of forming ice nuclei that lead to precipitation, and that are likely to be involved in triggering lightning, led us to postulate that natural electrotransformation in clouds may contribute to the adaptive potential of these bacteria. Here, we quantify the survival rate of 10 P. syringae strains in liquid and icy media under such electrical pulses and their capacity to acquire exogenous DNA. In comparison to two other bacteria (Pseudomonas sp. N3 and Escherichia coli TOP10), P. syringae CC0094 appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and to get a boost in its adaptive potential while being transported in clouds and falling back to Earth with precipitation from storms.
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Affiliation(s)
- Laurine S Blanchard
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Anaïs Monin
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Hounaïda Ouertani
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Lamia Touaibia
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Elisa Michel
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - François Buret
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Pascal Simonet
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
| | - Cindy E Morris
- INRA, UR0407 Pathologie Végétale, 84143 Montfavet Cedex, France
| | - Sandrine Demanèche
- Université de Lyon, École Centrale de Lyon, Laboratoire Ampére (CNRS UMR5005), Environmental Microbial Genomics, 69134 Ecully Cedex, France
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Demanèche S, Schauser L, Dawson L, Franqueville L, Simonet P. Microbial soil community analyses for forensic science: Application to a blind test. Forensic Sci Int 2017; 270:153-158. [DOI: 10.1016/j.forsciint.2016.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 12/03/2016] [Indexed: 10/20/2022]
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Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E, Pasternak Z. Soil characterisation by bacterial community analysis for forensic applications: A quantitative comparison of environmental technologies. Forensic Sci Int Genet 2017; 26:21-29. [DOI: 10.1016/j.fsigen.2016.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/20/2016] [Accepted: 10/06/2016] [Indexed: 12/01/2022]
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Miravitlles M, Monteagudo M, Rodríguez T, Barrecheguren M, Simonet P, Sáez ME, González-Pérez A, García Rodríguez LA, Mehtälä J, Iso-Mustajärvi I, Braun S, Haas J, Ringshausen FC, Juelich F, Korfmann G, Suzart-Woischnik K. Prevalence of bronchiectasis in four European countries. Pneumologie 2016. [DOI: 10.1055/s-0036-1592284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Smalla K, Simonet P, Tiedje J, Topp E. Editorial: Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance. FEMS Microbiol Ecol 2016; 92:fiw172. [DOI: 10.1093/femsec/fiw172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2016] [Indexed: 12/11/2022] Open
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Abstract
The present research investigated the relationship between handedness and performance on an attentional task for 24 skilled subjects. It is well known that in some sports the percentage of left-handed people is higher than in the normal population, e.g., tennis and fencing. It is also true that the most highly skilled in these sports are usually left-handed. Is this due to some disorientation of right-handed people when they face a left-handed opponent or are there some differences in competence? To test the last hypothesis an attentional task was constructed. In this task the subjects had to orient or to divide their attention between the two hemifields. An advantage for the left hand in the left-handed fencers was found only for the unattended situation. The results are discussed in the light of some anatomical evidence for right-hemispheric control of attention.
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Affiliation(s)
| | - H. Ripoll
- Institut National du Sport et de l'Education Physique
| | - J. F. Stein
- Institut National du Sport et de l'Education Physique
| | - P. Simonet
- Institut National du Sport et de l'Education Physique
| | - G. Azemar
- Institut National du Sport et de l'Education Physique
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Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P. Back to the Future of Soil Metagenomics. Front Microbiol 2016; 7:73. [PMID: 26903960 PMCID: PMC4748112 DOI: 10.3389/fmicb.2016.00073] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de LyonEcully, France; Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Neuherberg, Germany
| | - Wafa Achouak
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Spiros N Agathos
- Earth and Life Institute, Catholic University of LouvainLouvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech UniversityUrcuquí, Ecuador
| | - Mark Bailey
- Natural Environment Research Council, Centre for Ecology and Hydrology Oxford, UK
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences Praha, Czech Republic
| | - Dominique Brunel
- Institut National de la Recherche Agronomique, US1279, Etude du Polymorphisme des Génomes Végétaux, CEA, Institut de Génomique, Centre National de Génotypage Evry, France
| | - Åsa Frostegård
- NMBU Nitrogen Group, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
| | - Thierry Heulin
- Aix-Marseille Université, CEA, Centre National de la Recherche Scientifique, Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Biologie Végétale et de Microbiologie Environnementales Saint-Paul-lez-Durance, France
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Faculty of Agriculture, Food and Environment, The Otto Warburg-Minerva Center in Agricultural Biotechnology, The Hebrew University of Jerusalem Rehovot, Israel
| | - Kristiina L Kruus
- Enzymology of Renewable Biomass, VTT, Technical Research Centre of Finland Espoo, Finland
| | - George A Kowalchuk
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Antonio Lagares
- Departamento de Ciencia Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Centro Científico Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata La Plata, Argentina
| | | | - Philippe Lemanceau
- Institut National de la Recherche Agronomique, UMR 1347, Agroécologie, Université de Bourgogne Dijon, France
| | - Denis Le Paslier
- CEA/Direction des sciences du vivant/Institut de Génomique. Genoscope, Centre National de la Recherche Scientifiue UMR 8030, Université d'Evry Val d'Essonne Evry, France
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty- University of Ljubljana Ljubljana, Slovenia
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia Norwich, UK
| | - David D Myrold
- Department of Crop and Soil Science, Oregon State University Corvallis, OR, USA
| | | | - Paolo Nannipieri
- Department of Agrifood and Environmental Science, University of Florence Florence, Italy
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, National University of IrelandCork, Ireland; School of Biomedical Science, Curtin UniversityPerth, WA, Australia
| | - John J Parnell
- National Ecological Observatory Network Boulder, CO, USA
| | - Alfred Pühler
- Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University Bielefeld, Germany
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR/FIOCRUZ Belo Horizonte, Brazil
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | | | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Neuherberg, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Alexander Sczyrba
- Center for Biotechnology and Faculty of Technology, Computational Metagenomics, Bielefeld University Bielefeld, Germany
| | - Angela Sessitsch
- Health and Environment Department, Bioresources, AIT Austrian Institute of Technology GmbH Tulln, Austria
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University Huddinge, Sweden
| | - Jan Sørensen
- Section of Genetics and Microbiology, Department of Plant and Environmental Microbiology, University of Copenhagen Frederiksberg, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, Department of Biology, University of Western Ontario London, ON, Canada
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras Agrinio, Greece
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Geertje van Keulen
- Institute of Life Science, Medical School, Swansea University Swansea, UK
| | - Franco Widmer
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope Zürich, Switzerland
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna Vienna, Austria
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong Hong Kong, China
| | - Xiaojun Zhang
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liping Zhao
- Group of Microbial Ecology and Ecogenomics, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences Xiamen, China
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Pascal Simonet
- Institute of Life Science, Medical School, Swansea University Swansea, UK
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Ufarté L, Bozonnet S, Laville E, Cecchini DA, Pizzut-Serin S, Jacquiod S, Demanèche S, Simonet P, Franqueville L, Veronese GP. Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. Methods Mol Biol 2016; 1399:257-71. [PMID: 26791508 DOI: 10.1007/978-1-4939-3369-3_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.
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Affiliation(s)
- Lisa Ufarté
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France
- UMR5504, CNRS, 31400, Toulouse, France
| | - Sophie Bozonnet
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France
- UMR5504, CNRS, 31400, Toulouse, France
| | - Elisabeth Laville
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France
- UMR5504, CNRS, 31400, Toulouse, France
| | - Davide A Cecchini
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France
- UMR5504, CNRS, 31400, Toulouse, France
| | - Sandra Pizzut-Serin
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France
- UMR5504, CNRS, 31400, Toulouse, France
| | - Samuel Jacquiod
- Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | - Sandrine Demanèche
- Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | - Pascal Simonet
- Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | - Laure Franqueville
- Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | - Gabrielle Potocki Veronese
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France.
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France.
- UMR5504, CNRS, 31400, Toulouse, France.
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16
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Pivetal J, Frénéa-Robin M, Haddour N, Vézy C, Zanini LF, Ciuta G, Dempsey NM, Dumas-Bouchiat F, Reyne G, Bégin-Colin S, Felder-Flesh D, Ghobril C, Pourroy G, Simonet P. Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes. Environ Sci Pollut Res Int 2015; 22:20322-20327. [PMID: 26498963 DOI: 10.1007/s11356-015-5614-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
Horizontal gene transfers are critical mechanisms of bacterial evolution and adaptation that are involved to a significant level in the degradation of toxic molecules such as xenobiotic pesticides. However, understanding how these mechanisms are regulated in situ and how they could be used by man to increase the degradation potential of soil microbes is compromised by conceptual and technical limitations. This includes the physical and chemical complexity and heterogeneity in such environments leading to an extreme bacterial taxonomical diversity and a strong redundancy of genes and functions. In addition, more than 99 % of soil bacteria fail to develop colonies in vitro, and even new DNA-based investigation methods (metagenomics) are not specific and sensitive enough to consider lysis recalcitrant bacteria and those belonging to the rare biosphere. The objective of the ANR funded project “Emergent” was to develop a new culture independent approach to monitor gene transfer among soil bacteria by labeling plasmid DNA with magnetic nanoparticles in order to specifically capture and isolate recombinant cells using magnetic microfluidic devices. We showed the feasibility of the approach by using electrotransformation to transform a suspension of Escherichia coli cells with biotin-functionalized plasmid DNA molecules linked to streptavidin-coated superparamagnetic nanoparticles. Our results have demonstrated that magnetically labeled cells could be specifically retained on micromagnets integrated in a microfluidic channel and that an efficient selective separation can be achieved with the microfluidic device. Altogether, the project offers a promising alternative to traditional culture-based approaches for deciphering the extent of horizontal gene transfer events mediated by electro or natural genetic transformation mechanisms in complex environments such as soil.
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Abstract
BACKGROUND This paper reports on two case studies conducted by the Activity Clinic team to support the prevention of Work-Related Musculoskeletal Disorders (WRMSDs) in the workplace. Research so far qualifies WRMSDs as multifactorial and organizational pathologies. It has also demonstrated that in situ clinical analysis of the work activity improves the understanding of WRMSDs and their long-term prevention. OBJECTIVE In the two cases reported here (one in the car industry and the other among gravediggers in a large French city), the interventionist framework combined ergonomic observations, biomechanical monitoring, and a developmental methodology called Cross Self-Confrontation (CSC). The goal was to help workers and managers reflect on their work constraints, the impact of those constraints on health, and the possibility of transforming the work. METHOD Volunteers among the workers were prompted to engage in collective re-thinking of their work based on video-recordings and monitoring of their physical activity. In the CSC dialogues, biomechanical or ergonomic quantitative representations of the work activity were transformed by the researchers and the workers into argumentation and analysis tools for understanding and prevention of WRMSDs. CSC interviews were recorded and analyzed to track the dynamics of collective elaboration--both conceptual and practical--on WRMSDs prevention. RESULTS CSC discussions helped workers and managers transform their views on health, activity, and work constraints, and experiment with alternatives for health protection. The dialogical framework and quantitative representations were instrumental in the process of collective re-conceptualization of conflicts in the work activity and of resources for its transformation. CONCLUSION This research demonstrates how the integration of biomechanical and ergonomic mediations in the CSC framework promotes WRMSDs prevention in the workplace. This integration supports discussions within work teams and across organizational levels on work dimensions, which may lead to alternatives supporting health.
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Affiliation(s)
- Laure Kloetzer
- Equipe Psychologie du Travail et Clinique de l'Activité, CNAM Paris, Paris, France
| | - Edwige Quillerou-Grivot
- Equipe Psychologie du Travail et Clinique de l'Activité, CNAM Paris, Paris, France.,Working Life Department, Management, Organization for Health and Safety at Work Laboratory, Vandoeuvre-Les-Nancy, France
| | - Pascal Simonet
- Equipe Psychologie du Travail et Clinique de l'Activité, CNAM Paris, Paris, France.,Aix Marseille University, ENS Lyon, Marseille, France
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18
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Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol 2015; 6:358. [PMID: 25983722 PMCID: PMC4415585 DOI: 10.3389/fmicb.2015.00358] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/09/2015] [Indexed: 01/09/2023] Open
Abstract
Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Laboratoire Ampere, Centre National de la Recherche Scientifique, Ecole Centrale de Lyon, Université de Lyon Ecully, France ; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole MA, USA
| | - A Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole MA, USA
| | - Lorrie Maccario
- Environmental Microbial Genomics, Laboratoire Ampere, Centre National de la Recherche Scientifique, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Emmanuel Prestat
- Environmental Microbial Genomics, Laboratoire Ampere, Centre National de la Recherche Scientifique, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Özcan C Esen
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole MA, USA
| | - Eric Pelletier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope Evry, France ; UMR8030, Centre National de la Recherche Scientifique Evry, France ; Université d'Evry Val d'Essonne Evry, France
| | - Denis Le Paslier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope Evry, France ; UMR8030, Centre National de la Recherche Scientifique Evry, France ; Université d'Evry Val d'Essonne Evry, France
| | - Pascal Simonet
- Environmental Microbial Genomics, Laboratoire Ampere, Centre National de la Recherche Scientifique, Ecole Centrale de Lyon, Université de Lyon Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampere, Centre National de la Recherche Scientifique, Ecole Centrale de Lyon, Université de Lyon Ecully, France
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Nesme J, Simonet P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ Microbiol 2014; 17:913-30. [DOI: 10.1111/1462-2920.12631] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
| | - Pascal Simonet
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
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20
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Nesme J, Cécillon S, Delmont TO, Monier JM, Vogel TM, Simonet P. Large-scale metagenomic-based study of antibiotic resistance in the environment. Curr Biol 2014; 24:1096-100. [PMID: 24814145 DOI: 10.1016/j.cub.2014.03.036] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/01/2013] [Accepted: 03/13/2014] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance, including multiresistance acquisition and dissemination by pathogens, is a critical healthcare issue threatening our management of infectious diseases [1-3]. Rapid accumulation of resistance phenotypes implies a reservoir of transferable antibiotic resistance gene determinants (ARGDs) selected in response to inhibition of antibiotic concentrations, as found in hospitals [1, 3-5]. Antibiotic resistance genes were found in environmental isolates, soil DNA [4-6], secluded caves [6, 7], and permafrost DNA [7, 8]. Antibiotics target essential and ubiquitous cell functions, and resistance is a common characteristic of environmental bacteria [8-11]. Environmental ARGDs are an abundant reservoir of potentially transferable resistance for pathogens [9-12]. Using metagenomic sequences, we show that ARGDs can be detected in all (n=71) environments analyzed. Soil metagenomes had the most diverse pool of ARGDs. The most common types of resistances found in environmental metagenomes were efflux pumps and genes conferring resistance to vancomycin, tetracycline, or β-lactam antibiotics used in veterinary and human healthcare. Our study describes the diverse and abundant antibiotic resistance genes in nonclinical environments and shows that these genes are not randomly distributed among different environments (e.g., soil, oceans or human feces).
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Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Tom O Delmont
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Jean-Michel Monier
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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21
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Jacquiod S, Demanèche S, Franqueville L, Ausec L, Xu Z, Delmont TO, Dunon V, Cagnon C, Mandic-Mulec I, Vogel TM, Simonet P. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J Biotechnol 2014; 190:18-29. [PMID: 24721211 DOI: 10.1016/j.jbiotec.2014.03.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/24/2014] [Accepted: 03/28/2014] [Indexed: 11/27/2022]
Abstract
A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
| | - Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Luka Ausec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zhuofei Xu
- Molecular Microbial Ecology Group, Section of Microbiology, København Universitet, København, Denmark
| | - Tom O Delmont
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Vincent Dunon
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, University of Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Christine Cagnon
- Équipe Environnement et Microbiologie, IBEAS - UFR Sciences et Techniques, Université de Pau et des Pays de l'Adour, 64013 Pau, France
| | - Ines Mandic-Mulec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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23
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Gaze WH, Krone SM, Larsson DGJ, Li XZ, Robinson JA, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, Wright GD, Zhu YG. Influence of humans on evolution and mobilization of environmental antibiotic resistome. Emerg Infect Dis 2014; 19. [PMID: 23764294 PMCID: PMC3713965 DOI: 10.3201/eid1907.120871] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The clinical failure of antimicrobial drugs that were previously effective in controlling infectious disease is a tragedy of increasing magnitude that gravely affects human health. This resistance by pathogens is often the endpoint of an evolutionary process that began billions of years ago in non–disease-causing microorganisms. This environmental resistome, its mobilization, and the conditions that facilitate its entry into human pathogens are at the heart of the current public health crisis in antibiotic resistance. Understanding the origins, evolution, and mechanisms of transfer of resistance elements is vital to our ability to adequately address this public health issue.
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24
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Jacquiod S, Franqueville L, Cécillon S, M. Vogel T, Simonet P. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach. PLoS One 2013; 8:e79699. [PMID: 24278158 PMCID: PMC3835784 DOI: 10.1371/journal.pone.0079699] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- Microbial Molecular Ecology Group, Section of Microbiology, København Universitat, København, Denmark
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- * E-mail:
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25
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Abstract
The human skin microbiome could provide another example, after the gut, of the strong positive or negative impact that human colonizing bacteria can have on health. Deciphering functional diversity and dynamics within human skin microbial communities is critical for understanding their involvement and for developing the appropriate substances for improving or correcting their action. We present a direct PCR-free high throughput sequencing approach to unravel the human skin microbiota specificities through metagenomic dataset analysis and inter-environmental comparison. The approach provided access to the functions carried out by dominant skin colonizing taxa, including Corynebacterium, Staphylococcus and Propionibacterium, revealing their specific capabilities to interact with and exploit compounds from the human skin. These functions, which clearly illustrate the unique life style of the skin microbial communities, stand as invaluable investigation targets for understanding and potentially modifying bacterial interactions with the human host with the objective of increasing health and well being.
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Affiliation(s)
- Alban Mathieu
- Environmental Microbial Genomics group, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
- LibraGen, Toulouse, France
| | - Tom O. Delmont
- Environmental Microbial Genomics group, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics group, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
| | | | | | - Pascal Simonet
- Environmental Microbial Genomics group, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
- * E-mail:
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Engel K, Ashby D, Brady SF, Cowan DA, Doemer J, Edwards EA, Fiebig K, Martens EC, McCormac D, Mead DA, Miyazaki K, Moreno-Hagelsieb G, O'Gara F, Reid A, Rose DR, Simonet P, Sjöling S, Smalla K, Streit WR, Tedman-Jones J, Valla S, Wellington EMH, Wu CC, Liles MR, Neufeld JD, Sessitsch A, Charles TC. Meeting report: 1st international functional metagenomics workshop may 7-8, 2012, st. Jacobs, ontario, Canada. Stand Genomic Sci 2013; 8:106-11. [PMID: 23961315 PMCID: PMC3739178 DOI: 10.4056/sigs.3406845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.
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Affiliation(s)
- Katja Engel
- University of Waterloo, Waterloo, ON, Canada
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 2012; 6:1677-87. [PMID: 22297556 DOI: 10.1038/ismej.2011.197] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 × 10(9) bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although <50% of reads were assigned at an E value cutoff of 10(-5). In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of <10(-5), thus, considerable genomic reconstructions efforts still have to be performed.
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Demanèche S, Monier JM, Dugat-Bony E, Simonet P. Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria. FEMS Microbiol Ecol 2011; 78:129-36. [PMID: 21564143 DOI: 10.1111/j.1574-6941.2011.01126.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation. The results showed that among the 16 bacterial isolates tested, six were able to accept foreign DNA and acquire the spectinomycin resistance conferred by the aadA gene on plasmid, but none of them managed to integrate transgenic DNA in their chromosome. Our results provide no indication that the theoretical gene transfer-enhancing properties of transplastomic plants cause horizontal gene transfer at rates above those found in other studies with nuclear transgenes.
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Affiliation(s)
- Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire AMPERE, UMR CNRS 5005, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
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Lombard N, Prestat E, van Elsas JD, Simonet P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol Ecol 2011; 78:31-49. [PMID: 21631545 DOI: 10.1111/j.1574-6941.2011.01140.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.
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Affiliation(s)
- Nathalie Lombard
- Department of Marine Biotechnology, Institute of Marine Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA.
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Delmont TO, Robe P, Clark I, Simonet P, Vogel TM. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods 2011; 86:397-400. [PMID: 21723887 DOI: 10.1016/j.mimet.2011.06.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/15/2011] [Accepted: 06/18/2011] [Indexed: 11/26/2022]
Abstract
Full pyrosequencing runs of both direct-extracted (high yield, low DNA size) and indirect-extracted DNA (low yield, high DNA size) from the same prairie soil show that the sequence distribution of the majority of the metabolic functions and species detected were statistically similar. Although some microbial functions differed at the 95% confidence interval in bootstrap analyses, the overall functional diversity was the same.
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
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Abstract
Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. Although not all scientists have easy access to high-throughput sequencing technologies, they do have access to the sequences that have been deposited in databases, and therefore, can begin to intensively mine these metagenomic data to generate hypotheses that can be validated experimentally. Information about metabolic functions and microbial species compositions can already be compared among metagenomes from different ecosystems. These comparisons add to our understanding about microbial adaptation and the role of specific microbes in different ecosystems. Concurrent with the rapid growth of sequencing technologies, we have entered a new age of microbial ecology, which will enable researchers to experimentally confirm putative relationships between microbial functions and community structures.
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR, Vogel TM. Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 2011; 77:1315-24. [PMID: 21183646 PMCID: PMC3067229 DOI: 10.1128/aem.01526-10] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
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Affiliation(s)
- Tom O. Delmont
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Patrick Robe
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Sébastien Cecillon
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Ian M. Clark
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Florentin Constancias
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Penny R. Hirsch
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France, LibraGen, 3 Rue des Satellites, 31400 Toulouse, France, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
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Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Laval K, Lebeau T, Lemanceau P, Leyval C, Lindström K, Pandard P, Romero E, Sarr A, Schloter M, Simonet P, Smalla K, Wilke BM, Martin-Laurent F. Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples". J Microbiol Methods 2011; 84:454-60. [PMID: 21256879 DOI: 10.1016/j.mimet.2011.01.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/10/2011] [Accepted: 01/10/2011] [Indexed: 11/16/2022]
Abstract
Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, as well as the abundance and genetic structure of the total bacterial community in the DNA extracted from 12 different soils by the 13 laboratories. High quality DNA was successfully extracted from all 12 soils, despite different physical and chemical characteristics and a range of origins from arable soils, through forests to industrial sites. Quantification of the 16S rRNA gene abundances by real time PCR and analysis of the total bacterial community structure by automated ribosomal intergenic spacer analysis (A-RISA) showed acceptable to good levels of reproducibility. Based on the results of both ring-tests, the method was unanimously approved by the ISO as an international standard method and the normative protocol will now be disseminated within the scientific community. Standardization of a soil DNA extraction method will improve data comparison, facilitating our understanding of soil microbial diversity and soil quality monitoring.
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Affiliation(s)
- I Petric
- Wellience Agro-Environment, BP 66517, 21065 Dijon Cedex, France
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Nemir A, David MM, Perrussel R, Sapkota A, Simonet P, Monier JM, Vogel TM. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. Chemosphere 2010; 80:600-607. [PMID: 20444493 DOI: 10.1016/j.chemosphere.2010.03.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 02/15/2010] [Accepted: 03/28/2010] [Indexed: 05/29/2023]
Abstract
The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation.
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Affiliation(s)
- Audra Nemir
- Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Abstract
A hybridization procedure was developed to identify Frankia strains inside actinorhizae by direct probing of crushed root nodules. The probe consisted of an indigenous cryptic plasmid. This well-conserved, 8-kilobase plasmid was detected in Frankia isolates that were very close taxonomically (they possessed a very high DNA sequence homology). The probe did not hybridize to the DNA of Frankia isolates which did not carry the plasmid. Endophyte DNA was extracted by a modification of a technique originally developed for the detection of plasmids in Frankia isolates. The hybridization procedure applied to nodules collected in a stand of alder permitted determination of a distribution map of the plasmid-bearing Frankia strains.
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Affiliation(s)
- P Simonet
- Laboratoire de Biologie des Sols, U.A. Centre National de la Recherche Scientifique 697, Bâtiment 741, Université Lyon 1, Villeurbanne F-69622 Cedex, and Station d' Amélioration des Arbres Forestiers, Institut National de la Recherche Agronomique, Orléans, Ardon F-45160 Olivet, France
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Pontiroli A, Ceccherini MT, Poté J, Wildi W, Kay E, Nannipieri P, Vogel TM, Simonet P, Monier JM. Long-term persistence and bacterial transformation potential of transplastomic plant DNA in soil. Res Microbiol 2010; 161:326-34. [PMID: 20493252 DOI: 10.1016/j.resmic.2010.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/11/2010] [Accepted: 04/12/2010] [Indexed: 12/01/2022]
Abstract
The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up to 4 years. Total DNA was extracted from soil and the number of transgenes (aadA, which confers resistance to both spectinomycin and streptomycin) was quantified by quantitative PCR. The biological activity of these transgenes was assessed by transformation in the bacterial strain Acinetobacter sp. BD413(pBAB2) in vitro. While the proportion of transgenes recovered increased with the increasing amount of transplastomic DNA added, plant DNA was rapidly degraded over time. The number of transgenes recovered decreased about 10,000 fold within 2 weeks. Data reveal, however, that a small fraction of the plant DNA escaped degradation. Transgene sequences were still detected after 4 years and transformation assays showed that extracted DNA remained biologically active and could still transform competent cells of Acinetobacter sp. BD413(pBAB2). The approach presented here quantified the number of transgenes (based on quantitative PCR of 50% of the gene) released and persisting in the environment over time and provided new insights into the fate of transgenic plant DNA in soil.
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Affiliation(s)
- Alessandra Pontiroli
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France
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Abstract
The field of astrobiology lacks a universal marker with which to indicate the presence of life. This study supports the proposal to use nucleic acids, specifically DNA, as a signature of life (biosignature). In addition to its specificity to living organisms, DNA is a functional molecule that can confer new activities and characteristics to other organisms, following the molecular biology dogma, that is, DNA is transcribed to RNA, which is translated into proteins. Previous criticisms of the use of DNA as a biosignature have asserted that DNA molecules would be destroyed by UV radiation in space. To address this concern, DNA in plasmid form was deposited onto different surfaces and exposed to UVC radiation. The surviving DNA was quantified via the quantitative polymerase chain reaction (qPCR). Results demonstrate increased survivability of DNA attached to surfaces versus non-adsorbed DNA. The DNA was also tested for biological activity via transformation into the bacterium Acinetobacter sp. and assaying for antibiotic resistance conferred by genes encoded by the plasmid. The success of these methods to detect DNA and its gene products after UV exposure (254 nm, 3.5 J/m(2)s) not only supports the use of the DNA molecule as a biosignature on mineral surfaces but also demonstrates that the DNA retained biological activity.
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Affiliation(s)
- Delina Y Lyon
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Poté J, Teresa Ceccherini M, Rosselli W, Wildi W, Simonet P, Vogel TM. Leaching and transformability of transgenic DNA in unsaturated soil columns. Ecotoxicol Environ Saf 2010; 73:67-72. [PMID: 19828198 DOI: 10.1016/j.ecoenv.2009.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 09/08/2009] [Accepted: 09/10/2009] [Indexed: 05/28/2023]
Abstract
Unsaturated soil columns were used to examine the transport of the plasmid pLEPO1 and plant DNA (transplastomic tobacco DNA), both carrying an antibiotic resistance gene (aadA gene), and the capacity of bacteria to incorporate the gene in their genome after its passage through the soil. Soil columns containing a top leaf layer had sterile water percolated through them at a rate of 0.5mLh(-1). DNA from column leachate water was extracted and analyzed. Quantitative measurements included total DNA concentrations in the water and the transformation frequencies of Acinetobacter sp. BD413 by DNA in the column effluent. Qualitative measurements included the relative degradation of DNA after passage in the columns by agarose gel electrophoresis and the potential of effluent DNA to transform bacteria, leading to the production of antibiotic-resistant bacteria. The presence of aadA gene in the leachate water of soil columns suggests the mobility of DNA in unsaturated soil medium. The extent of DNA degradation was found to be proportional to its residence time in the soil column while a fraction of DNA was always able to incorporate into the Acinetobacter genome under all conditions studied. These results suggest that biologically active transgenic DNA might be transported downward by rain in unsaturated soils.
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Affiliation(s)
- John Poté
- Environmental Microbial Genomics Group, Laboratoire AMPERE, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
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Mercier A, Bertolla F, Passelègue-Robe E, Simonet P. Influence of DNA conformation and role of comA and recA on natural transformation in Ralstonia solanacearum. Can J Microbiol 2009; 55:762-70. [PMID: 19767847 DOI: 10.1139/w09-025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Naturally competent bacteria such as the plant pathogen Ralstonia solanacearum are characterized by their ability to take up free DNA from their surroundings. In this study, we investigated the efficiency of various DNA types including chromosomal linear DNA and circular or linearized integrative and (or) replicative plasmids to naturally transform R. solanacearum. To study the respective regulatory role of DNA transport and maintenance in the definite acquisition of new DNA by bacteria, the natural transformation frequencies were compared with those obtained when the bacterial strain was transformed by electroporation. An additional round of electrotransformation and natural transformation was carried out with the same set of donor DNAs and with R. solanacearum disrupted mutants that were potentially affected in competence (comA gene) and recombination (recA gene) functions. Our results confirmed the critical role of the comA gene for natural transformation and that of recA for recombination and, more surprisingly, for the maintenance of an autonomous plasmid in the host cell. Finally, our results showed that homologous recombination of chromosomal linear DNA fragments taken up by natural transformation was the most efficient way for R. solanacearum to acquire new DNA, in agreement with previous data showing competence development and natural transformation between R. solanacearum cells in plant tissues.
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Simonet P. L’examen méthodique d’un geste de métier pour une prévention durable des TMS : une intervention en clinique de l’activité. pistes 2009. [DOI: 10.4000/pistes.2404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel TM, Monier JM. Visual evidence of horizontal gene transfer between plants and bacteria in the phytosphere of transplastomic tobacco. Appl Environ Microbiol 2009; 75:3314-22. [PMID: 19329660 PMCID: PMC2681637 DOI: 10.1128/aem.02632-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 03/20/2009] [Indexed: 12/29/2022] Open
Abstract
Plant surfaces, colonized by numerous and diverse bacterial species, are often considered hot spots for horizontal gene transfer (HGT) between plants and bacteria. Plant DNA released during the degradation of plant tissues can persist and remain biologically active for significant periods of time, suggesting that soil or plant-associated bacteria could be in direct contact with plant DNA. In addition, nutrients released during the decaying process may provide a copiotrophic environment conducive for opportunistic microbial growth. Using Acinetobacter baylyi strain BD413 and transplastomic tobacco plants harboring the aadA gene as models, the objective of this study was to determine whether specific niches could be shown to foster bacterial growth on intact or decaying plant tissues, to develop a competence state, and to possibly acquire exogenous plant DNA by natural transformation. Visualization of HGT in situ was performed using A. baylyi strain BD413(rbcL-DeltaPaadA::gfp) carrying a promoterless aadA::gfp fusion. Both antibiotic resistance and green fluorescence phenotypes were restored in recombinant bacterial cells after homologous recombination with transgenic plant DNA. Opportunistic growth occurred on decaying plant tissues, and a significant proportion of the bacteria developed a competence state. Quantification of transformants clearly supported the idea that the phytosphere constitutes a hot spot for HGT between plants and bacteria. The nondisruptive approach used to visualize transformants in situ provides new insights into environmental factors influencing HGT for plant tissues.
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Affiliation(s)
- Alessandra Pontiroli
- Environmental Microbial Genomics Group, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R, Philippot L. TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 2009. [DOI: 10.1038/nrmicro2119] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Poté J, Mavingui P, Navarro E, Rosselli W, Wildi W, Simonet P, Vogel TM. Extracellular plant DNA in Geneva groundwater and traditional artesian drinking water fountains. Chemosphere 2009; 75:498-504. [PMID: 19171370 DOI: 10.1016/j.chemosphere.2008.12.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 05/27/2023]
Abstract
DNA, as the signature of life, has been extensively studied in a wide range of environments. While DNA analysis has become central to work on natural gene exchange, forensic analyses, soil bioremediation, genetically modified organisms, exobiology, and palaeontology, fundamental questions about DNA resistance to degradation remain. This paper investigated on the presence of plant DNA in groundwater and artesian fountain (groundwater-fed) samples, which relates to the movement and persistence of DNA in the environment. The study was performed in the groundwater and in the fountains, which are considered as a traditional artesian drinking water in Geneva Champagne Basin. DNA from water samples was extracted, analysed and quantified. Plant gene sequences were detected using PCR amplification based on 18S rRNA gene primers specific for eukaryotes. Physicochemical parameters of water samples including temperature, pH, conductivity, organic matter, dissolved organic carbon (DOC) and total organic carbon (TOC) were measured throughout the study. The results revealed that important quantities of plant DNA can be found in the groundwater. PCR amplification based on 18S rDNA, cloning, RFLP analysis and sequencing demonstrated the presence of plant DNA including Vitis rupestris, Vitis berlandieri, Polygonum sp. Soltis, Boopis graminea, and Sinapis alba in the water samples. Our observations support the notion of plant DNA release, long-term persistence and movement in the unsaturated medium as well as in groundwater aquifers.
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Affiliation(s)
- John Poté
- Environmental Microbial Genomics Group, Laboratoire AMPERE, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
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Coupat BÃ, Chaumeille-Dole F, Fall S, Prior P, Simonet P, Nesme X, Bertolla F. Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred. FEMS Microbiol Ecol 2008; 66:14-24. [DOI: 10.1111/j.1574-6941.2008.00552.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rizzi A, Pontiroli A, Brusetti L, Borin S, Sorlini C, Abruzzese A, Sacchi GA, Vogel TM, Simonet P, Bazzicalupo M, Nielsen KM, Monier JM, Daffonchio D. Strategy for in situ detection of natural transformation-based horizontal gene transfer events. Appl Environ Microbiol 2008; 74:1250-4. [PMID: 18165369 PMCID: PMC2258602 DOI: 10.1128/aem.02185-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 12/18/2007] [Indexed: 11/20/2022] Open
Abstract
A strategy is described that enables the in situ detection of natural transformation in Acinetobacter baylyi BD413 by the expression of a green fluorescent protein. Microscale detection of bacterial transformants growing on plant tissues was shown by fluorescence microscopy and indicated that cultivation-based selection of transformants on antibiotic-containing agar plates underestimates transformation frequencies.
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Affiliation(s)
- Aurora Rizzi
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
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Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM, Simonet P. Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms. PLoS One 2007; 2:e1055. [PMID: 17957239 PMCID: PMC2013936 DOI: 10.1371/journal.pone.0001055] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 10/02/2007] [Indexed: 12/01/2022] Open
Abstract
Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic “hot spots”, which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination “hot-spots” to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.
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Affiliation(s)
- Saliou Fall
- Environmental Microbial Genomics Group, Laboratoire AMPERE UMR CNRS 5005, Ecole Centrale de Lyon et Université de Lyon, Ecully, France
| | - Anne Mercier
- Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard–Lyon 1, Villeurbanne, France
| | - Franck Bertolla
- Ecologie Microbienne, UMR CNRS 5557, Université Claude Bernard–Lyon 1, Villeurbanne, France
| | - Alexandra Calteau
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard–Lyon 1, Villeurbanne, France
| | - Laurent Gueguen
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard–Lyon 1, Villeurbanne, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard–Lyon 1, Villeurbanne, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Laboratoire AMPERE UMR CNRS 5005, Ecole Centrale de Lyon et Université de Lyon, Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire AMPERE UMR CNRS 5005, Ecole Centrale de Lyon et Université de Lyon, Ecully, France
- * To whom correspondence should be addressed. E-mail:
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Mercier A, Bertolla F, Passelègue-Robe E, Simonet P. Natural transformation-based foreign DNA acquisition in a Ralstonia solanacearum mutS mutant. Res Microbiol 2007; 158:537-44. [PMID: 17618086 DOI: 10.1016/j.resmic.2007.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 05/11/2007] [Indexed: 11/29/2022]
Abstract
Mutator strains with defective methyl-mismatch repair (MMR) systems have been shown to play an important role in adaptation of bacterial populations to changing and stressful environments. In this report, we describe the impact of mutS::aacC3-IV inactivation on foreign DNA acquisition by natural transformation in the phytopathogenic bacterium Ralstonia solanacearum. A mutS mutant of R. solanacearum exhibited 33- to 60-fold greater spontaneous mutation frequencies, in accordance with a mutator phenotype. Transformation experiments indicated that intra- and interspecific DNA transfers increased up to 89-fold. To assess horizontal gene transfer (HGT) from genetically modified plants to R. solanacearum, fitness of the mutator was first evaluated in soil and plant environments. Competitiveness was not modified after 61 days in soil and 8 days in tomato, and the progress of plant decay symptoms was similar to that of the wild-type strain. Despite its survival in soil and in planta, and the powerful capacities of HGT, R. solanacearum was not genetically transformed by transgenic plant DNA in a wide range of in vitro and in planta tests.
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