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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Benavente D, Saiz-Jimenez C, Sanchez-Moral S. Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls. Microbiol Res 2023; 277:127511. [PMID: 37852679 DOI: 10.1016/j.micres.2023.127511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, 28805 Madrid, Spain.
| | | | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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2
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Chabas M, Pible O, Armengaud J, Alpha-Bazin B. Label-Free Multiplex Proteotyping of Microbial Isolates. Anal Chem 2023; 95:13163-13171. [PMID: 37590279 DOI: 10.1021/acs.analchem.3c01975] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
To meet clinical diagnostic needs and for general microbiological screening, it is essential to be able to accurately and rapidly identify any microorganisms from complex microbiota. To gain insight into the individual components of microbiota, culturomics has been proposed as a means to systematically test hundreds of possible cultivation conditions and generate numerous microbial isolates with very distinct characteristics. High-throughput identification methods must now be developed to quickly screen these isolates. Currently, most multiplexing methods involve labeling, which comes at a cost. In this paper, we present an innovative label-free multiplexing method for the identification of microorganisms using tandem mass spectrometry. The method is based on offline reversed-phase fractionation of individual peptidomes. Multiplexing is achieved by mixing fractions of staged hydrophobicity; thus, each sample is mapped to specific elution times. In this proof-of-concept study, multiplexed samples were analyzed by tandem mass spectrometry in a single run and microorganisms present in the mixture were resolved by phylopeptidomics proteotyping. Using this methodology, up to 21 microorganisms could be identified in a single 60 min run performed with a Q-Exactive HF high-resolution mass spectrometer, resulting in a rate of one microorganism identified per 3 min of mass spectrometry, without any need for the use of labeling reagents. This approach opens new perspectives for the application of high-throughput proteotyping of bacteria using tandem mass spectrometry in large culturomics projects.
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Affiliation(s)
- Madisson Chabas
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
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3
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Petit P, Hayoun K, Alpha-Bazin B, Armengaud J, Rivasseau C. First Isolation and Characterization of Bacteria from the Core's Cooling Pool of an Operating Nuclear Reactor. Microorganisms 2023; 11:1871. [PMID: 37630434 PMCID: PMC10456712 DOI: 10.3390/microorganisms11081871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial life can thrive in the most inhospitable places, such as nuclear facilities with high levels of ionizing radiation. Using direct meta-analyses, we have previously highlighted the presence of bacteria belonging to twenty-five different genera in the highly radioactive water of the cooling pool of an operating nuclear reactor core. In the present study, we further characterize this specific environment by isolating and identifying some of these microorganisms and assessing their radiotolerance and their ability to decontaminate uranium. This metal is one of the major radioactive contaminants of anthropogenic origin in the environment due to the nuclear and mining industries and agricultural practices. The microorganisms isolated when sampling was performed during the reactor operation consisted mainly of Actinobacteria and Firmicutes, whereas Proteobacteria were dominant when sampling was performed during the reactor shutdown. We investigated their tolerance to gamma radiation under different conditions. Most of the bacterial strains studied were able to survive 200 Gy irradiation. Some were even able to withstand 1 kGy, with four of them showing more than 10% survival at this dose. We also assessed their uranium uptake capacity. Seven strains were able to remove almost all the uranium from a 5 µM solution. Four strains displayed high efficiency in decontaminating a 50 µM uranium solution, demonstrating promising potential for use in bioremediation processes in environments contaminated by radionuclides.
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Affiliation(s)
- Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, F-38000 Grenoble, France;
| | - Karim Hayoun
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207 Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, F-38000 Grenoble, France;
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, F-91190 Gif-sur-Yvette, France
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4
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Mappa C, Alpha-Bazin B, Pible O, Armengaud J. Mix24X, a Lab-Assembled Reference to Evaluate Interpretation Procedures for Tandem Mass Spectrometry Proteotyping of Complex Samples. Int J Mol Sci 2023; 24:ijms24108634. [PMID: 37239979 DOI: 10.3390/ijms24108634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Correct identification of the microorganisms present in a complex sample is a crucial issue. Proteotyping based on tandem mass spectrometry can help establish an inventory of organisms present in a sample. Evaluation of bioinformatics strategies and tools for mining the recorded datasets is essential to establish confidence in the results obtained and to improve these pipelines in terms of sensitivity and accuracy. Here, we propose several tandem mass spectrometry datasets recorded on an artificial reference consortium comprising 24 bacterial species. This assemblage of environmental and pathogenic bacteria covers 20 different genera and 5 bacterial phyla. The dataset comprises difficult cases, such as the Shigella flexneri species, which is closely related to Escherichia coli, and several highly sequenced clades. Different acquisition strategies simulate real-life scenarios: from rapid survey sampling to exhaustive analysis. We provide access to individual proteomes of each bacterium separately to provide a rational basis for evaluating the assignment strategy of MS/MS spectra when recorded from complex mixtures. This resource should provide an interesting common reference for developers who wish to compare their proteotyping tools and for those interested in evaluating protein assignment when dealing with complex samples, such as microbiomes.
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Affiliation(s)
- Charlotte Mappa
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques Pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols sur Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
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5
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Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023; 14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.
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Affiliation(s)
- Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
| | - Gérard Steinmetz
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
- *Correspondence: Jean Armengaud,
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6
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Yan X, Ma J, Chen X, Lei M, Li T, Han Y. Characteristics of airborne bacterial communities and antibiotic resistance genes under different air quality levels. ENVIRONMENT INTERNATIONAL 2022; 161:107127. [PMID: 35180669 DOI: 10.1016/j.envint.2022.107127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/05/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Pathogenic bacteria and antibiotic resistance genes (ARGs) in bioaerosols are major threats to human health. In this study, the microbial community structure and ARG distribution characteristics of airborne bacteria in total suspended particulates (TSP) and PM2.5 were investigated under different air quality levels in Xinxiang, Central China. The results revealed that with the deterioration of air quality, the concentrations of airborne bacteria in both TSP and PM2.5 decreased; however, the relative amounts of pathogenic bacteria increased. The predominant genera in pathogenic bacteria of Bacillus, Sphingomonas, Corynebacterium, Rhodococcus, and Staphylococcus were identified in both TSP and PM2.5. Although the airborne bacteria concentrations and absolute abundances of ARGs in TSP were higher than those in PM2.5 under identical air quality conditions, the bacterial community structure and relative amounts of pathogenic bacteria were similar. In addition, the relationship between environmental factors of ions, metal elements, and meteorological parameters and the community structures of airborne bacteria and pathogenic bacteria were also analyzed. The effects of soluble ions and metal elements on several dominant genera of total bacteria and pathogenic bacteria differed, probably due to the strong tolerance of pathogenic bacteria to harsh atmospheric environments Different subtypes of ARGs showed various distribution characteristics with variations in air quality. The deterioration of air quality can inhibit the dissemination of ARGs, as the minimum values of all ARGs and class 1 integrase intI1 were observed under Severely Polluted conditions. This study provides a comprehensive understanding of the effect of air pollution levels on the airborne bacteria community composition and ARG distribution.
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Affiliation(s)
- Xu Yan
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China.
| | - Jiahui Ma
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Xinqing Chen
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Miao Lei
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Tianning Li
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Yunping Han
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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7
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Van Eesbeeck V, Props R, Mysara M, Petit PCM, Rivasseau C, Armengaud J, Monsieurs P, Mahillon J, Leys N. Cyclical Patterns Affect Microbial Dynamics in the Water Basin of a Nuclear Research Reactor. Front Microbiol 2021; 12:744115. [PMID: 34721343 PMCID: PMC8555696 DOI: 10.3389/fmicb.2021.744115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The BR2 nuclear research reactor in Mol, Belgium, runs in successive phases of operation (cycles) and shutdown, whereby a water basin surrounding the reactor vessel undergoes periodic changes in physico-chemical parameters such as flow rate, temperature, and radiation. The aim of this study was to explore the microbial community in this unique environment and to investigate its long-term dynamics using a 16S rRNA amplicon sequencing approach. Results from two sampling campaigns spanning several months showed a clear shift in community profiles: cycles were mostly dominated by two Operational Taxonomic Units (OTUs) assigned to unclassified Gammaproteobacterium and Pelomonas, whereas shutdowns were dominated by an OTU assigned to Methylobacterium. Although 1 year apart, both campaigns showed similar results, indicating that the system remained stable over this 2-year period. The community shifts were linked with changes in physico-chemical parameters by Non-metric Multidimensional Scaling (NMDS) and correlation analyses. In addition, radiation was hypothesized to cause a decrease in cell number, whereas temperature had the opposite effect. Chemoautotrophic use of H2 and dead cell recycling are proposed to be used as a strategies for nutrient retrieval in this extremely oligotrophic environment.
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Affiliation(s)
- Valérie Van Eesbeeck
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Food and Environmental Microbiology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Ruben Props
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Pauline C M Petit
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Paris, France
| | - Corinne Rivasseau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Paris, France
| | - Jean Armengaud
- Technological Innovations for Detection and Diagnosis Laboratory, CEA, Bagnols-sur-Cèze, France
| | - Pieter Monsieurs
- Protozoology Research Group, Department of Biomedical Sciences, Institute of Tropical Medicine (ITG), Antwerp, Belgium
| | - Jacques Mahillon
- Food and Environmental Microbiology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Natalie Leys
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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