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Châtillon E, Duran R, Rigal F, Cagnon C, Cébron A, Cravo-Laureau C. New insights into microbial community coalescence in the land-sea continuum. Microbiol Res 2022; 267:127259. [PMID: 36436444 DOI: 10.1016/j.micres.2022.127259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/30/2022] [Accepted: 11/13/2022] [Indexed: 11/23/2022]
Abstract
The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.
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Affiliation(s)
- Elise Châtillon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - François Rigal
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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Fernández-López C, Posada-Baquero R, García JL, Castilla-Alcantara JC, Cantos M, Ortega-Calvo JJ. Root-mediated bacterial accessibility and cometabolism of pyrene in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143408. [PMID: 33243519 DOI: 10.1016/j.scitotenv.2020.143408] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Partial transformation of pollutants and mobilization of the produced metabolites may contribute significantly to the risks resulting from biological treatment of soils polluted by hydrophobic chemicals such as polycyclic aromatic hydrocarbons (PAHs). Pyrene, a four-ringed PAH, was selected here as a model pollutant to study the effects of sunflower plants on the bacterial accessibility and cometabolism of this pollutant when located at a spatially distant source within soil. We compared the transformation of passively dosed 14C-labeled pyrene in soil slurries and planted pots that were inoculated with the bacterium Pseudomonas putida G7. This bacterium combines flagellar cell motility with the ability to cometabolically transform pyrene. Cometabolism of this PAH occurred immediately in the inoculated and shaken soil slurries, where the bacteria had full access to the passive dosing devices (silicone O-rings). Root exudates did not enhance the survival of P. putida G7 cells in soil slurries, but doubled their transport in column tests. In greenhouse-incubated soil pots with the same pyrene sources instead located centimeters from the soil surface, the inoculated bacteria transformed 14C-labeled pyrene only when the pots were planted with sunflowers. Bacterial inoculation caused mobilization of 14C-labeled pyrene metabolites into the leachates of the planted pots at concentrations of approximately 1 mg L-1, ten times greater than the water solubility of the parent compound. This mobilization resulted in a doubled specific root uptake rate of 14C-labeled pyrene equivalents and a significantly decreased root-to-fruit transfer rate. Our results show that the plants facilitated bacterial access to the distant pollutant source, possibly by increasing bacterial dispersal in the soil; this increased bacterial access was associated with cometabolism, which contributed to the risks of biodegradation.
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Affiliation(s)
- Carmen Fernández-López
- University Centre of Defense at the Spanish Air Force Academy, Santiago de la Ribera, Spain
| | - Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | | | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
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Chiapponi E, Henriot CP, Bertrand X, Hocquet D, Bornette G. Using GFP-Tagged Escherichia coli to Investigate the Persistence of Fecal Bacteria in Vegetated Wetlands: An Experimental Approach. Antibiotics (Basel) 2020; 9:E335. [PMID: 32570743 PMCID: PMC7344453 DOI: 10.3390/antibiotics9060335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 11/16/2022] Open
Abstract
The contamination of surface water by pathogenic bacteria of human origin is an important public health issue. Wetlands can be contaminated with fecal bacteria by water originating from different sources, such as wastewater treatment plants and agriculture. Escherichia coli is a commensal of the human gut flora and the major indication of fecal contamination in surface water. Little is known about the association between fecal bacteria and submerged macrophytes and how this may influence the water quality. We questioned whether macrophytes enhance or inhibit the bacterial growth in wetlands. For this purpose, we grew four different species of macrophytes (Mentha aquatica, Baldellia ranunculoides, Sparganium emersum and Elodea canadensis, in mono- or multispecies cultures) in aquatic rhizotrons and inoculated the devices with a fluorescent strain of Escherichia coli (producing a green fluorescent protein) to simulate the fecal contamination of wetlands. Bacterial survival was monitored by measuring the fluorescence for 19 days. We found (i) that contaminated sediments did not release E. coli in the water column in lentic conditions and (ii) that monocultures of E. canadensis, M. aquatica and S. emersum reduced the E. coli concentration in the water column. This suggests that aquatic plant species may be used in constructed wetlands to clear surface freshwater from bacteria of fecal origin.
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Affiliation(s)
- Emilia Chiapponi
- BIGEA–Biological, Geological and Environmental Sciences, Via S. Alberto 163, Ravenna Campus, University of Bologna, 40126 Bologna, Italy
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, 25030 Besançon, France; (X.B.); (D.H.); (G.B.)
| | - Charles P. Henriot
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, 25030 Besançon, France; (X.B.); (D.H.); (G.B.)
| | - Xavier Bertrand
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, 25030 Besançon, France; (X.B.); (D.H.); (G.B.)
- Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 Boulevard A. Fleming, 25030 Besançon, France
| | - Didier Hocquet
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, 25030 Besançon, France; (X.B.); (D.H.); (G.B.)
- Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 Boulevard A. Fleming, 25030 Besançon, France
| | - Gudrun Bornette
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, 25030 Besançon, France; (X.B.); (D.H.); (G.B.)
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Bourceret A, Leyval C, Faure P, Lorgeoux C, Cébron A. High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29556-29571. [PMID: 30136188 DOI: 10.1007/s11356-018-2744-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.
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Affiliation(s)
- Amélia Bourceret
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, Université de Lorraine, Bd des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
- Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany
| | - Corinne Leyval
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, Université de Lorraine, Bd des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Pierre Faure
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, Université de Lorraine, Bd des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Catherine Lorgeoux
- CNRS, CREGU, GeoRessourcesLab.,UMR 7359, Faculté des Sciences et Technologies, Université de Lorraine, Bd des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Aurélie Cébron
- CNRS, LIEC UMR7360 Faculté des Sciences et Technologies, Université de Lorraine, Bd des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy, France.
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