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Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiol Spectr 2024; 12:e0359023. [PMID: 38451230 DOI: 10.1128/spectrum.03590-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Yu Z, Wang Q, Pinilla-Redondo R, Madsen JS, Clasen KAD, Ananbeh H, Olesen AK, Gong Z, Yang N, Dechesne A, Smets B, Nesme J, Sørensen SJ. Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater. Ecotoxicol Environ Saf 2024; 271:115971. [PMID: 38237397 DOI: 10.1016/j.ecoenv.2024.115971] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/07/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
Wastewater treatment plants (WWTPs) are considered reservoirs of antibiotic resistance genes (ARGs). Given that plasmid-mediated horizontal gene transfer plays a critical role in disseminating ARGs in the environment, it is important to inspect the transfer potential of transmissible plasmids to have a better understanding of whether these mobile ARGs can be hosted by opportunistic pathogens and should be included in One Health's considerations. In this study, we used a fluorescent-reporter-gene based exogenous isolation approach to capture extended-spectrum beta-lactamases encoding mobile determinants from sewer microbiome samples that enter an urban water system (UWS) in Denmark. After screening and sequencing, we isolated a ∼73 Kbp IncN plasmid (pDK_DARWIN) that harboured and expressed multiple ARGs. Using a dual fluorescent reporter gene system, we showed that this plasmid can transfer into resident urban water communities. We demonstrated the transfer of pDK_DARWIN to microbiome members of both the sewer (in the upstream UWS compartment) and wastewater treatment (in the downstream UWS compartment) microbiomes. Sequence similarity search across curated plasmid repositories revealed that pDK_DARWIN derives from an IncN backbone harboured by environmental and nosocomial Enterobacterial isolates. Furthermore, we searched for pDK_DARWIN sequence matches in UWS metagenomes from three countries, revealing that this plasmid can be detected in all of them, with a higher relative abundance in hospital sewers compared to residential sewers. Overall, this study demonstrates that this IncN plasmid is prevalent across Europe and an efficient vector capable of disseminating multiple ARGs in the urban water systems.
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Affiliation(s)
- Zhuofeng Yu
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Qinqin Wang
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Kamille Anna Dam Clasen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Hanadi Ananbeh
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic
| | - Asmus Kalckar Olesen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Zhuang Gong
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Nan Yang
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, DK-2800 Kgs, Lyngby, Denmark
| | - Barth Smets
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, DK-2800 Kgs, Lyngby, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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3
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Yang N, Røder HL, Wicaksono WA, Wassermann B, Russel J, Li X, Nesme J, Berg G, Sørensen SJ, Burmølle M. Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth. ISME J 2024; 18:wrae012. [PMID: 38365935 PMCID: PMC10938371 DOI: 10.1093/ismejo/wrae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.
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Affiliation(s)
- Nan Yang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Henriette L Røder
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Section for Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen 2100, Denmark
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
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Yu Z, He W, Klincke F, Madsen JS, Kot W, Hansen LH, Quintela-Baluja M, Balboa S, Dechesne A, Smets B, Nesme J, Sørensen SJ. Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems. Environ Int 2024; 183:108351. [PMID: 38041983 DOI: 10.1016/j.envint.2023.108351] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/28/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023]
Abstract
Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.
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Affiliation(s)
- Zhuofeng Yu
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Wanli He
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Franziska Klincke
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark; Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark; Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Marcos Quintela-Baluja
- Department of Microbiology and Parasitology, University of Santiago de Compostela, Praza do Obradoiro, 0, 15705 Santiago de Compostela, A Coruña, Spain
| | - Sabela Balboa
- School of Engineering, Newcastle University, NE1 7RX Newcastle upon Tyne, United Kingdom
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, DK-2800 Kgs. Lyngby, Denmark
| | - Barth Smets
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, DK-2800 Kgs. Lyngby, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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Maccario L, Silva AF, Nesme J, Amador CI, Sørensen SJ, Cooper VS, Røder HL. Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea. Microbiol Resour Announc 2023; 12:e0052923. [PMID: 37966239 PMCID: PMC10720559 DOI: 10.1128/mra.00529-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/07/2023] [Indexed: 11/16/2023] Open
Abstract
We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the Pseudomonas and Pseudochrobactrum genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.
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Affiliation(s)
- Lorrie Maccario
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ana F. Silva
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cristina I. Amador
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Henriette L. Røder
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
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6
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Duan Y, Han M, Grimm M, Schierstaedt J, Imani J, Cardinale M, Le Jean M, Nesme J, Sørensen SJ, Schikora A. Hordeum vulgare differentiates its response to beneficial bacteria. BMC Plant Biol 2023; 23:460. [PMID: 37789272 PMCID: PMC10548682 DOI: 10.1186/s12870-023-04484-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/23/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored. RESULTS This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable. CONCLUSIONS Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.
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Affiliation(s)
- Yongming Duan
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Min Han
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Maja Grimm
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Jasper Schierstaedt
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) - Department Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, 14979, Großbeeren, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Jafargholi Imani
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, SP6 Lecce- Monteroni, Lecce, 73100, Italy
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Marie Le Jean
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360 CNRS, Université de Lorraine, 8 rue du Général Delestraint, Metz, 57070, France
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Adam Schikora
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany.
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Moradigaravand D, Li L, Dechesne A, Nesme J, de la Cruz R, Ahmad H, Banzhaf M, Sørensen SJ, Smets BF, Kreft JU. Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics 2023; 39:btad400. [PMID: 37348862 PMCID: PMC10318386 DOI: 10.1093/bioinformatics/btad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023] Open
Abstract
MOTIVATION Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.
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Affiliation(s)
- Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Roberto de la Cruz
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Huda Ahmad
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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8
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Major N, Jechalke S, Nesme J, Goreta Ban S, Černe M, Sørensen SJ, Ban D, Grosch R, Schikora A, Schierstaedt J. Influence of sewage sludge stabilization method on microbial community and the abundance of antibiotic resistance genes. Waste Manag 2022; 154:126-135. [PMID: 36242814 DOI: 10.1016/j.wasman.2022.09.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Municipal sewage sludge (MSS) and other biosolids are of high interest for agriculture. These nutrient-rich organic materials can potentially serve as organic fertilizers. Besides an increase of organic matter in soil, other positive effects were shown after their application. Especially the positive influence on circular economy increased the attention paid to management of MSS in recent years. Unfortunately, the use of sewage sludge has some drawbacks. Biosolids are frequently polluted with heavy metals, xenobiotic organic compounds and industrial chemicals, which may be hazardous for the environment and humans. Here, we investigated the influence of stabilization method and the size of wastewater treatment plant on the structure of microbial communities as well as the abundance of antibiotic resistance genes (ARG) and mobile genetic elements (MGE). All tested ARG and MGE were detectable in almost all of the samples. Interestingly, the presence of MGE as well as particular heavy metals correlated positively with the presence of several ARG. We conclude that the distribution of ARG and MGE in biosolids originated from municipal wastewater treatment plants, cannot be explained by the size of the facility or the applied stabilization method. Moreover, we postulate that the presence of pollutants and long-term impacts should be assessed prior to a possible use of sewage sludge as fertilizer.
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Affiliation(s)
- Nikola Major
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Sven Jechalke
- Institute for Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | | | - Marko Černe
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Dean Ban
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops, Department Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.
| | - Jasper Schierstaedt
- Leibniz Institute of Vegetable and Ornamental Crops, Department Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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He Z, Parra B, Nesme J, Smets BF, Dechesne A. Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages. Water Res 2022; 227:119320. [PMID: 36395568 DOI: 10.1016/j.watres.2022.119320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/27/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Plasmid-specific bacteriophages specifically infect bacteria carrying conjugal plasmids. While wastewater has been used as isolation source for such phages, to date, only the distribution and ecology of RNA phages specific to the F plasmid have been described, because they serve as a water quality indicator. Yet, several other plasmid classes have higher clinical and ecological relevance, and the distribution, fate, and ecology of the phages that target them remain uncharacterized. We aimed to (i) provide an experimental platform to quantify the abundance of plasmid-specific phages applicable to several different conjugal plasmid classes, (ii) describe the distribution of such phages in wastewater systems, and (iii) relate their abundance to plasmid abundance and to municipal wastewater treatment processes. We introduced four model conjugal plasmids, belonging to incompatibility groups IncP-1, IncN, IncHI1, or IncF into an avirulent Salmonella enterica strain, for which somatic phages are at low abundance in wastewater. These strains were used in double layer agar assays with waters from contrasting sources. Plasmid-specific phages were common in wastewater but rare in river water. Hospital wastewater contained significantly more IncP-1-, but fewer IncF- and IncN- specific phages than domestic wastewater. This pattern did not match that of plasmid abundance estimated by Inc group targeting high-throughput quantitative PCR. The comparison between influent and effluent of wastewater treatment plants revealed a reduction in phage concentration by ca. 2 log, without significant contribution of primary settling. Overall, the ubiquity of these phages hints at their importance for plasmid ecology, and can provide opportunities in water quality monitoring and in ecological management of mobile resistance genes.
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Affiliation(s)
- Zhiming He
- Technical University of Denmark, Department of Environmental and Resource Engineering, Bygningstorvet Bygning 115, 2800 Kgs. Lyngby, Denmark
| | - Boris Parra
- Technical University of Denmark, Department of Environmental and Resource Engineering, Bygningstorvet Bygning 115, 2800 Kgs. Lyngby, Denmark
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Barth F Smets
- Technical University of Denmark, Department of Environmental and Resource Engineering, Bygningstorvet Bygning 115, 2800 Kgs. Lyngby, Denmark
| | - Arnaud Dechesne
- Technical University of Denmark, Department of Environmental and Resource Engineering, Bygningstorvet Bygning 115, 2800 Kgs. Lyngby, Denmark.
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10
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Zadel U, Cruzeiro C, Raj Durai AC, Nesme J, May R, Balázs H, Michalke B, Płaza G, Schröder P, Schloter M, Radl V. Exudates from Miscanthus x giganteus change the response of a root-associated Pseudomonas putida strain towards heavy metals. Environ Pollut 2022; 313:119989. [PMID: 36028079 DOI: 10.1016/j.envpol.2022.119989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 05/29/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
The composition of root exudates is modulated by several environmental factors, and it remains unclear how that affects beneficial rhizosphere or inoculated microorganisms under heavy metal (HM) contamination. Therefore, we evaluated the transcriptional response of Pseudomonas putida E36 (a Miscanthus x giganteus isolate with plant growth promotion-related properties) to Cd, Pb and Zn in an in vitro study implementing root exudates from M. x giganteus. To collect root exudates and analyse their composition plants were grown in a pot experiment under HM and control conditions. Our results indicated higher exudation rate for plants challenged with HM. Further, out of 29 organic acids identified and quantified in the root exudates, 8 of them were significantly influenced by HM (e.g., salicylic and terephthalic acid). The transcriptional response of P. putida E36 was significantly affected by the HM addition to the growth medium, increasing the expression of several efflux pumps and stress response-related functional units. The additional supplementation of the growth medium with root exudates from HM-challenged plants resulted in a downregulation of 29% of the functional units upregulated in P. putida E36 as a result of HM addition to the growth medium. Surprisingly, root exudates + HM downregulated the expression of P. putida E36 functional units related to plant colonization (e.g., chemotaxis, motility, biofilm formation) but upregulated its antibiotic and biocide resistance compared to the control treatment without HM. Our findings suggest that HM-induced changes in root exudation pattern may attract beneficial bacteria that are in turn awarded with organic nutrients, helping them cope with HM stress. However, it might affect the ability of these bacteria to colonize plants growing in HM polluted areas. Those findings may offer an insight for future in vivo studies contributing to improvements in phytoremediation measures.
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Affiliation(s)
- Urška Zadel
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Catarina Cruzeiro
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Abilash Chakravarthy Raj Durai
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section for Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Robert May
- Labor Dr. Spranger & Partner, Lindberghstraße 9-13, 85051, Ingolstadt, Germany.
| | - Helga Balázs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Grażyna Płaza
- Silesian University of Technology, Faculty of Organization and Management, 26 Roosevelt street, 41-800 Zabrze, Poland.
| | - Peter Schröder
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Viviane Radl
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
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11
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Sommermann L, Babin D, Behr JH, Chowdhury SP, Sandmann M, Windisch S, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Long-Term Fertilization Strategy Impacts Rhizoctonia solani–Microbe Interactions in Soil and Rhizosphere and Defense Responses in Lettuce. Microorganisms 2022; 10:microorganisms10091717. [PMID: 36144319 PMCID: PMC9501836 DOI: 10.3390/microorganisms10091717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).
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Affiliation(s)
- Loreen Sommermann
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
- Correspondence:
| | - Doreen Babin
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Jan Helge Behr
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Sandmann
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Saskia Windisch
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Günter Neumann
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
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12
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Aguilar-Romero I, van Dillewijn P, Nesme J, Sørensen SJ, Nogales R, Delgado-Moreno L, Romero E. A novel and affordable bioaugmentation strategy with microbial extracts to accelerate the biodegradation of emerging contaminants in different media. Sci Total Environ 2022; 834:155234. [PMID: 35427621 DOI: 10.1016/j.scitotenv.2022.155234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
This study describes a new bioaugmentation alternative based on the application of aqueous aerated extracts from a biomixture acclimated with ibuprofen, diclofenac and triclosan. This bioaugmentation strategy was assayed in biopurification systems (BPS) and in contaminated aqueous solutions to accelerate the removal of these emerging contaminants. Sterilized extracts or extracts from the initial uncontaminated biomixture were used as controls. In BPS, the dissipation of 90% of diclofenac and triclosan required, respectively, 60 and 108 days less than in the controls. The metabolite methyl-triclosan was determined at levels 12 times lower than in controls. In the bioaugmented solutions, ibuprofen was almost completely eliminated (99%) in 21 days and its hydroxylated metabolites were also determined to be at lower levels than in the controls. The plasmidome of acclimated biomixtures and its extract appeared to maintain certain types of plasmids but degradation related genes became less evident. Several dominant OTUs found in the extract identified as Flavobacterium and Fluviicola of the phylum Bacteroidetes, Thermomicrobia (phylum Chloroflexi) and Nonomuraea (phylum Actinobacteria), may be responsible for the enhanced dissipation of these contaminants. This bioaugmentation strategy represents an advantageous tool to facilitate in situ bioaugmentation.
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Affiliation(s)
- Inés Aguilar-Romero
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rogelio Nogales
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Laura Delgado-Moreno
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
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13
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Pinilla-Redondo R, Russel J, Mayo-Muñoz D, Shah SA, Garrett RA, Nesme J, Madsen JS, Fineran PC, Sørensen SJ. CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Res 2022; 50:4315-4328. [PMID: 34606604 DOI: 10.1093/nar/gkab859/40506127/gkab859.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/08/2021] [Accepted: 10/02/2021] [Indexed: 05/27/2023] Open
Abstract
Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences highlight the genetic independence of plasmids and suggest a major role for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.
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Affiliation(s)
- Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Department of Technological Educations, University College Copenhagen, Sigurdsgade 26, 2200 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - David Mayo-Muñoz
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Roger A Garrett
- Danish Archaea Centre, Department of Biology, University of Copenhagen, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Jonas S Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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14
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Wolters B, Hauschild K, Blau K, Mulder I, Heyde BJ, Sørensen SJ, Siemens J, Jechalke S, Smalla K, Nesme J. Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes? Environ Microbiol 2022; 24:1573-1589. [PMID: 35192222 PMCID: PMC9306954 DOI: 10.1111/1462-2920.15938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 01/04/2023]
Abstract
Soil fertilization with wastewater treatment plant (WWTP) biosolids is associated with the introduction of resistance genes (RGs), mobile genetic elements (MGEs) and potentially selective pollutants (antibiotics, heavy metals, disinfectants) into soil. Not much data are available on the parallel analysis of biosolid pollutant contents, RG/MGE abundances and microbial community composition. In the present study, DNA extracted from biosolids taken at 12 WWTPs (two large-scale, six middle-scale and four small-scale plants) was used to determine the abundance of RGs and MGEs via quantitative real-time PCR and the bacterial and archaeal community composition was assessed by 16S rRNA gene amplicon sequencing. Concentrations of heavy metals, antibiotics, the biocides triclosan, triclocarban and quaternary ammonium compounds (QACs) were measured. Strong and significant correlations were revealed between several target genes and concentrations of Cu, Zn, triclosan, several antibiotics and QACs. Interestingly, the size of the sewage treatment plant (inhabitant equivalents) was negatively correlated with antibiotic concentrations, RGs and MGEs abundances and had little influence on the load of metals and QACs or the microbial community composition. Biosolids from WWTPs with anaerobic treatment and hospitals in their catchment area were associated with a higher abundance of potential opportunistic pathogens and higher concentrations of QACs.
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Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kristin Hauschild
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Khald Blau
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ines Mulder
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Benjamin Justus Heyde
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Siemens
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Sven Jechalke
- Justus Liebig University Giessen, Institute of Phytopathology, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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15
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Olesen AK, Pinilla-Redondo R, Hansen MF, Russel J, Dechesne A, Smets BF, Madsen JS, Nesme J, Sørensen SJ. IncHI1A plasmids potentially facilitate a horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage. Mol Ecol 2022; 31:1595-1608. [PMID: 35014098 DOI: 10.1111/mec.16346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/17/2021] [Revised: 11/29/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Abstract
Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, that R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer to other families, even other phyla. Indicating, that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of especially Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range as R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.
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Affiliation(s)
- Asmus K Olesen
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | | | - Mads F Hansen
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jakob Russel
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Jonas S Madsen
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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16
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Li X, Rensing C, Vestergaard G, Arumugam M, Nesme J, Gupta S, Brejnrod AD, Sørensen SJ. Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs. Environ Int 2022; 158:106899. [PMID: 34598063 DOI: 10.1016/j.envint.2021.106899] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 04/14/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR). This paper aims to elucidate this interplay and exploit differences in antibiotic usage to infer patterns of co-selection by the non-antibiotic factors metals and biocides in the context of pig farming. We examined 278 gut metagenomes from pigs with continuous antibiotic exposure, only at weaning and at no exposure. Metals as growth promoters and biocides as disinfectants are currently used with little restrictions in stock farming. The pigs under continuous antibiotic exposure displayed the highest co-occurrence of ARGs and other genetic elements while the pigs under limited use of antibiotics still showed abundant co-occurrences. Pathogens belonging to Enterobacteriaceae displayed increased co-occurrence phenomena, suggesting that this maintenance is not a random selection process from a mobilized pool but pertains to specific phylogenetic clades. These results suggest that metals and biocides displayed strong selective pressures on ARGs exerted by intensive farming, regardless of the current use of antibiotics.
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Affiliation(s)
- Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Gisle Vestergaard
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Shashank Gupta
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Asker Daniel Brejnrod
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, United States.
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
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17
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Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F, Venkateswaran K. Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov. Front Microbiol 2021; 12:765943. [PMID: 34938279 PMCID: PMC8685578 DOI: 10.3389/fmicb.2021.765943] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 of the Agrobacterium tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of Agrobacterium G3 strains to other Agrobacterium spp., which supports the description of a novel species. The G3 strains tested (n = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Agrobacterium. Phylogenetic analyses of the 16S rRNA gene, gyrB gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the Agrobacterium genus and they form a clade distinct from other validly described Agrobacterium species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and in silico digital DNA-DNA hybridization (dDDH) comparisons between the G3 tested strains and all known Agrobacterium species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were Agrobacterium sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of Agrobacterium G3, showing it is a bona fide bacterial species, well separated from previously named Agrobacterium species or other recognized genomic species. We thus propose the name Agrobacterium tomkonis for this species previously referred to as Agrobacterium genomospecies 3. The type strain of A. tomkonis is IIF1SW-B1T (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show A. tomkonis strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. A. tomkonis specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The A. tomkonis strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.
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Affiliation(s)
- Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Céline Lavire
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Vial
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Xavier Nesme
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Florent Lassalle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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18
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Hassoun-Kheir N, Stabholz Y, Kreft JU, de la Cruz R, Dechesne A, Smets BF, Romalde JL, Lema A, Balboa S, García-Riestra C, Torres-Sangiao E, Neuberger A, Graham D, Quintela-Baluja M, Stekel DJ, Graham J, Pruden A, Nesme J, Sørensen SJ, Hough R, Paul M. EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments. One Health 2021; 13:100339. [PMID: 34746357 PMCID: PMC8554267 DOI: 10.1016/j.onehlt.2021.100339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A One Health approach requires integrative research to elucidate antimicrobial resistance (AMR) in the environment and the risks it poses to human health. Research on this topic involves experts from diverse backgrounds and professions. Shortcomings exist in terms of consistent, complete, and transparent reporting in many environmental studies. Standardized reporting will improve the quality of scientific papers, enable meta-analyses and enhance the communication among different experts. In this study, we aimed to generate a consensus of reporting standards for AMR research in wastewater and related aquatic environments. METHODS Based on a risk of bias assessment of the literature in a systematic review, we proposed a set of study quality indicators. We then used a multistep modified Delphi consensus to develop the EMBRACE-WATERS statement (rEporting antiMicroBial ResistAnCE in WATERS), a checklist of recommendations for reporting in studies of AMR in wastewater and related aquatic environments. FINDINGS Consensus was achieved among a multidisciplinary panel of twenty-one experts in three steps. The developed EMBRACE-WATERS statement incorporates 21 items. Each item contains essential elements of high-quality reporting and is followed by an explanation of their rationale and a reporting-example. The EMBRACE-WATERS statement is primarily intended to be used by investigators to ensure transparent and comprehensive reporting of their studies. It can also guide peer-reviewers and editors in evaluation of manuscripts on AMR in the aquatic environment. This statement is not intended to be used to guide investigators on the methodology of their research. INTERPRETATION We are hopeful that this statement will improve the reporting quality of future studies of AMR in wastewater and related aquatic environments. Its uptake would generate a common language to be used among researchers from different disciplines, thus advancing the One Health approach towards understanding AMR spread across aquatic environments. Similar initiatives are needed in other areas of One Health research.
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Affiliation(s)
- Nasreen Hassoun-Kheir
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - Yoav Stabholz
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
| | - Jan-Ulrich Kreft
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Roberto de la Cruz
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Arnaud Dechesne
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Barth F. Smets
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Jesús L. Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Alberto Lema
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Sabela Balboa
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos García-Riestra
- Department of Microbiology and Parasitology, University Hospital Complex of Santiago (CHUS), Spain
| | - Eva Torres-Sangiao
- Escherichia coli Group, Research Foundation Institute (FIDIS), University Hospital Complex (CHUS), Santiago de Compostela, ES, Spain
| | - Ami Neuberger
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough LE12 5RD, UK
| | - Jay Graham
- University of California, Berkeley School of Public Health, Berkeley, CA, USA
| | - Amy Pruden
- The Charles Edward Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rupert Hough
- Information and Computational Sciences, The James Hutton Institute, Aberdeen AB15 8QH, Scotland, UK
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
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19
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Yang N, Nesme J, Røder HL, Li X, Zuo Z, Petersen M, Burmølle M, Sørensen SJ. Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis. NPJ Biofilms Microbiomes 2021; 7:82. [PMID: 34795326 PMCID: PMC8602335 DOI: 10.1038/s41522-021-00253-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 04/21/2021] [Accepted: 10/08/2021] [Indexed: 01/04/2023] Open
Abstract
Drought severely restricts plant production and global warming is further increasing drought stress for crops. Much information reveals the ability of individual microbes affecting plant stress tolerance. However, the effects of emergent bacterial community properties on plant drought tolerance remain largely unexplored. Here, we inoculated Arabidopsis plants in vivo with a four-species bacterial consortium (Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans, and Paenibacillus amylolyticus, termed as SPMX), which is able to synergistically produce more biofilm biomass together than the sum of the four single-strain cultures, to investigate its effects on plant performance and rhizo-microbiota during drought. We found that SPMX remarkably improved Arabidopsis survival post 21-day drought whereas no drought-tolerant effect was observed when subjected to the individual strains, revealing emergent properties of the SPMX consortium as the underlying cause of the induced drought tolerance. The enhanced drought tolerance was associated with sustained chlorophyll content and endogenous abscisic acid (ABA) signaling. Furthermore, our data showed that the addition of SPMX helped to stabilize the diversity and structure of root-associated microbiomes, which potentially benefits plant health under drought. These SPMX-induced changes jointly confer an increased drought tolerance to plants. Our work may inform future efforts to engineer the emergent bacterial community properties to improve plant tolerance to drought.
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Affiliation(s)
- Nan Yang
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Lyng Røder
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xuanji Li
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhangli Zuo
- grid.5254.60000 0001 0674 042XDepartment of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- grid.5254.60000 0001 0674 042XDepartment of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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20
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Pinilla-Redondo R, Russel J, Mayo-Muñoz D, Shah SA, Garrett RA, Nesme J, Madsen JS, Fineran PC, Sørensen SJ. CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Res 2021; 50:4315-4328. [PMID: 34606604 PMCID: PMC9071438 DOI: 10.1093/nar/gkab859] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/08/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences highlight the genetic independence of plasmids and suggest a major role for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.
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Affiliation(s)
- Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.,Department of Technological Educations, University College Copenhagen, Sigurdsgade 26, 2200 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - David Mayo-Muñoz
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Roger A Garrett
- Danish Archaea Centre, Department of Biology, University of Copenhagen, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Jonas S Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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21
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Li L, Nesme J, Quintela-Baluja M, Balboa S, Hashsham S, Williams MR, Yu Z, Sørensen SJ, Graham DW, Romalde JL, Dechesne A, Smets BF. Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage. Environ Sci Technol 2021; 55:5939-5949. [PMID: 33886308 DOI: 10.1021/acs.est.0c08548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum β-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (106-107 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (101-104 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum β-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.
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Affiliation(s)
- Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | | | - Sabela Balboa
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Syed Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing 48824, Michigan, USA
| | - Maggie R Williams
- School of Engineering and Technology, Central Michigan University, Mt. Pleasant 48859, Michigan, USA
| | - Zhuofeng Yu
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
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22
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Balbín-Suárez A, Jacquiod S, Rohr AD, Liu B, Flachowsky H, Winkelmann T, Beerhues L, Nesme J, J Sørensen S, Vetterlein D, Smalla K. Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis. FEMS Microbiol Ecol 2021; 97:6136273. [PMID: 33587112 DOI: 10.1093/femsec/fiab031] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 01/19/2023] Open
Abstract
A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents to spread in soil. 'M26' apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of operational taxonomic units affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility of the ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.
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Affiliation(s)
- Alicia Balbín-Suárez
- Julius Kühn-Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Samuel Jacquiod
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Annmarie-Deetja Rohr
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstr. 1, 38106 Braunschweig, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstr. 1, 38106 Braunschweig, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Bygning 1, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Bygning 1, 2100 Copenhagen, Denmark
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Kornelia Smalla
- Julius Kühn-Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
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23
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Cerecetto V, Smalla K, Nesme J, Garaycochea S, Fresia P, Sørensen SJ, Babin D, Leoni C. Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems. FEMS Microbiol Ecol 2021; 97:6129805. [PMID: 33547893 DOI: 10.1093/femsec/fiab023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/05/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
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Affiliation(s)
- Victoria Cerecetto
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.,Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Kornelia Smalla
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Pablo Fresia
- Unidad Mixta Institut Pasteur de Montevideo + Instituto Nacional de Investigación Agropecuaria INIA (UMPI), Mataojo 2020, 11400 Montevideo, Uruguay
| | - Søren Johannes Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Doreen Babin
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
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24
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. ISME J 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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Babin D, Sommermann L, Chowdhury SP, Behr JH, Sandmann M, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories. FEMS Microbiol Ecol 2021; 97:fiab027. [PMID: 33571366 DOI: 10.1093/femsec/fiab027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Received: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
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Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan H Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Martin Sandmann
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science, Department of Nutritional Crop Physiology, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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26
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Kang D, Huang Y, Nesme J, Herschend J, Jacquiod S, Kot W, Hansen LH, Lange L, Sørensen SJ. Metagenomic analysis of a keratin-degrading bacterial consortium provides insight into the keratinolytic mechanisms. Sci Total Environ 2021; 761:143281. [PMID: 33190895 DOI: 10.1016/j.scitotenv.2020.143281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/19/2020] [Revised: 10/11/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
Keratin is an insoluble fibrous protein from natural environments, which can be recycled to value-added products by keratinolytic microorganisms. A microbial consortium with efficient keratinolytic activity was previously enriched from soil, but the genetic basis behind its remarkable degradation properties was not investigated yet. To identify the metabolic pathways involved in keratinolysis and clarify the observed synergy among community members, shotgun metagenomic sequencing was performed to reconstruct metagenome-assembled genomes. More than 90% genera of the enriched bacterial consortium were affiliated to Chryseobacterium, Stenotrophomonas, and Pseudomonas. Metabolic potential and putative keratinases were predicted from the metagenomic annotation, providing the genetic basis of keratin degradation. Furthermore, metabolic pathways associated with keratinolytic processes such as amino acid metabolism, disulfide reduction and urea cycle were investigated from seven high-quality metagenome-assembled genomes, revealing the potential metabolic cooperation related to keratin degradation. This knowledge deepens the understanding of microbial keratinolytic mechanisms at play in a complex community, pinpointing the significance of synergistic interactions, which could be further used to optimize industrial keratin degradation processes.
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Affiliation(s)
- Dingrong Kang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Yuhong Huang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800 Kongens Lyngby, Denmark; Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, France
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Lene Lange
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800 Kongens Lyngby, Denmark; Bioeconomy, Research & Advisory, Karensgade 5, DK-2500 Valby, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Windisch S, Sommermann L, Babin D, Chowdhury SP, Grosch R, Moradtalab N, Walker F, Höglinger B, El-Hasan A, Armbruster W, Nesme J, Sørensen SJ, Schellenberg I, Geistlinger J, Smalla K, Rothballer M, Ludewig U, Neumann G. Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce. Front Microbiol 2021; 11:597745. [PMID: 33519736 PMCID: PMC7838544 DOI: 10.3389/fmicb.2020.597745] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
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Affiliation(s)
- Saskia Windisch
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Loreen Sommermann
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | | | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Narges Moradtalab
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Frank Walker
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Birgit Höglinger
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Abbas El-Hasan
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Wolfgang Armbruster
- Department of Food Chemistry and Analytical Chemistry, Institute of Food Chemistry, University of Hohenheim, Stuttgart, Germany
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ingo Schellenberg
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Jörg Geistlinger
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Günter Neumann
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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28
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Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
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Hassoun-Kheir N, Stabholz Y, Kreft JU, de la Cruz R, Romalde JL, Nesme J, Sørensen SJ, Smets BF, Graham D, Paul M. Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review. Sci Total Environ 2020; 743:140804. [PMID: 32758846 DOI: 10.1016/j.scitotenv.2020.140804] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [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: 05/25/2020] [Revised: 07/04/2020] [Accepted: 07/05/2020] [Indexed: 05/10/2023]
Abstract
Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded. Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis. Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.
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Affiliation(s)
- Nasreen Hassoun-Kheir
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel.
| | - Yoav Stabholz
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection & Centre for Computational Biology & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roberto de la Cruz
- Institute of Microbiology and Infection & Centre for Computational Biology & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
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Yim B, Baumann A, Grunewaldt-Stöcker G, Liu B, Beerhues L, Zühlke S, Sapp M, Nesme J, Sørensen SJ, Smalla K, Winkelmann T. Rhizosphere microbial communities associated to rose replant disease: links to plant growth and root metabolites. Hortic Res 2020; 7:144. [PMID: 32922816 PMCID: PMC7459328 DOI: 10.1038/s41438-020-00365-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 05/25/2023]
Abstract
Growth depression of Rosa plants at sites previously used to cultivate the same or closely related species is a typical symptom of rose replant disease (RRD). Currently, limited information is available on the causes and the etiology of RRD compared to apple replant disease (ARD). Thus, this study aimed at analyzing growth characteristics, root morphology, and root metabolites, as well as microbial communities in the rhizosphere of the susceptible rootstock Rosacorymbifera 'Laxa' grown in RRD-affected soil from two sites (Heidgraben and Sangerhausen), either untreated or disinfected by γ-irradiation. In a greenhouse bioassay, plants developed significantly more biomass in the γ-irradiated than in the untreated soils of both sites. Several plant metabolites detected in R. corymbifera 'Laxa' roots were site- and treatment-dependent. Although aloesin was recorded in significantly higher concentrations in untreated than in γ-irradiated soils from Heidgraben, the concentrations of phenylalanine were significantly lower in roots from untreated soil of both sites. Rhizosphere microbial communities of 8-week-old plants were studied by sequencing of 16S rRNA, ITS, and cox gene fragments amplified from total community DNA. Supported by microscopic observations, sequences affiliated to the bacterial genus Streptomyces and the fungal genus Nectria were identified as potential causal agents of RRD in the soils investigated. The relative abundance of oomycetes belonging to the genus Pythiogeton showed a negative correlation to the growth of the plants. Overall, the RRD symptoms, the effects of soil treatments on the composition of the rhizosphere microbial community revealed striking similarities to findings related to ARD.
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Affiliation(s)
- B. Yim
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, 30419 Hannover, Germany
- Julius Kühn-Institut (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - A. Baumann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - G. Grunewaldt-Stöcker
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - B. Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - L. Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - S. Zühlke
- Faculty of Chemistry and Chemical Biology (CCB), Technische Universität Dortmund, 44227 Dortmund, Germany
| | - M. Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Population Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - J. Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - S. J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - K. Smalla
- Julius Kühn-Institut (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - T. Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, 30419 Hannover, Germany
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Major N, Schierstaedt J, Jechalke S, Nesme J, Ban SG, Černe M, Sørensen SJ, Ban D, Schikora A. Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil. Microorganisms 2020; 8:microorganisms8071020. [PMID: 32660164 PMCID: PMC7409118 DOI: 10.3390/microorganisms8071020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/26/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/03/2022] Open
Abstract
Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of Salmonella enterica serovar Typhimurium strain 14028s and S.enterica serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of B.rapa grown on soil inoculated with Salmonella. We detected Salmonella in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens.
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Affiliation(s)
- Nikola Major
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia; (S.G.B.); (M.Č.); (D.B.)
- Correspondence: (N.M.); (A.S.)
| | - Jasper Schierstaedt
- Leibniz Institute of Vegetable and Ornamental Crops, Department Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany;
| | - Sven Jechalke
- Institute for Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany;
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; (J.N.); (S.J.S.)
| | - Smiljana Goreta Ban
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia; (S.G.B.); (M.Č.); (D.B.)
| | - Marko Černe
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia; (S.G.B.); (M.Č.); (D.B.)
| | - Søren J. Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; (J.N.); (S.J.S.)
| | - Dean Ban
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia; (S.G.B.); (M.Č.); (D.B.)
| | - Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
- Correspondence: (N.M.); (A.S.)
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Zadel U, Nesme J, Michalke B, Vestergaard G, Płaza GA, Schröder P, Radl V, Schloter M. Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus. Sci Total Environ 2020; 711:134433. [PMID: 31818597 DOI: 10.1016/j.scitotenv.2019.134433] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 07/26/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to non-contaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log2 fold change 1.9-4.1) and Micromonospora in endosphere (log2 fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils.
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Affiliation(s)
- Urška Zadel
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Joseph Nesme
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; University of Copenhagen, Institute for Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Bernhard Michalke
- Helmholtz Zentrum München, Research Unit Analytical Biogeochemistry, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Gisle Vestergaard
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Technical University of Denmark, Section of Bioinformatics, Department of Health Technology, 2800 Kgs. Lyngby, Denmark.
| | - Grażyna A Płaza
- Institute for Ecology of Industrial Areas, Department of Environmental Microbiology, 6 Kossutha Street, 40-844 Katowice, Poland.
| | - Peter Schröder
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Viviane Radl
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Technical University of Munich, Chair for Soil Ecology, Emil-Ramann-Straße 2, 85354 Freising, Germany.
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Schierstaedt J, Jechalke S, Nesme J, Neuhaus K, Sørensen SJ, Grosch R, Smalla K, Schikora A. Salmonella
persistence in soil depends on reciprocal interactions with indigenous microorganisms. Environ Microbiol 2020; 22:2639-2652. [DOI: 10.1111/1462-2920.14972] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Jasper Schierstaedt
- Plant‐Microbe SystemsLeibniz Institute of Vegetable and Ornamental Crops Großbeeren Germany
| | - Sven Jechalke
- Institute for Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen Giessen Germany
| | - Joseph Nesme
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Klaus Neuhaus
- ZIEL ‐ Institute for Food & Health, Core Facility Microbiome/NGS, Technische Universität München Freising Germany
| | - Søren J. Sørensen
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Rita Grosch
- Plant‐Microbe SystemsLeibniz Institute of Vegetable and Ornamental Crops Großbeeren Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn‐Institut, Federal Research Centre for Cultivated Plants Braunschweig Germany
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn‐Institut, Federal Research Centre for Cultivated Plants Braunschweig Germany
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Kang D, Jacquiod S, Herschend J, Wei S, Nesme J, Sørensen SJ. Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures. Front Microbiol 2020; 10:3010. [PMID: 31998278 PMCID: PMC6968696 DOI: 10.3389/fmicb.2019.03010] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 09/13/2019] [Accepted: 12/16/2019] [Indexed: 01/21/2023] Open
Abstract
The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10-9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.
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Affiliation(s)
- Dingrong Kang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaodong Wei
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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35
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Romero IA, van Dillewijn P, Nesme J, Sørensen SJ, Romero E. Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems. Sci Total Environ 2019; 691:749-759. [PMID: 31325872 DOI: 10.1016/j.scitotenv.2019.07.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/30/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Despite certain limitations, bioaugmentation enhances the efficiency of bioremediation systems. In this study, three aqueous extracts (APE, ACE and APE) from aged residual biomixtures in three biopurification systems (BPSs) exposed to pesticides at a pilot scale were found to improve pesticide removal. The addition of ACEs and AVEs to solutions containing the model compound diuron increased removal rates 6- and 17-fold, respectively, as compared to APEs. These extracts also increased the removal of the metabolite 3,4-dichloroaniline, while AVEs, in particular, were found to remove all pesticides within 9 days. Three metabolites less hazardous than 3,4-dichloroaniline were identified by SPME/GC/MS. AVEs, which also enhance linuron removal in liquid media, were found to increase diuron removal 6-fold in BPSs. We observed an increase in the relative abundance of taxa, such as Chloroflexi, Acidobacteria, Gemmatimonadetes, Firmicutes, Deinococcus-Thermus and especially Proteobacteria (10%), in AV biomixtures, as well as an enrichment of γ-proteobacteria and the actinobacterial genus Dokdonella in AVEs with respect to initial noncontaminated IV biomixture. We demonstrate that extracts containing a pollutant-acclimatized microbiome could be used as part of a bioaugmentation strategy to improve the functioning of on-farm BPSs and contaminated systems.
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Affiliation(s)
- Inés Aguilar Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
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Bernat P, Nesme J, Paraszkiewicz K, Schloter M, Płaza G. Characterization of Extracellular Biosurfactants Expressed by a Pseudomonas putida Strain Isolated from the Interior of Healthy Roots from Sida hermaphrodita Grown in a Heavy Metal Contaminated Soil. Curr Microbiol 2019; 76:1320-1329. [PMID: 31432210 DOI: 10.1007/s00284-019-01757-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/11/2019] [Accepted: 08/09/2019] [Indexed: 10/26/2022]
Abstract
Pseudomonas putida E41 isolated from root interior of Sida hermaphrodita (grown on a field contaminated with heavy metals) showed high biosurfactant activity. In this paper, we describe data from mass spectrometry and genome analysis, to improve our understanding on the phenotypic properties of the strain. Supernatant derived from P. putida E41 liquid culture exhibited a strong decrease in the surface tension accompanied by the ability for emulsion stabilization. We identified extracellular lipopeptides, putisolvin I and II expression but did not detect rhamnolipids. Their presence was confirmed by matrix-assisted laser desorption and ionization (MALDI) TOF/TOF technique. Moreover, ten phospholipids (mainly phosphatidylethanolamines PE 33:1 and PE 32:1) which were excreted by vesicles were also detected. In contrast the bacterial cell pellet was dominated by phosphatidylglycerols (PGs), which were almost absent in the supernatant. It seems that the composition of extracellular (secreted to the environment) and cellular lipids in this strain differs. Long-read sequencing and complete genome reconstruction allowed the identification of a complete putisolvin biosynthesis pathway. In the genome of P. putida E41 were also found all genes involved in glycerophospholipid biosynthesis, and they are likely responsible for the production of detected phospholipids. Overall this is the first report describing the expression of extracellular lipopeptides (identified as putisolvins) and phospholipids by a P. putida strain, which might be explained by the need to adapt to the highly contaminated environment.
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Affiliation(s)
- Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16 street, 90-237, Łódź, Poland
| | - Joseph Nesme
- Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Katarzyna Paraszkiewicz
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16 street, 90-237, Łódź, Poland
| | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Grażyna Płaza
- Institute for Ecology of Industrial Areas, Unit of Environmental Microbiology, Kossutha 6, 40-844, Katowice, Poland.
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Anjum M, Madsen JS, Nesme J, Jana B, Wiese M, Jasinskytė D, Nielsen DS, Sørensen SJ, Dalsgaard A, Moodley A, Bortolaia V, Guardabassi L. Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli. Antimicrob Agents Chemother 2019; 63:e02528-18. [PMID: 30885897 PMCID: PMC6496067 DOI: 10.1128/aac.02528-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical blaCMY-2-harboring plasmids introduced into the human fecal microbiota by two Escherichia coli strains isolated from a human and from poultry meat. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and green fluorescent protein [GFP]), allowing fluorescence-activated cell sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established in vitro gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6, and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 102 CFU/ml. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that the plasmids were predominantly acquired by Enterobacteriaceae species, such as E. coli and Hafnia alvei Our experimental data demonstrate that exogenous E. coli of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Small amounts of the exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Džiuginta Jasinskytė
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
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Sáenz JS, Marques TV, Barone RSC, Cyrino JEP, Kublik S, Nesme J, Schloter M, Rath S, Vestergaard G. Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. Microbiome 2019; 7:24. [PMID: 30773139 PMCID: PMC6378726 DOI: 10.1186/s40168-019-0632-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 09/12/2018] [Accepted: 01/21/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach. RESULTS The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase. CONCLUSIONS Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.
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Affiliation(s)
- Johan S Sáenz
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | | | - Rafael Simões Coelho Barone
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - José Eurico Possebon Cyrino
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Susanne Kublik
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Joseph Nesme
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany.
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany.
| | - Susanne Rath
- Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Gisle Vestergaard
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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39
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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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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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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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