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Romdhane S, Huet S, Spor A, Bru D, Breuil MC, Philippot L. Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly. Environ Microbiome 2024; 19:18. [PMID: 38504378 PMCID: PMC10953230 DOI: 10.1186/s40793-024-00559-4] [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] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors. RESULTS We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any "home field advantage" during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering. CONCLUSIONS Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.
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Affiliation(s)
- Sana Romdhane
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France.
| | - Sarah Huet
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Aymé Spor
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - David Bru
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Marie-Christine Breuil
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Laurent Philippot
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
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Li C, Li X, Romdhane S, Cheng Y, Li G, Cao R, Li P, Xu J, Zhao Y, Yang Y, Jiao J, Hu F, Wu J, Li H, Philippot L. Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes. Sci Total Environ 2024; 916:170180. [PMID: 38262533 DOI: 10.1016/j.scitotenv.2024.170180] [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: 10/29/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.
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Affiliation(s)
- Chunkai Li
- College of Chemical Engineering, Nanjing Forestry University, No. 159, Longpan Road, Nanjing, Jiangsu 210037, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Xianping Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Sana Romdhane
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroécologie, Dijon 21000, France.
| | - Yanhong Cheng
- Key Laboratory of Red Soil Cultivated Land Conservation, Jiangxi Institute of Red Soil and Germplasm Resource, Nanchang, Jiangxi 331717, China
| | - Gen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Rui Cao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Peng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jingjing Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Yexin Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Yang Yang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Jiaguo Jiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Jun Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Weigang, Nanjing 210014, China.
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroécologie, Dijon 21000, France.
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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Edlinger A, Garland G, Banerjee S, Degrune F, García-Palacios P, Herzog C, Pescador DS, Romdhane S, Ryo M, Saghaï A, Hallin S, Maestre FT, Philippot L, Rillig MC, van der Heijden MGA. The impact of agricultural management on soil aggregation and carbon storage is regulated by climatic thresholds across a 3000 km European gradient. Glob Chang Biol 2023; 29:3177-3192. [PMID: 36897740 DOI: 10.1111/gcb.16677] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/07/2023] [Indexed: 05/03/2023]
Abstract
Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (-56%) and SOC stocks (-35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.
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Affiliation(s)
- Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Environmental System Science, ETH Zurich, Zurich, Switzerland
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Soil Science and Environment Group, Changins, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - David Sánchez Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Sana Romdhane
- Department of Agroecology, INRA, AgroSup Dijon, University Bourgogne Franche Comte, Dijon, France
| | - Masahiro Ryo
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - Laurent Philippot
- Department of Agroecology, INRA, AgroSup Dijon, University Bourgogne Franche Comte, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Huet S, Romdhane S, Breuil MC, Bru D, Mounier A, Spor A, Philippot L. Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions. Microbiome 2023; 11:42. [PMID: 36871037 PMCID: PMC9985222 DOI: 10.1186/s40168-023-01480-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of interactions between microorganisms for assembly of the soil microbiome. RESULTS By combining experimental removal (taxa depletion in the community) and coalescence (mixing of manipulated and control communities) approaches, we demonstrated that interactions between microorganisms can play a key role in determining their fitness during soil recolonization. The coalescence approach not only revealed the importance of density-dependent interactions in microbial community assembly but also allowed to restore partly or fully community diversity and soil functions. Microbial community manipulation resulted in shifts in both inorganic nitrogen pools and soil pH, which were related to the proportion of ammonia-oxidizing bacteria. CONCLUSIONS Our work provides new insights into the understanding of the importance of microbial interactions in soil. Our top-down approach combining removal and coalescence manipulation also allowed linking community structure and ecosystem functions. Furthermore, these results highlight the potential of manipulating microbial communities for the restoration of soil ecosystems. Video Abstract.
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Affiliation(s)
- Sarah Huet
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - Sana Romdhane
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - Marie-Christine Breuil
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - David Bru
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - Arnaud Mounier
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - Ayme Spor
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
| | - Laurent Philippot
- University Bourgogne Franche-Comte, INRAE, Institut Agro Dijon, Agroecologie Department, 17 rue de Sully, Dijon, 21000 France
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6
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Romdhane S, Spor A, Banerjee S, Breuil MC, Bru D, Chabbi A, Hallin S, van der Heijden MGA, Saghai A, Philippot L. Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity. Environ Microbiome 2022; 17:1. [PMID: 34991714 PMCID: PMC8740439 DOI: 10.1186/s40793-021-00396-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/23/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. RESULTS We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. CONCLUSIONS Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
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Affiliation(s)
- Sana Romdhane
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Aymé Spor
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Samiran Banerjee
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Biological Sciences, North Dakota State University, Fargo, 58102, USA
| | - Marie-Christine Breuil
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - David Bru
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Abad Chabbi
- ECOSYS, UMR INRAE, AgroParisTech, Thiverval-Grignon, France
- CNRS, Institute of Ecology and Environmental Sciences-Paris (iEES-Paris, UMR Sorbonne Université, CNRS, INRAE), Thiverval-Grignon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Aurélien Saghai
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laurent Philippot
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France.
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Romdhane S, Spor A, Aubert J, Bru D, Breuil MC, Hallin S, Mounier A, Ouadah S, Tsiknia M, Philippot L. Unraveling negative biotic interactions determining soil microbial community assembly and functioning. ISME J 2022; 16:296-306. [PMID: 34321619 PMCID: PMC8692615 DOI: 10.1038/s41396-021-01076-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [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: 08/06/2020] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.
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Affiliation(s)
- Sana Romdhane
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Aymé Spor
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France
| | - David Bru
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Marie-Christine Breuil
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Sara Hallin
- grid.6341.00000 0000 8578 2742Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Arnaud Mounier
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Sarah Ouadah
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France
| | - Myrto Tsiknia
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France ,grid.10985.350000 0001 0794 1186Soil Science and Agricultural Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens, Greece
| | - Laurent Philippot
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
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Saghaï A, Banjeree S, Degrune F, Edlinger A, García-Palacios P, Garland G, van der Heijden MGA, Herzog C, Maestre FT, Pescador DS, Philippot L, Rillig MC, Romdhane S, Hallin S. Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol 2021; 24:341-356. [PMID: 34796612 DOI: 10.1111/1462-2920.15830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/28/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Anna Edlinger
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gina Garland
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Soil Quality and Use Group, Agroscope, Zurich, Switzerland.,Department of Environmental System Sciences, Soil Resources Group, ETH Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain.,Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - David S Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Móstoles, Spain
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Sana Romdhane
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Romdhane S, Spor A, Busset H, Falchetto L, Martin J, Bizouard F, Bru D, Breuil MC, Philippot L, Cordeau S. Cover Crop Management Practices Rather Than Composition of Cover Crop Mixtures Affect Bacterial Communities in No-Till Agroecosystems. Front Microbiol 2019; 10:1618. [PMID: 31338089 PMCID: PMC6629898 DOI: 10.3389/fmicb.2019.01618] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 10/19/2018] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures varying in species richness and functional diversity, three cover crop termination strategies (i.e., frost, rolling, and glyphosate) and two levels of irrigation at the cover crop sowing on soil nitrogen and carbon dynamics, soil microbial diversity, and structure as well as the abundance of total bacteria, archaea, and N-cycling microbial guilds. We found that total nitrogen and soil organic carbon were higher when cover crops were killed by frost compared to rolling and glyphosate termination treatments, while cover crop biomass was positively correlated to soil carbon and C:N ratio. Modifications of soil properties due to cover crop management rather than the composition of cover crop mixtures were related to changes in the abundance of ammonia oxidizers and denitrifiers, while there was no effect on the total bacterial abundance. Unraveling the underlying processes by which cover crop management shapes soil physico-chemical properties and bacterial communities is of importance to help selecting optimized agricultural practices for sustainable farming systems.
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Affiliation(s)
- Sana Romdhane
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Aymé Spor
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Hugues Busset
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | | | | | - Florian Bizouard
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - David Bru
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | | | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Stéphane Cordeau
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
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10
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Mallet C, Romdhane S, Loiseau C, Béguet J, Martin-Laurent F, Calvayrac C, Barthelmebs L. Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils. Front Microbiol 2019; 10:1024. [PMID: 31134038 PMCID: PMC6524154 DOI: 10.3389/fmicb.2019.01024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/14/2018] [Accepted: 04/24/2019] [Indexed: 01/10/2023] Open
Abstract
Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA revealed significant changes in fungal community structure and diversity in both soils. Xylariales, Hypocreales, Pleosporales and Capnodiales (Ascomycota phyla) fungi and those belonging to Sebacinales, Cantharellales, Agaricales, Polyporales, Filobasidiales and Tremellales orders (Basidiomycota phyla) were well represented in treated soil microcosms compared to control. Nevertheless, while for the treated SJF a complete recovery of the fungal community was observed at the end of the experiment, this was not the case for the P treated soil, although no more bioherbicide remained. Indeed, the relative abundance of most of the saprophytic fungi were lower in treated soil compared to control microcosms whereas fungi from parasitic fungi included in Spizellomycetales and Pezizales orders increased. To the best of our knowledge, this is the only study assessing the effect of the bioherbicide leptospermone on the composition and diversity of the fungal community in soil. This study showed that leptospermone has an impact on α- and β-diversity of the fungal community. It underlines the possible interest of microbial endpoints for environmental risk assessment of biopesticide.
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Affiliation(s)
- Clarisse Mallet
- Laboratoire Microorganismes : Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sana Romdhane
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
| | - Camille Loiseau
- Laboratoire Microorganismes : Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémie Béguet
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRA UMR1347 Agroécologie, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Christophe Calvayrac
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
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11
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Romdhane S, Devers-Lamrani M, Beguet J, Bertrand C, Calvayrac C, Salvia MV, Jrad AB, Dayan FE, Spor A, Barthelmebs L, Martin-Laurent F. Assessment of the ecotoxicological impact of natural and synthetic β-triketone herbicides on the diversity and activity of the soil bacterial community using omic approaches. Sci Total Environ 2019; 651:241-249. [PMID: 30236841 DOI: 10.1016/j.scitotenv.2018.09.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/03/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these two herbicides (i.e. dissipation and formation of transformation products) was monitored to assess the scenario of exposure of soil microorganisms to natural and synthetic herbicides. Ecotoxicological impact of both herbicides was explored by monitoring soil bacterial diversity and activity using next-generation sequencing of 16S rRNA gene amplicons and soil metabolomics. Both leptospermone and sulcotrione fully dissipated over the incubation period. During their dissipation, transformation products of natural and synthetic β-triketone were detected. Hydroxy-leptospermone was almost completely dissipated by the end of the experiment, while CMBA, the major metabolite of sulcotrione, remained in soil microcosms. After 8 days of exposure, the diversity and structure of the soil bacterial community treated with leptospermone was significantly modified, while less significant changes were observed for sulcotrione. For both herbicides, the diversity of the soil bacterial community was still not completely recovered by the end of the experiment (45 days). The combined use of next-generation sequencing and metabolomic approaches allowed us to assess the ecotoxicological impact of natural and synthetic pesticides on non-target soil microorganisms and to detect potential biomarkers of soil exposure to β-triketones.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France; Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France.
| | | | - Jérémie Beguet
- AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France
| | - Christophe Calvayrac
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
| | - Marie-Virginie Salvia
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France
| | - Amani Ben Jrad
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University, Fort Collins, CO, USA
| | - Aymé Spor
- AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France
| | - Lise Barthelmebs
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
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12
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Romdhane S, Devers-Lamrani M, Martin-Laurent F, Jrad AB, Raviglione D, Salvia MV, Besse-Hoggan P, Dayan FE, Bertrand C, Barthelmebs L. Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide. Environ Sci Pollut Res Int 2018; 25:29848-29859. [PMID: 28718021 DOI: 10.1007/s11356-017-9728-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Bioherbicides appear as an ecofriendly alternative to synthetic herbicides, generally used for weed management, because they are supposed to have low side on human health and ecosystems. In this context, our work aims to study abiotic (i.e., photolysis) and biotic (i.e,. biodegradation) processes involved in the fate of leptospermone, a natural β-triketone herbicide, by combining chemical and microbiological approaches. Under controlled conditions, the photolysis of leptospermone was sensitive to pH. Leptospermone has a half-life of 72 h under simulated solar light irradiations. Several transformation products, including hydroxy-leptospermone, were identified. For the first time, a bacterial strain able to degrade leptospermone was isolated from an arable soil. Based on its 16S ribosomal RNA (rRNA) gene sequence, it was affiliated to the Methylophilus group and was accordingly named as Methylophilus sp. LS1. Interestingly, we report that the abundance of OTUs, similar to the 16S rRNA gene sequence of Methylophilus sp. LS1, was strongly increased in soil treated with leptospermone. The leptospermone was completely dissipated by this bacteria, with a half-life time of 6 days, allowing concomitantly its growth. Hydroxy-leptospermone was identified in the bacterial culture as a major transformation product, allowing us to propose a pathway of transformation of leptospermone including both abiotic and biotic processes.
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Affiliation(s)
- Sana Romdhane
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France
- AgroSup Dijon, INRA, Univ. Bourgogne-Franche-Comté, Agroécologie, Dijon, France
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | | | | | - Amani Ben Jrad
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France
| | - Delphine Raviglione
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Marie-Virginie Salvia
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Pascale Besse-Hoggan
- Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), 63000, Clermont-Ferrand, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University, Fort Collins, CO, USA
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Lise Barthelmebs
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France.
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France.
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13
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Patil C, Calvayrac C, Zhou Y, Romdhane S, Salvia MV, Cooper JF, Dayan FE, Bertrand C. Environmental Metabolic Footprinting: A novel application to study the impact of a natural and a synthetic β-triketone herbicide in soil. Sci Total Environ 2016; 566-567:552-558. [PMID: 27236620 DOI: 10.1016/j.scitotenv.2016.05.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 02/26/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
This study presents a novel approach for assessing the risk of agrochemicals in soil microcosms through the use of non-targeted metabolomics. The metabolome of treated soils was extracted and tested through LCMS profiling in order to generate an "Environmental Metabolic Footprint" (EMF). A dynamic characterization of pollution biomarkers was obtained through a multivariate statistical analysis of EMF data, where our results show the possible evolution towards a state of resilience. The EMF methodology was applied to two β-triketone herbicides in soil microcosms: one natural, leptospermone, and one synthetic, sulcotrione. In spite of a four-fold higher application dose, leptospermone exhibited a lower resilience time than did sulcotrione (ca. 30 days vs ca. 45 days respectively).
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Affiliation(s)
- Chandrashekhar Patil
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Christophe Calvayrac
- Laboratoire BAE, EA4218, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Yuxiang Zhou
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Sana Romdhane
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Marie-Virginie Salvia
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Jean-Francois Cooper
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Franck E Dayan
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80521, USA
| | - Cédric Bertrand
- CRIOBE USR3278, Université de Perpignan, Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France.
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14
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Romdhane S, Devers-Lamrani M, Barthelmebs L, Calvayrac C, Bertrand C, Cooper JF, Dayan FE, Martin-Laurent F. Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils. Front Microbiol 2016; 7:775. [PMID: 27252691 PMCID: PMC4877392 DOI: 10.3389/fmicb.2016.00775] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 02/01/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via DomitiaPerpignan, France; Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via DomitiaPerpignan, France; Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDurDijon, France
| | - Marion Devers-Lamrani
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
| | - Lise Barthelmebs
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Christophe Calvayrac
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Jean-François Cooper
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University Fort Collins, CO, USA
| | - Fabrice Martin-Laurent
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
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15
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Romdhane S, Devers-Lamrani M, Martin-Laurent F, Calvayrac C, Rocaboy-Faquet E, Riboul D, Cooper JF, Barthelmebs L. Isolation and characterization of Bradyrhizobium sp. SR1 degrading two β-triketone herbicides. Environ Sci Pollut Res Int 2016; 23:4138-4148. [PMID: 25903192 DOI: 10.1007/s11356-015-4544-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/13/2015] [Indexed: 06/04/2023]
Abstract
In this study, a bacterial strain able to use sulcotrione, a β-triketone herbicide, as sole source of carbon and energy was isolated from soil samples previously treated with this herbicide. Phylogenetic study based on16S rRNA gene sequence showed that the isolate has 100 % of similarity with several Bradyrhizobium and was accordingly designated as Bradyrhizobium sp. SR1. Plasmid profiling revealed the presence of a large plasmid (>50 kb) in SR1 not cured under nonselective conditions. Its transfer to Escherichia coli by electroporation failed to induce β-triketone degrading capacity, suggesting that degrading genes possibly located on this plasmid cannot be expressed in E. coli or that they are not plasmid borne. The evaluation of the SR1 ability to degrade various synthetic (mesotrione and tembotrione) and natural (leptospermone) triketones showed that this strain was also able to degrade mesotrione. Although SR1 was able to entirely dissipate both herbicides, degradation rate of sulcotrione was ten times higher than that of mesotrione, showing a greater affinity of degrading-enzyme system to sulcotrione. Degradation pathway of sulcotrione involved the formation of 2-chloro-4-mesylbenzoic acid (CMBA), previously identified in sulcotrione degradation, and of a new metabolite identified as hydroxy-sulcotrione. Mesotrione degradation pathway leads to the accumulation of 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4 methylsulfonylbenzoic acid (AMBA), two well-known metabolites of this herbicide. Along with the dissipation of β-triketones, one could observe the decrease in 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibition, indicating that toxicity was due to parent molecules, and not to the formed metabolites. This is the first report of the isolation of bacterial strain able to transform two β-triketones.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyses Environnement (BAE), University of Perpignan Via Domitia, 66860, Perpignan, France
- Laboratoire de Chimie des Biomolécules et de l'Environnement-CRIOBE-USR 3278 CNRS EPHE, University of Perpignan Via Domitia, 66860, Perpignan, France
- INRA, UMR 1347 Agroécologie, Pole Ecoldur, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - Marion Devers-Lamrani
- INRA, UMR 1347 Agroécologie, Pole Ecoldur, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - Fabrice Martin-Laurent
- INRA, UMR 1347 Agroécologie, Pole Ecoldur, 17 rue Sully, BP 86510, 21065, Dijon Cedex, France
| | - Christophe Calvayrac
- Laboratoire de Chimie des Biomolécules et de l'Environnement-CRIOBE-USR 3278 CNRS EPHE, University of Perpignan Via Domitia, 66860, Perpignan, France
| | - Emilie Rocaboy-Faquet
- Biocapteurs Analyses Environnement (BAE), University of Perpignan Via Domitia, 66860, Perpignan, France
| | - David Riboul
- INPT, ENSIACET, Université de Toulouse, 31432, Toulouse, France
- Laboratoire de Génie Chimique (LGC UMR 5503), CNRS, 4 allée Emile Monso, BP 84234, 31432, Toulouse, France
| | - Jean-François Cooper
- Laboratoire de Chimie des Biomolécules et de l'Environnement-CRIOBE-USR 3278 CNRS EPHE, University of Perpignan Via Domitia, 66860, Perpignan, France
| | - Lise Barthelmebs
- Biocapteurs Analyses Environnement (BAE), University of Perpignan Via Domitia, 66860, Perpignan, France.
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Busset N, De Felice A, Chaintreuil C, Gully D, Fardoux J, Romdhane S, Molinaro A, Silipo A, Giraud E. The LPS O-Antigen in Photosynthetic Bradyrhizobium Strains Is Dispensable for the Establishment of a Successful Symbiosis with Aeschynomene Legumes. PLoS One 2016; 11:e0148884. [PMID: 26849805 PMCID: PMC4743980 DOI: 10.1371/journal.pone.0148884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
The photosynthetic bradyrhizobia are able to use a Nod-factor independent process to induce nitrogen-fixing nodules on some semi-aquatic Aeschynomene species. These bacteria display a unique LPS O-antigen composed of a new sugar, the bradyrhizose that is regarded as a key symbiotic factor due to its non-immunogenic character. In this study, to check this hypothesis, we isolated mutants affected in the O-antigen synthesis by screening a transposon mutant library of the ORS285 strain for clones altered in colony morphology. Over the 10,000 mutants screened, five were selected and found to be mutated in two genes, rfaL, encoding for a putative O-antigen ligase and gdh encoding for a putative dTDP-glucose 4,6-dehydratase. Biochemical analysis confirmed that the LPS of these mutants completely lack the O-antigen region. However, no effect of the mutations could be detected on the symbiotic properties of the mutants indicating that the O-antigen region of photosynthetic Bradyrhizobium strains is not required for the establishment of symbiosis with Aeschynomene.
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Affiliation(s)
- Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Antonia De Felice
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sana Romdhane
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
- * E-mail:
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El Borgi W, Romdhane S, Sdiri W, Longo S, Hafsia R, Boujnah MR. [Measurement of d-dimers in non-valvular atrial fibrillation. First prospective Tunisian study]. Ann Cardiol Angeiol (Paris) 2015; 64:279-284. [PMID: 25617058 DOI: 10.1016/j.ancard.2015.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 01/04/2015] [Indexed: 06/04/2023]
Abstract
Atrial fibrillation can expose to thrombo-embolic complications. Many biomarkers have been tested to refine the stratification of thrombo-embolic risk. The study aim was to assess the interest of the d-dimer testing in this pathology. We conducted a prospective observational study including 50 cases and 19 controls, enrolled at the cardiology department of the Mongi Slim Hospital, from July to November 2012. The d-dimer assay was performed on mini-VIDAS(®) and analyzed according to clinical, echocardiographic and biological data. The mean age of patients was 61.8±10.6years. The mean CHA2DS2-VASc score was 2.58±1.31. The average of D-dimer levels was 590±506ng/ml in patients and 225.26±112.95ng/ml in controls (P=0.02). No significant difference has been found between the d-dimer level and age, sex, type and etiology of atrial fibrillation, the CHA2DS2-VASc score, the left atrial surface. Among patients on acenocoumarol, d-dimer levels was significantly higher in patients with an INR<2 compared to those with an INR≥2 (P=0.004). We identified a positive d-dimer threshold (300ng/ml) in patients distinguishing them significantly with controls (P<0.001). In conclusion, the measurement of d-dimers could help clinicians to identify patients with atrial fibrillation having an increased coagulability and, therefore, an increased thrombo-embolic risk. It could be complementary to the determination of INR in monitoring anticoagulation therapy: d-dimers level refines the thrombo-embolic risk and INR measurement assesses the level of anticoagulation and the bleeding risk.
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Affiliation(s)
- W El Borgi
- Laboratoire d'hématologie biologique, hôpital Aziza Othmana, Tunis, Tunisie.
| | - S Romdhane
- Laboratoire d'hématologie biologique, hôpital Aziza Othmana, Tunis, Tunisie.
| | - W Sdiri
- Service de cardiologie, hôpital Mongi Slim La Marsa, Tunis, Tunisie.
| | - S Longo
- Service de cardiologie, hôpital Mongi Slim La Marsa, Tunis, Tunisie.
| | - R Hafsia
- Laboratoire d'hématologie biologique, hôpital Aziza Othmana, Tunis, Tunisie.
| | - M R Boujnah
- Service de cardiologie, hôpital Mongi Slim La Marsa, Tunis, Tunisie.
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Rocaboy-Faquet E, Noguer T, Romdhane S, Bertrand C, Dayan FE, Barthelmebs L. Novel bacterial bioassay for a high-throughput screening of 4-hydroxyphenylpyruvate dioxygenase inhibitors. Appl Microbiol Biotechnol 2014; 98:7243-52. [PMID: 24816780 DOI: 10.1007/s00253-014-5793-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/11/2014] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
Plant 4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of a range of synthetic β-triketone herbicides that are currently used commercially. Their mode of action is based on an irreversible inhibition of HPPD. Therefore, this inhibitory capacity was used to develop a whole-cell colorimetric bioassay with a recombinant Escherichia coli expressing a plant HPPD for the herbicide analysis of β-triketones. The principle of the bioassay is based on the ability of the recombinant E. coli clone to produce a soluble melanin-like pigment, from tyrosine catabolism through p-hydroxyphenylpyruvate and homogentisate. The addition of sulcotrione, a HPPD inhibitor, decreased the pigment production. With the aim to optimize the assay, the E. coli recombinant clone was immobilized in sol-gel or agarose matrix in a 96-well microplate format. The limit of detection for mesotrione, tembotrione, sulcotrione, and leptospermone was 0.069, 0.051, 0.038, and 20 μM, respectively, allowing to validate the whole-cell colorimetric bioassay as a simple and cost-effective alternative tool for laboratory use. The bioassay results from sulcotrione-spiked soil samples were confirmed with high-performance liquid chromatography.
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Affiliation(s)
- Emilie Rocaboy-Faquet
- Institut de Modélisation et d'Analyse en Géo-Environnement et Santé, Université Perpignan Via Domitia, EA 4218, 66860, Perpignan, France
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Calvayrac C, Bontemps N, Nouga-Bissoue A, Romdhane S, Coste CM, Cooper JF. Photolysis of tembotrione and its main by-products under extreme artificial conditions: comparison with another β-triketone herbicide. Sci Total Environ 2013; 452-453:227-232. [PMID: 23518282 DOI: 10.1016/j.scitotenv.2013.02.067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 06/01/2023]
Abstract
The photolytic behaviour of tembotrione, a new chemical herbicide intended for foliar application in corn, was investigated under unnatural and extreme photochemical exposure in aqueous solutions in the laboratory. It appeared that degradation was dependent on pH and occurred more rapidly under acidic and neutral conditions, leading predominantly to the formation of a xanthenedione type compound by intramolecular cyclisation with loss of HCl. Trace amounts of benzoic acid by-products appeared also during UV-C irradiation (λ=254 nm) of the parent compound. Results were comparable to those obtained with sulcotrione, another β-triketone herbicide. These extreme irradiation conditions clearly accelerated the phototransformation of sulcotrione vs. simulated sunlight irradiation. Furthermore, the photolysis of the degradation by-products, resulting from either photolysis, hydrolysis or biotic pathways of the two active ingredients, was also carried out. The benzoic acid by-products appeared more stable to photolysis than their parent molecules. Xanthenedione derivatives were degraded more rapidly with several differences depending on the pH value.
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Affiliation(s)
- Christophe Calvayrac
- Laboratoire de Chimie des Biomolécules et de l'Environnement (LCBE, EA 4215), Université de Perpignan Via Domitia (UPVD), Perpignan, France
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Mahjoub M, Jrad T, Touati S, Romdhane S. SFRP-P03 – Recherche clinique – Paralysies sciatiques secondaires aux injections intramusculaires chez l’enfant. Arch Pediatr 2008. [DOI: 10.1016/s0929-693x(08)72433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mahjoub M, Jrad T, Handous A, Romdhane S. SFRP-P04 – Recherche clinique – Leishmaniose viscérale infantile. Arch Pediatr 2008. [DOI: 10.1016/s0929-693x(08)72434-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Elhouichet H, Moadhen A, Oueslati M, Romdhane S, Roger JA, Bouchriha H. Structural, optical and electrical properties of porous silicon impregnated with SnO2:Sb. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/pssc.200461165] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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