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Christel A, Chemidlin Prevost-Bouré N, Dequiedt S, Saby N, Mercier F, Tripied J, Comment G, Villerd J, Djemiel C, Hermant A, Blondon M, Bargeot L, Matagne E, Horrigue W, Maron PA, Ranjard L. Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale. Sci Total Environ 2024; 906:167454. [PMID: 37783435 DOI: 10.1016/j.scitotenv.2023.167454] [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: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.
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Affiliation(s)
- A Christel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; AgroParisTech, 75732 Paris, France
| | | | - S Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Saby
- INRAE, US1106 Info&Sols, F-45075 Orleans, France
| | - F Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - J Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - G Comment
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - J Villerd
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - C Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - A Hermant
- Chambre d'agriculture de Côte d'Or, 1 rue des Coulots, 21110 Bretenière, France
| | - M Blondon
- Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - L Bargeot
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - E Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - W Horrigue
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - P A Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - L Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Djemiel C, Dequiedt S, Bailly A, Tripied J, Lelièvre M, Horrigue W, Jolivet C, Bispo A, Saby N, Valé M, Maron PA, Ranjard L, Terrat S. Biogeographical patterns of the soil fungal:bacterial ratio across France. mSphere 2023; 8:e0036523. [PMID: 37754664 PMCID: PMC10597451 DOI: 10.1128/msphere.00365-23] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Julie Tripied
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Mélanie Lelièvre
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | | | | | | | | | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. Sci Total Environ 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Djemiel C, Dequiedt S, Karimi B, Cottin A, Horrigue W, Bailly A, Boutaleb A, Sadet-Bourgeteau S, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L, Terrat S. Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production. Front Microbiol 2022; 13:889788. [PMID: 35847063 PMCID: PMC9280627 DOI: 10.3389/fmicb.2022.889788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023] Open
Abstract
Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Battle Karimi
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Novasol Experts, Dijon, France
| | - Aurélien Cottin
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Ali Boutaleb
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Lionel Ranjard,
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sébastien Terrat,
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Terrat S, Horrigue W, Dequiedt S, Saby NPA, Lelièvre M, Nowak V, Tripied J, Régnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Prévost-Bouré NC, Ranjard L. Correction: Mapping and predictive variations of soil bacterial richness across France. PLoS One 2022; 17:e0268101. [PMID: 35500020 PMCID: PMC9060351 DOI: 10.1371/journal.pone.0268101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Djemiel C, Maron PA, Terrat S, Dequiedt S, Cottin A, Ranjard L. Inferring microbiota functions from taxonomic genes: a review. Gigascience 2022; 11:giab090. [PMID: 35022702 PMCID: PMC8756179 DOI: 10.1093/gigascience/giab090] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
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Djemiel C, Dequiedt S, Karimi B, Cottin A, Girier T, El Djoudi Y, Wincker P, Lelièvre M, Mondy S, Chemidlin Prévost-Bouré N, Maron PA, Ranjard L, Terrat S. BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. BMC Bioinformatics 2020; 21:492. [PMID: 33129268 PMCID: PMC7603665 DOI: 10.1186/s12859-020-03829-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 02/21/2020] [Accepted: 10/21/2020] [Indexed: 01/04/2023] Open
Abstract
Background The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.
Results BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups. Conclusions The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Battle Karimi
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Thibault Girier
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Yassin El Djoudi
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Patrick Wincker
- CEA/Institut de Biologie François Jacob/Génoscope, 2, Rue Gaston Crémieux, CP5706, 91057, Evry Cedex, France
| | - Mélanie Lelièvre
- Agroécologie - Plateforme GenoSol, BP 86510, 21000, Dijon, France
| | - Samuel Mondy
- Agroécologie - Plateforme GenoSol, BP 86510, 21000, Dijon, France
| | | | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.
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Terrat S, Djemiel C, Journay C, Karimi B, Dequiedt S, Horrigue W, Maron P, Chemidlin Prévost‐Bouré N, Ranjard L. ReClustOR: a re‐clustering tool using an open‐reference method that improves operational taxonomic unit definition. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sébastien Terrat
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Christophe Djemiel
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Corentin Journay
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Battle Karimi
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Samuel Dequiedt
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Walid Horrigue
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | - Pierre‐Alain Maron
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
| | | | - Lionel Ranjard
- Agroécologie AgroSup Dijon INRAUniv. Bourgogne Franche‐Comté Dijon France
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Plassart P, Prévost-Bouré NC, Uroz S, Dequiedt S, Stone D, Creamer R, Griffiths RI, Bailey MJ, Ranjard L, Lemanceau P. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Sci Rep 2019; 9:605. [PMID: 30679566 PMCID: PMC6345909 DOI: 10.1038/s41598-018-36867-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 06/21/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
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Affiliation(s)
- Pierre Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Stéphane Uroz
- UMR 1136 Interactions Arbres Micro-organismes, INRA Univ Lorraine, F-54280, Champenoux, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Rachel Creamer
- TEAGASC, Johnstown Castle, Wexford, Ireland.,Wageningen University and Research, Wageningen, The Netherlands
| | - Robert I Griffiths
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Mark J Bailey
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
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10
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Carroll EL, Gallego R, Sewell MA, Zeldis J, Ranjard L, Ross HA, Tooman LK, O'Rorke R, Newcomb RD, Constantine R. Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Sci Rep 2019; 9:281. [PMID: 30670720 PMCID: PMC6342929 DOI: 10.1038/s41598-018-36478-x] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/22/2018] [Indexed: 01/26/2023] Open
Abstract
To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde's whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde's whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde's whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde's whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.
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Affiliation(s)
- E L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - R Gallego
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - M A Sewell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - J Zeldis
- National Institute of Water and Atmospheric Research, Christchurch, New Zealand
| | - L Ranjard
- Research School of Biology, the Australian National University, Canberra, ACT, Australia
| | - H A Ross
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - L K Tooman
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R O'Rorke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - R D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R Constantine
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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11
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Karimi B, Terrat S, Dequiedt S, Saby NPA, Horrigue W, Lelièvre M, Nowak V, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Maron PA, Bouré NCP, Ranjard L. Biogeography of soil bacteria and archaea across France. Sci Adv 2018; 4:eaat1808. [PMID: 29978046 PMCID: PMC6031370 DOI: 10.1126/sciadv.aat1808] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/23/2018] [Indexed: 05/03/2023]
Abstract
Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.
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Affiliation(s)
- Battle Karimi
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Walid Horrigue
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mélanie Lelièvre
- Agroécologie–Plateforme GenoSol, BP 86510, F-21000 Dijon, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | | | - Patrick Wincker
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Biologie François Jacob, Genoscope, 2, Rue Gaston Crémieux, CP5706, 91057 Evry cedex, France
| | - Corinne Cruaud
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Biologie François Jacob, Genoscope, 2, Rue Gaston Crémieux, CP5706, 91057 Evry cedex, France
| | - Antonio Bispo
- INRA Orléans, US 1106, Unité INFOSOL, Orléans, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Nicolas Chemidlin Prévost Bouré
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France
- Corresponding author.
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12
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Le Guillou C, Chemidlin Prévost-Bouré N, Karimi B, Akkal-Corfini N, Dequiedt S, Nowak V, Terrat S, Menasseri-Aubry S, Viaud V, Maron PA, Ranjard L. Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale. Microbiologyopen 2018; 8:e00676. [PMID: 29897676 PMCID: PMC6460278 DOI: 10.1002/mbo3.676] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/04/2018] [Accepted: 05/17/2018] [Indexed: 11/11/2022] Open
Abstract
Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long‐term research study catchment (12 km2) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape‐scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.
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Affiliation(s)
| | | | | | | | - Samuel Dequiedt
- INRA, UMR1347 Agroécologie, Dijon, France.,INRA, UMR1347 Agroécologie, Plateforme Genosol, Dijon, France
| | | | - Sébastien Terrat
- INRA, UMR1347 Agroécologie, Dijon, France.,Université de Bourgogne, UMR1347 Agroécologie, Dijon, France
| | - Safya Menasseri-Aubry
- INRA, UMR1069 Sol Agro et hydrosystème Spatialisation, Rennes, France.,Agrocampus Ouest, UMR1069 Sol Agro et hydrosystème Spatialisation, Rennes, France.,Université Européenne de Bretagne, Bretagne, France
| | - Valérie Viaud
- INRA, UMR1069 Sol Agro et hydrosystème Spatialisation, Rennes, France
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13
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Maron PA, Sarr A, Kaisermann A, Lévêque J, Mathieu O, Guigue J, Karimi B, Bernard L, Dequiedt S, Terrat S, Chabbi A, Ranjard L. High Microbial Diversity Promotes Soil Ecosystem Functioning. Appl Environ Microbiol 2018. [PMID: 29453268 DOI: 10.1128/aem.02738-2717] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO2 emission by up to 40%, and (ii) shaped the source of CO2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.
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Affiliation(s)
- Pierre-Alain Maron
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Amadou Sarr
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aurore Kaisermann
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Jean Lévêque
- UMR 6282 CNRS/uB Biogéosciences, Université de Bourgogne Franche-Comté, Dijon, France
| | - Olivier Mathieu
- UMR 6282 CNRS/uB Biogéosciences, Université de Bourgogne Franche-Comté, Dijon, France
| | - Julien Guigue
- UMR 6282 CNRS/uB Biogéosciences, Université de Bourgogne Franche-Comté, Dijon, France
| | - Battle Karimi
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laetitia Bernard
- Institut de Recherche pour le Développement, UMR Eco&Sols, Montpellier, France
| | - Samuel Dequiedt
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Terrat
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Abad Chabbi
- UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Lionel Ranjard
- UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
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14
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Terrat S, Horrigue W, Dequiedt S, Saby NPA, Lelièvre M, Nowak V, Tripied J, Régnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Prévost-Bouré NC, Ranjard L. Correction: Mapping and predictive variations of soil bacterial richness across France. PLoS One 2017; 12:e0190128. [PMID: 29253898 PMCID: PMC5734764 DOI: 10.1371/journal.pone.0190128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0186766.].
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15
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Terrat S, Horrigue W, Dequietd S, Saby NPA, Lelièvre M, Nowak V, Tripied J, Régnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L. Mapping and predictive variations of soil bacterial richness across France. PLoS One 2017; 12:e0186766. [PMID: 29059218 PMCID: PMC5653302 DOI: 10.1371/journal.pone.0186766] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/07/2017] [Indexed: 11/18/2022] Open
Abstract
Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.
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Affiliation(s)
- Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequietd
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | | | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | | | | | | | | | | | - Battle Karimi
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Pierre Alain Maron
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
- * E-mail:
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16
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Mougin C, Azam D, Caquet T, Cheviron N, Dequiedt S, Le Galliard JF, Guillaume O, Houot S, Lacroix G, Lafolie F, Maron PA, Michniewicz R, Pichot C, Ranjard L, Roy J, Zeller B, Clobert J, Chanzy A. A coordinated set of ecosystem research platforms open to international research in ecotoxicology, AnaEE-France. Environ Sci Pollut Res Int 2015; 22:16215-28. [PMID: 26315587 DOI: 10.1007/s11356-015-5233-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 06/20/2015] [Accepted: 08/11/2015] [Indexed: 05/25/2023]
Abstract
The infrastructure for Analysis and Experimentation on Ecosystems (AnaEE-France) is an integrated network of the major French experimental, analytical, and modeling platforms dedicated to the biological study of continental ecosystems (aquatic and terrestrial). This infrastructure aims at understanding and predicting ecosystem dynamics under global change. AnaEE-France comprises complementary nodes offering access to the best experimental facilities and associated biological resources and data: Ecotrons, seminatural experimental platforms to manipulate terrestrial and aquatic ecosystems, in natura sites equipped for large-scale and long-term experiments. AnaEE-France also provides shared instruments and analytical platforms dedicated to environmental (micro) biology. Finally, AnaEE-France provides users with data bases and modeling tools designed to represent ecosystem dynamics and to go further in coupling ecological, agronomical, and evolutionary approaches. In particular, AnaEE-France offers adequate services to tackle the new challenges of research in ecotoxicology, positioning its various types of platforms in an ecologically advanced ecotoxicology approach. AnaEE-France is a leading international infrastructure, and it is pioneering the construction of AnaEE (Europe) infrastructure in the field of ecosystem research. AnaEE-France infrastructure is already open to the international community of scientists in the field of continental ecotoxicology.
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Affiliation(s)
- Christian Mougin
- INRA/AgroParisTech, UMR1402 ECOSYS, Platform Biochem-Env, Route de St-Cyr, 78026, Versailles cedex, France.
- INRA/AgroParisTech, UMR1402 ECOSYS, Platform Biochem-Env, 78026, Versailles cedex, France.
| | - Didier Azam
- INRA, UE 1036 U3E, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France
| | - Thierry Caquet
- INRA, UAR1275 Département EFPA, 54280, Champenoux, France
| | - Nathalie Cheviron
- INRA/AgroParisTech, UMR1402 ECOSYS, Platform Biochem-Env, Route de St-Cyr, 78026, Versailles cedex, France
| | - Samuel Dequiedt
- INRA/Université de Bourgogne/AgroSup Dijon, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon cedex, France
| | - Jean-François Le Galliard
- CNRS/UPMC - UMR 7618, IEES Paris, Université Pierre et Marie Curie, Case 237, 7 Quai St Bernard, 75005, Paris, France
- CNRS/ENS - UMS 3194, CEREEP - Ecotron Ile-De-France, École Normale Supérieure, 78 rue du Château, 77140, St-Pierre-lès-Nemours, France
| | | | - Sabine Houot
- INRA/AgroParisTech, UMR 1402 ECOSYS, 78850, Thiverval-Grignon, France
| | - Gérard Lacroix
- CNRS/UPMC - UMR 7618, IEES Paris, Université Pierre et Marie Curie, Case 237, 7 Quai St Bernard, 75005, Paris, France
- CNRS/ENS - UMS 3194, CEREEP - Ecotron Ile-De-France, École Normale Supérieure, 78 rue du Château, 77140, St-Pierre-lès-Nemours, France
| | - François Lafolie
- INRA/UAPV, UMR 1114 EMMAH, Site Agroparc, 228 route de l'aérodrome, CS 40509, 84914, Avignon Cédex 9, France
| | - Pierre-Alain Maron
- INRA/Université de Bourgogne/AgroSup Dijon, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon cedex, France
| | | | - Christian Pichot
- INRA, UR0629 URFM, Site Agroparc, 228 route de l'aérodrome, CS 40509, 84914, Avignon Cédex 9, France
| | - Lionel Ranjard
- INRA/Université de Bourgogne/AgroSup Dijon, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon cedex, France
| | - Jacques Roy
- CNRS, UPS 3248 Ecotron Européen de Montpellier, Campus de Baillarguet, 1 chemin du Rioux, 34980, Montferrier-sur-Lez, France
| | | | | | - André Chanzy
- INRA/UAPV, UMR 1114 EMMAH, Site Agroparc, 228 route de l'aérodrome, CS 40509, 84914, Avignon Cédex 9, France
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17
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Tardy V, Chabbi A, Charrier X, de Berranger C, Reignier T, Dequiedt S, Faivre-Primot C, Terrat S, Ranjard L, Maron PA. Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil. PLoS One 2015; 10:e0130672. [PMID: 26102585 PMCID: PMC4478037 DOI: 10.1371/journal.pone.0130672] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [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: 12/09/2014] [Accepted: 05/22/2015] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.
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Affiliation(s)
| | - Abad Chabbi
- Centre de recherche Poitou-Charentes, INRA, Lusignan, France
| | - Xavier Charrier
- Centre de recherche Poitou-Charentes, INRA, Lusignan, France
| | | | | | - Samuel Dequiedt
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
| | | | | | - Lionel Ranjard
- INRA, UMR 1347 Agroecology, Dijon, France
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
| | - Pierre-Alain Maron
- INRA, UMR 1347 Agroecology, Dijon, France
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
- * E-mail:
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18
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Constancias F, Terrat S, Saby NPA, Horrigue W, Villerd J, Guillemin JP, Biju-Duval L, Nowak V, Dequiedt S, Ranjard L, Chemidlin Prévost-Bouré N. Mapping and determinism of soil microbial community distribution across an agricultural landscape. Microbiologyopen 2015; 4:505-17. [PMID: 25833770 PMCID: PMC4475391 DOI: 10.1002/mbo3.255] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 02/23/2015] [Accepted: 03/02/2015] [Indexed: 11/13/2022] Open
Abstract
Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.
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Affiliation(s)
| | - Sébastien Terrat
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
- Université de Bourgogne, UMR1347 AgroecologieBP 86510, F-21000 Dijon, France
| | | | - Walid Horrigue
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Jean Villerd
- INRA, UMR1121 Universite de Lorraine (Ensaia)F-54518, Vandoeuvre-les-Nancy, France
| | | | - Luc Biju-Duval
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
| | - Virginie Nowak
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Samuel Dequiedt
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Lionel Ranjard
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
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19
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Constancias F, Saby NPA, Terrat S, Dequiedt S, Horrigue W, Nowak V, Guillemin JP, Biju-Duval L, Chemidlin Prévost-Bouré N, Ranjard L. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape. Microbiologyopen 2015; 4:518-31. [PMID: 25922908 PMCID: PMC4475392 DOI: 10.1002/mbo3.256] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/23/2015] [Accepted: 03/02/2015] [Indexed: 12/03/2022] Open
Abstract
Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships) according to phyla. Altogether, this study provided valuable clues about the ecological behavior of soil bacterial and archaeal taxa at an agricultural landscape scale and could be useful for developing sustainable strategies of land management.
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Affiliation(s)
| | | | - Sébastien Terrat
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Samuel Dequiedt
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Wallid Horrigue
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Virginie Nowak
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | | | - Luc Biju-Duval
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
| | | | - Lionel Ranjard
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
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20
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Chemidlin Prévost-Bouré N, Dequiedt S, Thioulouse J, Lelièvre M, Saby NPA, Jolivet C, Arrouays D, Plassart P, Lemanceau P, Ranjard L. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale. PLoS One 2014; 9:e111667. [PMID: 25365044 PMCID: PMC4218796 DOI: 10.1371/journal.pone.0111667] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 10/01/2014] [Indexed: 11/24/2022] Open
Abstract
Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes<Burgundy≤Brittany<<South-East) using the systematic grid of French Soil Quality Monitoring Network to evaluate the communities’ composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.
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Affiliation(s)
- Nicolas Chemidlin Prévost-Bouré
- Unité Mixte de Recherche 1347 Agroécologie, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
- * E-mail:
| | - Samuel Dequiedt
- Unité Mixte de Recherche 1347 Agroécologie-Plateforme GenoSol, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
| | - Jean Thioulouse
- Unité Mixte de Recherche 555 Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1-Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Mélanie Lelièvre
- Unité Mixte de Recherche 1347 Agroécologie-Plateforme GenoSol, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
| | - Nicolas P. A. Saby
- Unité de Services 1106 InfoSol, Institut National de la Recherche Agronomique, Orléans, France
| | - Claudy Jolivet
- Unité de Services 1106 InfoSol, Institut National de la Recherche Agronomique, Orléans, France
| | - Dominique Arrouays
- Unité de Services 1106 InfoSol, Institut National de la Recherche Agronomique, Orléans, France
| | - Pierre Plassart
- Unité Mixte de Recherche 1347 Agroécologie-Plateforme GenoSol, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
| | - Philippe Lemanceau
- Unité Mixte de Recherche 1347 Agroécologie, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
| | - Lionel Ranjard
- Unité Mixte de Recherche 1347 Agroécologie, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
- Unité Mixte de Recherche 1347 Agroécologie-Plateforme GenoSol, Institut National de la Recherche Agronomique-AgroSup Dijon-Université de Bourgogne, Dijon, France
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Terrat S, Plassart P, Bourgeois E, Ferreira S, Dequiedt S, Adele-Dit-De-Renseville N, Lemanceau P, Bispo A, Chabbi A, Maron PA, Ranjard L. Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition. Microb Biotechnol 2014; 8:131-42. [PMID: 25195809 PMCID: PMC4321379 DOI: 10.1111/1751-7915.12162] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 04/25/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 11/29/2022] Open
Abstract
This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.
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22
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Deredjian A, Colinon C, Hien E, Brothier E, Youenou B, Cournoyer B, Dequiedt S, Hartmann A, Jolivet C, Houot S, Ranjard L, Saby NPA, Nazaret S. Low occurrence of Pseudomonas aeruginosa in agricultural soils with and without organic amendment. Front Cell Infect Microbiol 2014; 4:53. [PMID: 24809025 PMCID: PMC4010769 DOI: 10.3389/fcimb.2014.00053] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/09/2014] [Indexed: 01/05/2023] Open
Abstract
The occurrence of Pseudomonas aeruginosa was monitored at a broad spatial scale in French agricultural soils, from various soil types and under various land uses to evaluate the ability of soil to be a natural habitat for that species. To appreciate the impact of agricultural practices on the potential dispersion of P. aeruginosa, we further investigated the impact of organic amendment at experimental sites in France and Burkina Faso. A real-time quantitative PCR (qPCR) approach was used to analyze a set of 380 samples selected within the French RMQS (“Réseau de Mesures de la Qualité des Sols”) soil library. In parallel, a culture-dependent approach was tested on a subset of samples. The results showed that P. aeruginosa was very rarely detected suggesting a sporadic presence of this bacterium in soils from France and Burkina Faso, whatever the structural and physico-chemical characteristics or climate. When we analyzed the impact of organic amendment on the prevalence of P. aeruginosa, we found that even if it was detectable in various manures (at levels from 103 to 105 CFU or DNA targets (g drywt)−1 of sample), it was hardly ever detected in the corresponding soils, which raises questions about its survival. The only case reports were from a vineyard soil amended with a compost of mushroom manure in Burgundy, and a few samples from two fields amended with raw urban wastes in the sub-urban area of Ouagadougou, Burkina Faso. In these soils the levels of culturable cells were below 10 CFU (g drywt)−1.
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Affiliation(s)
- Amélie Deredjian
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
| | - Céline Colinon
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
| | - Edmond Hien
- UMR Ecosol, IRD-Université de Ouagadougou, UFR/SVT Ouagadougou, Burkina Faso
| | - Elisabeth Brothier
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
| | - Benjamin Youenou
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
| | - Benoit Cournoyer
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
| | - Samuel Dequiedt
- Plateforme GenoSol, INRA-Université Bourgogne, AgroSup, UMR1347 Agroécologie Dijon, France
| | - Alain Hartmann
- INRA-Université Bourgogne, AgroSup, UMR1347 Agroécologie Dijon, France
| | | | - Sabine Houot
- INRA, UMR 1091 Environnement et Grandes Cultures Thiverval-Grignon, France
| | - Lionel Ranjard
- Plateforme GenoSol, INRA-Université Bourgogne, AgroSup, UMR1347 Agroécologie Dijon, France
| | | | - Sylvie Nazaret
- CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Université de Lyon Villeurbanne, France
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Tardy V, Mathieu O, Lévêque J, Terrat S, Chabbi A, Lemanceau P, Ranjard L, Maron PA. Stability of soil microbial structure and activity depends on microbial diversity. Environ Microbiol Rep 2014; 6:173-83. [PMID: 24596291 DOI: 10.1111/1758-2229.12126] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/30/2013] [Indexed: 05/24/2023]
Abstract
Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
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Colinon C, Deredjian A, Hien E, Brothier E, Bouziri L, Cournoyer B, Hartman A, Henry S, Jolivet C, Ranjard L, Nazaret S. Detection and enumeration of Pseudomonas aeruginosa
in soil and manure assessed by an ecfX
qPCR assay. J Appl Microbiol 2013; 114:1734-49. [DOI: 10.1111/jam.12189] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 11/29/2022]
Affiliation(s)
- C. Colinon
- Université de Lyon, CNRS, Ecole Nationale Vétérinaire de Lyon Université Lyon 1, UMR 5557 Ecologie Microbienne; Villeurbanne Cedex France
| | - A. Deredjian
- Université de Lyon, CNRS, Ecole Nationale Vétérinaire de Lyon Université Lyon 1, UMR 5557 Ecologie Microbienne; Villeurbanne Cedex France
| | - E. Hien
- IRD UMR Eco-Sols; Université de Ouagadougou; UFR/SVT 03 BP 7021; Ouagadougou Burkina Faso
| | - E. Brothier
- Université de Lyon, CNRS, Ecole Nationale Vétérinaire de Lyon Université Lyon 1, UMR 5557 Ecologie Microbienne; Villeurbanne Cedex France
| | - L. Bouziri
- Centre de Recherches et de Technologies des Eaux; Laboratoire Traitement et Recyclage des Eaux; Hammam-Lif Tunisia
| | - B. Cournoyer
- Université de Lyon, CNRS, Ecole Nationale Vétérinaire de Lyon Université Lyon 1, UMR 5557 Ecologie Microbienne; Villeurbanne Cedex France
| | - A. Hartman
- INRA - Université Bourgogne; UMR 1229 Microbiologie du Sol et de l'Environnement; Dijon Cedex France
| | - S. Henry
- INRA - Université Bourgogne; UMR 1229 Microbiologie du Sol et de l'Environnement; Dijon Cedex France
| | | | - L. Ranjard
- INRA - Université Bourgogne; UMR 1229 Microbiologie du Sol et de l'Environnement; Dijon Cedex France
- INRA - Université Bourgogne; Plateforme Genosol; Dijon Cedex France
| | - S. Nazaret
- Université de Lyon, CNRS, Ecole Nationale Vétérinaire de Lyon Université Lyon 1, UMR 5557 Ecologie Microbienne; Villeurbanne Cedex France
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25
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Pascault N, Ranjard L, Kaisermann A, Bachar D, Christen R, Terrat S, Mathieu O, Lévêque J, Mougel C, Henault C, Lemanceau P, Péan M, Boiry S, Fontaine S, Maron PA. Stimulation of Different Functional Groups of Bacteria by Various Plant Residues as a Driver of Soil Priming Effect. Ecosystems 2013. [DOI: 10.1007/s10021-013-9650-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ranjard L, Dequiedt S, Chemidlin Prévost-Bouré N, Thioulouse J, Saby N, Lelievre M, Maron PA, Morin F, Bispo A, Jolivet C, Arrouays D, Lemanceau P. Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity. Nat Commun 2013; 4:1434. [DOI: 10.1038/ncomms2431] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/02/2013] [Indexed: 11/09/2022] Open
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27
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Plassart P, Terrat S, Thomson B, Griffiths R, Dequiedt S, Lelievre M, Regnier T, Nowak V, Bailey M, Lemanceau P, Bispo A, Chabbi A, Maron PA, Mougel C, Ranjard L. Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure. PLoS One 2012; 7:e44279. [PMID: 22984486 PMCID: PMC3439486 DOI: 10.1371/journal.pone.0044279] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/31/2012] [Indexed: 11/18/2022] Open
Abstract
Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.
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Affiliation(s)
- Pierre Plassart
- INRA, UMR1347 Agroécologie, Dijon, France
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
| | | | - Bruce Thomson
- Centre for Ecology & Hydrology, Wallingford, United Kingdom
| | | | - Samuel Dequiedt
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
| | | | | | - Virginie Nowak
- INRA, UMR1347 Agroécologie, Dijon, France
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
| | - Mark Bailey
- Centre for Ecology & Hydrology, Wallingford, United Kingdom
| | | | | | | | - Pierre-Alain Maron
- INRA, UMR1347 Agroécologie, Dijon, France
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
| | - Christophe Mougel
- INRA, UMR1347 Agroécologie, Dijon, France
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
| | - Lionel Ranjard
- INRA, UMR1347 Agroécologie, Dijon, France
- Plateforme GenoSol, INRA, UMR1347 Agroécologie, Dijon, France
- * E-mail:
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Krull CR, Ranjard L, Landers TJ, Ismar SMH, Matthews JL, Hauber ME. Analyses of sex and individual differences in vocalizations of Australasian gannets using a dynamic time warping algorithm. J Acoust Soc Am 2012; 132:1189-1198. [PMID: 22894237 DOI: 10.1121/1.4734237] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The study of the evolution of sexual differences in behavioral and morphological displays requires analyses of the extent of sexual dimorphism across various sensory modalities. In the seabird family Sulidae, boobies show dramatic sexual dimorphism in their vocalizations, and gannet calls have also been suggested to be dimorphic to human observers. This study aimed to evaluate the presence of sexually dimorphic calls in the Australasian gannet (Morus serrator) through the first comprehensive description of its vocalizations recorded at two localities; Cape Kidnappers, where individuals were banded and sexed from DNA samples, and at the Muriwai gannetry, both on the North Island of New Zealand. Calls were first inspected using basic bioacoustic features to establish a library of call element types for general reference. Extensive multivariate tests, based on a dynamic time warping algorithm, subsequently revealed that no sexual differences could be detected in Australasian gannet calls. The analyses, however, indicated extensive and consistent vocal variation between individuals, particularly so in female gannets, which may serve to signal individual identity to conspecifics. This study generates predictions to identify whether differences in Australasian gannet vocalizations play perceptual and functional roles in the breeding and social biology of this long-lived biparental seabird species.
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Affiliation(s)
- C R Krull
- School of Biological Sciences, University of Auckland, Auckland, Private Bag 92019, New Zealand
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Terrat S, Christen R, Dequiedt S, Lelièvre M, Nowak V, Regnier T, Bachar D, Plassart P, Wincker P, Jolivet C, Bispo A, Lemanceau P, Maron PA, Mougel C, Ranjard L. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb Biotechnol 2011; 5:135-41. [PMID: 21989224 PMCID: PMC3815280 DOI: 10.1111/j.1751-7915.2011.00307.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
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Affiliation(s)
- Sébastien Terrat
- INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France
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Chemidlin Prévost-Bouré N, Christen R, Dequiedt S, Mougel C, Lelièvre M, Jolivet C, Shahbazkia HR, Guillou L, Arrouays D, Ranjard L. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS One 2011; 6:e24166. [PMID: 21931659 PMCID: PMC3169588 DOI: 10.1371/journal.pone.0024166] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/01/2011] [Indexed: 11/19/2022] Open
Abstract
Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.
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Affiliation(s)
| | - Richard Christen
- Université de Nice and CNRS UMR 6543, Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valose, Nice, France
| | - Samuel Dequiedt
- Platform GenoSol, INRA-Université de Bourgogne, CMSE, Dijon, France
| | - Christophe Mougel
- INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, Dijon, France
- Platform GenoSol, INRA-Université de Bourgogne, CMSE, Dijon, France
| | - Mélanie Lelièvre
- Platform GenoSol, INRA-Université de Bourgogne, CMSE, Dijon, France
| | | | | | - Laure Guillou
- Université Pierre and Marie Curie and CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | | | - Lionel Ranjard
- INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, Dijon, France
- Platform GenoSol, INRA-Université de Bourgogne, CMSE, Dijon, France
- * E-mail:
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Colinon-Dupuich C, Février L, Ranjard L, Coppin F, Cournoyer B, Nazaret S. Radioecological risk assessment of low selenium concentrations through genetic fingerprints and metabolic profiling of soil bacterial communities. Microb Ecol 2011; 62:14-24. [PMID: 21409345 DOI: 10.1007/s00248-011-9831-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 10/02/2010] [Indexed: 05/30/2023]
Abstract
In a context of environmental risk assessment of nuclear (79)Se radionuclide, the impact of low Se-selenite concentrations (0.008 and 8 mg kg(-1)) on bacterial communities of two soils, a silty clay loam and a sandy soil, was investigated over a 6-month incubation time. This Se-selenite was partially labelled with (75)Se. The state of the Se-impacted bacterial communities was analyzed through total bacterial counts, DNA fingerprints (ARISA profiles) and metabolic profiling (carbon substrate utilization patterns). Furthermore, the genetic diversity of bacterial populations involved in Se volatilization was evaluated by tpm (thiopurine methyltransferase gene) profiling. Emissions of (75)Se and CaCl(2)-extractable (75)Se were measured by γ-spectrometry and scintillation analysis. Se-selenite inputs changed transiently the substrate utilization patterns of bacterial communities but did not affect the other indicators. Se volatilization was at its highest level just after adding Se-selenite and for about 1 week. This volatilization was proportional to the added Se-selenite concentrations. It was 100-fold higher in silty clay loam, even though Se bioavailability was reduced in this soil. The soils were amended with crushed grass 3 months after the addition of Se-selenite. This organic amendment affected the organization of bacterial communities and increased the Se-volatilizing activities of both soils. Original soil organic carbon and bacterial diversity and activities seemed responsible for the different levels of Se emissions observed in soils. tpm lineages, encoding Se methyltransferases, were detected in both soils, confirming the broad distribution of tpm-harbouring bacteria and their probable role in the emissions of volatile Se. Five distinct groups of tpm were recorded per soil, with tpmI lineage being detected throughout the incubation period. This study demonstrates the ability of bacterial communities at volatilizing Se concentrations inferior to geochemical backgrounds and suggests that a probable transfer of nuclear Se will occur through volatilization after an environmental spill.
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Affiliation(s)
- Céline Colinon-Dupuich
- Research Group on Bacterial Opportunistic Pathogens and Environment, UMR 5557 Ecologie Microbienne, Université de Lyon, CNRS and Ecole Nationale Vétérinaire de Lyon, Mendel Bldg., 69622, Villeurbanne Cedex, France
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Maron PA, Mougel C, Ranjard L. Soil microbial diversity: Methodological strategy, spatial overview and functional interest. C R Biol 2011; 334:403-11. [PMID: 21640949 DOI: 10.1016/j.crvi.2010.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 11/30/2010] [Indexed: 11/28/2022]
Abstract
Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.
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Affiliation(s)
- Pierre-Alain Maron
- UMR microbiologie du sol et de l'environnement, CMSE, INRA, université de Bourgogne, 17, rue Sully, BP 86510, 21065 Dijon cedex, France
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Pascault N, Cécillon L, Mathieu O, Hénault C, Sarr A, Lévêque J, Farcy P, Ranjard L, Maron PA. In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues. Microb Ecol 2010; 60:816-28. [PMID: 20593174 DOI: 10.1007/s00248-010-9705-7] [Citation(s) in RCA: 13] [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: 02/04/2010] [Accepted: 06/08/2010] [Indexed: 05/10/2023]
Abstract
Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in an 11-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass, and genetic structure of the soil microbial communities. Wheat, alfalfa, and rape residues were incorporated into the 0-15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near-infrared spectroscopy. Qualitative modifications in the genetic structure of the bacterial communities were determined by bacterial-automated ribosomal intergenic spacer analysis. Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial community dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process.
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Affiliation(s)
- Noémie Pascault
- UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne, CMSE, BP 86510, Dijon, France
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Pascault N, Nicolardot B, Bastian F, Thiébeau P, Ranjard L, Maron PA. In situ dynamics and spatial heterogeneity of soil bacterial communities under different crop residue management. Microb Ecol 2010; 60:291-303. [PMID: 20352206 DOI: 10.1007/s00248-010-9648-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 02/20/2010] [Indexed: 05/13/2023]
Abstract
The effect of the location of wheat residues (soil surface vs. incorporated in soil) on their decomposition and on soil bacterial communities was investigated by the means of a field experiment. Bacterial-automated ribosomal intergenic spacer analysis of DNA extracts from residues, detritusphere (soil adjacent to residues), and bulk soil evidenced that residues constitute the zone of maximal changes in bacterial composition. However, the location of the residues influenced greatly their decomposition and the dynamics of the colonizing bacterial communities. Sequencing of 16S rRNA gene in DNA extracts from the residues at the early, middle, and late stages of degradation confirmed the difference of composition of the bacterial community according to the location. Bacteria belonging to the γ-subgroup of proteobacteria were stimulated when residues were incorporated whereas the α-subgroup was stimulated when residues were left at the soil surface. Moreover, Actinobacteria were more represented when residues were left at the soil surface. According to the ecological attributes of the populations identified, our results suggested that climatic fluctuations at the soil surface select populations harboring enhanced catabolic and/or survival capacities whereas residues characteristics likely constitute the main determinant of the composition of the bacterial community colonizing incorporated residues.
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Affiliation(s)
- Noémie Pascault
- UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne CMSE, BP 86510, 17 rue de Sully, 21065 Dijon Cedex, France
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Bernard L, Maron PA, Mougel C, Nowak V, Lévêque J, Marol C, Balesdent J, Gibiat F, Ranjard L. Contamination of soil by copper affects the dynamics, diversity, and activity of soil bacterial communities involved in wheat decomposition and carbon storage. Appl Environ Microbiol 2009; 75:7565-9. [PMID: 19801474 PMCID: PMC2786425 DOI: 10.1128/aem.00616-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 09/24/2009] [Indexed: 11/20/2022] Open
Abstract
A soil microcosm experiment was conducted to evaluate the influence of copper contamination on the dynamics and diversity of bacterial communities actively involved in wheat residue decomposition. In the presence of copper, a higher level of CO(2) release was observed, which did not arise from greater wheat decomposition but from a higher level of stimulation of soil organic matter mineralization (known as the priming effect). Such functional modifications may be related to significant modifications in the diversity of active bacterial populations characterized using the DNA stable-isotope probing approach.
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Affiliation(s)
- L. Bernard
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - P. A. Maron
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - C. Mougel
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - V. Nowak
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - J. Lévêque
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - C. Marol
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - J. Balesdent
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - F. Gibiat
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
| | - L. Ranjard
- INRA Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17 Rue Sully, B.V. 86510, 21065 Dijon Cedex, France, UMR CNRS Biogeosciences, UMR 5561, Université de Bourgogne, 6 Boulevard Gabriel, F-21000 Dijon, France, CEA Cadarache, DSV/IBEB/SBVME/Groupement de Recherches Appliquées en Phytotechnologie, UMR 6191 Biologie Végétale & Microbiologie Environnementale, CEA/CNRS/Université Aix-Marseille, Saint-Paul-lez-Durance, F-13108, France, INRA Unité Géochimie des Sols et des Eaux Europole Méditerranéen de l'Arbois, BP 80, 13545 Aix en Provence Cedex 04, France
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Dequiedt S, Thioulouse J, Jolivet C, Saby NPA, Lelievre M, Maron PA, Martin MP, Prévost-Bouré NC, Toutain B, Arrouays D, Lemanceau P, Ranjard L. Biogeographical patterns of soil bacterial communities. Environ Microbiol Rep 2009; 1:251-5. [PMID: 23765854 DOI: 10.1111/j.1758-2229.2009.00040.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This study provides the first maps of variations in bacterial community structure on a broad scale based on genotyping of DNA extracts from 593 soils from four different regions of France (North, Brittany, South-East and Landes). Soils were obtained from the soil library of RMQS ('Réseau de Mesures de la Qualité des Sols' = French soil quality monitoring network). The relevance of a biogeographic approach for studying bacterial communities was demonstrated by the great variability in community structure and specific geographical patterns within and between the four regions. The data indicated that the distribution of bacterial community composition might be more related to local factors such as soil type and land cover than to more global factors such as climatic and geomorphologic characteristics. Furthermore, the regional pools of biodiversity could be ordered: South-East ≥ North > Brittany > Landes, according to the observed regional variability of the bacterial communities, which could be helpful for improving land use in accordance with soil biodiversity management.
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Affiliation(s)
- Samuel Dequiedt
- INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Université de Bourgogne, UMR 1229, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Platform GenoSol, INRA-Université de Bourgogne, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne Cedex, France. INRA Orléans - US 1106, Unité INFOSOL, Avenue de la Pomme de Pin - BP 20619 Ardon 45166 Olivet, Cedex, France
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Ranjard L, Dequiedt S, Lelievre M, Maron PA, Mougel C, Morin F, Lemanceau P. Platform GenoSol: a new tool for conserving and exploring soil microbial diversity. Environ Microbiol Rep 2009; 1:97-99. [PMID: 23765739 DOI: 10.1111/j.1758-2229.2009.00023.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Lionel Ranjard
- INRA, Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France. Platform GenoSol, INRA, Université de Bourgogne, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon, Cedex, France
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Philippot L, Cregut M, Chèneby D, Bressan MÃ, Dequiet S, Martin-Laurent F, Ranjard L, Lemanceau P. Effect of primary mild stresses on resilience and resistance of the nitrate reducer community to a subsequent severe stress. FEMS Microbiol Lett 2008; 285:51-7. [DOI: 10.1111/j.1574-6968.2008.01210.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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39
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Bressan M, Mougel C, Dequiedt S, Maron PA, Lemanceau P, Ranjard L. Response of soil bacterial community structure to successive perturbations of different types and intensities. Environ Microbiol 2008; 10:2184-7. [PMID: 18462402 DOI: 10.1111/j.1462-2920.2008.01641.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In soil, genetic structure modifications of indigenous bacterial community consecutively to a severe stress (mercury contamination) were delayed when the community was pre-exposed to various minor perturbations (heat, copper and atrazine). Such minor perturbations induced transitory community structure modifications leading to an increase of community stability towards a severe mercury stress. These results illustrated well the short-term pre-adaptation process for bacterial community hypothesizing that community submitted to perturbations become more resistant to withstand another stress.
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Affiliation(s)
- Mélanie Bressan
- INRA, Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France
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40
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Ranjard L, Nowak V, Echairi A, Faloya V, Chaussod R. The dynamics of soil bacterial community structure in response to yearly repeated agricultural copper treatments. Res Microbiol 2008; 159:251-4. [DOI: 10.1016/j.resmic.2008.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/27/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
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Lejon DPH, Martins JMF, Lévêque J, Spadini L, Pascault N, Landry D, Milloux MJ, Nowak V, Chaussod R, Ranjard L. Copper dynamics and impact on microbial communities in soils of variable organic status. Environ Sci Technol 2008; 42:2819-2825. [PMID: 18497129 DOI: 10.1021/es071652r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The effect of soil organic status on copper impact was investigated by means of a microcosm study carried out on a vineyard soil that had been amended with varying types of organic matter during a previous long-term field experiment. Soil microcosms were contaminated at 250 mg Cu kg(-1) and incubated for 35 days. Copper distribution and dynamics were assessed in the solid matrix by a sequential extraction procedure and in the soil solution by measuring total and free exchangeable copper concentrations. Copper bioavailability was also measured with a whole-cell biosensor. Modifications of microbial communities were assessed by means of biomass-C measurements and characterization of genetic structure using ARISA (automated-ribosomal-intergenic-spacer-analysis). The results showed that copper distribution, speciation, and bioavailability are strongly different between organically amended and nonamended soils. Surprisingly, in solution, bioavailable copper correlated with total copper but not with free copper. Similarly the observed differential copper impact on micro-organisms suggested that organic matter controlled copper toxicity. Bacterial-ARISA modifications also correlated with the estimated metal bioavailability and corresponded to the enrichment of the Actinobacteria. Contrarily, biomass-C and fungal-ARISA measurements did not relate trivially to copper speciation and bioavailability, suggesting that the specific composition of the indigenous-soil communities controls its sensitivity to this metal.
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Affiliation(s)
- David P H Lejon
- INRA-Université Bourgogne, UMR MSE, CMSE, 21065 Dijon, France
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Maron PA, Maitre M, Mercier A, Henri Lejon DP, Nowak V, Ranjard L. Protein and DNA fingerprinting of a soil bacterial community inoculated into three different sterile soils. Res Microbiol 2008; 159:231-6. [PMID: 18472249 DOI: 10.1016/j.resmic.2008.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 03/21/2008] [Accepted: 03/24/2008] [Indexed: 11/16/2022]
Abstract
The functional and genetic structures of a soil bacterial community were characterized after inoculation into three different sterile soils using a protein and DNA fingerprinting method, respectively. Principal component analysis (PCA) of profiles revealed that, depending on soil characteristics, bacterial communities with similar genetic structures harbored different functional structures and thus could potentially be of differing ecological significance for soil functioning. Co-inertia analysis between protein fingerprinting data and the corresponding sets of soil physicochemical characteristics demonstrated the correlation between the functional structure of the bacterial community and soil parameters, with pH, clay and CaCO(3) contents being the most discriminating factors.
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Affiliation(s)
- Pierre-Alain Maron
- UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, Dijon cedex, France.
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Lejon DPH, Nowak V, Bouko S, Pascault N, Mougel C, Martins JMF, Ranjard L. Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination. FEMS Microbiol Ecol 2007; 61:424-37. [PMID: 17696885 DOI: 10.1111/j.1574-6941.2007.00365.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A molecular fingerprinting assay was developed to assess the diversity of copA genes, one of the genetic determinants involved in bacterial resistance to copper. Consensus primers of the copA genes were deduced from an alignment of sequences from proteobacterial strains. A PCR detection procedure was optimized for bacterial strains and allowed the description of a novel copA genetic determinant in Pseudomonas fluorescens. The copA DNA fingerprinting procedure was optimized for DNA directly extracted from soils differing in their physico-chemical characteristics and in their organic status (SOS). Particular copA genetic structures were obtained for each studied soil and a coinertia analysis with soil physico-chemical characteristics revealed the strong influence of pH, soil texture and the quality of soil organic matter. The molecular phylogeny of copA gene confirmed that specific copA genes clusters are specific for each SOS. Furthermore, this study demonstrates that this approach was sensitive to short-term responses of copA gene diversity to copper additions to soil samples, suggesting that community adaptation is preferentially controlled by the diversity of the innate copA genes rather than by the bioavailability of the metal.
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Affiliation(s)
- David P H Lejon
- INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, Dijon, France
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Lejon DPH, Sebastia J, Lamy I, Chaussod R, Ranjard L. Relationships between soil organic status and microbial community density and genetic structure in two agricultural soils submitted to various types of organic management. Microb Ecol 2007; 53:650-63. [PMID: 17401597 DOI: 10.1007/s00248-006-9145-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 04/26/2006] [Accepted: 06/27/2006] [Indexed: 05/14/2023]
Abstract
The effects of soil organic management on indigenous microorganisms were studied by comparing mulching straw (S), conifer compost (CC), and conifer bark (CB) as well as grass landing with grass (G), clover (Cl), and fescue (F) in a silty-clay soil (Mâcon), and by incorporating vine shoot (VS) and single and double doses of farmyard manure (FM) and mushroom manure (MM) in a calcareous sandy soil (Chinon). Soil physicochemical and microbial characteristics were assessed at each site at two depths by sampling at 0-5 and 5-20 cm for the Mâcon site and 0-10 and 10-20 cm for the Chinon site. Changes in the quantity of soil organic matter (SOM), through an increase in C(org) and N(org) contents, and in its quality, through modifications in the C/N and humic acid/fulvic acid ratios, were essentially recorded at the surface layer of treated plots with differential magnitudes according to the inputs and soil type. Quantitative modifications in microbial communities were assessed by means of C-biomass measurements and resulted in an increase in microbial densities fitted with the increase of C(org) and N(org) contents. However, the deduced C incorporation in microbial biomass was negatively correlated with the C/N ratio, demonstrating a strong influence of the type of organic management on the rate of microbial processes. Qualitative modifications in microbial communities were evaluated by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using bacterial and fungal automated ribosomal intergenic spacer analysis. Organic amendments led to changes in the bacterial and fungal communities of both sites. However, the magnitude and the specificity of these changes were different between sites, organic amendments, and microorganisms targeted, revealing that the impact of organic management is dependent on the soil and organic input types as well as on the particular ecology of microorganisms. A co-inertia analysis was performed to specify the role of the quantity and quality of SOM on the modifications of the genetic structure. A significant costructure was only observed for Mâcon plots at 0-5 cm between the bacterial genetic structure and the SOM characteristics, demonstrating the influence of the relative amount of the different humic substances (humic and fulvic acids) on microbial composition.
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Affiliation(s)
- David P H Lejon
- UMR Microbiologie et Géochimie des sols, INRA/Université de Bourgogne, CMSE, Dijon Cedex, France
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Bernard L, Mougel C, Maron PA, Nowak V, Lévêque J, Henault C, Haichar FEZ, Berge O, Marol C, Balesdent J, Gibiat F, Lemanceau P, Ranjard L. Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 2007; 9:752-64. [PMID: 17298374 DOI: 10.1111/j.1462-2920.2006.01197.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work is the first report on the use of DNA-, RNA-SIP approaches to elucidate the dynamics and the diversity of bacterial populations actively assimilating C derived from plant residues labelled at more than 90% (13)C. Wheat-residues, were incorporated and incubated into soil microcosms for 28 days. At the end of the incubation time, no more than 55% of the total CO(2) released was (13)C-labelled, suggesting the occurrence of an important priming effect process. After 7 days, more than 30% of the whole DNA extracted were labelled, allowing an efficient separation of labelled from unlabelled DNA using density gradient centrifugation. The genetic structure of bacterial community, assessed by Automated Ribosomal Intergenic Spacer Analysis technique, was deduced from the (13)C- and (12)C-fractions of control and enriched conditions, over the time course of the experiment. Dynamics showed that wheat residues directly induced a rapid and durable stimulation of fresh organic matter (FOM) degrading populations ((13)C), while specific soil organic matter (SOM) degrading populations ((12)C) seemed to be indirectly stimulated only at the early time point (t7d). After 14 days of incubations, 16S rRNA clone libraries were elaborated on (12)C- and (13)C-RNA extracted from enriched microcosms, as well as (12)C-RNA extracted from control condition. Stimulation of the beta- and gamma-subgroups of proteobacteria, where numerous populations were previously described as r-strategists or copiotrophic organisms, was recorded in the (13)C-fraction. In the mean time, several phyla like Actinobacteria, Cyanobacteria, Candidate, Gemmatimonadetes and Planctomycetes were only present in (12)C fractions. Surprisingly, several sequences affiliated to species characterized as oligotrophic organisms were retrieved in both types of fraction. Trophic relationships between soil bacteria involved in FOM and SOM degradation were discussed on the basis of different hypotheses of Fontaine and colleagues (2003) concerning the mechanisms of the priming effect induction.
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Affiliation(s)
- Laetitia Bernard
- INRA-Université de Bourgogne, UMR Microbiologie et Géochimie des Sols, CMSE, 17, rue Sully, B. V. 86510, 21065 Dijon Cedex, France
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Maron PA, Ranjard L, Mougel C, Lemanceau P. Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 2007; 53:486-93. [PMID: 17431707 DOI: 10.1007/s00248-006-9196-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 11/17/2006] [Accepted: 11/26/2006] [Indexed: 05/14/2023]
Abstract
In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.
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Affiliation(s)
- Pierre-Alain Maron
- UMR Microbiologie et Géochimie des Sols, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, 21065, Dijon Cedex, France
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Haichar FEZ, Achouak W, Christen R, Heulin T, Marol C, Marais MF, Mougel C, Ranjard L, Balesdent J, Berge O. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 2007; 9:625-34. [PMID: 17298363 DOI: 10.1111/j.1462-2920.2006.01182.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. (13)C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the (13)C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.
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Affiliation(s)
- Feth El Zahar Haichar
- CEA, DSV, DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements extrêmes (LEMiRE), UMR 6191 CNRS, CEA, Aix Marseille-Univ, IFR-E 112, Saint-Paul-Lez-Durance F-13108, France
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Ranjard L, Echairi A, Nowak V, Lejon DPH, Nouaïm R, Chaussod R. Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils. FEMS Microbiol Ecol 2007; 58:303-15. [PMID: 17064271 DOI: 10.1111/j.1574-6941.2006.00157.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.
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Affiliation(s)
- Lionel Ranjard
- INRA-Université de Bourgogne, UMR Microbiologie et Géochimie des Sols, CMSE, Dijon, France.
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Favre-Bonté S, Ranjard L, Champier L, Cournoyer B, Nazaret S. Distribution and genetic diversity of bacterial thiopurine methyltransferases in soils emitting dimethyl selenide. Biochimie 2006; 88:1573-81. [PMID: 17007990 DOI: 10.1016/j.biochi.2006.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Accepted: 09/05/2006] [Indexed: 11/30/2022]
Abstract
Dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe) emissions by soil samples spiked with selenite or (methyl)selenocysteine, with or without a supplement of nutrient broth and glucose were measured. DMSe was the main form of volatile Se produced, and was observed for both Se-substrates. DMDSe was only emitted from soils spiked with (methyl)selenocysteine. Two bacterial thiopurine methyltransferases (TPMTs), TPMT-I and TPMT-E, have been reported to be involved in DMSe and DMDSe emissions [J. Bacteriol. 184 (2002) 3146; Appl. Environ. Microbiol. 69 (2003) 3784]. To establish if these TPMTs or other members of their gene family could have contributed to the DMSe emissions observed, the diversity of bTPMT gene (tpm) sequences among the soils of this study was investigated. Total DNAs from these soils were extracted and screened using the tpm PTCF2-PTCR2 consensus primers defined to PCR amplify this gene family. The PCR products obtained from two soils were cloned, analysed by PCR-RFLP, and sequenced. Their analysis showed an important diversity of tpm lineages (around 12) in soils. Phylogenetic analysis of the deduced TPMT sequences of these soils revealed lineages not previously recorded in the databases, sequences closely related or identical to freshwater TPMTs, or sequences encoding TPMTs closely related to those of Pseudomonas fragi TPMT-K, Pseudomonas Hsa.28 TPMT-I, or Colwellia psychrerythraea TPMT-Z. Nested PCRs, allowing detection of about 13 distinct tpm soil and freshwater lineages by PTCF2-PTCR2 PCR screenings, were performed on the soil total DNAs. These PCRs confirmed the sequencing data, and allowed to recover lineages not detected by the cloning strategy. These results indicate that soils, like the freshwater samples, harbour TPMT-I gene sequences but may also have distinct tpm lineages. This study further supports our hypothesis that TPMTs contribute to DMSe soil emissions.
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Affiliation(s)
- S Favre-Bonté
- UMR CNRS UCBL 5557 écologie microbienne (Centre for Microbial Ecology), Research Group on Bacterial Opportunistic Pathogens and Environment, université Claude-Bernard, Lyon-I, 69622 Villeurbanne cedex, France
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Abstract
In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg > or = Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the "hump-backed" relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S. P. McGrath, Soil Biol. Biochem. 30:1389-1414, 1998).
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Affiliation(s)
- L Ranjard
- INRA/Université de Bourgogne, UMR Microbiologie et Géochimie des Sols, CMSE, 17 rue de Sully, B.V. 86510, 21065 Dijon Cedex, France.
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