Publications by authors named "Pierre-Alain Maron"

35 Publications

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 Oct 31;21(1):492. Epub 2020 Oct 31.

Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.

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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http://dx.doi.org/10.1186/s12859-020-03829-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603665PMC
October 2020

Reduced microbial diversity induces larger volatile organic compound emissions from soils.

Sci Rep 2020 04 8;10(1):6104. Epub 2020 Apr 8.

INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France.

Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.
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http://dx.doi.org/10.1038/s41598-020-63091-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142124PMC
April 2020

µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria.

Sci Rep 2020 04 3;10(1):5915. Epub 2020 Apr 3.

Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France.

Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.
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http://dx.doi.org/10.1038/s41598-020-62555-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125122PMC
April 2020

The diversity of soil microbial communities matters when legumes face drought.

Plant Cell Environ 2020 04 3;43(4):1023-1035. Epub 2020 Feb 3.

Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France.

The cultivation of legumes shows promise for the development of sustainable agriculture, but yield instability remains one of the main obstacles for its adoption. Here, we tested whether the yield stability (i.e., resistance and resilience) of pea plants subjected to drought could be enhanced by soil microbial diversity. We used a dilution approach to manipulate the microbial diversity, with a genotype approach to distinguish the effect of symbionts from that of microbial diversity as a whole. We investigated the physiology of plants in response to drought when grown on a soil containing high or low level of microbial diversity. Plants grown under high microbial diversity displayed higher productivity and greater resilience after drought. Yield losses were mitigated by 15% on average in the presence of high soil microbial diversity at sowing. Our study provides proof of concept that the soil microbial community as a whole plays a key role for yield stability after drought even in plant species living in relationships with microbial symbionts. These results emphasize the need to restore soil biodiversity for sustainable crop management and climate change adaptation.
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http://dx.doi.org/10.1111/pce.13712DOI Listing
April 2020

Biogeography of soil bacteria and archaea across France.

Sci Adv 2018 07 4;4(7):eaat1808. Epub 2018 Jul 4.

Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France.

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 16 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 16 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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http://dx.doi.org/10.1126/sciadv.aat1808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031370PMC
July 2018

Profiles of volatile organic compound emissions from soils amended with organic waste products.

Sci Total Environ 2018 Sep 4;636:1333-1343. Epub 2018 May 4.

INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079 Dijon cedex, France.

Volatile Organic Compounds (VOCs) are reactive compounds essential to atmospheric chemistry. They are mainly emitted by living organisms, and mostly by plants. Soil microbes also contribute to emissions of VOCs. However, these emissions have not yet been characterised in terms of quality and quantity. Furthermore, long-term organic matter amendments are known to affect the microbial content of soils, and hence the quantity and quality of VOC emissions. This study investigates which and how much of these VOCs are emitted from soil amended with organic waste products (OWPs). Four OWPs were investigated: municipal solid waste compost (MSW), green waste and sludge co-compost (GWS), bio-waste compost (BIOW) and farmyard manure (FYM). These OWPs have been amended every two years since 1998 until now at a rate of ~4 tC ha. A soil receiving no organic inputs was used as a reference (CN). VOCs emissions were measured under laboratory conditions using a Proton Transfer Reaction-Quadrupole ion guide Time of Flight-Mass Spectrometry (PTR-QiToF-MS). A laboratory system was set up made of two Pyrex chambers, one for samples and the second empty, to be used as a blank. Our results showed that total VOC emissions were higher in BIOW than in MSW. Further findings outlined that the most emitted compounds were acetone, butanone and acetaldehyde in all treatments, suggesting a common production mechanism for these compounds, meaning they were not affected by the OWP amendment. We isolated 21 VOCs that had statistically different emissions between the treatments and could therefore be considered as good markers of soil biological functioning. Our results suggest that organic matter and pH jointly influenced total VOC emissions. In conclusion, OWPs in soil affect the type of VOC emissions and the total flux also depends on the pH of the soil and the quantity of organic matter.
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http://dx.doi.org/10.1016/j.scitotenv.2018.04.232DOI Listing
September 2018

Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale.

Microbiologyopen 2019 04 13;8(4):e00676. Epub 2018 Jun 13.

INRA, UMR1347 Agroécologie, Dijon, France.

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 km ) 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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http://dx.doi.org/10.1002/mbo3.676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460278PMC
April 2019

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data.

Sci Total Environ 2018 Feb 17;615:1207-1217. Epub 2017 Oct 17.

Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France. Electronic address:

In recent decades, show caves have begun to suffer from microorganism proliferation due to artificial lighting installations for touristic activity. In addition to the aesthetic problem, light encourages microorganisms that are responsible for physical and chemical degradation of limestone walls, speleothems and prehistoric paintings of cultural value. Microorganisms have previously been described by microscopy or culture-dependent methods, but data provided by new generation sequencing are rare. The authors identified, for the first time, microorganisms proliferating in one Swiss and in four French show caves using three different primers. The results showed that both photosynthetic and non-photosynthetic bacteria were the dominant taxa present in biofilms. Microalgae were heavily represented by the Trebouxiophyceae, Eustigmatophyceae and Chlorophyceae groups. Twelve diatoms were also recorded, with dominance of Syntrichia sp. (96.1%). Fungi were predominantly represented by Ascomycota, Zygomycota and Basidiomycota, fully half of the sampled biofilms where Fungi were detected. Comparing microbial communities from bleach-treated caves to those in untreated caves showed no significant difference except for a low-level change in the abundance of certain taxa. These findings provided by Illumina sequencing reveal a complex community structure in the 5 caves based on the assembly of bacteria, cyanobacteria, algae, diatoms, fungi and mosses.
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http://dx.doi.org/10.1016/j.scitotenv.2017.10.054DOI Listing
February 2018

High Microbial Diversity Promotes Soil Ecosystem Functioning.

Appl Environ Microbiol 2018 05 16;84(9). Epub 2018 Apr 16.

UMR 1347 Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France.

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 CO emission by up to 40%, and (ii) shaped the source of CO 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. 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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http://dx.doi.org/10.1128/AEM.02738-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930326PMC
May 2018

The interaction of soil phototrophs and fungi with pH and their impact on soil CO, COO and OCS exchange.

Soil Biol Biochem 2017 12;115:371-382

ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d'Ornon, France.

The stable oxygen isotope composition of atmospheric CO and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the 'community-integrated' CA activity differently for CO and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO, COO and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO sink and the CA-driven CO-HO isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO, OCS and COO fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO and OCS.
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http://dx.doi.org/10.1016/j.soilbio.2017.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666291PMC
December 2017

Mapping and predictive variations of soil bacterial richness across France.

PLoS One 2017 23;12(10):e0186766. Epub 2017 Oct 23.

Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186766PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653302PMC
November 2017

Soil microbial diversity drives the priming effect along climate gradients: a case study in Madagascar.

ISME J 2018 02 17;12(2):451-462. Epub 2017 Oct 17.

IRD, UMR 210 Eco&Sols, Montpellier Cedex 1, France.

The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.
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http://dx.doi.org/10.1038/ismej.2017.178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776458PMC
February 2018

Soil C and N models that integrate microbial diversity.

Environ Chem Lett 2016;14(3):331-344. Epub 2016 Jul 21.

UMR 1069 SAS, Agrocampus-Ouest, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France ; UMR 1069 SAS, INRA, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France ; Université Européenne de Bretagne, Rennes, France.

Industrial agriculture is yearly responsible for the loss of 55-100 Pg of historical soil carbon and 9.9 Tg of reactive nitrogen worldwide. Therefore, management practices should be adapted to preserve ecological processes and reduce inputs and environmental impacts. In particular, the management of soil organic matter (SOM) is a key factor influencing C and N cycles. Soil microorganisms play a central role in SOM dynamics. For instance, microbial diversity may explain up to 77 % of carbon mineralisation activities. However, soil microbial diversity is actually rarely taken into account in models of C and N dynamics. Here, we review the influence of microbial diversity on C and N dynamics, and the integration of microbial diversity in soil C and N models. We found that a gain of microbial richness and evenness enhances soil C and N dynamics on the average, though the improvement of C and N dynamics depends on the composition of microbial community. We reviewed 50 models integrating soil microbial diversity. More than 90 % of models integrate microbial diversity with discrete compartments representing conceptual functional groups (64 %) or identified taxonomic groups interacting in a food web (28 %). Half of the models have not been tested against an empirical dataset while the other half mainly consider fixed parameters. This is due to the difficulty to link taxonomic and functional diversity.
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http://dx.doi.org/10.1007/s10311-016-0571-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011482PMC
July 2016

Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source.

PLoS One 2016 23;11(8):e0161251. Epub 2016 Aug 23.

UMR SAS 1069, INRA, Rennes, France.

Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and confirmed with more experimental studies. Overall, along with other studies on relationships between microbial community composition and SOM dynamics, this study suggests that overall measures of microbial diversity may constitute relevant ways to include microbial diversity in models of SOM dynamics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161251PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995005PMC
July 2017

GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.

Methods Mol Biol 2016 ;1399:55-60

INRA, UMR Agroécologie, 17 Rue de Sully, 21065, Dijon Cedex, France.

In 2008, the platform "GenoSol" ( http://www.dijon.inra.fr/plateforme_genosol ) was created at the INRA (French National Institute for Agronomic Research) of Dijon. This platform was launched by several soil microbial ecologist senior scientists to provide a logistics and technical structure dedicated to the acquisition, conservation, characterization, and supply of genetic resources (DNA) of soils from very large-scale samplings (several hundred to several thousand corresponding to large spatial and/or temporal scales). Thanks to this structure metagenomic analysis of soil microbial communities has been standardized as well as a reliable reference system for analysis of the microbial genetic resources of the collected soils (more than 10,000 soil samples to date). This platform also illustrates the usefulness of existing soil archives in providing a readily available source of ecological information that is relevant to microbial ecology, probably more than we can currently fathom.
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http://dx.doi.org/10.1007/978-1-4939-3369-3_3DOI Listing
October 2016

A coordinated set of ecosystem research platforms open to international research in ecotoxicology, AnaEE-France.

Environ Sci Pollut Res Int 2015 Oct 29;22(20):16215-28. Epub 2015 Aug 29.

INRA/UAPV, UMR 1114 EMMAH, Site Agroparc, 228 route de l'aérodrome, CS 40509, 84914, Avignon Cédex 9, France.

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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http://dx.doi.org/10.1007/s11356-015-5233-9DOI Listing
October 2015

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil.

PLoS One 2015 23;10(6):e0130672. Epub 2015 Jun 23.

INRA, UMR 1347 Agroecology, Dijon, France; INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130672PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478037PMC
April 2016

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

Microb Biotechnol 2015 Jan 4;8(1):131-42. Epub 2014 Sep 4.

INRA, UMR1347 Agroécologie, Plateforme GenoSol, Dijon, France.

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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http://dx.doi.org/10.1111/1751-7915.12162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321379PMC
January 2015

Stability of soil microbial structure and activity depends on microbial diversity.

Environ Microbiol Rep 2014 Apr 2;6(2):173-83. Epub 2013 Dec 2.

UMR 1347 Agroecology, INRA, Dijon, France.

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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http://dx.doi.org/10.1111/1758-2229.12126DOI Listing
April 2014

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

PLoS One 2013 8;8(10):e76991. Epub 2013 Oct 8.

Université de Bourgogne, UMR1347 Agroécologie, Dijon, France ; INRA, UMR1347 Agroécologie, Dijon, France.

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076991PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792895PMC
August 2014

Loss in microbial diversity affects nitrogen cycling in soil.

ISME J 2013 Aug 7;7(8):1609-19. Epub 2013 Mar 7.

INRA, UMR 1347 Department of Agroecology, Dijon, France.

Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/10(3) and 1/10(5) dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4-5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversity-functioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.
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http://dx.doi.org/10.1038/ismej.2013.34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721106PMC
August 2013

Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure.

PLoS One 2012 11;7(9):e44279. Epub 2012 Sep 11.

INRA, UMR1347 Agroécologie, Dijon, France.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044279PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439486PMC
March 2013

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure.

Microb Biotechnol 2012 Jan 12;5(1):135-41. Epub 2011 Oct 12.

INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l'Environnement, CMSE, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France.

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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http://dx.doi.org/10.1111/j.1751-7915.2011.00307.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815280PMC
January 2012

Soil microbial diversity: Methodological strategy, spatial overview and functional interest.

C R Biol 2011 May 15;334(5-6):403-11. Epub 2011 Feb 15.

UMR microbiologie du sol et de l'environnement, CMSE, INRA, université de Bourgogne, 17, rue Sully, BP 86510, 21065 Dijon cedex, France.

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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http://dx.doi.org/10.1016/j.crvi.2010.12.003DOI Listing
May 2011

In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues.

Microb Ecol 2010 Nov 1;60(4):816-28. Epub 2010 Jul 1.

UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne, CMSE, BP 86510, Dijon, France.

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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http://dx.doi.org/10.1007/s00248-010-9705-7DOI Listing
November 2010

In situ dynamics and spatial heterogeneity of soil bacterial communities under different crop residue management.

Microb Ecol 2010 Aug 30;60(2):291-303. Epub 2010 Mar 30.

UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne CMSE, BP 86510, 17 rue de Sully, 21065 Dijon Cedex, France.

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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http://dx.doi.org/10.1007/s00248-010-9648-zDOI Listing
August 2010

Biogeographical patterns of soil bacterial communities.

Environ Microbiol Rep 2009 Aug 22;1(4):251-5. Epub 2009 Jun 22.

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.

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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http://dx.doi.org/10.1111/j.1758-2229.2009.00040.xDOI Listing
August 2009

Platform GenoSol: a new tool for conserving and exploring soil microbial diversity.

Environ Microbiol Rep 2009 Apr 3;1(2):97-9. Epub 2009 Mar 3.

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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http://dx.doi.org/10.1111/j.1758-2229.2009.00023.xDOI Listing
April 2009

Protein and DNA fingerprinting of a soil bacterial community inoculated into three different sterile soils.

Res Microbiol 2008 May 8;159(4):231-6. Epub 2008 Apr 8.

UMR Microbiologie du Sol et de l'Environnement, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, Dijon cedex, France.

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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http://dx.doi.org/10.1016/j.resmic.2008.03.004DOI Listing
May 2008
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