Publications by authors named "Sébastien Terrat"

24 Publications

  • Page 1 of 1

Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France.

PLoS One 2021 17;16(6):e0252216. Epub 2021 Jun 17.

UMR 1347 Agroécologie, INRAE, AgrosupDijon, Université Bourgogne Franche-Comté, Dijon, France.

According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0252216PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8211295PMC
June 2021

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

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages.

FEMS Microbiol Ecol 2020 07;96(7)

CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.

Basaltic rocks play a significant role in CO2 sequestration from the atmosphere during their weathering. Moreover, the primary microorganisms that colonize them, by providing mineral elements and nutrients, are shown to promote growth of diverse heterotrophic communities and plants, therefore positively impacting Earth's long-term climate balance. However, the first steps of microbial colonization and subsequent rock weathering remain poorly understood, especially regarding microbial communities over a chronological sequence. Here, we analyzed the microbial communities inhabiting the soil developed in crevices on lava flows derived from different eruptions on Fogo Island. Investigated soils show typically low carbon and nitrogen content and are relatively similar to one another regarding their phylogenetic composition, and similar to what was recorded in large soil surveys with dominance of Actinobacteria and Proteobacteria. Moreover, our results suggest a stronger effect of the organic carbon than the lava flow age in shaping microbial communities as well as the possibility of exogenous sources of bacteria as important colonizers. Furthermore, archaea reach up to 8.4% of the total microbial community, dominated by the Soil Crenarchaeotic Group, including the ammonium-oxidizer Candidatus Nitrososphaera sp. Therefore, this group might be largely responsible for ammonia oxidation under the environmental conditions found on Fogo.
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http://dx.doi.org/10.1093/femsec/fiaa104DOI Listing
July 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

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity.

Sci Rep 2019 03 7;9(1):3812. Epub 2019 Mar 7.

Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France.

Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.
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http://dx.doi.org/10.1038/s41598-019-40422-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405751PMC
March 2019

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

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

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region.

Front Microbiol 2018 4;9:568. Epub 2018 Apr 4.

Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France.

Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the , and genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera , and . Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against . Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.
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http://dx.doi.org/10.3389/fmicb.2018.00568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893819PMC
April 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

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

Bacterial Community Diversity Harboured by Interacting Species.

PLoS One 2016 3;11(6):e0155392. Epub 2016 Jun 3.

Université Rennes 1, UMR1349 IGEPP, F-35000, Rennes, France.

All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155392PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892616PMC
July 2017

FT-IR spectroscopy: A powerful tool for studying the inter- and intraspecific biodiversity of cultivable non-Saccharomyces yeasts isolated from grape must.

J Microbiol Methods 2016 Feb 12;121:50-8. Epub 2015 Dec 12.

UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France. Electronic address:

The efficiency of the FT-IR technique for studying the inter- and intra biodiversity of cultivable non-Saccharomyces yeasts (NS) present in different must samples was examined. In first, the capacity of the technique FT-IR to study the global diversity of a given sample was compared to the pyrosequencing method, used as a reference technique. Seven different genera (Aureobasidium, Candida, Cryptococcus, Hanseniaspora, Issatchenkia, Metschnikowia and Pichia) were identified by FT-IR and also by pyrosequencing. Thirty-eight other genera were identified by pyrosequencing, but together they represented less than 6% of the average total population of 6 musts. Among the species identified, some of them present organoleptic potentials in winemaking, particularly Starmerella bacillaris (synonym Candidazemplinina). So in a second time, we evaluated the capacity of the FT-IR technique to discriminate the isolates of this species because few techniques were able to study intraspecific NS yeast biodiversity. The results obtained were validated by using a classic method as ITS sequencing. Biodiversity at strain level was high: 19 different strains were identified from 58 isolates. So, FT-IR spectroscopy seems to be an accurate and reliable method for identifying major genera present in the musts. The two biggest advantages of the FT-IR are the capacity to characterize intraspecific biodiversity of non-Saccharomyces yeasts and the possibility to discriminate a lot of strains.
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http://dx.doi.org/10.1016/j.mimet.2015.12.009DOI Listing
February 2016

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

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

Microbiologyopen 2015 Jun 28;4(3):518-31. Epub 2015 Apr 28.

INRA, UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France.

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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http://dx.doi.org/10.1002/mbo3.256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475392PMC
June 2015

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

Microbiologyopen 2015 Jun 1;4(3):505-17. Epub 2015 Apr 1.

AgroSup Dijon, UMR1347 Agroecologie, BP 86510, F-21000, Dijon, France.

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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http://dx.doi.org/10.1002/mbo3.255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475391PMC
June 2015

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

High‑throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation.

J Ind Microbiol Biotechnol 2014 May;41(5):811-21

We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITSRFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods for studying the yeast community on grapes and during alcoholic fermentation. Indeed, this high-throughput sequencing method detected larger numbers of species on grapes and identified species present during alcoholic fermentation that were undetectable with the other techniques.
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http://dx.doi.org/10.1007/s10295-014-1427-2DOI Listing
May 2014

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

Annotation of microsporidian genomes using transcriptional signals.

Nat Commun 2012 ;3:1137

Clermont Université, Université d'Auvergne, Centre de Recherche en Nutrition Humaine Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, F63000 Clermont-Ferrand, France.

High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.
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http://dx.doi.org/10.1038/ncomms2156DOI Listing
March 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

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.

BMC Bioinformatics 2010 Sep 23;11:478. Epub 2010 Sep 23.

Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, BP 10448, F-63000 Clermont-Ferrand, France.

Background: Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.

Results: First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.

Conclusions: We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.
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http://dx.doi.org/10.1186/1471-2105-11-478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955052PMC
September 2010

Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation.

BMC Genomics 2009 Dec 15;10:607. Epub 2009 Dec 15.

Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, BP 10448, F-63000 CLERMONT-FERRAND.

Background: Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp) and highly compact (approximately 1 gene/kb) genome of the human parasite Encephalitozoon cuniculi has been fully sequenced. The aim of this study was to characterize noncoding motifs that could be involved in regulation of gene expression in E. cuniculi and to show whether these motifs are conserved among the phylum Microsporidia.

Results: To identify such signals, 5' and 3'RACE-PCR experiments were performed on different E. cuniculi mRNAs. This analysis confirmed that transcription overrun occurs in E. cuniculi and may result from stochastic recognition of the AAUAAA polyadenylation signal. Such experiments also showed highly reduced 5'UTR's (<7 nts). Most of the E. cuniculi genes presented a CCC-like motif immediately upstream from the coding start. To characterize other signals involved in differential transcriptional regulation, we then focused our attention on the gene family coding for ribosomal proteins. An AAATTT-like signal was identified upstream from the CCC-like motif. In rare cases the cytosine triplet was shown to be substituted by a GGG-like motif. Comparative genomic studies confirmed that these different signals are also located upstream from genes encoding ribosomal proteins in other microsporidian species including Antonospora locustae, Enterocytozoon bieneusi, Anncaliia algerae (syn. Brachiola algerae) and Nosema ceranae. Based on these results a systematic analysis of the approximately 2000 E. cuniculi coding DNA sequences was then performed and brings to highlight that 364 translation initiation codons (18.29% of total CDSs) had been badly predicted.

Conclusion: We identified various signals involved in the maturation of E. cuniculi mRNAs. Presence of such signals, in phylogenetically distant microsporidian species, suggests that a common regulatory mechanism exists among the microsporidia. Furthermore, 5'UTRs being strongly reduced, these signals can be used to ensure the accurate prediction of translation initiation codons for microsporidian genes and to improve microsporidian genome annotation.
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http://dx.doi.org/10.1186/1471-2164-10-607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803860PMC
December 2009
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