Publications by authors named "Stephane Uroz"

34 Publications

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria.

ISME J 2021 May 5. Epub 2021 May 5.

Institut Curie, Université Paris-Saclay, Paris, France.

Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm h. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.
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http://dx.doi.org/10.1038/s41396-021-00987-xDOI Listing
May 2021

The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system.

Environ Microbiol 2021 Apr 5. Epub 2021 Apr 5.

Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, F-54280, France.

Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.
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http://dx.doi.org/10.1111/1462-2920.15508DOI Listing
April 2021

Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain.

Microbiol Resour Announc 2020 Sep 10;9(37). Epub 2020 Sep 10.

Université de Lorraine, INRAe, UMR 1136 Interactions Arbres-Microorganismes, Champenoux, France

We announce the draft genome sequence of PMB3(1), isolated from the mycorrhizosphere. In addition to its mineral-weathering effectiveness and antifungal activity, this strain is characterized by genomic features that give it great potential as a biocontrol and plant growth-promoting agent in nutrient-poor soils.
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http://dx.doi.org/10.1128/MRA.00601-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484066PMC
September 2020

Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral.

Environ Microbiol 2020 09 7;22(9):3838-3862. Epub 2020 Sep 7.

Univ Lyon, INSA de Lyon, CNRS UMR 5240, Lyon, France, Univ Lyon, Villeurbanne, F-69622, France.

Minerals and rocks represent essential reservoirs of nutritive elements for the long-lasting functioning of forest ecosystems developed on nutrient-poor soils. While the presence of effective mineral weathering bacteria was evidenced in the rhizosphere of different plants, the molecular mechanisms involved remain uncharacterized. To fill this gap, we combined transcriptomic, proteomics, geo-chemical and physiological analyses to decipher the potential molecular mechanisms explaining the mineral weathering effectiveness of strain PML1(12) of Caballeronia mineralivorans. Considering the early-stage of the interaction between mineral and bacteria, we identified the genes and proteins differentially expressed when: (i) the environment is depleted of certain essential nutrients (i.e., Mg and Fe), (ii) a mineral is added and (iii) the carbon source (i.e., glucose vs mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of (i) mobilizing iron through the production of a non-ribosomal peptide synthetase-independent siderophore, (ii) inducing chemotaxis and motility in response to nutrient availability and (iii) strongly acidifying its environment in the presence of glucose using a suite of GMC oxidoreductases to weather mineral. These results provide new insights into the molecular mechanisms involved in mineral weathering and their regulation and highlight the complex sequence of events triggered by bacteria to weather minerals.
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http://dx.doi.org/10.1111/1462-2920.15159DOI Listing
September 2020

Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle .

Front Microbiol 2019 28;10:1437. Epub 2019 Jun 28.

Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 INRA - Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, France.

Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.
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http://dx.doi.org/10.3389/fmicb.2019.01437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611097PMC
June 2019

Plant Symbionts Are Engineers of the Plant-Associated Microbiome.

Trends Plant Sci 2019 10 6;24(10):905-916. Epub 2019 Jul 6.

Université de Lyon, Institut National des Sciences Appliquées (INSA) de Lyon, CNRS UMR, 5240, Villeurbanne, France.

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.
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http://dx.doi.org/10.1016/j.tplants.2019.06.008DOI Listing
October 2019

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect.

Sci Rep 2019 01 24;9(1):605. Epub 2019 Jan 24.

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

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
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http://dx.doi.org/10.1038/s41598-018-36867-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345909PMC
January 2019

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples.

Methods Mol Biol 2018 ;1775:21-35

Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, France.

Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction. In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements.
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http://dx.doi.org/10.1007/978-1-4939-7804-5_3DOI Listing
February 2019

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria.

Science 2017 05;356(6340)

Laboratory of Plant-Microbe Interactions (LIPM), INRA-CNRS-Toulouse University, 31326 Castanet-Tolosan, France.

Within the plant microbiota, mutualistic fungal and bacterial symbionts are striking examples of microorganisms playing crucial roles in nutrient acquisition. They have coevolved with their hosts since initial plant adaptation to land. Despite the evolutionary distances that separate mycorrhizal and nitrogen-fixing symbioses, these associations share a number of highly conserved features, including specific plant symbiotic signaling pathways, root colonization strategies that circumvent plant immune responses, functional host-microbe interface formation, and the central role of phytohormones in symbiosis-associated root developmental pathways. We highlight recent and emerging areas of investigation relating to these evolutionarily conserved mechanisms, with an emphasis on the more ancestral mycorrhizal associations, and consider to what extent this knowledge can contribute to an understanding of plant-microbiota associations as a whole.
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http://dx.doi.org/10.1126/science.aad4501DOI Listing
May 2017

HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase family.

Sci Rep 2017 04 19;7(1):943. Epub 2017 Apr 19.

Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.

The screening of a metagenomic library of 250,000 clones generated from a hypersaline soil (Spain) allowed us to identify a single positive clone which confers the ability to degrade N-acyl homoserine lactones (AHLs). The sequencing of the fosmid revealed a 42,318 bp environmental insert characterized by 46 ORFs. The subcloning of these ORFs demonstrated that a single gene (hqiA) allowed AHL degradation. Enzymatic analysis using purified HqiA and HPLC/MS revealed that this protein has lactonase activity on a broad range of AHLs. The introduction of hqiA in the plant pathogen Pectobacterium carotovorum efficiently interfered with both the synthesis of AHLs and quorum-sensing regulated functions, such as swarming motility and the production of maceration enzymes. Bioinformatic analyses highlighted that HqiA showed no sequence homology with the known prototypic AHL lactonases or acylases, thus expanding the AHL-degrading enzymes with a new family related to the cysteine hydrolase (CHase) group. The complete sequence analysis of the fosmid showed that 31 ORFs out of the 46 identified were related to Deltaproteobacteria, whilst many intercalated ORFs presented high homology with other taxa. In this sense, hqiA appeared to be assigned to the Hyphomonas genus (Alphaproteobacteria), suggesting that horizontal gene transfer had occurred.
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http://dx.doi.org/10.1038/s41598-017-01176-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430456PMC
April 2017

Soil networks become more connected and take up more carbon as nature restoration progresses.

Nat Commun 2017 02 8;8:14349. Epub 2017 Feb 8.

NIOO-KNAW, Microbial Ecology, Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
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http://dx.doi.org/10.1038/ncomms14349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309817PMC
February 2017

Screening for N-AHSL-Based-Signaling Interfering Enzymes.

Methods Mol Biol 2017 ;1539:271-286

Univ Lyon, INSA-Lyon, UCBL, CNRS UMR5240, 69621, Villeurbanne Cedex, France.

Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in their relation to the environment or their host. QS relies upon the production, accumulation and perception of small diffusable molecules by the bacterial population, hence linking high gene expression with high cell population densities. Among the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL). In pathogens such as Erwinia or Pseudomonas, N-AHSL based QS is crucial to overcome the host defenses and ensure a successful infection. Interfering with QS-regulation allows the algae Delisea pulcra to avoid surface colonization by bacteria. Thus, interfering the QS-regulation of pathogenic bacteria is a promising antibiotic-free antibacterial therapeutic strategy. To date, two N-AHSL lactonases and one amidohydrolase families of N-ASHL degradation enzymes have been characterized and have proven to be efficient in vitro to control N-AHSL-based QS-regulated functions in pathogens. In this chapter, we provide methods to screen individual clones or bacterial strains as well as pool of clones for genomic and metagenomic libraries, that can be used to identify strains or clones carrying N-ASHL degradation enzymes.
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http://dx.doi.org/10.1007/978-1-4939-6691-2_18DOI Listing
February 2018

Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development.

Mycorrhiza 2016 Jul 19;26(5):389-99. Epub 2016 Jan 19.

UMR1136 INRA Université de Lorraine, Interactions Arbres - Microorganismes, F-54280, Champenoux, France.

Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.
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http://dx.doi.org/10.1007/s00572-015-0679-7DOI Listing
July 2016

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities.

Trends Microbiol 2015 Dec 5;23(12):751-762. Epub 2015 Nov 5.

INRA, UMR1136, «Interactions Arbres - Microorganismes», F-54280 Champenoux, France; Université de Lorraine, UMR1136, «Interactions Arbres - Microorganismes», F-54500 Vandoeuvre-lès-Nancy, France.

Soil is composed of a mosaic of different rocks and minerals, usually considered as an inert substrata for microbial colonization. However, recent findings suggest that minerals, in soils and elsewhere, favour the development of specific microbial communities according to their mineralogy, nutritive content, and weatherability. Based upon recent studies, we highlight how bacterial communities are distributed on the surface of, and in close proximity to, minerals. We also consider the potential role of the mineral-associated bacterial communities in mineral weathering and nutrient cycling in soils, with a specific focus on nutrient-poor and acidic forest ecosystems. We propose to define this microbial habitat as the mineralosphere, where key drivers of the microbial communities are the physicochemical properties of the minerals.
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http://dx.doi.org/10.1016/j.tim.2015.10.004DOI Listing
December 2015

Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability.

Genome Announc 2015 Jul 23;3(4). Epub 2015 Jul 23.

CNRS UMR 5276, ENS de Lyon, Laboratoire de Géologie de Lyon, Lyon, France.

We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).
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http://dx.doi.org/10.1128/genomeA.00798-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513152PMC
July 2015

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay.

Environ Microbiol 2014 Jul 22;16(7):2238-52. Epub 2013 Dec 22.

Interactions Arbres - Microorganismes, UMR1136, INRA, Champenoux, France; Interactions Arbres - Microorganismes, UMR1136, Université de Lorraine, Vandoeuvre-lès-Nancy, France.

Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere.
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http://dx.doi.org/10.1111/1462-2920.12347DOI Listing
July 2014

Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles.

Environ Microbiol 2014 Sep 1;16(9):2831-47. Epub 2013 Nov 1.

INRA, Interactions Arbres - Microorganismes, UMR1136, F-54280, Champenoux, France; Interactions Arbres - Microorganismes, Université de Lorraine, UMR1136, F-54500, Vandoeuvre-lès-Nancy, France.

Although truffles are cultivated since decades, their life cycle and the conditions stimulating ascocarp formation still remain mysterious. A role for bacteria in the development of several truffle species has been suggested but few is known regarding the natural bacterial communities of Périgord Black truffle. Thus, the aim of this study was to decipher the structure and the functional potential of the bacterial communities associated to the Black truffle in the course of its life cycle and along truffle maturation. A polyphasic approach combining 454-pyrosequencing of 16S rRNA gene, TTGE, in situ hybridization and functional GeoChip 3.0 revealed that Black truffle ascocarps provide a habitat to complex bacterial communities that are clearly differentiated from those of the surrounding soil and the ectomycorrhizosphere. The composition of these communities is dynamic and evolves during the maturation of the ascocarps with an enrichment of specific taxa and a differentiation of the gleba and peridium-associated bacterial communities. Genes related to nitrogen and sulphur cycling were enriched in the ascocarps. Together, these data paint a new picture of the interactions existing between truffle and bacteria and of the potential role of these bacteria in truffle maturation.
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http://dx.doi.org/10.1111/1462-2920.12294DOI Listing
September 2014

Taxonomic and functional diversity of Streptomyces in a forest soil.

FEMS Microbiol Lett 2013 May 4;342(2):157-67. Epub 2013 Apr 4.

Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Vandoeuvre-lès-Nancy F-54506, France.

In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.
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http://dx.doi.org/10.1111/1574-6968.12126DOI Listing
May 2013

Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

PLoS One 2013 13;8(2):e55929. Epub 2013 Feb 13.

INRA, UMR 1136 INRA, Université de Lorraine Interactions Arbres Micro-organismes, Centre INRA de Nancy, Champenoux, France.

In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055929PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572175PMC
August 2013

Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis.

Environ Microbiol Rep 2011 Apr 1;3(2):203-10. Epub 2010 Sep 1.

INRA, UMR1136 INRA-Nancy Université, «Interactions Arbres/Micro-organismes», Centre de Nancy, IFR110, 54280 Champenoux, France. Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK. Department of Microbiology and Immunology, Dartmouth Medical School, 208 Vail Building, Hanover, NH 03755, USA.

The Mycorrhiza Helper Bacterium (MHB) Pseudomonas fluorescens BBc6R8 promotes the ectomycorrhizal symbiosis between Douglas fir roots and Laccaria bicolor. In this study, we identified a non-flagellar type III secretion system (T3SS) in the draft genome of BBc6R8 similar to that described in the biocontrol strain P. fluorescens SBW25. We examined whether this T3SS plays a role in the BBc6R8 mycorrhizal helper effect by creating a deletion in the rscRST genes encoding the central channel of the injectisome. The in vitro effect of BBc6R8 T3SS mutants on the radial growth rate of L. bicolor was unchanged compared with the parental strain. In contrast, T3SS mutants were unable to promote mycorrhization, suggesting that type III secretion plays an important role in the mycorrhizal helper effect of P. fluorescens BBc6R8 independent of the promotion of hyphal growth that BBc6R8 exhibits in vitro.
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http://dx.doi.org/10.1111/j.1758-2229.2010.00209.xDOI Listing
April 2011

Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems.

Res Microbiol 2011 Nov 22;162(9):820-31. Epub 2011 Feb 22.

INRA, UMR 1136 INRA Nancy Université Interactions Arbres Micro-Organismes, Centre INRA de Nancy, 54280 Champenoux, France.

Unlike farmland, forests growing on acidic soils are among the terrestrial ecosystems that are the least influenced or amended by man. Forests which developed on acidic soils are characterized by an important stock of inorganic nutrients entrapped in poorly weatherable soil minerals. In this context, the mineral-weathering process is of great importance, since such minerals are not easily accessible to tree roots. To date, several bacterial genera have been noted for their ability to weather minerals and, in the case of some of them, to improve tree nutrition. Nevertheless, few studies have focused their analyses on mineral-weathering bacterial communities in relation to geochemical cycles and soil characteristics, their ecological origin, associated tree species and forest management practices. Here we discuss the heterogeneity of the mineral-weathering process in forest soils and present what is known concerning the taxonomic and functional characteristics of mineral-weathering bacteria, as well as the different locations where they have been isolated in forest soils. We also discuss the biotic and abiotic factors that may influence the distribution of these bacteria, such as the effect of tree species or forest management practices.
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http://dx.doi.org/10.1016/j.resmic.2011.01.013DOI Listing
November 2011

Screening for N-AHSL-based-signaling interfering enzymes.

Methods Mol Biol 2010 ;668:203-17

Laboratoire de Sciences de la Terre, Ecole Normale Supérieure, Lyon, France.

Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in relation to their environment or host. QS relies upon the production, accumulation, and perception of small diffusible molecules by the bacterial population, hence linking high gene expression with high cell population densities. Amongst the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL) class. In pathogens such as Erwinia or Pseudomonas, N-AHSL-based QS is crucial to overcome the host defenses and ensure a successful infection. Interfering with QS regulation allows the alga Delisea pulchra to avoid surface colonization by bacteria. Thus, interfering in the QS regulation of pathogenic bacteria is a promising antibiotic-free antibacterial therapeutic strategy. To date, two N-AHSL lactonase and one amidohydrolase families of N-ASHL degradation enzymes have been characterized and proven to be efficient in vitro to control N-AHSL-based QS-regulated functions in pathogens.
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http://dx.doi.org/10.1007/978-1-60761-823-2_14DOI Listing
January 2011

Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere.

Appl Environ Microbiol 2010 Jul 28;76(14):4780-7. Epub 2010 May 28.

UMR 1136 INRA Nancy Université, Interactions Arbres-Microorganismes, 54280 Champenoux, France.

In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.
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http://dx.doi.org/10.1128/AEM.03040-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901721PMC
July 2010

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil.

Environ Microbiol Rep 2010 Apr 5;2(2):281-8. Epub 2010 Jan 5.

INRA, UMR1136 INRA-Nancy Université'Interactions Arbres-Microorganismes', IFR 110, Centre INRA de Nancy, 54280 Champenoux, France.

Several reports have highlighted that forest soil samples are more phylum-rich than agricultural soil samples. However, little is known about the structure and richness of the bacterial communities in forest soil. Using high-throughput next generation 454 pyrosequencing, we deeply investigated the diversity of bacterial communities colonizing the oak rhizosphere niche and the surrounding soil. From three spatially independent soil samples, we obtained over 300 000 partial 16S rRNA gene sequences. The most abundant bacterial groups were the Acidobacteria, Proteobacteria and unclassified bacteria. Multifactorial analysis of the relative proportions of the different phyla revealed a net differentiation of the bacterial communities present in the rhizosphere and soil environments, suggesting an oak rhizosphere effect. Significantly more β-, γ- and unclassified Proteobacteria inhabited the rhizosphere when compared with the surrounding soil. Conversely, significantly more unclassified bacteria were detected in the bulk soil than in the rhizosphere, demonstrating that the soil remains a challenging reservoir of complexity. This work increases our understanding of the niche effect on bacterial diversity and on the rare phylogenetic groups inhabiting the soil.
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http://dx.doi.org/10.1111/j.1758-2229.2009.00117.xDOI Listing
April 2010

Mineral weathering by bacteria: ecology, actors and mechanisms.

Trends Microbiol 2009 Aug 5;17(8):378-87. Epub 2009 Aug 5.

Institut National de la Recherche Agronomique (INRA), Nancy Université, UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France.

Soil microbes play an essential role in the environment by contributing to the release of key nutrients from primary minerals that are required not only for their own nutrition but also for that of plants. Although the role of fungi in mineral weathering is beginning to be elucidated, the relative impact of bacteria in this process and the molecular mechanisms involved remain poorly understood. Here, we discuss the ecological relevance of bacterial weathering, mainly in the soil and especially in acidic forest ecosystems, which strongly depend on mineral weathering for their sustainability. We also present highlights from recent studies showing molecular mechanisms and genetic determinants involved in the dissolution of complex minerals under aerobic conditions. Finally, we consider the potential applications of genomic resources to the study of bacterial weathering.
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http://dx.doi.org/10.1016/j.tim.2009.05.004DOI Listing
August 2009

The bacterial genus Collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments.

Environ Microbiol 2010 Feb 22;12(2):281-92. Epub 2009 Jul 22.

Department of Plant Pathology, University of California, Davis, CA 95616, USA.

This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so-called collimonads emerges a general picture of bacterial adaptation to low-nutrient soil environments. Among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). This unique combination of properties will be discussed in the context of other interactions that collimonads have with their biotic and abiotic surroundings, such as the ability to inhibit fungal growth (fungistasis), protect plant roots from fungal disease (biocontrol), and degrade natural polymers and synthetic pollutants (biodegradation). Future research on Collimonas is expected to take advantage of the genomic tools and resources that are becoming available to uncover and describe the genes and gene functions that distinguish this group of bacteria and are the basis for its phenotypes. Potential applications of collimonads include the control of unwanted fungi, for example in agriculture, their use as biological indicators of soil quality and fertility, and as a source of bioactive compounds.
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http://dx.doi.org/10.1111/j.1462-2920.2009.02010.xDOI Listing
February 2010

Quorum sensing and quorum quenching: the yin and yang of bacterial communication.

Chembiochem 2009 Jan;10(2):205-16

INRA-Nancy Université, UMR1136 Interactions Arbres Micro-organismes, 54280 Champenoux, France.

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http://dx.doi.org/10.1002/cbic.200800521DOI Listing
January 2009

Degradation of N-acyl homoserine lactone quorum sensing signal molecules by forest root-associated fungi.

FEMS Microbiol Ecol 2008 Aug 9;65(2):271-8. Epub 2008 Apr 9.

INRA/UHP UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, Champenoux, France.

A collection of mycorrhizal and nonmycorrhizal root-associated fungi coming from forest environments was screened for their ability to degrade N-acyl homoserine lactones (AHL) or to prevent AHL recognition by producing quorum sensing inhibitors (QSI). No production of QS-inhibitors or -activators was detected using the two biosensors Chromobacterium violaceum CV026 and Agrobacterium tumefaciens in the culture supernatant of these fungi. However, the ability to degrade C6- and 3O,C6-HSL was detected for three fungal isolates. Acidification assay revealed that the AHL were degraded by a lactonase activity for two of these isolates. These results demonstrated for the first time that the forest root-associated fungi are capable of degrading the AHL signal molecules.
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http://dx.doi.org/10.1111/j.1574-6941.2008.00477.xDOI Listing
August 2008

A Rhodococcus qsdA-encoded enzyme defines a novel class of large-spectrum quorum-quenching lactonases.

Appl Environ Microbiol 2008 Mar 11;74(5):1357-66. Epub 2008 Jan 11.

Interactions Plantes et Microorganismes de Rhizosphère, Institut des Sciences du Végétal, CNRS, Avenue de Terrasse, 91198 Gif-sur-Yvette Cedex, France.

A gene involved in N-acyl homoserine lactone (N-AHSL) degradation was identified by screening a genomic library of Rhodococcus erythropolis strain W2. This gene, named qsdA (for quorum-sensing signal degradation), encodes an N-AHSL lactonase unrelated to the two previously characterized N-AHSL-degrading enzymes, i.e., the lactonase AiiA and the amidohydrolase AiiD. QsdA is related to phosphotriesterases and constitutes the reference of a novel class of N-AHSL degradation enzymes. It confers the ability to inactivate N-AHSLs with an acyl chain ranging from C(6) to C(14), with or without substitution at carbon 3. Screening of a collection of 15 Rhodococcus strains and strains closely related to this genus clearly highlighted the relationship between the ability to degrade N-AHSLs and the presence of the qsdA gene in Rhodococcus. Bacteria harboring the qsdA gene interfere very efficiently with quorum-sensing-regulated functions, demonstrating that qsdA is a valuable tool for developing quorum-quenching procedures.
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http://dx.doi.org/10.1128/AEM.02014-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258624PMC
March 2008

N-acyl homoserine lactones are degraded via an amidolytic activity in Comamonas sp. strain D1.

Arch Microbiol 2007 Mar 29;187(3):249-56. Epub 2006 Nov 29.

CNRS, ISV, Bâtiment 23, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.

Comamonas strain D1 enzymatically inactivates quorum-sensing (QS) signal molecules of the N-acyl homoserine lactone (N-AHSL) family, and exhibits the broadest inactivation range of known bacteria. It degrades N-AHSL with acyl-side chains ranging from 4 to 16 carbons, with or without 3-oxo or 3-hydroxy substitutions. N-AHSL degradation yields HSL but not N-acyl homoserine: strain D1 therefore harbors an amidohydrolase activity. Strain D1 is the fifth bacterium species in which an N-AHSL amidohydrolase is described. Consistent with its N-AHSL degradation ability, strain D1 efficiently quenches various QS-dependent functions in other bacteria, such as violacein production by Chromobacterium violaceum and pathogenicity and antibiotic production in Pectobacterium.
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http://dx.doi.org/10.1007/s00203-006-0186-5DOI Listing
March 2007