Can differences in microbial abundances help explain enhanced N2O emissions in a permanent grassland under elevated atmospheric CO2?

The establishment of an introduced community of fluorescent pseudomonads in the soil and in the rhizosphere is affected by the soil type

Indigenous populations of fluorescent pseudomonads were previously shown to vary in two different soils (Châteaurenard and Dijon) and in the rhizosphere of a plant species (Linum usitatissimum L.) cultivated in these two soils. These differences could be related to the soil type and to their crop history. In the present study, the influence of the soil type on the diversity of fluorescent pseudomonads in bulk and rhizospheric soils was evaluated. The soils of Châteaurenard and Dijon were sterilized before being inoculated with the same community of fluorescent pseudomonads. Bacterial isolates from bulk and rhizospheric soils were characterized on the basis of their repetitive extragenic pal…

Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR.

Abstract Denitrification, the reduction of nitrate to nitrous oxide or dinitrogen, is the major biological mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Microorganisms capable of denitrification are widely distributed in the environment but little is known about their abundance since quantification is performed using fastidious and time-consuming MPN-based approaches. We used real-time PCR to quantify the denitrifying nitrite reductase gene (nirK), a key enzyme of the denitrifying pathway catalyzing the reduction of soluble nitrogen oxide to gaseous form. The real-time PCR assay was linear over 7 orders of magnitude and sensitive down to 102 copies by assa…

Abundance of narG, napA, nirK and nosZ genes of denitrifying bacteria in a Norway spruce forest under different N-deposition

Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management

Little is known about abundances of the major bacterial taxa in agricultural soils and how they are affected by fertilization or other agricultural practices. Our aim was to determine the abundance and relative distribution of several bacterial phyla and one class, as well as the archaeal and crenarchaeal communities, and how they were affected by different fertilization regimes to examine whether specific responses of microorganisms could be identified at these high taxonomic ranks. We used real-time PCR with taxa specific primers to quantify the abundance of the Actinobacteria, Acidobacteria, Bacteriodetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Alphaproteobacteria and Crenarchaeo…

Nitrogen cycling microbial communities: from diversity to interactions and functions

Soil microorganisms form one of the largest biodiversity reservoirs on earth. They also play essential roles in ecosystem functions such as biogeochemical cycling. However, the importance of microbial community diversity and composition for ecosystem functioning is still debated. A sound understanding of the ecological processes governing the assembly of these communities in the environment is also missing. In this talk, I will give examples of how we addressed these knowledge gaps using nitrogen cycling microorganisms as model functional guilds. Nitrogen is the most limiting nutrient for crop production in agriculture. The nitrogen cycle is also one which was pushed by human activities out…

Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation.

International audience; Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of th…

Abundance of NARG, NIRK and NOSZ genes of denirifying bacteria during primary successions of a glacier foreland

Primary succession changes diversity, abundance and function of soil microorganisms across glacier forelands

Quantification of denitrifiers by real-time PCR

Soil microbial diversity matters for denitrification and reduction of the greenhouse gas N2O

Use of functional genes to quantify denitrifiers in the environment.

During the last decade, application of molecular methods using cultivation-independent approaches has provided new insights into the composition and structure of denitrifying communities in various environments. However, little is known about their abundance, and quantification is still performed using cultivation-based approaches, which are not only biased by the inability to cultivate of many micro-organisms but also fastidious and time-consuming. Two types of cultivation-independent approaches have recently been developed to quantify denitrifiers. The first type, which is based on the hybridization technique, comprises the use of Southern hybridization and DNA arrays. The second type, ba…

Classé parmi les 6000 chercheurs mondiaux les plus influents selon Highly Cited Researchers de Clarivate analytics, dont environ 150 Français et 15 chercheurs de l’INRA

Un chercheur du centre Inra BFC parmi les plus influents du monde !Très belle nouvelle pour l’Inra Bourgogne-Franche-Comté. Laurent Philippot, Directeur de recherche au sein de l’UMR Agroécologie (Inra – AgroSup Dijon – université de Bourgogne), figurent dans le classement 2018 des Highly Cited Researchers de Clarivate analytics.Ce classement mondial rassemble 6000 chercheurs mondiaux parmi les plus influents, dont environ 150 Français. Parmi eux se classent 15 chercheurs de l’Inra, dont Laurent Philippot. A noter que le classement Highly Cited Researchers de Clarivate analytics est pris en compte dans le calcul de la note attribuée à un établissement d’enseignement supérieur par le fameux …

Traduction de la métagenomique des agrosystemes en services écologiques

International audience; En affectant les communautés microbiennes présentes dans le sol, les pratiques agricoles mettent en péril la biodiversité des agrosystèmes. La génomique environnementale est un nouveau moyen d’améliorer nos connaissances sur ces derniers et ce faisant, de concevoir des systèmes agricoles plus respectueux de l’environnement.

Genetic characterization of atrazine-degrading bacterial consortia isolated from maize rhizosphere

International audience

Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example

ABSTRACT We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.

Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis.

The ability of facultative anerobes to respire nitrate has been ascribed mainly to the activity of a membrane-bound nitrate reductase encoded by the narGHJI operon. Respiratory nitrate reduction is the first step of the denitrification pathway, which is considered as an important soil process since it contributes to the global cycling of nitrogen. In this study, we employed direct PCR, cloning, and sequencing of narG gene fragments to determine the diversity of nitrate-reducing bacteria occurring in soil and in the maize rhizosphere. Libraries containing 727 clones in total were screened by restriction fragment analysis. Phylogenetic analysis of 128 narG sequences separated the clone famili…

Novel bibliographic maps to guide research units

National audience; Publication is a major issue for research evaluation. As a consequence research units need strategies to improve their publications. Bibliometry and cartography are new tools to study the publications of research teams. In particular bibliometry give an overall picture and good criteria to choose a strategy for publishing and to guide the priorities of research. Here we studied the publications of the INRA Agroécologie research unit, Dijon. This unit has 107 scientists and professors, equivalent 80 full-time positions for research, and published 125 original articles in 2012. We present several examples of maps and measurements obtained using Web of science, Excel, Sphinx…

Effect of primary mild stresses on resilience and resistance of the nitrate reducer community to a subsequent severe stress

International audience; The factors regulating soil microbial stability (e.g. resistance and resilience) are poorly understood, even though microorganisms are essential for ecosystem functioning. In this study, we tested whether a functional microbial community subjected to different primary mild stresses was equally resistant or resilient to a subsequent severe stress. The nitrate reducers were selected as model community and analysed in terms of nitrate reduction rates and genetic structure by narG PCR-restriction fragment length polymorphism fingerprinting. Heat, copper and atrazine were used as primary stresses and mercury at a high concentration as a severe stress. None of the primary …

Effects of precipitation regime on soil bacterial and fungal activity upon rewetting of a plant-soil system using 18O-SIP: depth matters

EASPEBIOmEDOCT INRA; Climate change is predicted to affect not only the amount but also the temporal distribution of rain. Changes in frequency and amplitude of rain events, likely shape the activity of plants and soil microbes. Fluctuating water conditions will differ with soil depth between precipitation patterns, affecting plant growth and may result in differential microbial response upon rewetting. Our objective was to investigate, in plant-soil systems, the response of the metabolically active microbial communities to a rewetting event and to which extent this was modulated by 1) soil depth and 2) precipitation legacy. Wheat planted in soil mesocosms were subjected to frequent or infr…

Distinguished Scientist Award under the Chinese Academy of Science President’s international Fellowship Initiative 2020

Activity, size and structure of the nitrate reducer community in relation to land-use and fertilization regime in Madagascar

Communication orale, résumé; absent

Fitness in soil and rhizosphere of Pseudomonas fluorescens C7R12 compared with a C7R12 mutant affected in pyoverdine synthesis and uptake.

International audience; Fluorescent pseudomonads have evolved an efficient strategy of iron uptake based on the synthesis of the siderophore pyoverdine and its relevant outer membrane receptor. The possible implication of pyoverdine synthesis and uptake on the ecological competence of a model strain (Pseudomonas fluorescens C7R12) in soil habitats was evaluated using a pyoverdine minus mutant (PL1) obtained by random insertion of the transposon Tn5. The Tn5 flanking DNA was amplified by inverse PCR and sequenced. The nucleotide sequence was found to show a high level of identity with pvsB, a pyoverdine synthetase. As expected, the mutant PL1 was significantly more susceptible to iron starva…

Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes

In this study, we report the cloning and characterization of denitrifying gene clusters of Pseudomonas fluorescens C7R12 containing the narXLDKGHJI, nirPOQSM, norCB and nosRZDFYL genes. While consensus sequences for Fnr-like protein binding sites were identified in the promoter regions of the nar, nir, nor and nos genes, consensus sequences corresponding to the NarL binding sites were identified only upstream the nar genes. Monitoring by mRNA analysis the expression of the narG, nirS, norB and nosZ structural genes suggests a sequential induction of the denitrification system in P. fluorescens.

Technosols to reclaim industrial wastelands: depth distribution of abundance and activity of N-cycling microbial communities

International audience; Construction of Technosols through assemblage of treated soil and recycled wastes is an innovative option for the restoration of degraded lands and re-use of industrial wastes. Recent studies have evidenced that Technosols could support soil functions such as primary production but the knowledge about other ecosystemic services, such as nutrient cycling, is limited. In this work, we investigated the abundance and the activity of microbial communities involved in N-cycling in different horizons (0–15, 15–35, 35–70 cm) of two types of Technosols constructed to reclaim an industrial wasteland. The estimation by real-time PCR of the abundances of the different microbial …

Impact of maize mucilage on atrazine mineralization andatzC abundance

Soil was amended with maize mucilage, a major rhizodeposit, to study its role on the number of culturable soil micro-organisms, the structure of the bacterial community, atrazine mineralization and atzC abundance. The maximal percentage of atrazine mineralization was lower for mucilage-amended than for water-amended soil. Total culturable soil bacteria and 16S rDNA copy number, measured by RT-PCR, presented similar values and were not significantly (P < 0.05) different among treatments. Mucilage applied at a rate of 70 mu g C g(-1) dry soil day(-1) over two weeks did not modify the abundance of the total soil microflora. Global structure of soil bacterial communities revealed by RISA analys…

Spatiotemporal Variations in the Abundance and Structure of Denitrifier Communities in Sediments Differing in Nitrate Content

Spatial and temporal variations related to hydric seasonality in abundance and diversity of denitrifier communities were examined in sediments taken from two sites differing in nitrate concentration along a stream Do&ntilde

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms …

Artificial selection of root microbiota associated to plant phenotype changes

International audience; Artificial selection applied at community level is an important, but still growing topic in the field of ecology andexperimental evolution [1-3]. Its recent implementation to microbial communities holds not only appealingpromises in terms of fundamental knowledge about selection itself [3], but also in terms of relevant applicationsto our society, including bioremediation [4] and plant traits enhancement [5]. Here we transposed the conceptof artificial selection of communities to perform experimental evolution of root microbiota inducing relevantphenotypic changes in plants. We grew ten successive generations of four weeks old Brachypodiumdistachyon inoculated with a…

Local response of bacterial densities and enzyme activities to elevated atmospheric CO2 and different N supply in the rhizosphere of Phaseolus vulgaris L.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Altered flux of labile C from plant roots into soil is thought to influence growth and maintenance of microbial communities under elevated atmospheric CO2 concentrations. We studied the abundance and function of the soil microbial community at two levels of spatial resolution to assess the response of microorganisms in the rhizosphere of the whole root system and of apical root zones of Phaseolus vulgaris L. to elevated CO2 and high or low N supply. At the coarser resolution, microb…

Bridging microbial community ecology and ecosytem functioning

Contribution of bacteria to initial input and cycling of nitrogen in soils

Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils

ABSTRACT Microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. The diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. The narG gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. The use of narG is of special interest because the phylogeny of the narG gene closely reflects the 16S ribosomal DNA phylogeny. Therefore, targeting the narG gene provided for the first time a unique insight into the taxonomic composition of the nitrate-reducing community in planted an…

Bridging microbial community ecology and ecosystem functioning

Microbial communities have a central role in many ecosystem functions such as biogeochemical cycling. Large variation in N-fluxes has been widely documented, mirroring the complexity of the underlying mechanisms. However, application of molecular biology approaches during the last decade has given the opportunity to look beyond these fluxes and to study the genetic and the ecology of the microorganisms involved in N-cycling. In this talk, I will give examples of a trait-centered approach for bridging microbial community ecology, microbial processes and ecosystem functioning.

A plant perspective on microbial communities and nitrogen cycling in the rhizosphere

Promenade among terrestrial denitrifiers: from genetics to ecology

Maîtrise et gestion de la biodiversité dans les sols: quelles perspectives ?

National audience

N-cycling: Bridging microbial community ecology and terrestrial ecosystem functioning

Communication orale invitée, résuméEAEcolDur; Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles.

Benefits of plant controls on microbial nitrogen transformations for sustainable agroecosystems

Nitrogen is the major nutrient limiting plant growth in terrestrial ecosystems. The transformation of inert nitrogen to forms that can be assimilated by plants is mediated by soil microorganisms. However, global cycling of nitrogen has transgressed a critical threshold: the amount of atmospheric N2 industrially converted into ammonia to produce fertilizers now exceeds that produced from all of the Earth’s terrestrial biological processes. This excess reactive N from fertilizer use poses a threat to soil, water, and air quality due to nitrate leaching and emission of N2O, a potent greenhouse gas. The last decade has witnessed significant advances in understanding of plant-microbe interaction…

Direct seeding mulch-based cropping increases both the activity and the abundance of denitrifier communities in a tropical soil

International audience; This study evaluated the impact of direct seeding mulch-based cropping (DMC), as an alternative to conventional tilling (CT), on a functional community involved in N cycling and emission of greenhouse gas nitrous oxide (N2O). The study was carried out for annual soybean/rice crop rotation in the Highlands of Madagascar. The differences between the two soil management strategies (direct seeding with mulched crop residues versus tillage without incorporation of crop residues) were studied along a fertilization gradient (no fertilizer, organic fertilizer, organic plus mineral fertilizers). The activity and size of the denitrifier community were determined by denitrifica…

Use of functional traits to study microbial diversity

Microbial communities have a central role in many ecosystem functions such as biogeochemical cycling, filtering and climate regulation. However, while functional trait-based approaches are commonly used for at least two decades in microbiology, most microbial ecology studies are still carried out with the rRNA genes. This talk will highlight the advantages of trait-based approaches for studying microbial diversity and its relationship with ecosystem functions. For this purpose, denitrification, a microbial process involved in N-cycling, was selected as a model functional trait. Using both naturally assembled and artificially manipulated communities, we will show how the diversity of the den…

Mitigation of N2O emissions in agroecosystems: the role of N2O-reducers

CT3 ; EnjS4 ; Département EA; Mitigation of N2O emissions in agroecosystems: the role of N2O-reducers. 16. International Symposium on Microbial Ecology - ISME16

Génétique et amélioration des plantes au sein du réseau PhytoMic

National audience

Additional file 1 of Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions

Additional file 1: Supplementary Table 1. Number of OTUs significantly differentially abundant among all treatments as estimated using a generalized linear mixed model, among the 515 most abundant 16S rRNA OTUs and the 439 most abundant 18S rRNA OTUs. Supplementary Figure 1. Abundances of total bacteria and total fungi. Quantification of 16S rRNA (a and c) and ITS (b and d) gene copy numbers in the original soil, the removal treatments and the control (Step 1; a and b) and in the coalescence treatment, the self-mixed removal treatment and the control samples (Step 2; c and d) (mean ± s.e. of log10-transformed data expressed as gene copy g-1 dry soil). Letters indicate significantly differen…

Relative abundance of the membrane bound and periplasmic nitrate reductase in the environment

Mapping spatial patterns of denitrifiers at large scale

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distributio…

Ecology of Denitrifying Prokaryotes in Agricultural Soil

Denitrification is a microbial respiratory process during which soluble nitrogen oxides are used as an alternative electron acceptor when oxygen is limiting. It results in considerable loss of nitrogen, which is the most limiting nutrient for crop production in agriculture. Denitrification is also of environmental concern, since it is the main biological process responsible for emissions of nitrous oxide, one of the six greenhouse gases considered by the Kyoto protocol. In addition to natural variations, agroecosystems are characterized by the use of numerous practices, such as fertilization and pesticide application, which can influence denitrification rates. This has been widely documente…

Genetic characterization of the nitrate reducing community in French soils

International audience

Linking microbial diversity and ecosystem functioning: The nitrogen cycle example

Microbial communities have a central role in ecosystem processes by driving the Earth’s biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. While functional trait-based approaches are commonly used for at least two decades in microbiology, most microbial diversity studies are still carried out with the rRNA genes. This talk will show how metagenomic approaches targeting microbial guilds involved in nitrogen cycling can help bridging microbial community ecology and ecosystem processes in terrestrial environments.

The influence of climate change on N-cycling microorganisms in soil

International audience

Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils

A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical …

Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of ino…

Legacy effects of contrasting water and N-availability patterns on plantmicrobial response to rewetting

National audience; Introduction. Shifts in the frequency and magnitude of rain events (precipitation regime) associated with climate change may affect plant morphological and physiological strategies as well as soil microbial activity.Objectives. The objective of this study was to determine i) how precipitation history shapes the response dynamics of soil bacterial and fungal communities to rewetting, as well as plant-microbial competition for N, and ii) how the N status of the system may modulate the effect of precipitation regime.Materials & methods. The legacy effects of 12 weeks of contrasting precipitation (frequent or infrequent watering, equal total water input) and N inputs was asse…

GENEFISHING: AN ALTERNATE METAGENOMIC APPROACH FOR CAPTURING TARGETED BACTERIAL DIVERSITY IN AN ENGINEERED RECIPIENT E. COLI STRAIN

International audience; The metagenomic approach, defined as the direct recovery and cloning of bacterial DNA from the environment in domesticated bacterial hosts has been widely used to study bacterial populations and their functional genes in numerous environments. The advantage of this approach over conventional culture based techniques is that it encompasses a wider range of bacteria by bypassing the bias of uncultivability of more than 99% of the bacteria in soil. However, in complex and rich environments such as soils, the huge level of bacterial diversity requires construction, handling and screening of several million clones in order to cover a significant proportion of bacterial ge…

Deciphering biotic interactions and their role in soil microbial community assembly

National audience; Soil microbial communities play key roles in ecosystem functioning. Yet, little is known aboutthe importance of microbe-microbe interactions in soil microbial community assembly andfunctions. To address this knowledge gap, the objective of my thesis is to assess the role ofinteractions between micro-organisms in soil microbial communities. For this purpose, we willmanipulate the interactions between microorganisms within complex soil microbialcommunities by (i) removing different members of the soil community, (ii) adding microbialtaxa to the soil community and (iii) increasing the physical distance between members of thesoil community. How shifts in microbial interaction…

La communauté nitrate-réductrice : modèle d'évaluation de l'impact du type de fertilisant et du mode de travail du sol à Madagascar

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality -- Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Insights into the unexplored diversity of the nitrous oxide reducing microbial community

Nitrous oxide (N2O) is a major radiative forcing and stratospheric ozone depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to N2 by bacteria and archaea harboring the nitrous oxide reductase (N2OR), which is the only known N2O sink in the biosphere. Despite its crucial role in mitigating N2O emissions, knowledge of the N2OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N2O reducing communities. Examination of N2OR structural el…

Microorganisms acting as a N2O sink in soil

International audience

Spatial distribution of ammonia oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Unraveling biotic interactions determining soil microbial community assembly and functioning

National audience; Microbial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial …

Scale, spatial pattern and metagenomic

Dynamics of changes in the soil organic matter, functional diversity and C and N fluxes after shift in agricultural practices of an annual crops rotation under conventional agriculture

International audience; Introduction and objectives Agricultural practices (e.g. crop rotation, tillage) lead to profound changes in soil properties, ecosystem structure (e.g. biodiversity) and functioning (e.g. ecosystem services). Whereas this has been very often characterized in the medium and long terms, little is known so far about how fast soil properties respond to changing practices at the time scale (year to several years) in which farmers take their decision in the management of their crops. In agricultural systems, increasing consideration is given to soil biodiversity, whose role has long been overlooked by agronomists, but whose preservation in now recognized as key for maintai…

Membres du comité d’organisation scientifique

International audience; Biodiversity loss has become a global concern as increasing evidence highlights the importance of diverse species interactions as the main drivers of the ecosystem services on which society depends. This symposium focuses on the importance of above and belowground biodiversity for ecosystem functioning, multifunctionality and sustainability. Various talks will highlight the importance of biodiversity for agro-ecosystem functioning as this symposium is linked to the Biodiversa research project “Agricultural Diversification: Digging Deeper” investigating the importance of agricultural crop diversification.

Towards food, feed and energy crops mitigating climate change

Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH 4 ) and nitrous oxide (N 2 O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant–microbe interactions in relation to the CH 4 and N 2 O budgets and show how this is promoting new generations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security.

Soil microorganisms can act as sinks for the greenhouse gas N2O

Relative abundance of the membrane bound- and periplasmic nitrate-reductases in the environment

Do tropical soil engineer stimulate the bacterial communities link to N2O emission?

National audience

Rôle de la nitrate réductase et de la pyoverdine dans la compétence tellurique et rhizosphérique de la souche Pseudomonas fluorescens C7R12

National audience

Effect of integrated weed management in cropping system on soils, microbial activity and N2O fluxes

National audience

Changement d'usage des terres et fonctionnement microbien : le cas du semis direct sous couverture végétale à Madagascar

National audience

Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment

Few studies have been conducted on adaptations of microbial communities to low and fluctuating temperatures using environmentally relevant conditions. In this study, six Himalayan and two temperate soils were selected as candidates for low-temperature/freeze-thaw (FT)-adapted and susceptible soils, respectively. Redundancy analysis with forward selection was used to create a model of environmental parameters explaining variability in the initial microbial abundance and 4 °C activities. The best predictor was soil carbon, explaining more than 74% of data variability (P=0.002), despite significant differences in the soil characteristics and environmental history. We tested the hypothesis that…

Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of ino…

Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates.

International audience; To determine to which extent root-derived carbon contributes to the effects of plants on nitrate reducers and denitrifiers, four solutions containing different proportions of sugar, organic acids and amino acids mimicking maize root exudates were added daily to soil microcosms at a concentration of 150 μg C g−1 of soil. Water-amended soils were used as controls. After 1 month, the size and structure of the nitrate reducer and denitrifier communities were analysed using the narG and napA, and the nirK, nirS and nosZ genes as molecular markers respectively. Addition of artificial root exudates (ARE) did not strongly affect the structure or the density of nitrate reduce…

A tale of two stories from the underground: soil microbial diversity and N cycling

International audience; Dr. Laurent Philippot is Director of Research at the French Institute for Agricultural Research (INRA) and is leading a research group at the department of Agroecology in Dijon. He did a sabbatical at Georgia Tech in Atlanta and at the Swedish University of Agricultural Science (SLU) in Uppsala in 2000 and 2009, respectively. His research focuses on bridging microbial community ecology, microbial processes and ecosystem functioning using microbial guilds involved in nitrogen cycling and greenhouse gas. He is serving as Senior Editor of The ISME Journal and as editorial board member for FEMS Microbiology Ecology, Applied and Environmental Microbiology and Frontiers in…

Molecular tools to assess the diversity and density of denitrifying bacteria in their habitats

Publisher Summary This chapter describes the molecular tools to assess the diversity and density of denitrifying bacteria in their habitats. Genome sequencing and metagenomic projects might even provide new denitrification gene sequences, which could aid in designing more broad range primers. Most information is obtained by cloning and sequencing the polymerase chain reaction (PCR) amplicons, but a more rapid analysis is achieved using fingerprinting techniques. As all PCR-based analyses, the fingerprinting techniques are subjected to well-known biases introduced by, e.g., DNA extraction procedures, primer selection, and PCR conditions. For denitrifiers, the PCR-RFLP (restriction fragment l…

Biogeography of microorganisms in grassland

Bridging microbial community ecology and nitrogen cycling in soil

Pas de résumé

Biodiversity-functioning relations in microorganisms

The role of microorganisms as key components in the functioning of ecosystems and biodiversity is discussed. The latest methodologies developed to study microbial diversity and functioning of ecosystems are considered, as DNA extraction and isotope labeling, fluorescent in situ hybridization and microautoradiography, and tracking of a substrate labeled with a stable isotope. Investigations related to correlations between microbial diversity and functioning in situ are considered. An example is illustrated of a correlation of erosion of microbial diversity of natural microbial community in prairie soil and erosion of species diversity in an ecosystem.

Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, gra…

Loss in microbial diversity affects nitrogen cycling in soil

International audience; Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 s…

Structure and activity of the nitrate-reducing community in the rhizosphere of Lolium perenne and Trifolium repens under long-term elevated atmospheric pCO2

Rhizosphere soil was sampled in monocultures of Lolium perenne and Trifolium repens in June and October 2002, at two different nitrogen fertilisation levels (14 and 56 g N m−2 year−1) and under two pCO2 atmospheres (360 and 600 ppmv) at the Swiss FACE (Free Air Carbon dioxide Enrichment) site. Directly extracted soil DNA was analysed with restriction fragment length polymorphism (PCR-RFLP) by use of degenerated primers for the narG gene encoding the active site of the membrane-bound nitrate reductase. The corresponding enzyme activity of the nitrate reductase was determined colorimetrically after 24 h of anaerobic incubation. The narG PCR-RFLP fingerprints showed that the structure of the n…

Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis

International audience; Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil microbial processes, we analysed metagenomes of community-level virus-enriched suspensions by tangential flow filtration obtained from two French agricultural soils. We found viral sequences representing a total of 239 viral operational taxonomic units that corresponded to 29.5% of the mapping reads in the metagenomic datasets.…

Soil microbial community fragmentation reveals indirect effects of pesticide application mediated through biotic interactions between taxa

In soil ecosystems, microorganisms exist in complex and diverse communities where microbial taxa are linked through different types of interactions. Therefore, pesticide application will not only directly affect certain microbial taxa, but will also have indirect effects throughout the community mediated through these interactions. These indirect effects may also influence ecosystem functions. In this study, a naturally occurring soil microbial community was fragmented by filtering a soil suspension and inoculating sterile soil microcosms. The effect of the fungicide Hymexazol on community structure and function was tested on the separate fractions and on the unfragmented community after a …

Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG , nirK , and nosZ Genes in Soils

ABSTRACT Nitrous oxide (N 2 O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N 2 O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different …

Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR

Abstract Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR® Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08×108 and 1.12×1011 copies per gram of dry weight of environmental sample. Environmental real-…

Involvement of nitrate reductase and pyoverdine in competitiveness of Pseudomonas fluorescens strain C7R12 in soil

ABSTRACT Involvement of nitrate reductase and pyoverdine in the competitiveness of the biocontrol strain Pseudomonas fluorescens C7R12 was determined, under gnotobiotic conditions, in two soil compartments (bulk and rhizosphere soil), with the soil being kept at two different values of matric potential (−1 and −10 kPa). Three mutants affected in the synthesis of either the nitrate reductase (Nar − ), the pyoverdine (Pvd − ), or both (Nar − Pvd − ) were used. The Nar − and Nar − Pvd − mutants were obtained by site-directed mutagenesis of the wild-type strain and of the Pvd − mutant, respectively. The selective advantage given by nitrate reductase and pyoverdine to the wild-type strain was as…

Nitrous oxide production in the terrestrial environment

Chapitre : 11; Terrestrial ecosystems are a major source of nitrous oxide (N2O), with soils accounting for ~70% of the atmospheric loading of this greenhouse gas. Here we provide a synthesis of current understanding of the environmental regulation of N2O production and reduction through different microbial pathways, presenting examples of where measured emissions have been related to characterizations of the underpinning microbial communities. We explore the direct and indirect influence of plants on rhizosphere N2O production, reduction and net emission, and the interactions between N2O production and methane oxidation, as examples of coupling between the C and N cycles that need to be con…

Influence of maize mucilage on structure and activity of the denitrifying community

International audience

Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach

International audience; Denitrification is a microbial respiratory process contributing to the emission of greenhouse gas. The study of denitrifying bacteria, like that of others, is hindered by characteristics that can prevent up to 99% of soil bacteria from being cultivated in vitro. New approaches based on the direct extraction of DNA from the natural environment and PCR amplifications can overcome limitations due to bacterial unculturability, but until now their application to denitrification genes has led only to the recovery of partial sequences for some of these genes.Our goals in this study were to apply a metagenomic approach characterized by cloning of DNA extracted from soil and …

Effects of nitrogen fertilization on soil N2O reducing bacteria and their importance for mitigating N2O emissions

EABIOmECT3; Arable soils are a major source of nitrous oxide (N2O). The only known sink in Earth’s biosphere is the reduction of N2O to N2 via the N2O reductase encoded by the nosZ gene, identified as nosZ clade I and II. The nosZI gene is mainly found among denitrifying bacteria, whereas >50% of microorganisms with nosZII lack other denitrification genes. The abundance and phylogenetic diversity of nosZII was previously shown to correlate with a soils N2O sink capacity. To provide a proof of principle, we manipulated 11 indigenous soil microbial communities by increasing the abundance of a non-denitrifying N2O-reducing strain capable of growth with N2O as the only electron acceptor. Conseq…

Corrigendum to “Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR” [J. Microbiol. Methods 59 (2004) 327–335]

Recurrent inoculation: a strategy for a better survival of Pseudomonas fluorescens strain in soil

A growing interest is shown for microbial inoculants as a promising alternative to agrochemicals for sustainable agricultural. However, biotic and abiotic stresses are known to affect their establishment and effectiveness, leading to inconsistent performance in field conditions. At the same time, a poor survival of the strain is often observed, which constitutes a main hamper for bacterial inoculant development. We hypothesize that recurrent inoculations would improve the survival of the strain in soil. For this purpose, we tested different scenarios of inoculation of the plant growth promoting rhizobacteria Pseudomonas fluorescens in soil microcosms: a single inoculation, two inoculations …

Artificial selection of rhizosphere microbiota associated to phenotypical changes in plant functions

International audience; Artificial selection applied at community level is an important, but still growing topic at the interface of ecology and evolution. Its recent implementation to microbial communities holds appealing promises not only in terms of fundamental knowledge about selection itself and the levels at which it may be used, but also in terms of relevant applications to our societies, including bioremediation and agroecology. In this experimental evolution study, we performed an artificial selection of rhizosphere microbial communities inducing relevant phenotypic changes in plants. In total, we grew more than 2200 Brachypodium distachyon plants, consisting in ten consecutive gen…

Managing biotic interactions for ecological intensification of agroecosystems.

9 pages; International audience; Agriculture faces the challenge of increasing food production while simultaneously reducing the use of inputs and delivering other ecosystem services. Ecological intensification of agriculture is a paradigm shift, which has recently been proposed to meet such challenges through the manipulation of biotic interactions. While this approach opens up new possibilities, there are many constraints related to the complexity of agroecosystems that make it difficult to implement. Future advances, which are essential to guide agricultural policy, require an eco-evolutionary framework to ensure that ecological intensification is beneficial in the long term.

Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent Pseudomonads

ABSTRACT The diversity of the membrane-bound nitrate reductase ( narG ) and nitrous oxide reductase ( nosZ ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overa…

La dénitrification et la production de N2O dans la rhizosphère de maïs : diversité et activité des populations bactériennes impliquées

Denitrification

Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses

Land-use practices aiming at increasing agro-ecosystem sustainability, e.g. no-till systems and use of temporary grasslands, have been developed in cropping areas, but their environmental benefits could be counterbalanced by increased N2O emissions produced, in particular during denitrification. Modelling denitrification in this context is thus of major importance. However, to what extent can changes in denitrification be predicted by representing the denitrifying community as a black box, i.e. without an adequate representation of the biological characteristics (abundance and composition) of this community, remains unclear. We analysed the effect of changes in land uses on denitrifiers for…

Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile

A field-scale manipulation experiment conducted for 16 years in a Norway spruce forest at Solling, Central Germany, was used to follow the long-term response of total soil bacteria, nitrate reducers and denitrifiers under conditions of reduced N deposition. N was experimentally removed from throughfall by a roof construction (‘clean rain plot’). We used substrate-induced respiration (SIR) to characterize the active fraction of soil microbial biomass and potential nitrate reduction to quantify the activity of nitrate reducers. The abundance of total bacteria, nitrate reducers and denitrifiers in different soil layers was analysed by quantitative PCR of 16S rRNA gene, nitrate reduction and de…

Factors influencing spatial patterns of activity of denitrifying bacteria in a grassland soil

International audience

Denitrification in pathogenic bacteria : for better or worst ?

A large variety of physiological and taxonomic groups have the ability to use nitrogen oxides as alternative electron acceptors. Brucella spp. is an alpha-proteobacteriaceae that induces a persistent disease in some mammals. Recent work has revealed that a denitrifying gene cluster is important in the interaction of Brucella neotomoae with its host.

Insights into the effect of soil pH on N(2)O and N(2) emissions and denitrifier community size and activity.

ABSTRACT The objective of this study was to investigate how changes in soil pH affect the N 2 O and N 2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H 2 SO 4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N 2 O and N 2 emissions using the 15 N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG , napA ,…

Gaz à effet de serre. Un nouveau groupe de microorganismes du sol lié à l'élimination de l'oxyde nitreux (N2O : un puissant gaz à effet de serre) découvert par une équipe de l'UMR Agroécologie

Recurrent inoculation: a strategy for a better survival of Pseudomonas fluorescens strain in soil

A growing interest is shown for microbial inoculants as a promising alternative to agrochemicals for sustainable agricultural. However, biotic and abiotic stresses are known to affect their establishment and effectiveness, leading to inconsistent performance in field conditions. At the same time, a poor survival of the strain is often observed, which constitutes a main hamper for bacterial inoculant development. We hypothesize that recurrent inoculations would improve the survival of the strain in soil. For this purpose, we tested different scenarios of inoculation of the plant growth promoting rhizobacteria Pseudomonas fluorescens in soil microcosms: a single inoculation, two inoculations …

Diversity of the nitrate reductase genes in the Pseudomonas genus

How agricultural practices affect the different bacterial communities involved in the denitrification process: the case of direct seeding in Madagascar

International audience

Mapping field-scale spatial patterns of size and activity of the denitrifier community

International audience; There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6–16 m) and mapped the dis…

Mapping spatial patterns of denitrifiers for bridging community ecology and microbial processes along environmental gradients

International audience; While there is ample evidence that microbial processes can exhibit large variations at a field scale, very little is known about the spatial distribution of the communities mediating these processes. The objective of this study was to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We used geostatistical modeling to map the distribution of size and activity of the denitrifier community in the pasture. Size of the denitrifier community was estimated by PCR quantification of the denitrification gene copy numbers while its activity w…

Modification de la structure de la communauté nitrate réductrice dans la rhizosphère

National audience

Effect of repeated organic waste applications on soil microorganisms involved in N cycle and their activities at the plot scale

Shifts in the nitrate-reducing community induced by the maize rhizosphere

International audience

Les émissions de protoxyde d'azote (N2O) d'origine agricole : évaluation au niveau du territoire français

National audience

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions

Abstract Background Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of interactions between microorganisms for assembly of the soil microbiome. Results By combining experimental removal (taxa depletion in the community) and coalescence (mixing of manipulated and control communities) approaches, we demonstrated that interactions between microorganisms can play a key role in determining their fitness during soi…

Effects of precipitation regime and N-availability on the dynamics of plant-microbial and soil biogeochemical cycling responses to rewetting

International audience; Introduction. Shifts in the frequency and magnitude of rain events (precipitation regime) associated with climate change may affect plant morphological and physiological strategies as well as soil microbial activity. Objectives. The objective of this study was to determine i) how precipitation history shapes the response dynamics of soil bacterial and fungal communities to rewetting, as well as plant-microbial competition for N, and ii) how the N status of the system may modulate the effect of precipitation regime. Materials & methods. The legacy effects of 12 weeks of contrasting precipitation (frequent or infrequent watering, equal total water input) and N inputs w…

Spatial distribution of N-cycling microbial communities showed complex patterns in constructed wetland sediments.

International audience; Constructed wetlands are used for biological treatment of wastewater from agricultural lands carrying pollutants such as nitrates. Nitrogen removal in wetlands occurs from direct assimilation by plants and through microbial nitrification and denitrification. We investigated the spatial distribution of N-cycling microbial communities and genes involved in nitrification and denitrification in constructed wetland sediments receiving irrigation water. We used quantitative real-time PCR (qPCR) to characterize microbial communities. Geostatistical variance analysis was used to relate them with vegetation cover and biogeochemical sediment properties. The spatial distributio…

La face visible des microorganismes dénitrifiants

Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment.

The relative importance of size and composition of microbial communities in ecosystem functioning is poorly understood. Here, we investigated how community composition and size of selected functional guilds in the nitrogen cycle correlated with agroecosystem functioning, which was defined as microbial process rates, total crop yield and nitrogen content in the crop. Soil was sampled from a 50-year fertilizer trial and the treatments comprised unfertilized bare fallow, unfertilized with crop, and plots with crop fertilized with calcium nitrate, ammonium sulfate, solid cattle manure or sewage sludge. The size of the functional guilds and the total bacterial community were greatly affected by …

Fonctionnement des cycles biogéochimiques et communautés microbiennes rhizosphériques : quels enjeux ?

Recently identified microbial guild mediates soil N2O sink capacity

Impact of fertilization, tillage and direct seeding on nitrate reducers in Madagascar

Microbial communities of the kanchenjunga mountains, nepal himalaya: factors affecting abundance, culturability and activity of the high-altitude cold-tolerant microbes

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape-scale

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities. In this manuscript, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites using a grid with a 16 km lag distance within Burgundy, a 31 500 km2 region in France. After quantifying the abundances of the total bacterial, crenarchaeal, nitrate-reducing, denitrifying and ammonia-oxidizing communit…

La faune du sol tropicale, un facteur de régulation des communautés bactériennes liées aux émissions de gaz à effet de serre

Mapping field-scale spatial distribution patterns of size and activity of the denitrifier community

International audience

Evidence of a core microbiota shaped by plant and earthworm interactions across soils

Prod 2018-139a EA AGROSUP INRA BIOME IPM; International audience; While having distinct niches, plants and earthworms have occupied soils over geological times, mutually influencing each-others. These macroorganisms are considered “ecosystem engineers”, actively modifying soil physical structure, which notably provides specific habitats for microorganisms: the rhizosphere and the drilosphere (casts/burrows produced by earthworms). In this study, we aimed to disentangle the relative importance of both macroorganisms in shaping microbial community assembly in different soil types, and determine the extent and modalities of how rhizosphere and drilosphere communities may coalesce with each-oth…

DNA extraction from soils: old bias for new microbial diversity analysis methods.

ABSTRACT The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure o…

Microbial terrestrial pathways to Nitrous Oxyde

Impact of spatial heterogeneity created by the termite building activity (Cubitermes niokoloensis) on the activity and genetic structure of the denitrifying community

Translation of metagenomics agroecosystems in ecological services

National audience

Accelerated mineralisation of atrazine in maize rhizosphere soil

International audience; The mineralisation rate of atrazine measured in soil pre-treated with this herbicide, was significantly higher in the maize rhizosphere than in bulk soil. Maize rhizosphere was also shown to significantly increase microbial biomass C as compared with bulk soil. Ribosomal intergenic spacer analysis conducted on nucleic acids extracted directly from soil samples revealed that the structure of microbial communities observed in the rhizosphere was slightly different from that of bulk soil. The quantification of the relative amount of the gene atzC, which encodes an enzyme involved in atrazine mineralisation, was carried out on soil nucleic acids by using quantitative-com…

Traking nitrate reducers and denitrifiers in the environment

The ability to respire nitrate when oxygen is limited has been described in taxonomically diverse microorganisms including members of the alpha-, beta-, gamma- and epsilon-proteobacteria, high and low GC Gram-positive bacteria and even Archaea. Respiratory nitrate reduction is the first step of the denitrification pathway, which is important since it is the main biological process responsible for the return of fixed nitrogen to the atmosphere, thus completing the nitrogen cycle. During the last decade, considerable knowledge has been accumulated on the biochemistry and genetics of the nitrate reductases. In this paper, we summarize the recent progress in molecular approaches for studying th…

Présentation du projet PIA4 ExcellenceS HARMI

Differential Responses of Nitrate Reducer Community Size, Structure, and Activity to Tillage Systems

ABSTRACT The main objective of this study was to determine how the size, structure, and activity of the nitrate reducer community were affected by adoption of a conservative tillage system as an alternative to conventional tillage. The experimental field, established in Madagascar in 1991, consists of plots subjected to conventional tillage or direct-seeding mulch-based cropping systems (DM), both amended with three different fertilization regimes. Comparisons of size, structure, and activity of the nitrate reducer community in samples collected from the top layer in 2005 and 2006 revealed that all characteristics of this functional community were affected by the tillage system, with increa…

Un Dijonnais parmi les chercheurs les plus cités au monde

International audience

Sélection artificielle de microbiote rhizosphériques associés à des changements phénotypiques de traits de plante

International audience; La sélection artificielle appliquée au niveau des communautés est un sujet grandissant à l’interface de l’écologie et de l’évolution. Son implémentation relativement récente à l’écologie microbienne s’avère prometteuse non seulement en termes de connaissance fondamentale sur le principe de sélection en luimême, mais aussi en termes de potentiel d’application, notamment en bioremédiation et en agroécologie.Nous avons utilisé l’évolution expérimentale afin de sélectionner artificiellement des communautés microbiennes rhyzosphériques induisant des changements phénotypiques chez leurs hôtes. Durant dix générations consécutives, nous avons fait pousser plusieurs lignées d…

Contribution of Bacteria to Initial Input and Cycling of Nitrogen in Soils

Nitrogen was discovered by the Scottish chemist and physician Daniel Rutherford in 1772 by removing oxygen and carbon dioxide from air. At the same time, the French chemist, Antoine Laurent Lavoisier, isolated what we would call nitrogen and named it azote, meaning without life since it did not support life or combustion. However, nitrogen is the fourth most common element in many biomolecules, which are essential for life, being outrankedonly by carbon, hydrogen andoxygen. Thus, nitrogen is found in amino acids that form proteins and in the nucleoside phosphates of nucleic acids. The cycle of nitrogen in soil has been studied more extensively than any other nutrient cycle. Nevertheless, de…

Involvement of pyoverdine and nitrate reductase in the soil and rhizospheric competence of biocontrol Pseudomonas fluorescens strain C7R12

International audience

Microbes : 14 millions d’euros pour les chercheurs de la région

L’université Bourgogne-Franche-Comté vient d’être lauréate d’un appel à projets qui va permettre à quelque 250 chercheurs de la région de bénéficier d’une manne de 14 millions d’euros, pour mener à bien des travaux sur les microbes.Laurent Philippot, directeur de recherche à l’Inrae, à Dijon, sera en charge de coordonner le projet Harmi en Bourgogne-Franche-Comté.

La PCR compétitive un outil moléculaire permettant de détecter et quantifier les gènes atzC, de l'ADNr 16S et 18S d'ADN extraits directement du sol

National audience

Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions

Competition between different isogenic mutants of Pseudomonas fluorescens unable to carry out the first steps of the denitrification pathway was compared in soil micro-columns non-planted or planted with maize. A new isogenic mutant of P. fluorescens YT101 affected in both nitrate and nitrite respirations was constructed and used as a model of non-denitrifying strain (FM69MS strain). The outcome of the selection exerted by the plant after co-inoculation of FM69MS at the same ratio either with an isogenic denitrifier unable to reduce nitrate (Nar(-) mutant) or with an isogenic NO2 (-) accumulator (Nir(-) mutant) was investigated in non-limiting NO3 (-) conditions. Regardless of the inoculate…

Role of plant residues in determining temporal patterns of the activity, size and structure of nitrate reducer communities in soil

ABSTRACT The incorporation of plant residues into soil not only represents an opportunity to limit soil organic matter depletion resulting from cultivation but also provides a valuable source of nutrients such as nitrogen. However, the consequences of plant residue addition on soil microbial communities involved in biochemical cycles other than the carbon cycle are poorly understood. In this study, we investigated the responses of one N-cycling microbial community, the nitrate reducers, to wheat, rape, and alfalfa residues for 11 months after incorporation into soil in a field experiment. A 20- to 27-fold increase in potential nitrate reduction activity was observed for residue-amended plot…

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Linking N2O concentrations in different soil depths to denitrification genes abundances under the influence of an elevated atmospheric CO2 concentration

Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree

International audience; Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5–6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high t…

Multiple-scale distribution and function of soil microorganisms

Is soil fauna an important driver of the structure and activities of denitrifier communities in tropical soils?

International audience

Classé parmi les 6000 chercheurs mondiaux les plus influents selon Highly Cited Researchers de Clarivate analytics (Microbiology), dont environ 170 Français et 10 chercheurs de l’INRA

Abundance and activity of nitrate reducers in an arable soil are more affected by temporal variation and soil depth than by elevated atmospheric [CO2]

Elevated atmospheric carbon dioxide concentrations ([CO2]) might change the abundance and the function of soil microorganisms in the depth profile of agricultural soils by plant-mediated reactions. The seasonal pattern of abundance and activity of nitrate-reducing bacteria was studied in a Mini-FACE experiment planted with oilseed rape (Brassica napus). Three depths (0–10, 10–20 and 20–30 cm) were sampled. Analyses of the abundances of total (16S rRNA gene) and nitrate-reducing bacteria (narG, napA) revealed strong influences of sampling date and depth, but no [CO2] effects. Abundance and activity of nitrate reducers were higher in the top soil layer and decreased with depth but were not re…

Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

Abstract Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing…

Impact of land use, pesticide application and agricultural management practices on the phosphorus foraging capacity of mycorrhizal fungi in 217 european agricultural soils

More than 80% of vascular plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Several studies have shown the potential of AMF to provide plants with phosphorus (P) via their hyphal network. Most of these studies have been performed in the greenhouse under controlled conditions using standardized soil mixtures. However, few studies have investigated hyphal P transfer in natural soils, severely limiting our understanding of the main drivers of P transfer by AMF in real agricultural soils. As a consequence, the potential of using AMF as a tool to increase crop yield remains a mystery. Using agricultural soils from a large field observation study in Europe, we aimed at a…

Influencce of elevated atmospheric pCO2 on the culturable nitrate-dissimilating Pseudomonas and their nitrate reductases in the rhizosphere of perennial grasses

Impact of elevated CO2 on structure and activity of the nitrate-reducing community in grassland ecosystems

Qu’attendre des recherches en microbiologie du sol ?

SPE EA EcolDur GenoSol MERS IPM Résumé du livre : La fertilité des sols est au carrefour des enjeux de sécurité alimentaire, de protection de l’environnement et de rentabilité économique de l’activité agricole. Cet ouvrage présente les résultats d’une réflexion prospective sur le contexte de la fertilisation dans les 5-10 ans à venir. Il définit les besoins en termes de méthodes et d'outils pour la gestion des cycles biogéochimiques et le raisonnement de la fertilisation en agriculture. Mots clés du livre : agriculture - agronomie - eau - effluent - engrais - environnement - fertilisation - pollution - prévention - production végétale - prospective - sol Description du chapitre 10 (partie 3…

Shifts in size, genetic structure and activity of the soil denitrifier community by nematode grazing

International audience; Bacterial-feeding nematodes represent an important driver of the soil microbial activity and diversity. This study aimed at characterizing the impact of nematode grazing on a model functional bacterial guild involved in N-cycling, the denitrifiers. Bacterial-feeding nematodes (Cephalobus pseudoparvus) were inoculated into soil microcosms whose indigenous nematofauna had previously been removed. The size, genetic structure and activity of the soil denitrifier community were characterized 15 and 45 days after nematodes inoculation using quantitative PCR of the nirK, nirS and nosZ denitrification genes, fingerprinting of the nirK and nirS genes and denitrification enzym…

Dissimilatory nitrate reductase in bacteria

184 ref.

Estimation of atrazine-degrading genetic potential and activity in three French agricultural soils

The impact of organic amendment (sewage sludge or waste water) used to fertilize agricultural soils was estimated on the atrazine-degrading activity, the atrazine-degrading genetic potential and the bacterial community structure of soils continuously cropped with corn. Long-term application of organic amendment did not modify atrazine-mineralizing activity, which was found to essentially depend on the soil type. It also did not modify atrazine-degrading genetic potential estimated by quantitative PCR targeting atzA, B and C genes, which was shown to depend on soil type. The structure of soil bacterial community determined by RISA fingerprinting was significantly affected by organic amendmen…

Effect of soil type and plant species on the fluorescent pseudomonads nitrate dissimilating community

International audience

Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community

The recent development and application of numerous methods mainly based on 16S rDNA analyses have brought insights into the questions of which and how many bacterial populations can be found in a given ecosystem. A new and challenging question for microbial ecologists has emerged from the exploration of this diversity: what is its significance for ecosystem functioning? We propose the denitrifying bacteria as a model microbial community for understanding the relationship between community structure and activity, and have summarized the recent progress in studies of this functional community.

Loss in microbial diversity affects nitrogen cycling in soil

National audience; Microbial communities have a central role in ecosystem processes by driving the Earth’s biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequen…

Mapping spatial patterns of denitrifiers for bridging community ecology and microbial processes along environmental gradients

While there is ample evidence that microbial processes can exhibit large variations at a field scale, very little is known about the spatial distribution of the communities mediating these processes. The objective of this study was to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We used geostatistical modeling to map the distribution of size and activity of the denitrifier community in the pasture. Size of the denitrifier community was estimated by PCR quantification of the denitrification gene copy numbers while its activity was estimated by measurin…

Microbial diversity in relation to soil functional operating range

Monitoring of atrazine treatment on soil bacterial, fungal and atrazine-degrading communities by quantitative competitive PCR

We report the development of quantitative competitive (QC) PCR assays for quantifying the 16S, 18S ribosomal and atzC genes in nucleic acids directly extracted from soil. QC-PCR assays were standardised, calibrated and evaluated with an experimental study aiming to evaluate the impact of atrazine application on soil microflora. Comparison of QC-PCR 16S and 18S results with those of soil microbial biomass showed that, following atrazine application, the microbial biomass was not affected and that the amount of 16S rDNA gene representing 'bacteria' increased transitorily, while the amount of 18S rDNA gene representing fungi decreased in soil. In addition, comparison of atzC QC-PCR results wit…

Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps

International audience; Changes in community structure and activity of the dissimilatory nitrate-reducing community were investigated across a glacier foreland in the Central Alps to gain insight into the successional pattern of this functional group and the driving environmental factors. Bulk soil and rhizosphere soil of Poa alpina was sampled in five replicates in August during the flowering stage and in September after the first snowfalls along a gradient from 25 to 129 years after deglaciation and at a reference site outside the glacier foreland (> 2000 years deglaciated). In a laboratory-based assay, nitrate reductase activity was determined colorimetrically after 24 h of anaerobic inc…

Diversity of denitrifying community in three soils and ability to reduce nitrous oxide

International audience

Impact of fertilization and direct seeding on activity and abundance of key denitrifier communities in a tropical soil

Affiche, résumé; The aim of this work was to investigate to which extent different practices impacted on the bacterial communities involved in N2O emission.

Monitoring microbial diversity in European soils: ongoing projects and challenges

SPEEcolDurGenoSolCT3communication orale invitée, résumé et slides; According to the Convention of Biological Diversity (Rio de Janeiro, 1992), biodiversity is the variation in life from genes to species, communities, ecosystems, and landscapes. Soils represent a huge reservoir of biodiversity which varies in terms of taxonomic richness, relative abundance and distribution according to soil types, climatic conditions, vegetation and land uses. The key functions supporting ecosystem services as identified in the Millennium Ecosystem Assessment (MEA, 2005) largely depend upon organisms that inhabit the soil. Thus, the design and implementation of a sustainable soil management strategy requires…

Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils

International audience; Introduction Agriculture is the main source of terrestrial N2O emissions, a potent greenhouse gas and the main cause of ozone depletion ((Hu et al., 2015). The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers (nosZII) was related to the potential capacity of the soil to act as a N2O sink (see Hallin et al., 2017 and references therein). However little is known about how this group responds to different agricultural practices. Here, we investigated how N2O-producers and N2O-reducers were …

Change in nitrate reducer community structure in wheat residue amended soil revealed by stable isotope probing

Long-term impact of 19 years' farmyard manure or sewage sludge application on the structure, diversity and density of the protocatechuate-degrading bacterial community

International audience; Impact of long-term biosolids application on soil-living micro-organisms key players of ecosystemic services is scarcely reported. Here, the impact of the 19 year-long application of farmyard manure (FM) and sewage sludge (SS) organic fertilisation regimes on the protocatechuate-degrading bacterial (pca) community was estimated by comparison to a mineral fertilisation regime (U). The structure, diversity and density of the pca community were determined using pcaH, a gene encoding the protocatechuate 3,4-dioxygenase. Ten years after the last application, the structure of the pca community in soils amended with 55100 (100 t/ha/2 years) and to a lesser extent with FM (1…

Relative Abundances of Proteobacterial Membrane-Bound and Periplasmic Nitrate Reductases in Selected Environments

ABSTRACT Dissimilatory nitrate reduction is catalyzed by a membrane-bound and a periplasmic nitrate reductase. We set up a real-time PCR assay to quantify these two enzymes, using the narG and napA genes, encoding the catalytic subunits of the two types of nitrate reductases, as molecular markers. The narG and napA gene copy numbers in DNA extracted from 18 different environments showed high variations, with most numbers ranging from 2 × 10 2 to 6.8 × 10 4 copies per ng of DNA. This study provides evidence that, in soil samples, the number of proteobacteria carrying the napA gene is often as high as that of proteobacteria carrying the narG gene. The high correlation observed between narG an…

Abundance of narG , nirS , nirK , and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

ABSTRACT Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 10 5 to 8.9 × 10 5 copies per nanogram of DNA but smaller amounts of narG , nirK , and nosZ target molecules. Thus, numbers of narG , nirK , nirS , and nosZ copies per nanogram of DNA ranged from 2.1 × 10 3 to 2.6 × 10 4 , 7.4 × 10 2 to 1.4 × 10 3 , 2.5 × 10 2 to 6.4 × 10 3 , and 1.2 × 10 3 to 5.5 × 10 3 , respectively. The densities of 16S rRNA genes per gram of soil increased with…

Effects of integrated weed management in cropping systems on soils, microbial activity and N2O fluxes

International audience; Cultivated soils have been widely highlighted as a major source of nitrous oxide (N2O) emissions. This suggests that greenhouse gas emissions should be taken in account when evaluating the impact of new cropping systems. The development of integrated weed management in cropping systems introduces new agricultural practices (combinations of crop rotation, soil management, fertilization, and mechanical and chemical weed control, etc.), which may affect the microbial processes responsible for N2O production in soils. However, the effect of those practices remains to be assessed. Thus, the main objectives of our study is to provide (i) an accurate estimation of the inten…

Functional stability of the nitrate-reducing community in grassland soils towards high nitrate supply

Abstract To study the effects of short-term fluctuation of nitrate concentrations on the nitrate-reducing community, repacked soil cores were amended with 0, 100 and 300 μ g NO 3 - ‐ N g - 1 soil and incubated for 3, 7 and 14 days, respectively. The nitrate reductase activity was determined in a laboratory-based enzyme assay. In parallel, the community structure of nitrate-reducing microorganisms was characterised by RFLP-PCR using the functional gene narG , which encodes the catalytic site of the membrane-bound nitrate reductase. The community structure remained constant over the experimental period indicating that this functional community is characterised by a high resistance towards flu…

16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils

Bacteria capable of denitrification are spread among phylogenetically diverse groups. In the present investigation, molecular methods (amplified ribosomal DNA restriction analysis (ARDRA) and partial 16S rDNA gene sequencing) were used to determine the genetic diversity of culturable denitrifying soil bacteria. The purpose of this work was to study the microbial density and diversity of denitrifying communities isolated from two luvisols and a rendosol. The denitrifying bacterial density was significantly higher in the two luvisols (3x10(6) and 4x10(6) bacteria g(-1) dry soil) than in the rendosol (4x10(5) bacteria g(-1) dry soil). Denitrifying isolates from soils were grouped according to …