Impact of repeated treatments of the pesticides chlorpyrifos or tebuconazole on soil microorganisms using alternative methods

International audience

Estimation of the density of the protocatechuate-degrading bacterial community in soil by real-time PCR

Summary The β-ketoadipate pathway is the major route for degradation of aromatic compounds by various soil microorganisms. Protocatechuate 3,4-dioxygenase, a key enzyme of this pathway and which is encoded by pcaGH genes, catalyses the ring cleavage of protocatechuate. Microorganisms harbouring pcaGH genes are widely distributed in the environment but little is known about their relative abundance within the total microflora. Hence, this paper reports the development of a real-time PCR assay to quantify the bacterial pcaH sequence that encodes the β sub-unit of the protocatechuate 3,4-dioxygenase. This real-time PCR assay was linear over seven orders of magnitude with a calculated efficienc…

Depth matters : Effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

International audience; 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, i.e. precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used 18O stable isotope probing (SIP) to investigate bacterial and fungal communities that actively grew or not upon rewetting, at three different depths in plant-soil mesocosms previously subjected to frequent or infrequent watering for 12 weeks (equal total water input). Phylogenetic marker genes for bacteria and fungi were sequenced after rewetting,…

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…

Quantification of denitrifiers by real-time PCR

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.

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…

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 …

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…

Assessment of pesticides ecotoxicology on soil microorganism

National audience

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

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

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…

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…

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…

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 …

Phytotoxicité et écotoxicité d’un extrait de cyanobactéries

La présence de cyanobactéries dans les eaux de surface est souvent accompagnée par la production d'une grande quantité de cyanotoxines ayant des effets néfastes sur certains certains organes de mammifères. La plus communément trouvée dans l'environnement est la microcystine leucine-arginine (MC-LR), une hépatotoxine très toxique qui induit l'inhibition des protéines phosphatase de type 1A et 2A (MacKintosh et al., 1990) et dont les concentrations, dans les eaux douces, excèdent souvent la limite de 1 µg équi. MC-LR L-1 établie par l’Organisation Mondiale de la Santé pour l’eau potable. Des études ont démontré les effets phytotoxiques des microcystines (El Khalloufi et al., 2012; Pflugmacher…

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

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

National audience

[div]Long-term dynamics of the atrazine mineralization potential in surface and subsurface soil in an agricultural field as a response to atrazine applications[/div]

Abstract The dynamics of the atrazine mineralization potential in agricultural soil was studied in two soil layers (topsoil and at 35–45 cm depth) in a 3 years field trial to examine the long term response of atrazine mineralizing soil populations to atrazine application and intermittent periods without atrazine and the effect of manure treatment on those processes. In topsoil samples, 14 C-atrazine mineralization lag times decreased after atrazine application and increased with increasing time after atrazine application, suggesting that atrazine application resulted into the proliferation of atrazine mineralizing microbial populations which decayed when atrazine application stopped. Decay …

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…

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…

Use of PCAH as a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in soil environment

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling. The pcaH gene encoding a key ring-cleaving enzyme of the β -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two soils. The RFLP screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70 % identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This gene constitutes a suitable molecular marker to study the diversity of this functional group.

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 …

Bacterial hppd: a biomarker of exposure of soils to beta-triketone herbicides?

National audience; β-triketone herbicides are among the most used herbicides in corn crop to control broadleaf weeds.These herbicides inhibit the 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) and lead to bleaching anddeath of weeds. This enzyme is not only found in plants but in all living organisms, includingmicroorganisms where it takes part to the tyrosine degradation pathway. Thus, microorganismsclassified as “non-target organisms” by current EU regulation for pesticide authorization, might beimpacted by β-triketones, with possible domino effect on microbial functions supporting soilecosystem services (Thiour-Mauprivez et al. 2019). Since microorganisms have been proposed by EFSAas key-d…

Evaluation of the ecotoxicological impact of pesticides on the diversity and the abundance of soil microorganisms

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 ,…

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 …

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…

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…

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…

Response of the PCB-contaminated soil bacterial community to applied bioremediation treatments

For full field implementation of the bioremediation as a strategy for cleaning PCB-contaminated soils, the impact of the applied treatment on the microbial community needs to be clarified. An ideal bioremediation should have positive effects on PCB-removal but should pose no treats to the health of the soil ecosystem. Microbes, playing an essential role in maintenance of the soil ecosystem, are the first indicators of a negative impact of soil manipulation to ecosystem. A small-scale bioremediation experiment was conducted in order to get insight into behavior of the microbial community during bioremediation of PCB-contaminated soil, targeting both functional PCB-degrading community (by bph…

Utiliser les symbiotes des Légumineuses pour favoriser la réduction du gaz à effet de serre N2O dans les sols

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

International audience

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…

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…

Quantification of metal-resistant genes from the microbial community of uranium mine soils

Background: Bacteria can thrive in environments presenting unique, extreme and/or stressful conditions, partly due to the diverse resistome they evolved as a result of physiological, metabolic and genetic adaptations. In this context, the microbial communities in soils from abandoned uranium mines may have peculiar genetic profiles that sustain valuable metal-resistance mechanisms. Getting further knowledge on the genetic potential of these microbial communities can be a contribute for developing bioremediation strategies towards the reclamation of highly contaminated uranium mine soils. Objectives: To quantify metal-resistance genes harboured by the microbial community of soil samples coll…

Sensitive measure of prevalence and parasitaemia of haemosporidia from European blackbird (Turdus merula) populations: value of PCR-RFLP and quantitative PCR.

8 pages; International audience; Haemosporidian parasites are common in birds in which they act as an important selective pressure. While most studies so far have focused on the effect of their prevalence on host life-history traits, no study has measured the effect of parasitaemia. We developed molecular methods to detect, identify and quantify haemosporidia in 2 natural populations of the Blackbird Turdus merula. Three different parasite genotypes were found - 1 Haemoproteus and 2 Plasmodium. A PCR-RFLP screening revealed that only approximately 3% of blackbirds were free of parasites, compared to the 34% of uninfected birds estimated by blood smear screening. A quantitative PCR (q-PCR) a…

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…

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

pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pai…

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.

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 …

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…