Diuron mineralisation in a Mediterranean vineyard soil: impact of moisture content and temperature

BACKGROUND: The diuron-mineralising ability of the microbiota of a Mediterranean vineyard soil exposed each year to this herbicide was measured. The impact of soil moisture and temperature on this microbial activity was assessed. RESULTS: The soil microbiota was shown to mineralise diuron. This mineralising activity was positively correlated with soil moisture content, being negligible at 5% and more than 30% at 20% soil moisture content. According to a double Gaussian model applied to fit the dataset, the optimum temperature/soil moisture conditions were 27.9 °C/19.3% for maximum mineralisation rate and 21.9 °C/18.3% for maximum percentage mineralisation. The impact of temperature and soil…

Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil

Abstract The level of expression of highly conserved, plasmid-borne, and widely dispersed atrazine catabolic genes ( atz ) was studied by RT-qPCR in two telluric atrazine-degrading microbes. RT-qPCR assays, based on the use of real-time PCR, were developed in order to quantify atzABCDEF mRNAs in Pseudomonas sp. ADP and atzABC mRNAs in Chelatobacter heintzii . atz gene expression was expressed as mRNA copy number per 10 6 16S rRNA. In Pseudomonas sp. ADP, atz genes were basally expressed. It confirmed atrazine-degrading kinetics indicating that catabolic activity starts immediately after adding the herbicide. atz gene expression increased transitorily in response to atrazine treatment. This …

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

International audience

Spatial variability of 2,4-dichlorophenoxyacetic acid (2,4-D) mineralisation potential at a millimetre scale in soil

Abstract We analysed the ability of soil units of millimetre size to mineralise a herbicide, 2,4-D, using incubations of individual aggregates (2–7 mm diameter) and 6×6×6 mm 3 cubes dissected from soil cores, under standard conditions. Mineralisation of 14 C-ring labelled 2,4-D was measured using a barite paper trap and a Phosphorimager to record the evolved 14 C-CO 2 from these very small soil samples. We found a large variability of 2,4-D mineralisation potential between aggregate size classes, between individual aggregates of the same size and between the different dissected cubes from a given core. We explained this variability by an uneven distribution of the degrading microorganisms a…

Microbial aspects of atrazine biodegradation in relation to history of soil treatment

Among 15 soils with different cropping practices, seven which had an history of repeated atrazine applications showed accelerated degradation of this herbicide. By contrast, grassland or agricultural soils with no recorded atrazine application, at least for the last three years, had a low degradation potential. No direct relation was found between the rate of atrazine mineralisation and the size of the microbial biomass. In adapted soils, the amounts of extractable residues were lowered and the very high percentages of radioactivity from [ring-14C]atrazine recovered as [14C]carbon dioxide demonstrated that N-dealkylation and deamidation were the only processes for micro-organisms to derive …

Regulating role of lumbricid macrofauna in Atrazine biodegradation in temperate cropped soil.

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Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of physicochemical and microbiological soil parameters, 411-417

International audience

Heterogeneity of pesticide mineralisation among individual soil aggregates of millimetre size

*INRA Science du Sol 78026 Versailles (FRA) Diffusion du document : INRA Science du Sol 78026 Versailles (FRA)

Study of diuron in soil solution by means of a novel simple technique using glass microfibre filters

International audience

Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils

The capacity of 12 soils to degrade atrazine was studied in laboratory incubations using radiolabelled atrazine. Eight soils showed enhanced degradation of this compound. Twenty-five bacterial strains able to degrade atrazine were isolated by an enrichment method from 10 of these soils. These soils were chosen for their wide range of physico-chemical characteristics. Their history of treatment with atrazine was also variable. The genetic diversity of atrazine degraders was determined by amplified ribosomal restriction analysis (ARDRA) of the 16S rDNA gene with three restriction endonucleases. The 25 bacterial strains were grouped into five ARDRA types. By sequencing and aligning the 16S rDN…

Rétention et dégradation des pesticides dans les sols

National audience

Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil

FR2116; In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s- triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atr…

Interactions biotiques entre macrofaune lombricienne et les communautés microbiennes, indigènes et bioaugmentées, dégradant l'atrazine en sol tempéré.

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Spatial variability of a microbial function. 2,4-D degradation as a test case

Isolation and characterisation of an isoproturon-mineralisingMethylopilasp. TES from French agricultural soil

Using enrichment culture three isoproturon (IPU) mineralising bacterial isolates were isolated from a French agricultural soil mineralising up to 50% of the initially added 14C-ring labelled IPU within only eight days. These isolates showed similar metabolic (BIOLOG GN) and amplified rDNA restriction (ARDRA) profiles. Partial 16S rDNA sequencing revealed that they were identical and identified as Methylopila sp TES. This strain harbours a large plasmid (220 kb) putatively bearing essential IPU-degrading genes as demonstrated by a curing experiment. Methylopila sp. TES transformed IPU and its known metabolites to CO2 and biomass but did not degrade chlorotoluron, monolinuron, diuron and linu…

Plasmid localisation of atrazine-degrading genes in newly described Chelatobacter and Arthrobacter strains

Abstract In a previous study, we isolated a collection of atrazine-degrading bacteria from various soils. The aim of this study was to localise the atrazine-degrading genes in these 25 atrazine-degrading strains. In the case of the Gram-negative strains of Chelatobacter heintzii, six to seven plasmids were observed. The atzABC and trzD genes were located on two or three plasmids with variable molecular masses. For the Gram-positive strains of Arthrobacter crystallopoietes, the atzBC genes were located on a single plasmid of 117 kb. The organisation of atrazine-degrading genes seems to be highly variable between the strains studied. We have shown by a specific PCR the occurrence of IS1071-li…

Indicateurs pour l'évaluation de l'impact de produits phytosanitaires sur la composante microbienne de la qualité biologique des sols

National audience

Ecologie microbienne appliquée et dépollution - Les micro-organismes acteurs majeurs de l'élimination des pollutions qui affectent l'environnement

Chapitre 16; National audience

Enhanced isoproturon mineralisation in a clay silt loam agricultural soil

International audience; 14C-ring-labelled isoproturon mineralisation was investigated in a French agricultural soil previously exposed to isoproturon. 50 different soil samples collected every 2 m along a transect of 100 m in length were treated one or two times with isoproturon under laboratory conditions and analysed by radiorespirometry. 94% of the soil samples showed a high ability to mineralise isoproturon with a relatively low variability in the cumulative percentage of mineralisation ranging from 30 to 51% of the initially added radioactivity for the samples treated once with the herbicide. About 45 to 67% of the initially added radioactivity was transformed into 14CO2 in soil sample…

Bioremediation of atrazine-contaminated soil

International audience

Analyse et modélisation des mécanismes de transfert de produits phytosanitaires aux échelles de la parcelle agricole et du bassin versant. Le cas d'un système hydrologique en milieu méditerranéen cultivé

National audience

Dependence of accelerated degradation of atrazine on soil pH in French and Canadian soils

Abstract A series of agricultural soils varying in their atrazine treatment history were sampled from 12 sites in France and two sites in Canada. The soils varied widely with respect to soil chemical, physical and microbiological (total microbial biomass, kinetics of C and N mineralization) properties. Soils treated with as few as two successive atrazine field applications mineralized [U- ring - 14 C]atrazine significantly more rapidly in 35 d laboratory incubations than did soils which had never received atrazine. Longer treatment history tended to favour more rapid mineralization in the so-called “adapted” soils. Up to 80% of the initially applied 14 C-atrazine was mineralized at the end …

Inoculation of an atrazine-degrading strain, Chelobacter heintzii Cit1, in four different soils : effects of different inoculum densities

International audience

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…

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…

Biodégradation de l'atrazine en sols tempérés : rôle régulateur d'un modèle d'interaction biotique macrofaune/bactérie.

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Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil

In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s-triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atrazine-deg…

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

Isolement et caractérisation physiologique et moléculaire de consortia bactériens dégradant l'atrazine à partir de sol ou de rhizosphère de maïs

National audience

Analyse de la biodégradation accélérée dans un sol cultivé avec du maïs

National audience

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…

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…

Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil

International audience; We report the characterisation of Nocardioides sp. SP12, an atrazine-degrading bacteria isolated from atrazine-treated bulk- and maize rhizosphere soil. Based on 16S rDNA alignment, strain SP12 showed close phylogenic relationships with Nocardioides sp. C157 and Nocardioides simplex. Internal transcribed spacer (ITS) sequences of strain SP12 were longer than those of other Nocardioides sp. and present Ala- and Ile-tRNA unlike Actinomycetales. Nocardioides sp. SP12 presents a novel atrazine catabolic pathway combining trzN with atzB and atzC. Atrazine biodegradation ends in a metabolite that co-eluted in HPLC with cyanuric acid. This metabolite shows an absorption spe…

Reassessement of the Kec coefficient of the fumigation-extraction method in a soil profile

Perspectives and limitations in assessing side-effects of pesticides on the soil microflora

International audience

Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil

Abstract The main objective of this work was to characterize an atrazine-mineralizing community originating from agrochemical factory soil, especially to elucidate the catabolic pathway and individual metabolic and genetic potentials of culturable members. A stable four-member bacterial community, characterized by colony morphology and 16S rDNA sequencing, was rapidly able to mineralize atrazine to CO 2 and NH 3 . Two primary organisms were identified as Arthrobacter species (ATZ1 and ATZ2) and two secondary organisms (CA1 and CA2) belonged to the genera Ochrobactrum and Pseudomonas, respectively. PCR assessment of atrazine-degrading genetic potential of the community, revealed the presence…

Effect of cropping cycles and repeated herbicide applications on the degradation of diclofop-methyl, bentazone, diuron, isoproturon and pendimethalin in soil.

A greenhouse study was conducted to investigate the ability of four crops (wheat, corn, oilseed rape and soybean) to influence the degradation of bentazone, diclofop-methyl, diuron, isoproturon and pendimethalin in soil. The present study showed that microbial biomass-carbon was significantly higher in planted soils than in bulk soil, especially with wheat and corn, after several cropping cycles. The biomass in corn and soybean planted soils was adversely affected by bentazone but recovered after three cropping cycles. In wheat-planted soils, diclofop-methyl application resulted in persistent increase of the amount of microbial biomass. Bentazone did not show accelerated degradation even af…