Philippe Delfosse - Academia.edu (original) (raw)

Papers by Philippe Delfosse

ABSTRACT Tan spot caused by Drechslera tritici-repentis was identified for the first time in the ... more ABSTRACT Tan spot caused by Drechslera tritici-repentis was identified for the first time in the Grand-Duchy of Luxembourg (GDL) in 1999 on the basis of morphological characters. In order to optimise disease control measures in the GDL, tillage methods, cultivar resistance, and fungicides effects were investigated during 1999-2009 in four sites. Over this period, only three years (i.e. 1999, 2000, and 2009) with epidemic outbreak were recorded. Field experiments showed a significant difference in disease severity between sites ( P< 0.001), cultivars ( P< 0.0001) and years ( P< 0.001) . In years with epidemic outbreak, the interaction of cultivars with non-inversion tillage, intensive winter wheat production, and favourable weather conditions caused an early expansion of the disease and a significant severity at GS 83 (early dough). Non-inversion tillage was found to be a major factor increasing the tan spot severity compared with conventional tillage. Furthermore, the analysis revealed that the disease severity was related to the cultivar’s susceptibility. For cultivars with similar phenology, the severity differed between the most and the weakly susceptible cultivar by a factor of two to four. The study also showed that no fungicide (mix of triazoles and strobilurin) effect has been observed in the epidemic years, except in 2000.

Phytopathology, Jun 1, 2013

Environmental microbiology, Jan 16, 2015

Although viruses are not the key players of the anaerobic digestion process, they may affect the ... more Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat, therefore as a first step toward their characterisation we optimised a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro-food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant-infecting viruses. Interestingly, less than 2 % of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends t...

Phytopathology

... S1 The efficacy of carbofuran at 1 mg ai/kg soil, Serratia marcescens (1 × 109 bacteriumcells... more ... S1 The efficacy of carbofuran at 1 mg ai/kg soil, Serratia marcescens (1 × 109 bacteriumcells/ml water ... Given the nature of the RB mutation, the objective of this work was to determine if RB variants can ... Agar plates contained a continuous concentration gradient for each fungicide ...

Azoxystrobin and epoxiconazole sensitivity profiles of Mycosphaerella graminicola populations fro... more Azoxystrobin and epoxiconazole sensitivity profiles of Mycosphaerella graminicola populations from the Grand-Duchy of Luxembourg in 2007 and 2008

The reconstruction of complete or nearly-complete microbial genomes from metagenomic reads is reg... more The reconstruction of complete or nearly-complete microbial genomes from metagenomic reads is regarded as an important step toward a better characterization of the genetic potential of microbes present in a studied environment that contains mostly novel and uncultured species. However, even though the depth of sequencing is continuously increasing, current computational analyses of metagenomic data, especially the binning step (aggregation of the contigs into biological entities), are largely dependent on comparisons to reference genomes from cultivated species. These reference genomes represent only a fraction of the real microbial diversity present in nature. Therefore, here we present a new non taxonomy-dependent iterative approach for contig binning, which relies on a series of samples, e.g. sequential time series samples from one specific environment or different samples from environments that could be characterized by similar microflora. The key concept is that bacteria (archa...

JOURNAL OF PLANT PATHOLOGY

Re-emergence of Fusarium head blight (FHB) on wheat should be taken into account in the global ma... more Re-emergence of Fusarium head blight (FHB) on wheat should be taken into account in the global management of cropped fields, especially with respect to fungicide application schemes, due to harmful toxin production. The aim of this study was to assess, in three experimental fields representative of the various topoclimatological zones of Luxembourg, the impact of timing of fungicide spray application on the prevalence and severity of FHB, the concentration of mycotoxins, and Fusarium strain pattern in winter wheat. It was found that fungicide treatments and the time of application had a significant impact on the amount of deoxynivalenol (DON) detected (P=0.027, ANOVA). In our experimental design, the application of fungicides at 3 different times increased the amount of DON in winter wheat compared to two and single applications. The importance of the timing of fungicide application is discussed in relation to limiting toxin contamination in the field.

Wheat stripe rust (WSR) (caused by Puccinia striiformis sp. tritici) i continues to be a major th... more Wheat stripe rust (WSR) (caused by Puccinia striiformis sp. tritici) i continues to be a major threat in most wheat growing regions of the world, with potential to inflict regular yield losses where susceptible cultivars are grown and when weather conditions are favourable. A recently isolated strain of P. striiformis sp. tritici, ‘warrior’, first identified in 2011 in Europe, is now virulent on adult plants of susceptible wheat cultivars throughout most wheat growing regions, including Luxembourg. Daily weather conditions were monitored and related to development of WSR during the 2012-2014 seasons in Luxembourg. Favourable weather conditions were determined by (i) analysing Dennis model outputs generated through a Monte Carlo method, and (ii) identifying the best correlation between the frequencies of weather condition classes and the area under the disease progress curve on the uppermost three leaves (L1, L2, and L3; L1 being the flag leaf). Our results showed that a combination ...

Batch anaerobic digesters were fed with increasing amounts of maize silage in order to reach a fa... more Batch anaerobic digesters were fed with increasing amounts of maize silage in order to reach a failure in the biomethanation process. A methodology for quantitative and qualitative analysis was developed to follow the progress of volatile fatty acids (VFA) related to the biogas production. In overfed digesters, process failure was characterized by a decreased biogas production and a higher CO2/CH4 ratio compared to the reasonably fed digesters. No fixed value in terms of total or individual VFA concentration was found to be a good indicator of process imbalance but the results indicated that the microbial consortium was able to degrade up to 837, 674 and 697 mg.L-1 of acetic, propionic and butyric acids, respectively. This study also highlighted the importance of quantifying the substrate to inoculum ratio in batch anaerobic digestion assays to get significant and valid estimation of biomethane potential and production kinetics.

The bacterial and archaeal communities’ genetic structures of four mesophilic CSTRs were monitore... more The bacterial and archaeal communities’ genetic structures of four mesophilic CSTRs were monitored during a gradual overfeeding experiment aiming at causing acidosis. The 16S rRNA T-RFLP patterns showed overt changes in the structure of both microbial communities during acidosis installation (decreasing of the reactor pH value) and after process recovery. The lower the pH value during the acidosis, the more the composition of the microbial community was altered between the beginning and the end of the experiment.

Bacteriophages are the most abundant biological entities on Earth, with an estimated population o... more Bacteriophages are the most abundant biological entities on Earth, with an estimated population of 10 31 total particles . Early studies have confirmed the presence of viruses in the different stages of wastewater treatment plants, including anaerobic digestion (AD) tanks, at concentrations 10 -1000 times higher than in natural aquatic environments . Although the performance and the stability of AD greatly relies on its microbial community that carry out the different metabolic processes, bacteriophages may largely shape the dynamics of these communities by infecting and lysing the dominant microbial populations ("phage kills the winner" strategy); thus potentially impacting the overall process of the anaerobic digestion (no literature dealing with this topic!). Nevertheless, to date very limited information is available on the viromes (total viral communities) of AD. Most of the available metagenomic data concerning AD underestimated the viral communities present in the reactor, particularly owing to our incomplete methods of recognizing them. This is due to the fact that most of the sequenced bacterial genomes, used as a reference in metagenomic analyses, contain a large number of unrecognized intact or defective prophages, and more importantly because there is a prevalence of host metabolic genes being carried by viruses as well. Therefore, in this study we have applied a metagenomic approach to investigate a phylogenetic and functional diversity of DNA and RNA viral communities in different anaerobic reactors fed with distinct substrates, including: (1) wastewater, (2) agricultural residues, and (3) bio -waste. The complete analysis consisted of the isolation of virus like particles by filtration, using both 0.22 and 0.45µm filters, and their concentration by ultracentrifugation. Subsequently, the RNA/DNA were extracted, two types of libraries were prepared for RNA and DNA viromes respectively, and finally sequenced on Miseq. Following our preliminary analyses we have realized that AD environments are indeed very reach in numerous viruses (also studied by TEM), including bacteriophages, most of which have never been characterized before. Based on the taxonomic classification, the dominant viral families included Siphoviridae, Myoviridae and Podoviridae. Subsequent, functional analysis should help to select adequate molecular markers useful to monitor, on the regular basis, different reactors (both in the laboratory as well as the biogas units) for the presence of different viruses/bacteriophages. This will allow evaluating the real impact of viruses on the overall process of anaerobic digestion.

Various factors may affect the anaerobic digestion process (AD), by causing rapid changes within ... more Various factors may affect the anaerobic digestion process (AD), by causing rapid changes within its microbial community. It has been widely recognized that biodiversity, which is particularly manifest at the species and strain level, can in fact maintain or boost ecosystem functioning when such system faces environmental changes. Therefore, it is clear that a better characterization of microbial diversity of AD will help to better understand the dynamics of these communities; especially a significant impact of species and strain variations under suboptimal conditions. For this reason, we monitored microbial communities in mesophilic AD, using 16S rRNA high throughput gene sequencing and metagenomics, under two sub–optimal conditions, both reflected by different pH values, namely alkalosis (ammonium intoxication) and acidosis (toxicity due to high volatile fatty acids [VFAs] concentration).

Biotechnology for Biofuels, 2015

Background: Volatile fatty acid intoxication (acidosis), a common process failure recorded in ana... more Background: Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steadystate reactor.

Phytopathology

Bias (over and underestimates) in estimates of disease severity, and the impact of that inaccurac... more Bias (over and underestimates) in estimates of disease severity, and the impact of that inaccuracy on hypothesis testing using different disease scales was explored. Nearest percent estimates (NPE), the Horsfall-Barratt (H-B) scale and four different linear category scales (5% and 10% increments, with and without additional grades at low severity) were compared. Actual values and estimates by 4 different raters of the severity (0 to 100%) of Septoria leaf blotch on leaves of winter wheat were used to develop distributions for a simulation model. The simulations were based on i) all the 4 raters data combined, ii) only the most accurate rater estimates, and iii) only the most biased rater. Regardless of the effect of rater ability, we found that, there were lower type II error rates with NPEs as compared with the other category scales at severities of 80 to 100%. On the other hand, with lower severities (0 to 20%), the 5% and 10% scales with additional grades had type II error rates ...

ABSTRACT Tan spot caused by Drechslera tritici-repentis was identified for the first time in the ... more ABSTRACT Tan spot caused by Drechslera tritici-repentis was identified for the first time in the Grand-Duchy of Luxembourg (GDL) in 1999 on the basis of morphological characters. In order to optimise disease control measures in the GDL, tillage methods, cultivar resistance, and fungicides effects were investigated during 1999-2009 in four sites. Over this period, only three years (i.e. 1999, 2000, and 2009) with epidemic outbreak were recorded. Field experiments showed a significant difference in disease severity between sites ( P< 0.001), cultivars ( P< 0.0001) and years ( P< 0.001) . In years with epidemic outbreak, the interaction of cultivars with non-inversion tillage, intensive winter wheat production, and favourable weather conditions caused an early expansion of the disease and a significant severity at GS 83 (early dough). Non-inversion tillage was found to be a major factor increasing the tan spot severity compared with conventional tillage. Furthermore, the analysis revealed that the disease severity was related to the cultivar’s susceptibility. For cultivars with similar phenology, the severity differed between the most and the weakly susceptible cultivar by a factor of two to four. The study also showed that no fungicide (mix of triazoles and strobilurin) effect has been observed in the epidemic years, except in 2000.

Phytopathology, Jun 1, 2013

Environmental microbiology, Jan 16, 2015

Although viruses are not the key players of the anaerobic digestion process, they may affect the ... more Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat, therefore as a first step toward their characterisation we optimised a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro-food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant-infecting viruses. Interestingly, less than 2 % of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends t...

Phytopathology

... S1 The efficacy of carbofuran at 1 mg ai/kg soil, Serratia marcescens (1 × 109 bacteriumcells... more ... S1 The efficacy of carbofuran at 1 mg ai/kg soil, Serratia marcescens (1 × 109 bacteriumcells/ml water ... Given the nature of the RB mutation, the objective of this work was to determine if RB variants can ... Agar plates contained a continuous concentration gradient for each fungicide ...

Azoxystrobin and epoxiconazole sensitivity profiles of Mycosphaerella graminicola populations fro... more Azoxystrobin and epoxiconazole sensitivity profiles of Mycosphaerella graminicola populations from the Grand-Duchy of Luxembourg in 2007 and 2008

The reconstruction of complete or nearly-complete microbial genomes from metagenomic reads is reg... more The reconstruction of complete or nearly-complete microbial genomes from metagenomic reads is regarded as an important step toward a better characterization of the genetic potential of microbes present in a studied environment that contains mostly novel and uncultured species. However, even though the depth of sequencing is continuously increasing, current computational analyses of metagenomic data, especially the binning step (aggregation of the contigs into biological entities), are largely dependent on comparisons to reference genomes from cultivated species. These reference genomes represent only a fraction of the real microbial diversity present in nature. Therefore, here we present a new non taxonomy-dependent iterative approach for contig binning, which relies on a series of samples, e.g. sequential time series samples from one specific environment or different samples from environments that could be characterized by similar microflora. The key concept is that bacteria (archa...

JOURNAL OF PLANT PATHOLOGY

Re-emergence of Fusarium head blight (FHB) on wheat should be taken into account in the global ma... more Re-emergence of Fusarium head blight (FHB) on wheat should be taken into account in the global management of cropped fields, especially with respect to fungicide application schemes, due to harmful toxin production. The aim of this study was to assess, in three experimental fields representative of the various topoclimatological zones of Luxembourg, the impact of timing of fungicide spray application on the prevalence and severity of FHB, the concentration of mycotoxins, and Fusarium strain pattern in winter wheat. It was found that fungicide treatments and the time of application had a significant impact on the amount of deoxynivalenol (DON) detected (P=0.027, ANOVA). In our experimental design, the application of fungicides at 3 different times increased the amount of DON in winter wheat compared to two and single applications. The importance of the timing of fungicide application is discussed in relation to limiting toxin contamination in the field.

Wheat stripe rust (WSR) (caused by Puccinia striiformis sp. tritici) i continues to be a major th... more Wheat stripe rust (WSR) (caused by Puccinia striiformis sp. tritici) i continues to be a major threat in most wheat growing regions of the world, with potential to inflict regular yield losses where susceptible cultivars are grown and when weather conditions are favourable. A recently isolated strain of P. striiformis sp. tritici, ‘warrior’, first identified in 2011 in Europe, is now virulent on adult plants of susceptible wheat cultivars throughout most wheat growing regions, including Luxembourg. Daily weather conditions were monitored and related to development of WSR during the 2012-2014 seasons in Luxembourg. Favourable weather conditions were determined by (i) analysing Dennis model outputs generated through a Monte Carlo method, and (ii) identifying the best correlation between the frequencies of weather condition classes and the area under the disease progress curve on the uppermost three leaves (L1, L2, and L3; L1 being the flag leaf). Our results showed that a combination ...

Batch anaerobic digesters were fed with increasing amounts of maize silage in order to reach a fa... more Batch anaerobic digesters were fed with increasing amounts of maize silage in order to reach a failure in the biomethanation process. A methodology for quantitative and qualitative analysis was developed to follow the progress of volatile fatty acids (VFA) related to the biogas production. In overfed digesters, process failure was characterized by a decreased biogas production and a higher CO2/CH4 ratio compared to the reasonably fed digesters. No fixed value in terms of total or individual VFA concentration was found to be a good indicator of process imbalance but the results indicated that the microbial consortium was able to degrade up to 837, 674 and 697 mg.L-1 of acetic, propionic and butyric acids, respectively. This study also highlighted the importance of quantifying the substrate to inoculum ratio in batch anaerobic digestion assays to get significant and valid estimation of biomethane potential and production kinetics.

The bacterial and archaeal communities’ genetic structures of four mesophilic CSTRs were monitore... more The bacterial and archaeal communities’ genetic structures of four mesophilic CSTRs were monitored during a gradual overfeeding experiment aiming at causing acidosis. The 16S rRNA T-RFLP patterns showed overt changes in the structure of both microbial communities during acidosis installation (decreasing of the reactor pH value) and after process recovery. The lower the pH value during the acidosis, the more the composition of the microbial community was altered between the beginning and the end of the experiment.

Bacteriophages are the most abundant biological entities on Earth, with an estimated population o... more Bacteriophages are the most abundant biological entities on Earth, with an estimated population of 10 31 total particles . Early studies have confirmed the presence of viruses in the different stages of wastewater treatment plants, including anaerobic digestion (AD) tanks, at concentrations 10 -1000 times higher than in natural aquatic environments . Although the performance and the stability of AD greatly relies on its microbial community that carry out the different metabolic processes, bacteriophages may largely shape the dynamics of these communities by infecting and lysing the dominant microbial populations ("phage kills the winner" strategy); thus potentially impacting the overall process of the anaerobic digestion (no literature dealing with this topic!). Nevertheless, to date very limited information is available on the viromes (total viral communities) of AD. Most of the available metagenomic data concerning AD underestimated the viral communities present in the reactor, particularly owing to our incomplete methods of recognizing them. This is due to the fact that most of the sequenced bacterial genomes, used as a reference in metagenomic analyses, contain a large number of unrecognized intact or defective prophages, and more importantly because there is a prevalence of host metabolic genes being carried by viruses as well. Therefore, in this study we have applied a metagenomic approach to investigate a phylogenetic and functional diversity of DNA and RNA viral communities in different anaerobic reactors fed with distinct substrates, including: (1) wastewater, (2) agricultural residues, and (3) bio -waste. The complete analysis consisted of the isolation of virus like particles by filtration, using both 0.22 and 0.45µm filters, and their concentration by ultracentrifugation. Subsequently, the RNA/DNA were extracted, two types of libraries were prepared for RNA and DNA viromes respectively, and finally sequenced on Miseq. Following our preliminary analyses we have realized that AD environments are indeed very reach in numerous viruses (also studied by TEM), including bacteriophages, most of which have never been characterized before. Based on the taxonomic classification, the dominant viral families included Siphoviridae, Myoviridae and Podoviridae. Subsequent, functional analysis should help to select adequate molecular markers useful to monitor, on the regular basis, different reactors (both in the laboratory as well as the biogas units) for the presence of different viruses/bacteriophages. This will allow evaluating the real impact of viruses on the overall process of anaerobic digestion.

Various factors may affect the anaerobic digestion process (AD), by causing rapid changes within ... more Various factors may affect the anaerobic digestion process (AD), by causing rapid changes within its microbial community. It has been widely recognized that biodiversity, which is particularly manifest at the species and strain level, can in fact maintain or boost ecosystem functioning when such system faces environmental changes. Therefore, it is clear that a better characterization of microbial diversity of AD will help to better understand the dynamics of these communities; especially a significant impact of species and strain variations under suboptimal conditions. For this reason, we monitored microbial communities in mesophilic AD, using 16S rRNA high throughput gene sequencing and metagenomics, under two sub–optimal conditions, both reflected by different pH values, namely alkalosis (ammonium intoxication) and acidosis (toxicity due to high volatile fatty acids [VFAs] concentration).

Biotechnology for Biofuels, 2015

Background: Volatile fatty acid intoxication (acidosis), a common process failure recorded in ana... more Background: Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steadystate reactor.

Phytopathology

Bias (over and underestimates) in estimates of disease severity, and the impact of that inaccurac... more Bias (over and underestimates) in estimates of disease severity, and the impact of that inaccuracy on hypothesis testing using different disease scales was explored. Nearest percent estimates (NPE), the Horsfall-Barratt (H-B) scale and four different linear category scales (5% and 10% increments, with and without additional grades at low severity) were compared. Actual values and estimates by 4 different raters of the severity (0 to 100%) of Septoria leaf blotch on leaves of winter wheat were used to develop distributions for a simulation model. The simulations were based on i) all the 4 raters data combined, ii) only the most accurate rater estimates, and iii) only the most biased rater. Regardless of the effect of rater ability, we found that, there were lower type II error rates with NPEs as compared with the other category scales at severities of 80 to 100%. On the other hand, with lower severities (0 to 20%), the 5% and 10% scales with additional grades had type II error rates ...