Publications by authors named "Céline Vandecasteele"

13 Publications

  • Page 1 of 1

Characterisation of hydrocarbon degradation, biosurfactant production, and biofilm formation in Serratia sp. Tan611: a new strain isolated from industrially contaminated environment in Algeria.

Antonie Van Leeuwenhoek 2021 Apr 15;114(4):411-424. Epub 2021 Feb 15.

Génétique Moléculaire, Génomique et Microbiologie (GMGM), UMR 7156, Université de Strasbourg, Strasbourg, France.

A novel bacterial strain was isolated from industrially contaminated waste water. In the presence of crude oil, this strain was shown to reduce the rate of total petroleum hydrocarbons (TPH) up to 97.10% in 24 h. This bacterium was subsequently identified by 16S rRNA gene sequence analysis and affiliated to the Serratia genus by the RDP classifier. Its genome was sequenced and annotated, and genes coding for catechol 1,2 dioxygenase and naphthalene 1,2-dioxygenase system involved in aromatic hydrocarbon catabolism, and LadA-type monooxygenases involved in alkane degradation, were identified. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of crude oil after biological treatment showed that Serratia sp. Tan611 strain was able to degrade n-alkanes (from C to C). This bacterium was also shown to produce a biosurfactant, the emulsification index (E24) reaching 43.47% and 65.22%, against vegetable and crude oil, respectively. Finally, the formation of a biofilm was increased in the presence of crude oil. These observations make Serratia sp. Tan611 a good candidate for hydrocarbon bioremediation.
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http://dx.doi.org/10.1007/s10482-021-01527-5DOI Listing
April 2021

Complete Genome Sequences of Four Atrazine-Degrading Bacterial Strains, sp. Strain ADPe, sp. Strain TES, sp. Strain 38R, and sp. Strain SR38.

Microbiol Resour Announc 2021 Jan 7;10(1). Epub 2021 Jan 7.

AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France

We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.
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http://dx.doi.org/10.1128/MRA.01080-20DOI Listing
January 2021

Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato.

Mol Biol Evol 2021 May;38(5):1792-1808

LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.

The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen's physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.
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http://dx.doi.org/10.1093/molbev/msaa320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097285PMC
May 2021

Complete Genome Sequence of sp. Strain Nx66, Isolated from Waters Contaminated with Petrochemicals in El Saf-Saf Valley, Algeria.

Microbiol Resour Announc 2020 Nov 19;9(47). Epub 2020 Nov 19.

Génétique Moléculaire, Génomique et Microbiologie, Université de Strasbourg, Strasbourg, France

sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb.
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http://dx.doi.org/10.1128/MRA.01130-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679099PMC
November 2020

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Microbiol Resour Announc 2020 Aug 6;9(32). Epub 2020 Aug 6.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, Gif-sur-Yvette, France

is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of SS95, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.
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http://dx.doi.org/10.1128/MRA.00420-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409842PMC
August 2020

Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.

Microorganisms 2020 Jun 13;8(6). Epub 2020 Jun 13.

Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.

Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.
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http://dx.doi.org/10.3390/microorganisms8060895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356628PMC
June 2020

Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): gen. nov. sp. nov.

Front Microbiol 2019 16;10:1497. Epub 2019 Jul 16.

Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France.

Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10-25°C and pH 8.5 showed that and were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-A was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named is a novel species of a new genus within the newly described family (order , phylum ). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-A. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.
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http://dx.doi.org/10.3389/fmicb.2019.01497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647913PMC
July 2019

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.

Nature 2017 06 22;546(7656):148-152. Epub 2017 May 22.

Department of Plant Sciences, University of California, Davis, California 95616, USA.

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
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http://dx.doi.org/10.1038/nature22380DOI Listing
June 2017

Comparative Analysis of Methylomes.

Front Plant Sci 2017 13;8:504. Epub 2017 Apr 13.

Center for Research in Agricultural Genomics, CSIC- IRTA- UAB -UBBarcelona, Spain.

is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of is unknown. Sequencing of strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete spp. genomes and across the , as well as a methylation motif associated to a phage-borne methylase unique to UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in evolution and its adaptation to different plants.
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http://dx.doi.org/10.3389/fpls.2017.00504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390034PMC
April 2017

ABI5 Is a Regulator of Seed Maturation and Longevity in Legumes.

Plant Cell 2016 11 15;28(11):2735-2754. Epub 2016 Nov 15.

IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France

The preservation of our genetic resources and production of high-quality seeds depends on their ability to remain viable and vigorous during storage. In a quantitative trait locus analysis on seed longevity in Medicago truncatula, we identified the bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5). Characterization of Mt-abi5 insertion mutant seeds revealed that both the acquisition of longevity and dormancy were severely impaired. Using transcriptomes of developing Mt-abi5 seeds, we created a gene coexpression network and revealed ABI5 as a regulator of gene modules with functions related to raffinose family oligosaccharide (RFO) metabolism, late embryogenesis abundant (LEA) proteins, and photosynthesis-associated nuclear genes (PhANGs). Lower RFO contents in Mt-abi5 seeds were linked to the regulation of SEED IMBIBITION PROTEIN1 Proteomic analysis confirmed that a set of LEA polypeptides was reduced in mature Mt-abi5 seeds, whereas the absence of repression of PhANG in mature Mt-abi5 seeds was accompanied by chlorophyll and carotenoid retention. This resulted in a stress response in Mt-abi5 seeds, evident from an increase in α-tocopherol and upregulation of genes related to programmed cell death and protein folding. Characterization of abi5 mutants in a second legume species, pea (Pisum sativum), confirmed a role for ABI5 in the regulation of longevity, seed degreening, and RFO accumulation, identifying ABI5 as a prominent regulator of late seed maturation in legumes.
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http://dx.doi.org/10.1105/tpc.16.00470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155344PMC
November 2016

Characterization of a dual-affinity nitrate transporter MtNRT1.3 in the model legume Medicago truncatula.

J Exp Bot 2011 Nov 23;62(15):5595-605. Epub 2011 Aug 23.

University of Angers, UMR-1191 Physiologie Moléculaire des Semences, IFR 149 Quasav, 2 Boulevard Lavoisier, 49045 Angers cedex 01, France.

Primary root growth in the absence or presence of exogenous NO(3)(-) was studied by a quantitative genetic approach in a recombinant inbred line (RIL) population of Medicago truncatula. A quantitative trait locus (QTL) on chromosome 5 appeared to be particularly relevant because it was seen in both N-free medium (LOD score 5.7; R(2)=13.7) and medium supplied with NO(3)(-) (LOD score, 9.5; R(2)=21.1) which indicates that it would be independent of the general nutritional status. Due to its localization exactly at the peak of this QTL, the putative NRT1-NO(3)(-) transporter (Medtr5g093170.1), closely related to Arabidopsis AtNRT1.3, a putative low-affinity nitrate transporter, appeared to be a significant candidate involved in the control of primary root growth and NO(3)(-) sensing. Functional characterization in Xenopus oocytes using both electrophysiological and (15)NO(3)(-) uptake approaches showed that Medtr5g093170.1, named MtNRT1.3, encodes a dual-affinity NO(3)(-) transporter similar to the AtNRT1.1 'transceptor' in Arabidopsis. MtNRT1.3 expression is developmentally regulated in roots, with increasing expression after completion of germination in N-free medium. In contrast to members of the NRT1 superfamily characterized so far, MtNRT1.3 is environmentally up-regulated by the absence of NO(3)(-) and down-regulated by the addition of the ion to the roots. Split-root experiments showed that the increased expression stimulated by the absence of NO(3)(-) was not the result of a systemic signalling of plant N status. The results suggest that MtNRT1.3 is involved in the response to N limitation, which increases the ability of the plant to acquire NO(3)(-) under N-limiting conditions.
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http://dx.doi.org/10.1093/jxb/err243DOI Listing
November 2011

Quantitative trait loci analysis reveals a correlation between the ratio of sucrose/raffinose family oligosaccharides and seed vigour in Medicago truncatula.

Plant Cell Environ 2011 Sep 28;34(9):1473-87. Epub 2011 Jun 28.

Institut National de la Recherche Agronomique, Physiologie Moléculaire des Semences, IFR 149 QUASAV, 49045 Angers, France.

Seed vigour is important for successful establishment and high yield, especially under suboptimal environmental conditions. In legumes, raffinose oligosaccharide family (RFO) sugars have been proposed as an easily available energy reserve for seedling establishment. In this study, we investigated whether the composition or amount of soluble sugars (sucrose and RFO) is part of the genetic determinants of seed vigour of Medicago truncatula using two recombinant inbred line (RIL) populations. Quantitative trait loci (QTL) mapping for germination rate, hypocotyl and radicle growth under water deficit and nutritional stress, seed weight and soluble sugar content was performed using RIL populations LR1 and LR4. Seven of the 12 chromosomal regions containing QTL for germination rate or post-germinative radicle growth under optimal or stress conditions co-located with Suc/RFO QTL. A significant negative correlation was also found between seed vigour traits and Suc/RFO. In addition, one QTL that explained 80% of the variation in the ratio stachyose/verbascose co-located with a stachyose synthase gene whose expression profile in the parental lines could explain the variation in oligosaccharide composition. The correlation and co-location of Suc/RFO ratio with germination and radicle growth QTL suggest that an increased Suc/RFO ratio in seeds of M. truncatula might negatively affect seed vigour.
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http://dx.doi.org/10.1111/j.1365-3040.2011.02346.xDOI Listing
September 2011

Genetic Structure of Mycosphaerella populorum (Anamorph Septoria musiva) Populations in North-Central and Northeastern North America.

Phytopathology 2005 Jun;95(6):608-16

ABSTRACT In order to characterize the genetic variation of the poplar pathogen Mycosphaerella populorum (anamorph Septoria musiva), we have studied seven North American populations using the polymerase chain reaction random amplified polymorphic DNA (RAPD) technique. The fungal populations were sampled in 2001 and 2002 by obtaining 352 isolates from cankers and leaf spots in hybrid poplar plantations and adjacent eastern cottonwood (Populus deltoides). A total of 21 polymorphic RAPD markers were obtained with the six RAPD primers used. A fine-level scale analysis of the genetic structure within the populations revealed that subpopulations sampled on P. deltoides and on hybrid trees were not significantly differentiated. In contrast, analyses performed on the entire data set showed high levels of haplotypic diversity and moderate to high genetic differentiation, with 20% of the expected genetic diversity found at the interpopulation level. Moreover, a high and significant correlation between genetic and geographic distances among populations was found, suggesting isolation by distance of the sampled populations. Although the occurrence of the sexual stage of this fungus remained unclear in field populations, five of the six populations were at gametic equilibrium for RAPD loci, suggesting the occurrence of recombination episodes in Septoria musiva populations. Overall, S. musiva appears to consist of differentiated subpopulations, with both asexual and sexual recombination contributing to the local level of genetic structure.
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http://dx.doi.org/10.1094/PHYTO-95-0608DOI Listing
June 2005