Dr. Joël Pothier

Work at ZHAW

Position at the ZHAW

Senior Researcher - Environmental Genomics und Systems Biology Research Group

Education and Continuing education

Expertise and research interests

Microbial Ecology
Biochemistry
Molecular biology
Bioinformatics
Genomics
Transcriptomics
Proteomics
Teaching assistant ("moniteur" and "ATER" University Lyon 1)

Educational background

PhD of Microbial Ecology - 2007 – University Lyon 1 (France)
Master of Science - Year 2: Microbial Ecology - 2003 - University Lyon 1 (France)
Master of Science - Year 1: Molecular and Cellular Biology - 2002 – University of Limoges (France)
Bachelor of Science in Biochemistry - 2001 – University of Limoges (France)

Membership of networks

• Swiss Society for Microbiology SGM-SSM (since 2010)
• Société Française de Phytopathologie SFP (2009-2015)
• Swiss Group for Mass Spectrometry SGMS (since 2015)
• COST 873 (2008-2012)
• COST FA1104 (2013-2016)
• Q-Detect (2010-2013)
• NRP68 (2013-2016)
• Dropsa (2014-2018)
• COST CA16107 (since 2016)
• COST CA16110 (since 2016)

Projects

• ToViPoRe: massive detection of tomato brown rugose fruit virus by high-throughput sequencing / Project leader / Project ongoing
• Modernes Biodiversitätsmonitoring mit Next-Generation Sequencing (NGS-Methoden) / Team member / Project ongoing
• EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions / Deputy project leader / Project ongoing
• ChitinOMix – A multidisciplinary project to understand the effect of chitin soil amendment on the plant response, natural microbial community and the fate of human pathogenic bacteria / Project leader / Project ongoing
• Comparative genomics of the plant pathogen Xanthomonas arboricola pv. pruni and related xanthomonads / Project leader / Project ongoing
• MALDI-TOF MS for microorganism identification: from pattern recognition towards marker based approaches / Project leader / Project ongoing
• Fire Blight App for Central Asia / Deputy project leader / Project completed
• Acceptance of an app for contact-tracing of SARS-CoV-2 in the Swiss population / Team member / Project completed
• Silent pathway awakening to discover novel antibacterial compounds from actinomycetes / Project co-leader / Project completed
• MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology / Project co-leader / Project completed
• XhortOMICs: Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies / Project co-leader / Project completed
• Effect of cryopreservation on genome mutation rate - examples of grapevine / Deputy project leader / Project completed
• Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples / Project co-leader / Project completed
• Characterization of nitrogen dynamics in an aquaponic system / Team member / Project completed
• Comparative genomics to untangle insect pathogenicity in plant-associated pseudomonads / Team member / Project completed
• Sepsis-Associated Microorganisms in Brazilian Ambulatories (SAMBA) / Team member / Project completed
• MycoTOF -Determining mycotoxigenic molds and mycotoxins / Project co-leader / Project completed
• COST Action – Sustainable production of high quality cherries for the European market / Project leader / Project completed
• DROPSA – Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens / Project leader / Project completed
• High-throughput proteomics of Thiodictyon synthrophicum strain Cad16T / Project leader / Project completed
• Genomics and transcriptomics of Erwinia and Pantoea / Team member / Project completed
• In-depth molecular analysis of stool and water samples collected in Kampala, Uganda / Project leader / Project completed

Publications

• Kałużna, Monika; Prokić, Andjelka; Obradović, Aleksa; Weldon, William A.; Stockwell, Virginia O.; Pothier, Joël F.,

  2023.

  Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics.

  Frontiers in Plant Science.

  14(1254107).

  Available from: https://doi.org/10.3389/fpls.2023.1254107

• Orfei, Benedetta; Pothier, Joël F.; Fenske, Linda; Blom, Jochen; Moretti, Chiaraluce; Buonaurio, Roberto; Smits, Theo H. M.,

  2023.

  Race-specific genotypes of Pseudomonas syringae pv. tomato are defined by the presence of mobile DNA elements within the genome.

  Frontiers in Plant Science.

  14(1197706).

  Available from: https://doi.org/10.3389/fpls.2023.1197706

• Li, Leilei; Kaufmann, Moritz; Makechemu, Moffat; Van Poucke, Christof; De Keyser, Ellen; Uyttendaele, Mieke; Zipfel, Cyril; Cottyn, Bart; Pothier, Joël F.,

  2023.

  Assessment of transcriptional reprogramming of lettuce roots in response to chitin soil amendment.

  Frontiers in Plant Science.

  14(1158068).

  Available from: https://doi.org/10.3389/fpls.2023.1158068

• Arend, Lavinia N.V.S.; Bergamo, Ricardo; Rocha, Fabiano B.; Bail, Larissa; Ito, Carmen; Baura, Valter A.; Balsanelli, Eduardo; Pothier, Joël F.; Rezzonico, Fabio; Pilonetto, Marcelo; Smits, Theo H.M.; Tuon, Felipe Francisco,

  2023.

  Dissemination of NDM-producing bacteria in Southern Brazil.

  Diagnostic Microbiology and Infectious Disease.

  106(2), pp. 115930.

  Available from: https://doi.org/10.1016/j.diagmicrobio.2023.115930

• Pothier, Joël F.; Bolt, Valentin; Arn, Fabienne; Frasson, David; Rhyner, Nicola; Sievers, Martin,

  2023.

  High-quality draft genome sequence of Streptomyces albidoflavus CCOS 2040, isolated from a Swiss soil sample.

  Microbiology Resource Announcements.

  12(3), pp. e01225-22.

  Available from: https://doi.org/10.1128/mra.01225-22

• Sulja, Arburon; Pothier, Joël F.; Blom, Jochen; Moretti, Chiaraluce; Buonaurio, Roberto; Rezzonico, Fabio; Smits, Theo H. M.,

  2022.

  Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734.

  BMC Genomics.

  23(742).

  Available from: https://doi.org/10.1186/s12864-022-08966-y

• Schmautz, Zala; Walser, Jean-Claude; Espinal, Carlos A.; Gartmann, Florentina; Scott, Benjamin; Pothier, Joël F.; Frossard, Emmanuel; Junge, Ranka; Smits, Theo H. M.,

  2022.

  Microbial diversity across compartments in an aquaponic system and its connection to the nitrogen cycle.

  Science of the Total Environment.

  852(158426).

  Available from: https://doi.org/10.1016/j.scitotenv.2022.158426

• Dia, Nay C.; Cottyn, Bart; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2022.

  Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays.

  Frontiers in Agronomy.

  4(898778).

  Available from: https://doi.org/10.3389/fagro.2022.898778

• Silva, Kayla Gisela; Martins, Leonor; Teixeira, Miguel; Pothier, Joël F.; Tavares, Fernando,

  2022.

  DNA markers for detection and genotyping of Xanthomonas euroxanthea.

  Microorganisms.

  10(6), pp. 1078.

  Available from: https://doi.org/10.3390/microorganisms10061078

• Kałużna, Monika; Pothier, Joël F.,

  2022.

  Complete genome sequence data of two Xanthomonas arboricola strains isolated from blueberry plants displaying bacterial leaf blight in Poland.

  Phytopathology.

  112(8), pp. 1814-1818.

  Available from: https://doi.org/10.1094/PHYTO-11-21-0484-A

• Ruinelli, Michela; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2022.

  Comparative genomics of Prunus-associated members of the Pseudomonas syringae species complex reveals traits supporting co-evolution and host adaptation.

  Frontiers in Microbiology.

  13(804681).

  Available from: https://doi.org/10.3389/fmicb.2022.804681

• Dia, Nay C.; Morinière, Lucas; Cottyn, Bart; Bernal, Eduardo; Jacobs, Jonathan M.; Koebnik, Ralf; Osdaghi, Ebrahim; Potnis, Neha; Pothier, Joël F.,

  2022.

  Xanthomonas hortorum – beyond gardens : current taxonomy, genomics, and virulence repertoires.

  Molecular Plant Pathology.

  23(5), pp. 597-621.

  Available from: https://doi.org/10.1111/mpp.13185

• Hakalová, Eliška; Čechová, Jana; Tekielska, Dorota A.; Eichmeier, Ales; Pothier, Joël F.,

  2022.

  Combined effect of thyme and clove phenolic compounds on Xanthomonas campestris pv. campestris and biocontrol of black rot disease on cabbage seeds.

  Frontiers in Microbiology.

  13.

  Available from: https://doi.org/10.3389/fmicb.2022.1007988

• Knecht, Leandra E.; Born, Yannick; Pelludat, Cosima; Pothier, Joël F.; Smits, Theo H. M.; Loessner, Martin J.; Fieseler, Lars,

  2022.

  Spontaneous resistance of Erwinia amylovora against bacteriophage Y2 affects infectivity of multiple phages.

  Frontiers in Microbiology.

  13(908346).

  Available from: https://doi.org/10.3389/fmicb.2022.908346

• Dia, Nay C.; Van Vaerenbergh, Johan; Van Malderghem, Cinzia; Blom, Jochen; Smits, Theo H. M.; Cottyn, Bart; Pothier, Joël F.,

  2021.

  Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens.

  International Journal of Systematic and Evolutionary Microbiology.

  71(12).

  Available from: https://doi.org/10.1099/ijsem.0.005163

• Kałużna, Monika; Fischer‐Le Saux, Marion; Pothier, Joël; Jacques, Marie‐Agnès; Obradović, Aleksa; Tavares, Fernando; Stefani, Emilio,

  2021.

  Xanthomonas arboricola pv. juglandis and pv. corylina: Brothers or distant relatives? : genetic clues, epidemiology, and insights for disease management.

  Molecular Plant Pathology.

  22(12), pp. 1481-1499.

  Available from: https://doi.org/10.1111/mpp.13073

• Cottyn, B.; De Paepe, B.; Dia, Nay; Van Malderghem, C.; Pothier, Joël; Van Vaerenbergh, J.,

  2021.

  First report of bacterial leaf spot of Hydrangea in retail nurseries in Belgium caused by strains assigned to a new Xanthomonas hortorum clade.

  New Disease Reports.

  43(2), pp. e12008.

  Available from: https://doi.org/10.1002/ndr2.12008

• Catara, Vittoria; Cubero, Jaime; Pothier, Joël; Bosis, Eran; Bragard, Claude; Đermić, Edyta; Holeva, Maria C.; Jacques, Marie-Agnès; Petter, Francoise; Pruvost, Olivier; Robène, Isabelle; Studholme, David J.; Tavares, Fernando; Vicente, Joana G.; Koebnik, Ralf; Costa, Joana,

  2021.

  Trends in molecular diagnosis and diversity studies for phytosanitary regulated Xanthomonas.

  Microorganisms.

  9(4), pp. 862.

  Available from: https://doi.org/10.3390/microorganisms9040862

• Fernandes, Camila; Martins, Leonor; Teixeira, Miguel; Blom, Jochen; Pothier, Joël; Fonseca, Nuno A.; Tavares, Fernando,

  2021.

  Comparative genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis strains isolated from a single walnut host tree.

  Microorganisms.

  9(3), pp. 624.

  Available from: https://doi.org/10.3390/microorganisms9030624

• Pothier, Joël F.; Kałużna, Monika; Prokić, Andjelka; Obradovic, Aleksa; Rezzonico, Fabio,

  2021.

  Complete genome and plasmid sequence data of three Xanthomonas arboricola pv. corylina strains, the bacterium responsible for bacterial blight of hazelnut.

  Phytopathology.

  112(4), pp. 956-960.

  Available from: https://doi.org/10.1094/PHYTO-08-21-0356-A

• Puławska, Joanna; Kałużna, Monika; Warabieda, Wojciech; Pothier, Joël F.; Gétaz, Michael; van der Wolf, Jan M.,

  2020.

  Transcriptome analysis of Xanthomonas fragariae in strawberry leaves.

  Scientific Reports.

  10(20582).

  Available from: https://doi.org/10.1038/s41598-020-77612-y

• Dia, Nay C.; Rezzonico, Fabio; Smits, Theo H. M.; Pothier, Joël F.,

  2020.

  Complete or high-quality draft genome sequences of six Xanthomonas hortorum strains sequenced with short- and long-read technologies.

  Microbiology Resource Announcements.

  9(41), pp. e00828-20.

  Available from: https://doi.org/10.1128/MRA.00828-20

• Martins, Leonor; Fernandes, Camila; Blom, Jochen; Dia, Nay C.; Pothier, Joël F.; Tavares, Fernando,

  2020.

  Xanthomonas euroxanthea sp. nov. : a new xanthomonad species including pathogenic and non-pathogenic strains of walnut.

  International Journal of Systematic and Evolutionary Microbiology.

  70(12), pp. 6024-6031.

  Available from: https://doi.org/10.1099/ijsem.0.004386

• Gétaz, Michael; Puławska, Joanna; Smits, Theo H.M.; Pothier, Joël F.,

  2020.

  Host–pathogen interactions between Xanthomonas fragariae and its host Fragaria × ananassa investigated with a dual RNA-Seq analysis.

  Microorganisms.

  8(8), pp. 1253.

  Available from: https://doi.org/10.3390/microorganisms8081253

• Gétaz, Michael; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2020.

  Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations.

  Phytopathology Research.

  2020(2), pp. 17.

  Available from: https://doi.org/10.1186/s42483-020-00061-y

• Rothen, Julian; Sapugahawatte, Dulmini Nanayakkara; Li, Carmen; Lo, Norman; Vogel, Guido; Foucault, Frédéric; Pflüger, Valentin; Pothier, Joël; Blom, Jochen; Daubenberger, Claudia; Ip, Margaret,

  2020.

  A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS.

  Scientific Reports.

  10(8788).

  Available from: https://doi.org/10.1038/s41598-020-65707-5

• Fossou, Romain K.; Pothier, Joël F.; Zézé, Adolphe; Perret, Xavier,

  2020.

  Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d’Ivoire.

  International Journal of Systematic and Evolutionary Microbiology.

  70(2), pp. 1421-1430.

  Available from: https://doi.org/10.1099/ijsem.0.003931

• Arn, Fabienne; Frasson, David; Kroslakova, Ivana; Rezzonico, Fabio; Pothier, Joël; Riedl, Rainer; Sievers, Martin,

  2020.

  Isolation and identification of actinomycetes strains from Switzerland and their biotechnological potential.

  Chimia.

  74(5), pp. 382-390.

  Available from: https://doi.org/10.2533/chimia.2020.382

• Schneeberger, Pierre H. H.; Fuhrimann, Samuel; Becker, Sören L.; Pothier, Joël F.; Duffy, Brion; Beuret, Christian; Frey, Jürg E.; Utzinger, Jürg,

  2019.

  Qualitative microbiome profiling along a wastewater system in Kampala, Uganda.

  Scientific Reports.

  9(1), pp. 17334.

  Available from: https://doi.org/10.1038/s41598-019-53569-5

• Luedin, Samuel M.; Storelli, Nicola; Danza, Francesco; Roman, Samuele; Wittwer, Matthias; Pothier, Joël F.; Tonolla, Mauro,

  2019.

  Mixotrophic growth under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum".

  Frontiers in Microbiology.

  10(384).

  Available from: https://doi.org/10.3389/fmicb.2019.00384

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H.M.,

  2019.

  Comparative genomic analysis of the biotechnological potential of the novel species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T.

  Diversity.

  2019(11), pp. 204.

  Available from: https://doi.org/10.3390/d11110204

• Ruinelli, Michela; Blom, Jochen; Smits, Theo; Pothier, Joël,

  2019.

  Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp.

  BMC Genomics.

  20(172).

  Available from: https://doi.org/10.1186/s12864-019-5555-y

• Luedin, Samuel; Liechti, Nicole; Cox, Raymond P.; Danza, Francesco; Frigaard, Niels-Ulrik; Posth, Nicole; Pothier, Joël F.; Roman, Samuele; Storelli, Nicola; Wittwer, Matthias; Tonolla, Mauro,

  2019.

  Draft genome sequence of Chromatium okenii isolated from the stratified alpine Lake Cadagno.

  Scientific Reports.

  9(1), pp. 1936.

  Available from: https://doi.org/10.1038/s41598-018-38202-1

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H. M.,

  2019.

  High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T.

  Microbiology Resource Announcements.

  8(3).

  Available from: https://doi.org/10.1128/MRA.01502-18

• Rothen, Julian; Pothier, Joël F.; Foucault, Frédéric; Blom, Jochen; Nanayakkara, Dulmini; Li, Carmen; Ip, Margaret; Tanner, Marcel; Vogel, Guido; Pflüger, Valentin; Daubenberger, Claudia A.,

  2019.

  Subspecies typing of Streptococcus agalactiae based on ribosomal subunit protein mass variation by MALDI-TOF MS.

  Frontiers in Microbiology.

  10(471).

  Available from: https://doi.org/10.3389/fmicb.2019.00471

• Smits, Theo H.M.; Rezzonico, Fabio; Frasson, David; Vesga, Pilar; Vacheron, Jordan; Blom, Jochen; Pothier, Joël F.; Keel, Christoph; Maurhofer, Monika; Sievers, Martin,

  2019.

  Updated genome sequence and annotation for the full genome of Pseudomonas protegens CHA0.

  Microbiology Resource Announcements.

  8(39).

  Available from: https://doi.org/10.1128/MRA.01002-19

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël; Smits, Theo,

  2018.

  High-quality draft genome sequence of pseudomonas wadenswilerensis CCOS 864T.

  Microbiology Resource Announcements.

  7(16).

  Available from: https://doi.org/10.1128/MRA.01059-18

• Fernandes, Camila; Blom, Jochen; Pothier, Joël F.; Tavares, Fernando,

  2018.

  High-quality draft genome sequence of xanthomonas arboricola pv. juglandis CPBF 1521, isolated from leaves of a symptomatic walnut tree in Portugal without a past of phytosanitary treatment.

  Microbiology Resource Announcements.

  7(16).

  Available from: https://doi.org/10.1128/MRA.00887-18

• Fernandes, Camila; Blom, Jochen; Pothier, Joël F.; Tavares, Fernando,

  2018.

  High-Quality draft genome sequence of xanthomonas sp. strain CPBF 424, a walnut-pathogenic strain with atypical features.

  Microbiology Resource Announcements.

  7(15).

  Available from: https://doi.org/10.1128/MRA.00921-18

• Normand, Philippe; Nouioui, Imen; Pujic, Petar; Fournier, Pascale; Dubost, Audrey; Schwob, Guillaume; Klenk, Hans-Peter; Nguyen, Agnès; Abrouk, Danis; Herrera-Belaroussi, Aude; Pothier, Joël F.; Pflüger, Valentin; Fernandez, Maria P.,

  2018.

  Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa.

  International Journal of Systematic and Evolutionary Microbiology.

  68, pp. 3001-3011.

  Available from: https://doi.org/10.1099/ijsem.0.002939

• Luedin, Samuel M.; Pothier, Joël F.; Danza, Francesco; Storelli, Nicola; Frigaard, Niels-Ulrik; Wittwer, Matthias; Tonolla, Mauro,

  2018.

  Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

  Standards in Genomic Sciences.

  13(14).

  Available from: https://doi.org/10.1186/s40793-018-0317-z

• Knecht, Leandra E.; Born, Yannick; Pothier, Joël F.; Loessner, Martin J.; Fieseler, Lars,

  2018.

  Complete genome sequences of erwinia amylovora phages vB_EamP-S2 and vB_EamM-Bue1.

  Microbiology Resource Announcements.

  7(3).

  Available from: https://doi.org/10.1128/MRA.00891-18

• Gétaz, Michael; Krijger, Marjon; Rezzonico, Fabio; Smits, Theo; van der Wolf, Jan M.; Pothier, Joël F.,

  2018.

  Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description.

  Microbial Genomics.

  4(7).

  Available from: https://doi.org/10.1099/mgen.0.000189

• Gétaz, Michael; Baeyen, Steve; Blom, Jochen; Maes, Martine; Cottyn, Bart; Pothier, Joël F.,

  2018.

  High-quality draft genome sequences of five xanthomonas arboricola pv. fragariae isolates.

  Genome Announcements.

  6(7).

  Available from: https://doi.org/10.1128/genomeA.01585-17

• Rezzonico, Fabio; Duffy, Brion; Smits, Theo H.M.; Pothier, Joël F.,

  2017.

  Erwinia species identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry.

  Journal of Plant Pathology.

  99(Special issue), pp. 121-129.

  Available from: https://doi.org/10.4454/jpp.v99i0.3916

• Gétaz, Michael; Bühlmann, Andreas; Schneeberger, Pierre H. H.; Van Malderghem, Cinzia; Duffy, Brion; Maes, Martine; Pothier, Joël F.; Cottyn, Bart,

  2017.

  A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics.

  Plant Pathology.

  66(7), pp. 1094-1102.

  Available from: https://doi.org/10.1111/ppa.12665

• Kamber, Tim; Pothier, Joël; Pelludat, Cosima; Rezzonico, Fabio; Duffy, Brion; Smits, Theo,

  2017.

  Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host.

  BMC Genomics.

  16(628), pp. 1-12.

  Available from: https://doi.org/10.1186/s12864-017-4010-1

• Gétaz, Michael; van der Wolf, Jan; Blom, Jochen; Pothier, Joël F.,

  2017.

  Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants.

  Genome Announcements.

  5(32).

  Available from: https://doi.org/10.1128/genomeA.00642-17

• Ruinelli, Michela; Blom, Jochen; Pothier, Joël F.,

  2017.

  Complete genome sequence of Pseudomonas viridiflava CFBP 1590: isolated from diseased cherry in France.

  Genome Announcements.

  5(30).

  Available from: https://doi.org/10.1128/genomeA.00662-17

• Rothen, Julian; Schindler, Tobias; Pothier, Joël F.; Younan, Mario; Certa, Ulrich; Daubenberger, Claudia; Pflüger, Valentin; Jores, Joerg,

  2017.

  Draft genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius at the horn of Africa.

  Genome Announcements.

  5(28).

  Available from: https://doi.org/10.1128/genomeA.00525-17

• Schneeberger, Pierre H.H.; Pothier, Joël F.; Bühlmann, Andreas; Duffy, Brion; Beuret, Christian; Utzinger, Jürg; Frey, Jürg E.,

  2017.

  Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection.

  PLOS ONE.

  12(5).

  Available from: https://doi.org/10.1371/journal.pone.0178195

• Kałużna, Monika; Willems, Anne; Pothier, Joël F.; Ruinelli, Michela; Sobiczewski, Piotr; Puławska, Joanna,

  2016.

  Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry.

  Systematic and Applied Microbiology.

  39(6), pp. 370-377.

  Available from: https://doi.org/10.1016/j.syapm.2016.05.005

• Ruinelli, Michela; Schneeberger, Pierre H.H; Ferrante, Patrizia; Bühlmann, Andreas; Scortichini, Marco; Vanneste, Joel L.; Duffy, Brion; Pothier, Joël F.,

  2016.

  Comparative genomics-informed design of two LAMP detection assays for detection of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae and discrimination of isolates belonging to the pandemic biovar 3.

  Plant Pathology.

  66(1), pp. 140-149.

  Available from: https://doi.org/10.1111/ppa.12551

• Schneeberger, Pierre H.H.; Becker, Sören L.; Pothier, Joël F.; Duffy, Brion; N'Goran, Eliézer K.; Beuret, Christian; Frey, Jürg E.; Utzinger, Jürg,

  2016.

  Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study.

  Infection, Genetics and Evolution.

  40, pp. 389-397.

  Available from: https://doi.org/10.1016/j.meegid.2015.08.044

• Puławska, Joanna; Kuzmanović, Nemanja; Willems, Anne; Pothier, Joël F.,

  2016.

  Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks.

  Systematic and Applied Microbiology.

  39(3), pp. 164-169.

  Available from: https://doi.org/10.1016/j.syapm.2016.03.002

• Kamber, Tim; Buchmann, Jan P.; Pothier, Joël; Smits, Theo; Wicker, Thomas; Duffy, Brion,

  2016.

  Fire blight disease reactome : RNA-seq transcriptional profile of apple host plant defence responses to Erwinia amylovora pathogen infection.

  Scientific Reports.

  6(21600).

  Available from: https://doi.org/10.1038/srep21600

• Konavko, Dmitrijs; Malchev, Svetoslav; Pothier, Joël F.; Jundzis, Māris; Moročko-Bičevska, Inga; Rezzonico, Fabio,

  2016.

  Diversity and host range of Pseudomonas in fruit tree species in Latvia.

  Acta Horticulturae.

  1149, pp. 25-30.

  Available from: https://doi.org/10.17660/ActaHortic.2016.1149.5

• Smits, Theo H. M.; Pothier, Joël F.; Ruinelli, Michela; Blom, Jochen; Frasson, David; Koechli, Chantal; Fabbri, Carlotta; Brandl, Helmut; Duffy, Brion; Sievers, Martin,

  2015.

  Complete genome sequence of the cyanogenic phosphate-solubilizing Pseudomonas sp. strain CCOS 191 : a close relative of Pseudomonas mosseli.

  Genome Announcements.

  3(3).

  Available from: https://doi.org/10.1128/genomeA.00616-15

• Palacio-Bielsa, Ana; López-Soriano, Pablo; Bühlmann, Andreas; van Doorn, Joop; Pham, Khanh; Cambra, Miguel A.; Berruete, Isabel M.; Pothier, Joël F.; Duffy, Brion; Olmos, Antonio; López, María M.,

  2015.

  Evaluation of a real-time PCR and a loop-mediated isothermal amplification for detection of Xanthomonas arboricola pv. pruni in plant tissue samples.

  Journal of Microbiological Methods.

  112, pp. 36-39.

  Available from: https://doi.org/10.1016/j.mimet.2015.03.005

• Ziegler, Dominik; Pothier, Joël F.; Ardley, Julie; Kouakou Fossou, Romain; Pflüger, Valentin; de Meyer, Sofie; Vogel, Guido; Tonolla, Mauro; Howieson, John; Reeve, Wayne; Perret, Xavier,

  2015.

  Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS.

  Applied Microbiology and Biotechnology.

  99(13), pp. 5547-5562.

  Available from: https://doi.org/10.1007/s00253-015-6515-3

• Brankatschk, Kerstin; Kamber, Tim; Pothier, Joël F.; Duffy, Brion; Smits, Theo H.M.,

  2014.

  Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization.

  Microbial Biotechnology.

  7(6), pp. 528-544.

  Available from: https://doi.org/10.1111/1751-7915.12104

• Bühlmann, Andreas; Dreo, Tanja; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H. M.; Ravnikar, Maja; Frey, Jürg E.; Duffy, Brion,

  2014.

  Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

  Environmental Microbiology.

  16(7), pp. 2112-2125.

  Available from: https://doi.org/10.1111/1462-2920.12289

• van der Wolf, Jan M.; Nijhuis, Els H.; Kowalewska, Malgorzata J.; Saddler, Gerry S.; Parkinson, Neil; Elphinstone, John G.; Pritchard, Leighton; Toth, Ian K.; Lojkowska, Ewa; Potrykus, Marta; Waleron, Malgorzata; de Vos, Paul; Cleenwerck, Ilse; Pirhonen, Minna; Garlant, Linda; Hélias, Valérie; Pothier, Joël F.; Pflüger, Valentin; Duffy, Brion; Tsror, Leah; Manulis, Shula,

  2014.

  Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).

  International Journal of Systematic and Evolutionary Microbiology.

  64, pp. 768-774.

  Available from: https://doi.org/10.1099/ijs.0.052944-0

• Vandroemme, Joachim; Cottyn, Bart; Pothier, Joël F.; Pflüger, Valentin; Duffy, Brion; Maes, Martine,

  2013.

  Xanthomonas arboricola pv. fragariae : what's in a name?.

  Plant Pathology.

  62(5), pp. 1123-1131.

  Available from: https://doi.org/10.1111/ppa.12028

• Socquet-Juglard, Didier; Duffy, Brion; Pothier, Joël F.; Christen, Danilo; Gessler, Cesare; Pattochi, Andrea,

  2013.

  Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot.

  Tree Genetics & Genomes.

  9(2), pp. 409-421.

  Available from: https://doi.org/10.1007/s11295-012-0562-z

• Bühlmann, Andreas; Pothier, F.; Rezzonico, Fabio; Smits, Theo H. M.; Andreou, Michael; Boonham, Neil; Duffy, Brion; Frey, Jürg E.,

  2013.

  Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.

  Journal of Microbiological Methods.

  92(3), pp. 332-339.

  Available from: https://doi.org/10.1016/j.mimet.2012.12.017

• Socquet-Juglard, Didier; Kamber, Tim; Pothier, Joël F.; Christen, Danilo; Gessler, Cesare; Duffy, Brion; Patocchi, Andrea,

  2013.

  Comparative RNA-Seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.

  PLOS ONE.

  8(1).

  Available from: https://doi.org/10.1371/journal.pone.0054196

• Bühlmann, Andreas; Pothier, Joël F.; Tomlinson, Jennifer A.; Frey, Jürg F.; Boonham, N.; Smits, Theo H.M.; Duffy, Brion,

  2012.

  Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level.

  Plant Pathology.

  62(2), pp. 475-484.

  Available from: https://doi.org/10.1111/j.1365-3059.2012.02654.x

• Kaufmann, Moritz; Schüle, Martin; Smits, Theo; Pothier, Joël,

  2020.

  Typing plasmids with distributed sequence representation [paper].

  In:

  Schilling, Frank-Peter; Stadelmann, Thilo, eds.,

  Artificial Neural Networks in Pattern Recognition.

  9th IAPR TC 3 Workshop on Artificial Neural Networks for Pattern Recognition (ANNPR'20), Winterthur, Switzerland, 2-4 September 2020.

  Cham:

  Springer.

  pp. 200-210.

  Lecture Notes in Computer Science ; 12294.

  Available from: https://doi.org/10.1007/978-3-030-58309-5_16

• Kałużna, Monika; Willems, Anne; Pothier, Joël F.; Ruinelli, Michela; Sobiczewski, Piotr; Puławska, Joanna,

  2016.

  Characterization and genetic diversity of causal agent of stone fruit bacterial canker Pseudomonas cerasi : a new pathogen of cherry [paper].

  In:

  II International Workshop on Bacterial Diseases of Stone Fruits and Nuts.

  II International Workshop on Bacterial Diseases of Stone Fruits and Nuts, Izmir, Turkey, 21 April 2015.

  International Society for Horticultural Science.

  pp. 9-14.

  Available from: https://doi.org/10.17660/ActaHortic.2016.1149.2

• Aspin, Andrew; Cole, Jennifer; Pothier, Joël,

  2023.

  PM 7/65 (2) Xanthomonas fragariae.

  EPPO Bulletin

  ; 53(2).

  Wiley.

  Available from: https://doi.org/10.1111/epp.12916

• Costa, Joana; Pothier, Joël F.; Boch, Jens; Stefani, Emilio; Koebnik, Ralf,

  2022.

  Integrating science on Xanthomonas and Xylella for integrated plant disease management.

  Microorganisms.

  11(1), pp. 6.

  Available from: https://doi.org/10.3390/microorganisms11010006

• Costa, Joana; Pothier, Joël F.; Boch, Jens; Stefani, Emilio; Jacques, Marie-Agnès; Catara, Vittoria; Koebnik, Ralf,

  2021.

  Integrating science on Xanthomonadaceae for sustainable plant disease management in Europe.

  Molecular Plant Pathology.

  22(12), pp. 1461-1463.

  Available from: https://doi.org/10.1111/mpp.13150

• Stefani, Emilio; Loreti, Stefania; Costa, Joana; Cunty, Amandine; Pothier, Joël F.,

  2021.

  PM 7/120 (2) Pseudomonas syringae pv. actinidiae.

  EPPO Bulletin

  ; 51(3).

  Wiley.

  Available from: https://doi.org/10.1111/epp.12782

• Saponari, Maria; Gétaz, Michael; Palkovics, László; Kuzmanović, Nemanja; Puławska, Joanna; Ruinelli, Michela; Pothier, Joël; Obradović, Aleksa; Boscia, Donato; Végh, Anita; Kałużna, Monika,

  2017.

  Bacterial diseases

  .

  In:

  Quero-García, José; Iezzoni, Amy; Puławska, Joanna; Lang, Gregory, eds.,

  Cherries : botany, production and uses.

  Wallingford:

  CAB International.

Publications before appointment at the ZHAW

Cesbron S., Pothier J., Gironde S., Jacques M.-A., Manceau C. (2014). Development of multilocus variable-number tandem repeat analysis (MLVA) for Xanthomonas arboricola pathovars. Journal of Microbiological Methods. 100, 84-90.

Brankatschk K., Kamber T., Pothier J.F., Duffy B., Theo HM Smits T.H.M. (2014). Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization. Microbial biotechnology. 7, 528-544.

Palacio-Bielsa A., Pothier J.F., Roselló M., Duffy B., López M.M. (2012). Xanthomonas arboricola pv. pruni detection and identification methods. Journal of Plant Pathology. 94, S1.135-S1.146.

Campillo T., Lavire C., Malek S., Pothier J.F., Pulawska J. (2012). Tumorigenic Agrobacterium spp. Journal of Plant Pathology. 94, S1.97-S1.104.

Socquet-Juglard D., Patocchi A., Pothier J.F., Christen D., Duffy B. (2012). Evaluation of Xanthomonas arboricola pv. pruni inoculation techniques to screen for bacterial spot resistance in apricot. Journal of Plant Pathology. 94, S1.91-S1.96.

Bergsma-Vlami M., Martin W., Koenraadt H., Teunissen H., Pothier J.F., Duffy B., van Doorn J. (2012). Molecular typing of Dutch isolates of Xanthomonas arboricola pathovar pruni isolated from ornamental cherry laurel. Journal of Plant Pathology. 94, S1.29-S1.35.

Frappoli M.*, Pothier J.F.*, Défago G., Moënne-Loccoz Y. (2012). Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads. Molecular Phylogenetics and Evolution. 63, 877-890.
*Contributed equally as first authors

Hajri A., Pothier J.F., Fischer-Le Saux M., Bonneau S., Poussier S., Boureau T., Duffy B., Manceau C. (2012). Type three effector genes distribution and sequence analysis provides new insights into pathogenicity of plant pathogenic Xanthomonas arboricola. Applied and Environmental Microbiology. 78, 371-374.

Pothier J.F., Vorhölter F.-J., Blom J., Goesmann A., Pühler A., Smits T.H.M., Duffy B. (2011). The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. FEMS Microbiology Letters. 323, 52-60.

Pothier J.F.*, Pagani M.C.*, Pelludat C., Ritchie D.F., Duffy B. (2011). A duplex-PCR method for species- and pathovar-level identification and detection of the quarantine plant pathogen Xanthomonas arboricola pv. pruni. Journal of Microbiological Methods. 86, 16-24.
*Contributed equally as first authors

Combes-Meynet E., Pothier J.F., Moënne-Loccoz Y., Prigent-Combaret C. (2011). The Pseudomonas secondary metabolite 2,4-diacetylphloroglucinol is a signal inducing rhizoplane expression of Azospirillum genes involved in plant-growth promotion. Molecular Plant-Microbe Interactions, 24, 271-284.

Couillerot O., Combes-Meynet E., Pothier J.F., Bellvert F., Challita E., Poirier M.-A., Rohr R., Comte G. Moënne-Loccoz Y., Prigent-Combaret C. (2011). Role of the antimicrobial compound 2,4-diacetylphloroglucinol in the impact of biocontrol Pseudomonas fluorescens F113 on Azospirillum brasilense phytostimulators. Microbiology. 157, 1694-1705.

Pothier J.F., Pelludat C., Bünter M., Genini M., Vogelsanger J., Holliger E., Duffy B. (2010). First report of the quarantine pathogen Xanthomonas arboricola pv. pruni on apricot and plum in Switzerland. Plant Pathology. 59, 404.

Pothier J.F., Prigent-Combaret C., Haurat J., Moënne-Loccoz Y., Wisniewski-Dyé F. (2008). Functional duplication of plasmid-borne nitrite reductase gene nirK in the wheat-associated plant growth-promoting rhizobacterium Azospirillum brasilense Sp245. Molecular Plant-Microbe Interactions. 21, 831-842.

Prigent-Combaret C., Blaha D., Pothier J.F., Poirier M.A., Vial L., Wisniewski F., Bally R., Moënne-Loccoz Y. (2008). Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria. FEMS Microbiology Ecology. 65, 202-219.

Pothier J.F., Prigent-Combaret C., Weiss M., Wisniewski-Dyé F., Moënne-Loccoz Y. (2007). Promoter trap identification of wheat seed extract-induced genes in the plant growth-promoting rhizobacterium Azospirillum brasilense Sp245. Microbiology. 153, 3608-3622.

Vial L., Pothier J.F., Normand P., Moënne-Loccoz Y., Bally R., Wisnievski-Dyé F. (2004). Construction of a recA mutant of Azospirillum lipoferum and involvement of recA in phase variation. FEMS Microbiology Letter. 236, 291-299.

Other publications

ORCID ID: orcid.org/0000-0002-9604-7780

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