publications

2025

1. Year-long, multiple-timepoint field studies show the importance of spatiotemporal dynamics and microbial functions in agricultural soil microbiomes

   Lisa Joos, Sarah Ommeslag, Steve Baeyen, Wouter Asselberg, {Koen Van} Loo, Lieven Clement, Jane Debode, Bart Vandecasteele, and {Caroline De} Tender

   mSystems, Jul 2025

   Abs DOI

   Despite the recognition of the complexity of soil ecosystem dynamics, most soil microbiome studies sample one field, take one sample per field, or use limited samples throughout the year. This limits our understanding of the spatiotemporal role of the soil microbiome in relation to management practices. To address these limitations, we conducted a year-long investigation of the soil microbiome in two agricultural fields, sampling multiple plots at different soil depths every 5 weeks. We examined spatial and temporal variabilities in response to the application of organic amendments (one-time biochar and annual compost application) on bacterial and fungal communities, studying both the microbial composition (metabarcoding, phospholipid fatty acids [PLFA], hot-water extractable-carbon) and activity (metatranscriptomics). Indicated by metabarcoding and PLFA, fungal communities were less affected over time per field, whereas bacteria exhibited more pronounced temporal trends. In contrast, fungi displayed clear spatial effects, while bacterial spatial differences within the field were predominantly observed in the deeper soil layer. Effects on functional roles and metabolic processes of the active microbial community were mainly related to temporal trends, especially in the topsoil. Organic amendments did not affect the microbial activity and affected fewer than 2 emphasizing the importance of field-specific factors, sampling depth, and community type. This ushers in the need for a well-considered experimental design and sampling strategy that accounts for spatiotemporal trends.IMPORTANCE This study addresses a critical gap in soil microbiome research by investigating spatiotemporal effects on soil bacterial and fungal composition and activity in relation to field management practices. Moving beyond single-field and limited sampling approaches, this research conducted monthly sampling events on two fields at various depths. By combining metabarcoding, phospholipid fatty acid analysis, and metatranscriptomics, the study examined bacterial and fungal community composition, biomass, and functionality. Key findings reveal distinct responses of bacterial and fungal communities to spatiotemporal variability and management practices. Functional categories were predominantly driven by temporal trends rather than compost amendments. Temporal changes were more pronounced in the topsoil. These insights into the complex interactions between soil microbial communities, management practices, and spatiotemporal dynamics contribute significantly to soil microbiome research and sampling strategies.

2024

1. The “Key” to Bringing DNA Collections to the Next Level: A DiSSCo Flanders Working Group Product

   Emily Veltjen, Pieter Asselman, Wim Baert, Steve Baeyen, Lise Beirinckx, Liselot Breyne, Dimitri Brosens, Tim Claerhout, Sari Cogneau, Karen Cox, Laura Cuypers, Lynn Delgat, Philippe Desmeth, Jordi Raad, Lore Esselens, Maria-Rose Eves Down, Frederik Leliaert, Kenny Meganck, Zjef Pereboom, Nathalie Smitz, Gontran Sonet, Maarten Trekels, An Vanden Broeck, Charlotte Van Driessche, and Aaike De Wever

   Biodiversity Information Science and Standards, Nov 2024

   DOI
2. The key to bringing DNA collections to the next level

   Emily Veltjen, Pieter Asselman, Wim Baert, Steve Baeyen, Lise Beirinckx, Liselot Breyne, Dimitri Brosens, Tim Claerhout, Sari Cogneau, Karen Cox, Laura Cuypers, Lynn Delgat, Philippe Desmeth, Jordi Raad, Lore Esselens, Maria-Rose Eves Down, Philippe Helsen, Frederik Leliaert, Kenny Meganck, Zjef Pereboom, Nathalie Smitz, Gontran Sonet, Maarten Trekels, An Vanden Broeck, Charlotte Van Driessche, and Aaike De Wever

   Research Ideas and Outcomes, Nov 2024

   DOI
3. Snakemake workflow for Illumina bacterial assembly and QC

   Steve Baeyen

   Nov 2024

   DOI
4. Snakemake workflow for Nanopore-only bacterial assembly and QC

   Steve Baeyen

   Nov 2024

   DOI
5. Snakemake workflow for bacterial assembly QC

   Steve Baeyen

   Nov 2024

   DOI
6. Snakemake workflow for bacterial assembly QC

   Steve Baeyen

   Nov 2024

   DOI
7. Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum

   E. Osdaghi, S.M. Taghavi, M. Hamidizade, M. Kariminejhad, A. Fazliarab, H. Hajian Maleki, S. Baeyen, G. Taghouti, M.-A. Jacques, J. Van Vaerenbergh, and P. Portier

   Systematic and Applied Microbiology, Nov 2024

2023

1. Presence of Curtobacterium flaccumfaciens in Belgian and Dutch greenhouse poinsettia production – Ruining the Christmas spirit?

   Jolien Venneman, M.J.C. Pel, J.L.J. Bilt}, Cinzia {Van Malderghem}, Margo {De Smet}, Steve Baeyen, and Johan {Van Vaerenbergh}

   Aug 2023

   12th International Congress of Plant Pathology (ICPP) ; Conference date: 20-08-2023 Through 25-08-2023
2. The fate of Xylella fastidiosa in common woody plant species in Belgium.

   Jolien Venneman, Cinzia {Van Malderghem}, Paul Quataert, Brigitte {De Paepe}, Yannick {Van Moerkercke}, Steve Baeyen, and Johan {Van Vaerenbergh}

   Aug 2023

   4th European Conference on Xylella fastidiosa ; Conference date: 20-08-2023
3. Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses

   K.J. Fortuna, D. Holtappels, J. Venneman, S. Baeyen, M. Vallino, P. Verwilt, H. Rediers, B. De Coninck, M. Maes, J. Van Vaerenbergh, R. Lavigne, and J. Wagemans

   Applied and Environmental Microbiology, Aug 2023
4. First Report of Black Rot Disease in Eruca vesicaria subsp. sativa Caused by Xanthomonas campestris pv. campestris in Belgium

   D. Holtappels, B. De Paepe, C. Malderghem, S. Baeyen, J. Venneman, J. Wagemans, and J. Van Vaerenbergh

   Plant Disease, Aug 2023

2022

1. Exploring Acidovorax strains causing leaf spot on Calathea.

   Johan {Van Vaerenbergh}, Jolien Venneman, Brigitte {De Paepe}, Cinzia {Van Malderghem}, and Steve Baeyen

   Jul 2022

   14th International Conference on Plant Pathogenic Bacteria (ICPPB) ; Conference date: 03-07-2022 Through 08-07-2022
2. Uncommon Curtobacterium flaccumfaciens pathovars revive in other plant hosts: pv. betae in sugar beet and pv. oortii in garden lily.

   Johan {Van Vaerenbergh}, Jolien Venneman, Brigitte {De Paepe}, Cinzia {Van Malderghem}, Steve Baeyen, and A. Wauters

   Jul 2022

   14th International Conference on Plant Pathogenic Bacteria (ICPPB) ; Conference date: 03-07-2022 Through 08-07-2022
3. The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development

   Dominique Holtappels, Kiandro J. Fortuna, Lauren Moons, Nand Broeckaert, Léon E. Bäcker, Sofie Venneman, Sofie Rombouts, Louis Lippens, Steve Baeyen, Sabien Pollet, Jean-Paul Noben, Frank Oechslin, Marta Vallino, Abram Aertsen, Martine Maes, Johan Van Vaerenbergh, Rob Lavigne, and Jeroen Wagemans

   Microbial Biotechnology, Jan 2022

   DOI
4. Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description

   B. Lebas, I. Adams, M. Al Rwahnih, S. Baeyen, G. Bilodeau, A.G. Blouin, N. Boonham, T. Candresse, A. Chandelier, K. De Jonghe, A. Fox, Y.Z.A. Gaafar, P. Gentit, A. Haegeman, W. Ho, O. Hurtado-Gonzales, W. Jonkers, J. Kreuze, D. Kutjnak, B. Landa, M. Liu, F. Maclot, M. Malapi-Wight, H.J. Maree, F. Martoni, N. Mehle, A. Minafra, D. Mollov, A. Moreira, M. Nakhla, F. Petter, A.M. Piper, J. Ponchart, R. Rae, B. Remenant, Y. Rivera, B. Rodoni, J. Roenhorst, J. Rollin, P. Saldarelli, J. Santala, R. Souza-Richards, D. Spadaro, D.J. Studholme, S. Sultmanis, R. Vlugt, L. Tamisier, C. Trontin, I. Vazquez-Iglesias, C.S.L. Vicente, B.T.L.H. Vossenberg, T. Wetzel, H. Ziebell, and S. Massart

   EPPO Bulletin, Jan 2022
5. Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

   S. Massart, I. Adams, M. Al Rwahnih, S. Baeyen, G.J. Bilodeau, A.G. Blouin, N. Boonham, T. Candresse, A. Chandellier, K. De Jonghe, A. Fox, Y.Z.A. Gaafar, P. Gentit, A. Haegeman, W. Ho, O. Hurtado-Gonzales, W. Jonkers, J. Kreuze, D. Kutjnak, B.B. Landa, M. Liu, F. Maclot, M. Malapi-Wight, H.J. Maree, F. Martoni, N. Mehle, A. Minafra, D. Mollov, A.G. Moreira, M. Nakhla, F. Petter, A.M. Piper, J.P. Ponchart, R. Rae, B. Remenant, Y. Rivera, B. Rodoni, M. Botermans, J.W. Roenhorst, J. Rollin, P. Saldarelli, J. Santala, R. Souza-Richards, D. Spadaro, D.J. Studholme, S. Sultmanis, R. Vlugt, L. Tamisier, C. Trontin, I. Vazquez-Iglesias, C.S.L. Vicente, B.T.L.H. Vossenberg, M. Westenberg, T. Wetzel, H. Ziebell, and B.S.M. Lebas

   Peer Community Journal, Jan 2022
6. Promising epiphytic antagonistic Pseudomonas strains from the Citrus phyllosphere in the biocontrol of Pseudomonas syringae pv. syringae, causing bacterial citrus blast and black pit

   E. Abdellatif, A. Mikici?ski, M. Ka?u?na, B.A. Bahri, A. Mougou-Hamdane, J. Vaerenberg, S. Baeyen, A. Rhouma, and J.D. Janse

   Journal of Plant Pathology, Jan 2022

2021

1. Effects of bioavailable phosphorus and soil biota on typical Nardus grassland species in competition with fast-growing plant species

   S. Schelfhout, S. Wasof, J. Mertens, M. Vanhellemont, A. Demey, A. Haegeman, E. DeCock, I. Moeneclaey, P. Vangansbeke, N. Viaene, S. Baeyen, N. De Sutter, M. Maes, W.H. Putten, K. Verheyen, and A. De Schrijver

   Ecological Indicators, Jan 2021

2020

1. Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

   Lisa Joos, Stien Beirinckx, Annelies Haegeman, Jane Debode, Bart Vandecasteele, Steve Baeyen, Sofie Goormachtig, Lieven Clement, and Caroline De Tender

   BMC Genomics, Oct 2020

   DOI
2. Phylogenetic, genetic, and phenotypic diversity of Pseudomonas syringae pv. syringae strains isolated from citrus blast and black pit in Tunisia

   Emna Abdellatif, Monika Kałużna, Patrizia Ferrante, Marco Scortichini, Bochra Bahri, Jaap D. Janse, Johan Vaerenberg, Steve Baeyen, Piotr Sobiczewski, and Ali Rhouma

   Plant Pathology, Aug 2020

   DOI
3. Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers

   Lonneke Onrust, Steve Baeyen, Freddy Haesebrouck, Richard Ducatelle, and Filip Van Immerseel

   Veterinary Research, Apr 2020

   DOI

2019

1. Differential efficiency of wild type rhizogenic strains for rol gene transformation of plants

   Siel Desmet, Ellen De Keyser, Johan Van Vaerenbergh, Steve Baeyen, Johan Van Huylenbroeck, Danny Geelen, and Emmy Dhooghe

   Applied Microbiology and Biotechnology, Jul 2019

   DOI

2018

1. Reduced-Particle-Size Wheat Bran Is Efficiently Colonized by a Lactic Acid-Producing Community and Reduces Levels of Enterobacteriaceae in the Cecal Microbiota of Broilers

   Karen Vermeulen, Joran Verspreet, Christophe M. Courtin, Freddy Haesebrouck, Steve Baeyen, Annelies Haegeman, Richard Ducatelle, and Filip Van Immerseel

   Applied and Environmental Microbiology, Nov 2018

   DOI
2. High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae Isolates

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

   Genome Announcements, Feb 2018

   DOI

2017

1. Pathogenicity and virulence gene content of Xanthomonas strains infecting Araceae, formerly known as Xanthomonas axonopodis pv. dieffenbachiae

   E. C. Constantin, A. Haegeman, J. Van Vaerenbergh, S. Baeyen, C. Van Malderghem, M. Maes, and B. Cottyn

   Plant Pathology, Mar 2017

   DOI
2. EFFECT OF FOOD-BORNE FUSARIUM MYCOTOXINS ON THE GUT MICROBIOME COMPOSITION IN BROILER CHICKENS AND IN PIGS

   Gunther Antonissen, Filip {Van Immerseel}, A. Michiels, Venessa Eeckhaut, K. Vermeulen, N. Reisinger, Steve Baeyen, Annelies Haegeman, K Audenaert, Sarah {De Saeger}, Dominiek Maes, Freddy Haesebrouck, Richard Ducatelle, and Siska Croubels

   Sep 2017

   abstract for the first MycoKey international Conferenceheld in Ghent, Belgium from 11 to 14 September 2017; 1st MycoKey International Conference ; Conference date: 11-09-2017 Through 14-09-2017

   Abs

   The mycotoxins deoxynivalenol (DON) and fumonisins (FBs) exert toxicity toward the intestinal epithelial barrier and immune system. Besides, following ingestion of contaminated feed, the intestinal microbiota will be exposed to these toxins. The gut harbours a complex community of over trillions microbial cells which influence animal physiology, metabolism, nutrition and immune function, while disruption of the gut microbiota has been linked with poor intestinal health. The aim of this presentation is to discuss comparatively the impact of mycotoxins on intestinal microbiota composition in broiler chickens and pigs. In a first study, the impact of DON and FBs on the composition of the intestinal microbiota in broiler chickens of different ages was assessed. Chickens of 1 day old were fed either a control diet, a DON contaminated diet (3.3-3.7 mg DON/kg feed) or a FBs contaminated diet (15.5-18.3 mg FB1+FB2/kg feed). Subsequently, after a feeding period of one, three and five weeks chickens were euthanized and ileal and caecal content samples were collected. In a second study, the impact of DON and its acetylated forms on the gut microbiome in piglets of 3 weeks old was investigated. Piglets were fed either a control diet or a DON contaminated diet (0.4 mg DON, 0.3 mg 3-acetylDON, and 0.8 mg 15-acetylDON/kg feed) for 5 weeks. Following euthanasia, colon content samples were collected. Intestinal microbiome profiling was performed by next-generation sequencing of 16S ribosomal DNA. The hyper-variable V4 region was amplified by using the 515F-806R primer set, and the amplicon library was prepared with Nextera adaptors. Subsequently, PCR fragments were sequenced by MiSeq Illumina sequencing (96 samples per lane, 2x300bp 5Gb raw data per lane). The results showed that the impact of DON and FBs on the intestinal microbiota is species- and age-dependent. Mycotoxin exposure modulated the abundance of several members of the family of Lachnospiraceae, Ruminococcacceae, Peptococaceae, Coriobacteriaceae, Bifidobacteriaceae, Clostridiaceae, and Veillonellaceae. Several of the affected microbial genera are involved in the production of short-chain fatty acids such as butyric acid.

2015

1. Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex

   E. C. Constantin, I. Cleenwerck, M. Maes, S. Baeyen, C. Van Malderghem, P. De Vos, and B. Cottyn

   Plant Pathology, Oct 2015

   DOI
2. Isolation and characterization of Pseudomonas syringae pv. porri from leek in Flanders

   S. Rombouts, J. Van Vaerenbergh, A. Volckaert, S. Baeyen, T. De Langhe, B. Declercq, R. Lavigne, and M. Maes

   European Journal of Plant Pathology, Sep 2015

   DOI
3. Effects of biochar addition on bacterial populations of the lettuce and strawberry rhizosphere

   Caroline {De Tender}, Jane Debode, Annelies Haegeman, Tom Ruttink, Steve Baeyen, Pieter Cremelie, Bart Vandecasteele, Peter Dawyndt, and Martine Maes

   Jun 2015

   Bageco 13 ; Conference date: 14-06-2015 Through 18-06-2015
4. Effects of biochar addition on bacterial populations of the lettuce and strawberry rhizosphere

   Caroline {De Tender}, Jane Debode, Annelies Haegeman, Tom Ruttink, Steve Baeyen, Pieter Cremelie, Bart Vandecasteele, Peter Dawyndt, and Martine Maes

   May 2015

   BIG N2N annual symposium ; Conference date: 21-05-2015 Through 21-05-2015
5. Towards population genomics and metagenomics in agriculture and marine environments

   Annelies Haegeman, Thijs {De Mulder}, Caroline {De Tender}, Marie-Alice Fraiture, Ilia Kirov, Gil Luypaert, Frederik Parijs}, Elisabeth Veeckman, Christophe Verwimp, Steve Baeyen, Jane Debode, Ellen {De Keyser}, Jan {De Riek}, Lisa Devriese, Karen Goossens, Sara Maes, Hilde Muylle, Nico Peiren, Geertrui Rasschaert, Isabel Taverniers, Els {Van Coillie}, Leen Vandaele, Katrijn {Van Laere}, Sam {De Campeneere}, Marc {De Loose}, Marc Heyndrickx, Martine Maes, Johan Robbens, Isabel Roldán-Ruiz, Johan {Van Huylenbroeck}, and Tom Ruttink

   May 2015

   BIG N2N annual symposium ; Conference date: 21-05-2015 Through 21-05-2015

2014

1. Metagenome analysis of a soil and marine environment

   Caroline {De Tender}, Jane Debode, Lisa Devriese, Annelies Haegeman, Tom Ruttink, Steve Baeyen, Pieter Cremelie, Sara Maes, Peter Dawyndt, Martine Maes, and Johan Robbens

   May 2014

   4th MRP N2N Bioinformatics symposium ; Conference date: 21-05-2014 Through 21-05-2014
2. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle

   Joanna Załuga, Pieter Stragier, Steve Baeyen, Annelies Haegeman, Johan Van Vaerenbergh, Martine Maes, and Paul De Vos

   BMC Genomics, May 2014

   DOI
3. DGGE fingerprinting for microbial community monitoring as a new tool for anthropogenic impact assessment on the Belgian part of the North Sea

   Lisa Devriese, Sara Maes, Caroline {De Tender}, Steve Baeyen, Karen Bekaert, Pieter Cremelie, and Johan Robbens

   May 2014

   Studiedag Zandwinning ; Conference date: 20-10-2014 Through 20-10-2014
4. Population genomics @ ILVO - Plant Sciences Unit

   Annelies Haegeman, Tom Ruttink, Hilde Muylle, Christophe Verwimp, Frederik Parijs}, Sabine {Van Glabeke}, Isabel Roldán-Ruiz, Jane Debode, Steve Baeyen, Caroline {De Tender}, and Martine Maes

   May 2014

   Agricultural -Omics course (European Bioinformatics Institute) ; Conference date: 17-02-2014 Through 21-02-2014

2013

1. ISSR-PCR fingerprinting of plant pathogen strains using the QIAxcel\textregistered system and BioNumerics\textregistered

   Steve Baeyen, Joanna Zaluga, Paul {De Vos}, and Martine Maes

   Apr 2013

   Qiagen Application Note

   Abs

   A reliable method for genotypic fingerprinting of plant pathogen strains would be an important tool for tracking sources of infections and determining effective control strategies. This application note describes a reliable method for this purpose using the QIAxcel Advanced System in combination with BioNumerics software. The plant pathogen model used was bacterial canker of tomato (Clavibacter michiganensis subsp. michiganensis).

2. Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains

   Leighton Pritchard, Sonia Humphris, Steve Baeyen, Martine Maes, Johan Van Vaerenbergh, John Elphinstone, Gerry Saddler, and Ian Toth

   Genome Announcements, Aug 2013

   DOI
3. Draft genome sequence of Xanthomonas fragariaereveals reductive evolution and distinct virulence-related gene content

   Joachim Vandroemme, Bart Cottyn, Steve Baeyen, Paul De Vos, and Martine Maes

   BMC Genomics, Nov 2013

   DOI

2012

1. Draft genome sequencing of Xanthomonas fragariae reveals reduced genome size and distinct virulence related gene content

   Joachim Vandroemme, Steve Baeyen, Bart Cottyn, Paul {De Vos}, and Martine Maes

   Jul 2012

   4th Xanthomonas Genomics Conference ; Conference date: 09-07-2012 Through 12-07-2012

   Abs

   Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is known for its rather weak pathogenicity, fastidious growth on artificial media, its narrow host range and its taxonomically distinct but homogenous position within the otherwise complex genus Xanthomonas. As part of a broader pathogenicity study of Xf, the genome of a recent Belgian isolate (LMG 25863) was sequenced and assembled to draft status, with 105 contigs of more than 200 bp long. Remarkably, the Xf draft genome (4.2 Mb) was considerably smaller than most other Xanthomonas genomes (~5 Mb). Compared to other plant pathogenic Xanthomonas, Xf appeared to miss several genes/regions with a possible relevance to pathogenicity: i) an operon involved in the breakdown of phenolic compounds, ii) one of the two Type II Secretion System coding regions in Xanthomonas, iii) isocitrate lyase and malate synthase, responsible for the glyoxylate shunt pathway, and iv) two genes of the rfp gene cluster, rpfD and rpfI. Also, only half of the cellulolytic, hemicellulolytic and pectinolytic enzyme coding genes typically present in other Xanthomonas genomes were found in Xf. On the other hand, we identified possible virulence-related gene regions in Xf that are not common in other Xanthomonas genomes, with a Type VI Secretion System coding region being the most obvious one. Also, the Type III Secretion System effector repertoire in the Xf genome included several rare variable effectors such as xopC, xopE4, xopAF and xopAS, and some putatively new effectors. The Xf draft genome further revealed a high content of externally derived DNA: i) multiple copies of several Insertion Sequence (IS) elements, comparable to Xanthomonas oryzae, ii) a phage coding region, iii) 18-19 kb of sequence fragments with high similarity to Plasmid III (27 kb) of X. albilineans GPE GP73, and iv) a CRISPR associated gene cluster of the Yersinia pestis subtype with 40 related spacer sequences. The draft genome sequence of LMG 25863 affirms the distinct position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired pathogenicity related functions. It’s pathogenicity related distinguishing features may help explain the specific, mostly endophytic association of Xf with the strawberry plant system.

2. Xanthomonas arboricola genomics and type three effector gene distribution

   {Joël F.} Pothier, J. Blom, Steve Baeyen, S. Essakhi, Ahmed Hajri, Sophie Cesbron, Joachim Vandroemme, Bart Cottyn, A. Goesmann, Martine Maes, Charles Manceau, Theo Smits, and Brion Duffy

   Jul 2012

   4th Xanthomonas Genomics Conference ; Conference date: 09-07-2012 Through 12-07-2012

   Abs

   Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot on commercial, ornamental and forest Prunus species. Outbreaks can result in severe economic losses to fruit quality and yield, branch/tree dieback, and orchard devastation, particularly on peach, apricot, nectarine and plum. This stone is endemic in the USA, NZ and is a quarantine regulated pathogen in Europe and elsewhere, compounding economic loss with eradication and regulatory expenses. Wide host range and climate change patterns portend potential increased invasion risk of this pathogen. Despite the regulatory and economic significance of Xap, almost nothing is known about the genetics of Xap compared to other xanthomonads. To fill this gap, a genome sequencing and comparative genomics approach were undertaken. We have sequenced the complete genome of a genotypic-representative Xap strain from Europe (Italy, CFBP 5530). This is the first complete genome sequence for this species. Paired-end 454-pyrosequencing and primer walking on a fosmid library gave 3 contigs. The chromosome is 4.85 Mb with 65.6% GC ratio and 3,912 predicted CDS. Xap has a unique 41.2 kb plasmid with a 62.3% GC ratio and 45 CDS. Comparative genomics with other Xanthomonads was used to identify X. arboricola-specific genes indicating features relevant to differential host specificity and virulence mechanisms. Among those, composition and role of type III secretion system effectors repertoires was surveyed within all six X. arboricola pathovars. Applied genomics has identified over 90 VNTR, several of which are currently being used to examine biodiversity and epidemiology of Xap and related pathovars, and design of improved diagnostics. This first complete genome sequence was also successfully used as a template to perform genomic assembly via mapping of short reads of several isolates from related pathovars. For example, the genome of a Xap isolate GBBC 2038 from the ornamental P. laurocerasus was assembled into 93 contigs. These two genomes show very high identity, the main difference being the presence of 10 kb genomic island in the ornamental isolate. Applied and comparative genomics improved our knowledge on host specificity and biodiversity of Xap, and allowed the development of efficient methods for detection of this plant disease. Overall, the availability of the first genome of X. arboricola constitutes a precious knowledge base for better comprehension of all other X. arboricola pathovars.

3. Xanthomonas arboricola genomics and type three effector gene distribution

   {Joël F.} Pothier, Steve Baeyen, Jochem Blom, S. Essakhi, Ahmed Hajri, Sophie Cesbron, Joachim Vandroemme, Bart Cottyn, A. Goesmann, Martine Maes, Charles Manceau, {Theo H.M.} Smits, and Brion Duffy

   Feb 2012

   First International Congress for Bacterial Diseases of Stone Fruits and Nuts ; Conference date: 14-02-2012 Through 17-02-2012

   Abs

   Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot on commercial, ornamental and forest Prunus species. Outbreaks can result in severe economic losses to fruit quality and yield, branch/tree dieback, and orchard devastation, particularly on peach, apricot, nectarine and plum. This stone is endemic in the USA, NZ and is a quarantine regulated pathogen in Europe and elsewhere, compounding economic loss with eradication and regulatory expenses. Wide host range and climate change patterns portend potential increased invasion risk of this pathogen. Despite the regulatory and economic significance of Xap, almost nothing is known about the genetics of Xap compared to other xanthomonads. To fill this gap, a genome sequencing and comparative genomics approach were undertaken. We have sequenced the complete genome of a genotypic-representative Xap strain from Europe (Italy, CFBP 5530). This is the first complete genome sequence for this species. Paired-end 454-pyrosequencing and primer walking on a fosmid library gave 3 contigs. The chromosome is 4.85 Mb with 65.6% GC ratio and 3,912 predicted CDS. Xap has a unique 41.2 kb plasmid with a 62.3% GC ratio and 45 CDS. Comparative genomics with other Xanthomonads was used to identify X. arboricola-specific genes indicating features relevant to differential host specificity and virulence mechanisms. Among those, composition and role of type III secretion system effectors repertoires was surveyed within all six X. arboricola pathovars. Applied genomics has identified over 90 VNTR, several of which are currently being used to examine biodiversity and epidemiology of Xap and related pathovars, and design of improved diagnostics. This first complete genome sequence was also successfully used as a template to perform genomic assembly via mapping of short reads of several isolates from related pathovars. For example, the genome of a Xap isolate GBBC 2038 from the ornamental P. laurocerasus was assembled into 97 contigs. These two genomes present very high identity, the main difference being the presence of 10 kb genomic island in the ornamental isolate. Applied and comparative genomics improved our knowledge on host specificity and biodiversity of Xap, and allowed the development of efficient methods for detection of this plant disease. Overall, the availability of the first genome of X. arboricola constitutes a precious knowledge base for better comprehension of all other X. arboricola pathovars.

4. Sequence Diversity in the Dickeya fliC Gene: Phylogeny of the Dickeya Genus and TaqMan® PCR for “D. solani”, New Biovar 3 Variant on Potato in Europe

   Johan Van Vaerenbergh, Steve Baeyen, Paul De Vos, and Martine Maes

   PLoS ONE, May 2012

   DOI

2010

1. Development of a real‐time PCR assay for Pseudomonas cichorii, the causal agent of midrib rot in greenhouse‐grown lettuce, and its detection in irrigating water

   B. Cottyn, S. Baeyen, E. Pauwelyn, I. Verbaendert, P. De Vos, P. Bleyaert, M. Höfte, and M. Maes

   Plant Pathology, Nov 2010

   DOI

2009

1. Molecular detection of Puccinia horiana in Chrysanthemum x morifolium through conventional and real-time PCR

   Hossein Alaei, Steve Baeyen, Martine Maes, Monica Höfte, and Kurt Heungens

   Journal of Microbiological Methods, Feb 2009

   DOI
2. Quantitative detection and monitoring of Colletotrichum acutatum in strawberry leaves using real‐time PCR

   J. Debode, W. Van Hemelrijck, S. Baeyen, P. Creemers, K. Heungens, and M. Maes

   Plant Pathology, May 2009

   DOI

2008

1. First Record of Bacterial Blight Caused by Pseudomonas syringae pv. syringae on Pyracantha coccinea and an Amelanchier sp. in Bulgaria

   S. G. Bobev, S. Baeyen, J. Van Vaerenbergh, and M. Maes

   Plant Disease, Aug 2008

   DOI
2. Sensitive real‐time PCR detection of Xanthomonas fragariae in strawberry plants

   J. Vandroemme, S. Baeyen, J. Van Vaerenbergh, P. De Vos, and M. Maes

   Plant Pathology, Feb 2008

   DOI

2006

1. First Report of Cochliobolus sativus on Guzmania sp. in Belgium

   C. Crepel, S. Inghelbrecht, S. Baeyen, and M. Maes

   Plant Disease, Oct 2006

   DOI

2005

1. First Report of Leaf Spots on Laurus nobilis Caused by Phytophthora citricola in Belgium

   C. Crepel, S. Inghelbrecht, S. Baeyen, M. Maes, and S. G. Bobev

   Plant Disease, Jan 2005

   DOI

2004

1. First Report of Fire Blight Caused by Erwinia amylovora on Pyracantha coccinea in Bulgaria

   S. G. Bobev, S. Baeyen, C. Crepel, and M. Maes

   Plant Disease, Apr 2004

   DOI

2003

1. Experiences and perspectives for the use of a Paenibacillus strain as a plant protectant.

   Steve Baeyen, Maes M, and Baeyen S

   Apr 2003
2. Experiences and perspectives for the use of a Paenibacillus strain as a plant protectant.

   M. Maes and S. Baeyen

   Communications in agricultural and applied biological sciences, Apr 2003
3. First Report of Phytophthora cactorum on American Ginseng (Panax quinquefolius) in Bulgaria

   S. G. Bobev, S. Baeyen, C. Crepel, and M. Maes

   Plant Disease, Jun 2003

   DOI