Joël F. Pothier

ZHAW Zurich University of Applied Sciences | ZHAW · Institute of Natural Resource Sciences (IUNR)

Sunflower is a short-season crop of the Asteraceae family and the Helianthus genus and is the fourth most important oilseed crop in the world. During a field campaign, unusual symptoms (necrosis and longitudinal cracking of the petiole) were observed in a sunflower crop grown in the region of Kavarna (Dobrich district, Bulgaria) and strains of the...

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen with 6,534 annual reported cases in the EU in 2021. This pathotype generally contains strains with smooth LPS with O-antigen serogroup O157 being the predominant serogroup in the US. However, non-O157 STEC serogroups are becoming increasingly prevalent. Here we announce the compl...

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen with 6,534 annual reported cases in the EU in 2021. This pathotype generally contains strains with smooth LPS with O-antigen serogroup O157 being the predominant serogroup in the US. However, non-O157 STEC serogroups are becoming increasingly prevalent. Here we announce the compl...

Plants and its microbiome are subjected to several abiotic and biotic stresses, including new plant pathogens, that will be more frequent and intense in the current climate change scenario. Current agricultural practices in Europe depend on agrochemicals and high amounts of water and will therefore not be sufficient to face the upcoming stresses. T...

Here, we report the draft genome sequence of Xanthomonas arboricola pv. pruni strain PVCT 262.1, isolated from almond (Prunus dulcis) leaves affected by bacterial spots in Italy in 2020. Genome size is 5,076,418 bp and G+C content is 65.44%. A total of 4,096 protein-coding genes and 92 RNAs are predicted.

Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, i...

Chitin amendment of peat substrate has been proven effective in promoting lettuce growth and increasing phenolic compounds in lettuce seedlings. However, the effect of chitin soil amendment on lettuce growth in mineral soil remains unexplored. The effect of chitin amendment of mineral soil on lettuce growth and metabolite changes was investigated f...

Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with...

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck of tomato, an important disease that results in severe crop production losses worldwide. Currently, two races within phylogroup 01a (PG01a) are described for this pathogen. Race 0 strains have avirulence genes for the expression of type III system-associated effectors AvrPto1 an...

Chitin soil amendment is known to improve soil quality, plant growth and stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of...

Background: The dissemination of NDM-1 carbapenemases (New Delhi Metallo-β-lactamase) is a global public health problem, mainly in developing countries. The aim of this study was to characterize the spread of NDM-producing bacteria in the Southern Brazilian states analyzing epidemiological, molecular, and antimicrobial susceptibility aspects. Met...

Here, we report the high-quality draft genome sequence of the actinomycete Streptomyces albidoflavus CCOS 2040, isolated from a Swiss soil sample. The genome contains 7,136,301 bp with 73.35% GC content. In total, 22 biosynthetic gene clusters, including polyketides and terpenes, were predicted within the sequenced genome.

Present, emerging or re-emerging plant diseases due to infection by bacteria of the Lysobacteraceae (syn: Xanthomonadaceae) family are continually challenging food security and cause significant losses to the economies of European countries each year [...]

Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5′396...

The seed-borne bacterium Xanthomonas campestris pv. campestris (Xcc) as a causal organism of black rot disease remains the most serious bacterial problem of agricultural production of cruciferous plants worldwide. The eradication of a primary inoculum originating in seeds is available, but no treatment is totally effective. With the threat of devel...

Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of non-pathogenic and taxonomically un-validated strains are also designated as X. arboricola leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole genome resources of...

Broad application of antibiotics gave rise to increasing numbers of antibiotic resistant bacteria. Therefore, effective alternatives are currently investigated. Bacteriophages, natural predators of bacteria, could work as such an alternative. Although phages can be highly effective at eliminating specific bacteria, phage resistance can be observed...

Aquaponics combines hydroponic crop production with recirculating aquaculture. These systems comprise various compartments (fish tank, biofilter, sump, hydroponic table, radial flow settler and anaerobic digester), each with their own specific environmental pressures, which trigger the formation of unique microbial communities. Triplicated aquaponi...

The seven pathovars of Xanthomonas hortorum and Xanthomonas hydrangeae, referred to as the X. hortorum – X. hydrangeae species complex, cause disease on a multitude of plants, including crops, ornamental and wild plants. Cross-pathogenicity was proven for some of the strains within this species complex. It is thus important to have highly specific...

Xanthomonas euroxanthea is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as X. arboricola. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight X. euroxanthea-specific...

Taxonomy Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. Host ran...

Members of the Pseudomonas syringae species complex cause symptoms that are ranging from leaf spots to cankers on a multitude of plant species, including some of the genus Prunus. To date, a total of two species of the P. syringae species complex and six different pathovars have been associated with diseases on Prunus spp., which were shown to belo...

This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia . Analysis using MALDI-TOF...

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence...

Xanthomonas arboricola pv. corylina is the causal agent of bacterial blight of hazelnut. The bacterium is listed as A2 quarantine pathogen in Europe since 1978 and on the Regulated Non-Quarantine Pest (RNQP) list since 2020. Three strains from various geographic regions and isolated at different times were sequenced using a hybrid approach with sho...

Background: The species Xanthomonas arboricola comprises up to nine pathovars, two of which affect nut crops: pv. juglandis, the causal agent of walnut bacterial blight, brown apical necrosis, and the vertical oozing canker of Persian (English) walnut; and pv. corylina, the causal agent of the bacterial blight of hazelnut. Both pathovars share a c...

Specific scope This Standard describes a diagnostic protocol for Pseudomonas syringae pv. actinidiae. It should be used in conjunction with PM 7/76 Use of EPPO Diagnostic Protocols.¹ Specific approval and amendment Approved in 2014–09. Revised in 2021–06. Authors and contributors are given in the Acknowledgements section.

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence...

The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unv...

Abstract The quarantine bacterium Xanthomonas fragariae causes angular leaf spots on strawberry. Its population structure was recently found to be divided into four (sub)groups resulting from two distinct main groups. Xanthomonas arboricola pv. fragariae causes bacterial leaf blight, but the bacterium has an unclear virulence status on strawberry....

Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink’s medium and from infected strawberry cv. Elsanta plants...

We report the genome sequences of six Xanthomonas hortorum species-level clade members, X. hortorum pathovars taraxaci, pelargonii, cynarae, and gardneri (complete genome sequences) and X. hortorum pathovars carotae and vi-tians (high-quality draft genome sequences). Both short-and long-read sequencing technologies were used.

We describe a novel species isolated from walnut (Juglans regia) which comprises non-pathogenic and pathogenic strains on walnut. The isolates, obtained from a single ornamental walnut tree showing disease symptoms, grew on yeast extract-dextrose-carbonate agar as mucoid yellow colonies characteristic of Xanthomonas species. Pathogenicity assays sh...

Multidrug resistant bacteria represent an increasing challenge for medicine. In bacteria, most antibiotic resistances are transmitted by plasmids. Therefore, it is important to study the spread of plasmids in detail in order to initiate possible countermeasures. The classification of plasmids can provide insights into the epidemiology and transmiss...

Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta...

Actinomycetes strains isolated from different habitats in Switzerland were investigated for production of antibacterial and antitumoral compounds. Based on partial 16S rRNA gene sequences, the isolated strains were identified to genus level. Streptomyces as the largest genus of Actinobacteria was isolated the most frequently. A screening assay usin...

For many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d'Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1BT, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) g...

Kampala, the capital city of Uganda, is rapidly expanding without adequate wastewater treatment facilities to accommodate the current estimated population of 1.68 million people. Hence, freshwater bodies and natural ecosystems around the city are heavily polluted with organic and inorganic contaminants. Yet, there is a paucity of data on pathogenic...

In recent years, the use of whole-cell biocatalysts and biocatalytic enzymes in biotechnological applications originating from the genus Pseudomonas has greatly increased. In 2014, two new species within the Pseudomonas putida group were isolated from Swiss forest soil. In this study, the high quality draft genome sequences of Pseudomonas wadenswil...

Minor differences in the previously obtained genome of Pseudomonas protegens CHA0 were detected after resequencing the strain. Based on this, the genome size slightly increased. Additionally, we performed a manual annotation of genes involved in biocontrol and insect pathogenicity. This annotation version will be the basis for upcoming genome studi...

Background: A ribosomal subunit protein (rsp)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method was developed for fast subspecies-level typing of Streptococcus agalactiae (Group B Streptococcus, GBS), a major cause of neonatal sepsis and meningitis. Methods: A total of 796 GBS whole genome sequ...

Background Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe lack of genomic information of these pathogens. The high phylogenetic diversity observed within strains causing disease on Prun...

The microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively in order to understand structure and functioning of the anoxygenic phototrophic sulfur bacteria community living in the chemocline. It has been found that the purple sulfur bacterium “Thiodictyon syntrophicum” strain Cad16T, belonging to the Chr...

Blooms of purple sulfur bacteria (PSB) are important drivers of the global sulfur cycling oxidizing reduced sulfur in intertidal flats and stagnant water bodies. Since the discovery of PSB Chromatium okenii in 1838, it has been found that this species is characteristic of for stratified, sulfidic environments worldwide and its autotrophic metabolis...

We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865 T , which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. The genome of this species may provide an important resource for the discovery of novel...

“Thiodictyon syntrophicum” sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven b...

Here, we report the draft genome sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, isolated from symptomatic leaves of an ornamental walnut in a public site in Portugal without any record of phytosanitary treatment. This isolate may constitute a genomic reference of a wild-type strain in comparative genomics studies.

Pseudomonas wadenswilerensis CCOS 864T was isolated in 2014 from forest soil. The organism belongs taxonomically to the Pseudomonas putida group, members of which have been well studied for their potential in biotechnological applications. We present here the draft genome sequence of P. wadenswilerensis CCOS 864T.

We report here the draft genome sequence of Xanthomonas sp. strain CPBF 424, isolated from a diseased walnut tree. Multilocus sequence analysis showed that this walnut-pathogenic isolate is located between the nonpathogenic X. arboricola and X. prunicola clusters. These features make this strain a promising reference to disclose new genetic determi...

The microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively to understand metabolic functions driven by the highly abundant anoxygenic phototrophic sulfur bacteria of the families Chromatiaceae and Chlorobiaceae. It was found that the sequenced isolate "Thiodictyon syntrophicum" nov. sp. str. Cad16T, bel...

Phages vB_EamP-S2 (S2) and vB_EamM-Bue1 (Bue1) infect the plant pathogen Erwinia amylovora . S2 has a genome size of 45,495 bp and belongs to the genus SP6virus . The genome size of Bue1, related to Salmonella phage Vil, is 164,037 bp. Both phages possess a depolymerase enzyme, a frequent feature of E. amylovora phages.

Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia . 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus F...

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing t...

Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of fiveX. arboricolapv. fragariae isolates from Italy and France.

Rapid and reliable identification of plant pathogenic bacteria is critical for effective implementation of phytosanitary measures. The genus Erwinia includes a number of economically important plant pathogens such as fire blight agent Erwinia amylovora or Asian pear pathogen Erwinia pyrifoliae, together with closely related plant epiphytes of unkno...

Background: Type VI secretion systems (T6SS) are widespread among Gram-negative bacteria and have a potential role as essential virulence factors or to maintain symbiotic interactions. Three T6SS gene clusters were identified in the genome of E. amylovora CFBP 1430, of which T6SS-1 and T6SS-3 represent complete T6SS machineries, while T6SS-2 is re...

Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf spots, thus reducing the yield of production for strawberry fruits. Three isolates with various geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genome sequences of virulent strains and observe the variability i...

Pseudomonas viridiflava causes foliar and stem necrosis, as well as stem and root rot on a wide range of plants. We report here the first complete genome of a P. viridiflava strain, isolated from diseased tissue of a cherry tree.