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DEC. 4 - 7, 2017

In cooperation with the "Phytobiomes" journal

Phytobiomes journal

Satellite Workshops

Update Nov 18., 2015: The venue of the workshops has been added and the programm timetable has been updated.

IMPORTANT: Please be aware that these workshops are parallel events and you can therefore only register for one of the workshops.

Venue of the workshops: AIT, Konrad-Lorenz-straße 24, 3430 Tulln. 09:30-15:00. Details on transport will be provided to the participants by the workshop organizer and during the miCROPe symposium.

How to get there:

Take U4 to Heiligenstadt; from there take train at 8:38 (platform 1)

buy a train ticket first :)

Applications of endophytes and their secondary metabolites to combat phytopathogens (26.11.2015)

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Workshop organizers: Marc Stadler (marc.stadler@helmholtz-hzi.de) and Anna Maria Pirttilä (am.pirttila@oulu.fi)

On 26 November, a joint workshop between members of WG4 of COST Action FA1103 and COST Action FP1103 will be held at the UFT in Tulln. The topic of this workshop relates to practical applications of non-systemic endophytes as natural enemies of important phytopathogens, including classical biocontrol agents, as well as “biofertilizers” and “biofumigants”. Special emphasis will be given to the recent invasive ash dieback pathogen, Hymenoscyphus fraxineus (aka Chalara fraxinea and H. pseudoalbidus), but contributions dealing with the application of endophytes to combat other pathogens, including other fungi, invertebrates and bacteria, are also welcome.

In addition, some contributions will deal with the discovery of novel bioactive secondary metabolites from endophytic bacteria and fungi with potential to become agrochemicals, e.g. fungicides or insecticides. The workshop will be co-organised by Anna Maria Pirttilä and Marc Stadler (WG 4 leaders), who will also be glad to answer any questions.

The workshop will be open to all participants, even though only up to 18 contributions (six thereof reserved for FP1103 members) can be reimbursed. Active participation as speaker or poster presenter will be regarded as major criterion for those who wish to be considered for reimbursement. In case there are too many requests for oral talks, the organisation committee, comprising members of WG 4 of COST Action FA1103, will make the selections.

There are still some open slots for oral presentations and, in particular, poster presentations.


The registration for this workshop is now closed. Any questions regarding this workshop should be addressed directly to the workshop organizer Marc Stadler marc.stadler@helmholtz-hzi.de.

Emergence of human pathogens from natural and agricultural environments (26.11.2015)

Workshop organizer: Leo van Overbeek (leo.vanoverbeek@wur.nl)

Incidences of intestinal diseases occurring after consumption of contaminated fresh vegetables have frequently been reported. Pathogenic bacteria causing disease symptoms in humans were presumed to be present in clinical and veterinary environments only. However, these pathogens and their closest resembling relatives have frequently been detected in alternative habitats like water ecosystems, (manured) soils and even in plants. For example, species closely resembling human pathogens frequently have been found in the plant microbiome. It is thus a relevant question whether alternative habitats are indeed hostile for invading human pathogens and whether adaptation or even emergence of human pathogens is taking place in alternative habitats like present in intensive agriculture. 

Intriguing questions on the origin of human pathogens, taxonomical relationship with members of the plant microbiome, adaptation to alternative habitats and possibilities for genetic exchanges between human pathogens and taxonomic relatives in biomes of plants and of other habitats relevant for plant growth (soil, water, manure) need to be addressed.  Typical questions are:

  • How to discriminate human pathogens from non-pathogenic taxonomic relatives in environmental samples?
    • What are typical risk factors for different groups of human pathogens that commonly are found to be present in non-clinical environments?
    • What are the best tools for detection of human pathogens in non-clinical environments?
    • How must data be interpreted with respect to human/ animal pathogenicity?
  • What is the taxonomical relationship of human pathogens with closest non-pathogenic relatives in the plant biome?
    • Are there taxonomical distinctions between pathogens and closest resembling non-pathogens?
    • Can mobile genetic elements be transferred between human pathogens and non-pathogens?
    • What can be the consequences of genetic exchanges with respect to emergence of pathogens and circulation of potential ‘risk factors’ (e.g. virulence and antibiotic resistance genes) among plant-associated communities?
  • What are the roles of different biomes in alternative environments (plant, soil, water) in buffering against invasive human pathogens?
    • What are the intervention strategies to control dissemination of human pathogens to food/ feed production chains

In this proposal we call for presentations on this topic to emphasize the scientific and societal relevance of this subject.

Tentative program "Emergence of human pathogens from natural and agricultural environments", Nov. 26, 2015

09:30 Leo van Overbeek Opening workshop


Leo van Overbeek

Cycling of food-borne human pathogens across animal and plant ecosystems


Gabriele Berg

Human pathogens from the plants – a novel perspective


Coffee break



Adam Schikora

Salmonella can use effector proteins and avoid the plant immune system during colonization


Birgt Mitter

The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements


László Kredic

Filamentous fungi from the environment emerging as causal agents of keratomycosis


Lunch break



Kornelia Smalla



Armin Erlacher

The lettuce microbiome: susceptibility for microbiome perturbation

13:50 Anton Hartmann Closely related plant beneficial and opportunistic human pathogens amongst different diazotrophic PGPR


General discussion on European collaboration


Finish of the workshop and round trip to AIT facilities organized by Stéphane Compant


To register for the satellite workshop please login to the meeting registration system with your account data from the miCROPe registration confirmation e-mail and then click the "Satellite registration" button in the left menu. Any questions regarding this workshop should be addressed directly to the workshop organizer Leo van Overbeek (leo.vanoverbeek@wur.nl)