Post written by Thomas Badet (SNSF postdoc)
Even though I was raised in the city, I have always been more attracted by what was happening in the wild, somehow escaping from human control. Studying biology was therefore a natural choice for me. I was introduced to fungi during my childhood, spending hours roaming French forests trying to find a valuable mushroom. Fungi are feeding human imagination since old times. Upon my scientific education I had the chance to tackle the amazing capacities of fungi to live in either beneficial or detrimental interaction with plants. Since, my research focus on the genetics of the interaction between fungal pathogens and their host plants. After investigating the genetics of generalist parasitism in fungi with Sclerotinia sclerotiorum as a model broad-host range plant pathogen during my PhD, I am now working on the evolution of gene expression in the specialist wheat fungal pathogen Zymoseptoria tritici and the emergence of host-induced genes from non-coding DNA in a local field population. Besides these specific questions related to my research, I also enjoy taking part to scientific popularization through radio talks or articles. As an illustration, here is a short article (written in French) published in a university newspaper during my master degree.
Des saprophytes qui nous veulent du bien
On a tendance à les bouder depuis Tchernobyl, mais ils sont de retour chaque année, envahisseurs silencieux et gardiens de nos forêts. Rendons leur hommage.
Vous l’aurez compris, les températures de ces derniers jours ne mentent pas, l’hiver est en marche. J’en entends se plaindre de ce refroidissement soudain, et peut-être en faites-vous partie. Je profite donc de cette tribune pour faire une annonce qui devrait vous réchauffer un peu le cœur. Et oui, car avant l’hiver vient l’automne; saison aux couleurs énigmatiques, et propice à certaines coutumes bien trop souvent oubliées.
Voyez le rougissement des feuilles du chêne comme un signe. Mais ne vous y trompez pas, ce n’est pas sur la canopée de la forêt que j’attire votre attention mais sur ce qui s’y passe plus bas, le nez collé à l’humus. Voici en effet venu le temps de se dandiner au son des Trompettes de la mort, accompagnées à la voix par leur sœur Chanterelle. En cette période où les Tricholomes, moins prétentieux, s‘abritent sous le tapis d’aiguilles du pin, je vous le dis : il fait bon courir les sous-bois les yeux rivés au sol. C’est ici que vous aurez peut-être le privilège de croiser un Tête de Nègre, fier, tout juste écorché par une limace.
Comment décrire le plaisir procuré par la découverte d’un de ces mystérieux spécimens ou bien celui offert une fois passés à la casserole ? Aaah, tomber à genoux devant un de ces « bouchons de champagne », priceless!
D’autres préfèreront sûrement courir les prés, à la recherche d’un rond de Mousserons rôdant autour d’une bouse. À déguster à la sauce tomates-olives accompagnant un gâteau de foie de lapin. Bien sûr j’en vois venir, la mine renfrognée : beurk, pas bon. Je conçois (bien que mal) qu’on puisse ne pas apprécier les champignons dans l’assiette. Rassurez-vous, les champignons, Tchernobyl ou pas, sont pleins de ressources et assouviront la curiosité des plus récalcitrants. Saviez-vous par exemple qu’un champignon du joli nom de Magnaporthe oryzae était capable de percer du Kevlar ? Braah ! Pilobolus quant à lui se nourrit de crottin de cheval et éjecte ses spores à pas moins de 1,8 million de mètres par seconde ramenés à échelle humaine. À cette vitesse là on serait tenté de troquer les épinards pour du crottin avouez-le.
Et les champignons ne s’illustrent pas que par leurs prouesses physiques, ce sont aussi des As de la chimie. Les plus téméraires d’entre vous pourront ainsi se laisser hypnotiser par les couleurs chatoyantes de la Tue Mouches ou par le téton du Psilocybe. Le temps de planer serein jusqu’à décembre, et atterrir sous un vieux chêne truffier.
Blog post written by Sabina Tralamazza
I was always driven by curiosity. Choosing Biology and academic studies seemed like a natural path to take. Since the beginning, I was intrigued by fungi and how much they affect everything around them. In my research, I am especially interested in the phylogeny, monitoring and control aspects of mycotoxigenic fungi in cereal crops. With the ongoing growth of information, I realized I needed to start using bioinformatic tools to comprehend more complex concepts in my field. The lab here gave me the opportunity to start this learning process, focusing on the whole-genome phylogenetic analysis of mycotoxigenic fungi. In my current project, we will perform genome assemblies and analyze the genomes of strains within the Fusarium graminearum species complex isolated from wheat grains from Brazil. We will investigate the genetic variation and phylogeny of the Brazilian FGSC found on cereals.
Blog post by our new postdoc Emilie Chanclud
If water or food is missing, animals will seek for it. If a predator is threatening, they fight or run away. So how do plants manage? I've always been amazed by looking at a 100-year-old oak or a 1000-year-old pine, how do they deal with all these environmental constrains? Therefore, I started to study plant biology and I'm still fascinated to observe that if water is missing, plants induce precipitation; if food is missing, they are working in network; if a pathogen attacks, they respond with a very sophisticated immune system. After a BSc degree in plant physiology and botany, I moved to the south of France for a MSc in plant functional biology and got enthralled by plant-microbe interactions. I did a master thesis in plant pathology and stayed on the dark side of the force in PhD to study how a pathogenic fungus manipulates its host with fungal derived plant-hormones. By seeking deeper in the roles of these hormones, we discovered that they were useful for the fungus itself, and that this seemed to be conserved in microbes (even those that do not interact with plants such as human pathogens). Then, by joining a plant physiology lab and by working with a specialist of plant hormones, I could explore the hypothesis that plant hormones could act as universal communication compounds between organisms. After a year, missing plant pathology so hard, I moved to England for a second post-doc and have been initiated to evolution concepts in plant-microbe interactions. There I met Prof. Croll and was really looking forward joining his group. The Laboratory of Evolutionary Genetics and the University of Neuchâtel are amazing environments to be emerged in biotic interactions evolution and to become fully skilled in computational biology. My project aims to unravel how fungal pathogens evolved to overcome crop resistance in the agricultural ecosystems. To date, plant pathogens are threatening food security and the modern agricultural landscapes are highly conducive for virulent pathogens emergence. A better understanding of pathogens adaptation is crucial for developing sustainable crop production. In a farther future, I hope to apply this knowledge to unravel how the microbiota affects the physiology of their hosts and how they co-evolve, making a parallel between plants and humans.
We had a great day of talks last Friday. Thanks to all who came and contributed. For more information see here.
Nikhil and Thomas organized a super nice BBQ down at the lake serving Tandoori chicken and more. (And sorry for the loud baby ;-)
Blog post by Leen Abraham who joined our lab in August 2017
“Look deep into nature, and you will understand everything better” - Albert Einstein-
I believe that nature has a solution to every problem. Even in the most modern era of science, all our research is seeking answers from nature to solve the many unanswered questions. This mystery of nature always fascinated me. My quest for nature and science destined me to an agriculture college where I did my bachelors and masters. This gave me a new insight into the inter play of science and nature and I could familiarise myself with plant breeding programmes, development of transgenic crops, different agronomic practices, extension services to the farmers etc. All this ignited my research interest in plant science and I undertook my masters study with the objective of developing an efficient transformation protocol for elephant foot yam. A considerable reduction in tuber yield was reported due to the incidence of mosaic disease in yam. To develop disease resistance and improve nutritional characteristics, transgenic technology was preferred due to low germplasm variability in the crop. The study yielded an efficient protocol for the development of transgenic elephant foot yam. The next project I worked on was a collaborative work between the network partners in India (ICAR- Central Tuber Crops Research Institute) and ETH, Zurich. The project aims to develop Cassava mosaic disease (CMD) resistant transgenic cassava via a RNA silencing strategy.
My research career so far was focussed on developing crops resistant to pathogens but for my doctoral studies I am interested in evolution of plant pathogens especially a devastating pathogen of wheat (the fungus Zymoseptoria tritici) by exploiting the tools of population genetics. My PhD project aims to analyse adaptive evolution driven by the regulation of effector gene expression in Z. tritici using transcriptome sequence. I will analyse how polymorphism in the genome influences gene expression both in pure cultures and during leaf infections. I hope that my project findings will make an important contribution to the control of wheat diseases.
We had to say goodbye to Clémence Plissonneau last Friday. Clémence was an essential part of our lab since January 2016 when she joined us on a INRA Young Scientist fellowship
Clémence built up an incredible skill set in genomics and transcriptomics very quickly. For a sample of her work look here and here. In addition to her own work, she was also highly prolific in helping out numerous collaborators at the ETH and beyond. Clémence now moves on to a career in industry in Southern France. Best of wishes from the whole lab - You will be missed!
Thomas Badet joins us on a 3-month fellowship to work on the genomics of Sclerotinia sclerotiorum. Thomas is doing his PhD at the National Institute for Agronomic Research (INRA), Toulouse, France.
His research interests:
Thomas’ work in Toulouse aims at identifying molecular actors underlying quantitative disease resistance to the pathogenic fungus Sclerotinia sclerotiorum using natural populations of Arabidopsis thaliana and association genomics. He’s hosted in our lab for a three month period to develop population genomic and phylogenomic tools within the Sclerotiniaceae family with a focus on understanding the genetic basis of Sclerotinia sclerotiorum multi-parasitism.
November 2014-present: PhD student, Laboratory of Plant Microbe Interactions, National Institute for Agronomic Research, Toulouse, France.
2013-2014: Master thesis in S. Raffaele’s team, University of Toulouse Paul Sabatier, France.
Thesis title: “Functional analysis of an Arabidopsis putative quantitative disease resistance gene to Sclerotinia sclerotiorum”
2012-2014: Master in Plant Biology, University of Toulouse Paul Sabatier, France.
2008-2011: Bachelor in Biology, University of Rennes I, France.
We hiked up Creux du Van near Neuchâtel. We were joined by the good people from the Plant Pathology at the ETH Zürich and it was a fun day out. Creux du Van is a pretty stunning rock formation left behind by a retreating glacier (long ago).
Post by Nikhil Kumar Singh who started his PhD in March 2017 in our lab.
From the beginning of my academic career, I was more inclined towards investigating the behaviour of microbes, their inter- and intraspecies interactions and their response towards a changing environment. My master thesis was based on understanding the spatial and temporal dynamics of the soil microbial population that were exposed to an exogenous bacterial species in different environmental conditions. We all have witnessed a global rise in all kinds of pollution. However, the microbial community in any specific habitat is usually not specialized to degrade a particular pollutant. A very popular biological approach to eliminate such pollutants is the use of microbial species that have evolved the ability to transform a specific pollutant into less toxic or non-toxic forms. The question here is how will the original endogenous microbial population behave if such specialised “pollutant degraders” species are introduced into their habitat. My Masters project aimed to use fluorescence and time-lapse microscopy, and systems biology tools to understand the community dynamics when exposed to toxic compounds in the presence of exogenous species.
After my masters, I got more interested in understanding the genetic basis microbial adaptations with respect to their immediate environment. The environment that a specific microbe inhabits can be very variable, for example, it could be a toxic soil environment or the body of a host in case of pathogens. My PhD project will focus on understanding the genetic basis of host-pathogen interactions between wheat and Zymoseptoria tritici which is a major pathogenic fungus of wheat. I will use genome wide association (GWA) mapping as a tool to identify the genetic basis of different phenotypes including the pathogenicity of Z. tritici under different environmental conditions.
Please see here (PDF) for the announcement details.
Post by Ursula Oggenfuss who started her PhD in our lab in January 2017.
Three months ago, I started my PhD project in the evolutionary genetics group at University Neuchâtel. After a month in the “old” plant pathology group at ETH Zurich, where I learned the most important lab methods and got in touch with a lot of researchers on Zymoseptoria tritici, I started in the lab in Neuchâtel.
Although my research and personal interests are very broad, I mostly worked with fungi during my studies. During my bachelor at ETH Zurich I was introduced to forest pathology, and I was working for my bachelor thesis with the fungal endophytes in Fraxinus excelsior leaves that are already infected with the new fungal disease Hymenoscyphus fraxineus. With this work, I got a first insight into laboratory work. After I wrote my term paper on Clavicipitaceae, fungal grass endophytes that can act antagonistically against herbivores, I went back to H. fraxineus for my master thesis. I had the opportunity to work on the population structure of a newly found Mitovirus (a virus inside of the mitochondria of a fungi) in H. fraxineus. For this thesis, I could expand my experiences into the wet laboratory work, and I learned how to work with level 2 organisms in the newly built plant protection lab at WSL Birmensdorf. Next to the laboratory work, I had an extended insight into bioinformatics and phylogenetics.
After my Master, I shortly worked in the plant pathology group at ETH, where I helped developing a qPCR protocol for two agricultural filamentous plant pathogens. After that I worked in the mycorrhiza group at WSL Birmensdorf, mostly with Cenococcum geophilum and different truffle species.
In my PhD project, I would like to concentrate on the diversity, population dynamics and influence on the infection potential of transposable elements in Z. tritici. I’m looking forward to work in this dynamic and well connected laboratory, as well as in the very diverse institute of biology.
By Fanny and Daniel
How a fungal pathogen evolved host specialization by chromosomal rearrangements
Our paper on host specialization by chromosomal rearrangements in a fungal pathogen of wheat just came out in The ISME Journal and is now available online:
Despite the use of fungicides and resistant crop varieties, fungi cause major economic losses in agriculture. One major concern is the ability of plant pathogens to circumvent crop resistance and adapt to exploit the host. In plant-pathogen interactions, the specific recognition of a pathogen effector by a host resistance protein can trigger plant defences and prevent invasion by the pathogen. Mutations or deletions in pathogen effector genes are thought to enable pathogens to escape host recognition. However, we know very little about the loci and the mechanisms enabling virulence evolution in pathogen populations. A better understanding of these mechanisms is essential for the control of fungal diseases.
Our study system was the highly damaging fungal pathogen Zymoseptoria tritici. This pathogen is causing Septoria tritici blotch (STB) on wheat that leads to large economic losses worldwide. We obtained a collection of 106 Z. tritici isolates sampled in four locations across the geographical range of the pathogen. For all strains, we assessed virulence on two Swiss wheat cultivars that had different levels of resistance. We generated whole-genome sequences for each strain and performed genome-wide association studies (GWAS) to identify loci linked to virulence.
We identified multiple loci in the pathogen genome associated with virulence on each cultivar. However, the loci identified for the two different cultivars hardly overlapped showing that the pathogen evolved distinct loci to exploit genetically different wheat. The strongest association in the pathogen genome was linked to the deletion of a gene. This gene encoded a small secreted protein that was highly expressed during the appearance of the first disease symptoms. The deletion of the gene was associated to a gain in virulence on one cultivar only. This is likely due to the fact that this cultivar has the ability to detect this specific protein and activate defences. The pathogen gene seems to be very young, because we found no evidence in any of the most closely related species. We also found that the deletion of the gene happened thanks to the action of a large block of repetitive DNA containing selfish genomic elements (transposable elements). Hence, the pathogen likely benefited from the action of selfish elements to become more virulent on wheat. In summary, our study demonstrates that chromosomal rearrangements can play a major role in host specialization in fungal pathogens.
Fanny very convincingly passed her PhD defence at the ETH Zurich Friday 20 January! Warmest congratulations from the entire group. See below for the enthusiastic tweet by Fanny's external examiner Pascal Frey (@pascal_frey) from the INRA Nancy (France). Now, it's time to celebrate.
The pathogen genomics group has now officially become the Laboratory of Evolutionary Genetics at the University of Neuchâtel. Also, the lab was just joined by its first new member, Ursula Oggenfuss - welcome! But we still maintain a presence at the ETH Zürich with Norfarhan, Clémence, Fanny and Simone staying on for a while.
More updates of what's happening in Neuchâtel will be posted in the coming months.
View from the new offices in Neuchâtel. Definitely the place to be to watch pretty sunsets.
Daniel was invited to speak at Peter Solomon's (Australian National University) fantastic annual meeting on molecular plant pathology near Canberra. The meeting took place up at the Stromlo observatory overlooking the beautiful surroundings. For more information about the meeting, check this link here: http://www.wheatbiosecurity.com/stromlo
by Farhan and Daniel
The evolution of azole resistance in agricultural fields
Our paper on multilocus resistance evolution to azoles in a fungal plant pathogen is online now.
The evolution of fungicide resistance is truly worrisome for farmers and at the same time extremely fascinating as a case study of rapid adaptive evolution.
One of the most commonly used classes of fungicides are azoles. Resistance to azoles has been well established in human and animal pathogenic fungi, and includes a wide array of mechanisms to cope with stress induced by fungicides. The analysis of resistance in plants pathogens was largely focused on mutations in a specific gene called CYP51. This gene encodes the protein that is directly targeted by azoles. Additional mechanisms were rarely explored in field populations.
We studied an ubiquitous pathogen of barley called Rhynchosporium commune. We obtained a pathogen collection across the world comprising regions where fungicides were used frequently and others were the pathogen was unlikely to have been exposed yet. Then, we sequenced the entire genome of all strains and screened for loci associated with increased resistance to azoles. For this, we used genome-wide association mapping (or GWAS), which is a widely used tool in human and plant genetics.
Our study that just came out in Molecular Ecology showed that several previously unknown genes contributed to azole resistance. These genes encoded for proteins related to stress responses, regulation of transcription and other processes. Then, we analyzed whether some mutations that conferred higher resistance had an impact on the growth of the fungus. We found that some mutations had no detectable impact on growth and are likely to become fixed in resistant populations. But we also found resistance mutations that were associated with slower growth. Such trade-offs in the evolution of resistance (or "cost of resistance") are important, because we may be able to exploit such "weaknesses" of the pathogen to devise more sustainable control strategies.