Blog post written by Sandra Milena Gonzalez Sayer (visiting PhD student from Colombia)
One of my biggest passions is facing challenges related to molecular pattern discovery. Ever since I was doing my undergraduate program, I have been interested in understanding the pathogen role in plant disease and the molecular component in the pathogenicity process. My study model since that time has been Pseudocercospora ulei, an ascomycete biotrophic pathogenic fungus that causes a disease known as the South American Leaf Blight (SALB) in natural rubber plants (Hevea brasiliensis). Because of P. ulei’s biotrophic lifestyle, the isolation and in vitro culture has been one of the biggest challenges studying this pathogen. The obtention of P. ulei isolates from infected leaves could take up to 50 days, but once it occurs, maintaining the strains alive becomes another challenge. The common practice to preserve them is through periodic transference to fresh medium. However, it is well-known that this practice can affect the isolates genetic stability and generate phenotypic changes like the loss of pathogenicity. In my undergraduate thesis, I assessed long term preservation methods to maintain the P. ulei strains collection. As a result, I standardized conidia lyophilization conditions which allow maintaining the P. ulei isolations viability for more than one year.
Stroma of Pseudocercospora ulei
H. brasiliensis is a perennial species which presents an unproductive period of approximately six years. Because of that, plant breeding programs advance slowly, and unconventional genetic breeding strategies based on genetic engineering technics are still necessary. Aware that molecular knowledge is crucial to improving plant breeding programs and before to its draft genome release, I worked in searching for polymorphic molecular markers (Microsatellites and RAPDs) for discriminating a natural rubber population constituted by Asiatic and Latin American clones. These markers were used in a national service of H. brasiliensis varieties identification whose aim was organizing the clonal gardens that produce seedlings for future rubber plantations in Colombia. In this sense, the farmers could know the identity of the planted clones (SALB resistance or highly rubber yield clones) before the economic investment during the unproductive period.
My scientific career has been developed in the natural rubber group from the biotechnology institute of the National University of Colombia. The work of this group is focused on studying the natural rubber crop since a holistic perspective encompassing the pre and post cultivate stages as well as the productive period. It has been amazing to me having the opportunity to choose my research line through this integral view, so my decision was studying the SALB disease. Currently, I am doing my PhD studying the P. ulei pathogenicity mechanisms through genomic and transcriptomic perspective. The main goal of my thesis project is to improve the knowledge of P. ulei genome architecture and identify pathogenicity determinants deployed by this fungus to cause SALB disease. For this purpose, whole-genome shotgun sequencing and assembly of the P. ulei genome was done using Pacific BioScience, Oxford nanopore, and Illumina platforms. One of my more relevant findings is the P. ulei size genome is the biggest genome so far reported in the Mycosphaerellaceae family. Furthermore, this genome showed an exceptionally high repeat content that could be associated with a genome a size expansion event and could play an essential role in the environment fungal adaptation as well in the pathogenicity mechanism evolved.
Crepe rubber sheet
Natural rubber plantation and rubber tapping process (Mavalle S.A Villavicencio-Colombia)
Blog post written by Luzia Stalder who started her PhD in our lab in spring 2019.
Understanding how characteristics of organisms arise and interact with each other – this is the fundamental aim of biological research. As researchers, we want to unveil the complex relationships between physiological, molecular and genetic traits. Importantly, these relationships evolved in a highly branched network. Thus, to untangle complex relationships, we need to be able to measure a large set of variables at different levels simultaneously. For example, to understand the virulence of a pathogen on a host, we require knowledge of genomes of pathogen strains with different virulence, and test how these affect different hosts, which themselves are in different environments and inhabit different microbes. I believe that large datasets with information collections at different levels – together with modern bioinformatic tools – are key to uncover complex relationships of biological networks in a systematic manner.
Since I started to work on biological questions, I was fascinated how new meaningful relationships are revealed using large datasets. During my master studies at ETH Zurich, I extracted complex relationships from high-throughput genomic, transcriptomic - and proteomic data. In my first project, I used genomic data collected around the world with 114 populations of Rhynchosporium commune, a major fungal pathogen of barley, to understand how genomic changes influence its adaptation to fungicide. For my second project, I used transcriptomic datasets of hippocampal brain tissue of mice that have been subjected to either a stressful or a non-stressful situation, to understand how stress influences the expression network of different hippocampal regions. In a third project, I used large proteomic datasets of yeast, fly, mouse and human to understand how basic protein networks evolve across evolution.
For my PhD project, I joined the lab of Daniel Croll at the University of Neuchâtel, to focus on the complex microbiome network that influences plant health and disease. Typically, researchers study pathogen- host interactions in an isolated one pathogen – one host system. However, it has been shown that the presence of a second microbe on the host plant can either aid the arriving pathogen in a way that it becomes far more virulent – or on the contrary, can prevent the arriving pathogen from infecting the plant completely. One prominent example of such microbes are Pseudomonas bacteria, which are omnipresent on plant leaves and roots. Different Pseudomonas species either promote or inhibit fungal pathogen growth, and therefore significantly affect plant disease. I am intrigued by such microbe-microbe interactions and their impact on plant health. I hope to untangle a part of this complex interplay in the coming years. For this, I will focus on the tripartite system of wheat, the fungus Zymoseptoria tritici - the major pathogen of wheat - and the bacteria Pseudomonas. I want to understand how the diverse bacteria-fungal interactions affect plant health on a genetic and functional level. I will use high-throughput genomic and transcriptomic approaches to do so. My ultimate goal is to understand complex relationships that can be used for sustainable crop production in the first place, but also allow to draw parallels to complex microbiome systems in human.
Please find the details below and don't hesitate to contact email@example.com with questions.
Camille Kessler (MSc student in our lab) develops the genomic markers to save the Alpine ibex. Here's a video explaining the bigger context of the project.
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).