Microbes are everywhere in the food system
Indeed, microbes are everywhere in the food system! They circulate in the open ocean where they serve as the basis of the marine food chain, they dwell in the intestines of our livestock or they are sitting on the roots, leaves and fruits of all the crop plants. While some of these microbes are specifically used to produce and preserve food and others just sit there with no obvious function, many are well known for the devastating diseases they cause on animals and plants.
Root diseases of pea
I am a doctoral student at the Institute of Agricultural Sciences, ETH Zurich and FiBL, the Research Institute of Organic Agriculture, Switzerland. I am interested in microbes that make our crops sick, but along my way I also encountered microbes that maybe, hopefully can protect plants against pathogens. More specifically, I am interested in root diseases of pea. These so-called root-rots are caused by various fungi and other fungal-like microbes that often simultaneously infect the plant – a very hard stand for the poor pea plant. Peas were bred by humans to produce juicy sugars eventually ending up as a tasty vegetable; but clearly, we are not the only ones that fancy this yummy dish. However, help might come from the microbes as well. Fungal microbes can also exist in a mutually beneficial symbiosis with the plants. Mycorrhizas, for example, strengthen the plants they infect and protect them from pathogens, just in exchange for a little bit of plant assimilated sugars. Or Clonostachys, a veritable fungi predator strangles other fungi and sucks them dry – So you are truly a happy pea when you have these fungi around your roots.
Microbial composition of different pea lines
Plants have the ability to selectively attract beneficial microbes and we know that this ability has a genetic basis. In our research we want to find out if pea lines with contrasting levels of root-rot resistance have different microbial compositions in and around the roots. To this end we assessed the resistance of over 300 pea lines from various geographic origins. We then tested a subset of pea lines in the field in order to analyze the microbial composition, the microbiome, with next-generation-sequencing. This sequencing process generates millions of snippets of barcode-like DNA-sequences that we compare to databases of known microbes. Sending out 100 samples of diseased pea roots for sequencing gets us terabits of data back – and that’s just simple text files with four letters: A, T, G and C! So, here it is, our complex food system; ready to be analyzed...
I presented part of my work at the World Food System Center Research Symposium 2018 with a scientific poster – and won the Mercator award for the best poster. I was awarded CHF 1000.- and decided to use this money to get help for my microbial data analysis.
Microbes are everywhere - Schematic illustration of the different roles micro-organisms play in our food systems; for instance they are at the basis of the food chain in the oceans, they increase nutrient uptake of crop plants and they are, since ancient times, key players in food production. However, they are also causal agents of many diseases challenging food production. Source: https://www.microbiomesupport.eu/
Microbial data analysis late at night
Ming-Hui “Maggie” Hsung did her studies in agricultural sciences at ETH Zurich and did her master thesis project in summer 2019 in the Plant Breeding Group at FiBL. We were together in the field at two different locations, digging out diseased pea plants, carefully assessing root-rot visually before wrapping them up in zip-lock bags and transporting them back to the lab on ice. We then extracted the DNA, containing the microbial DNA, present in the root and sent it for sequencing in a Canadian lab. Maggie analyzed a very similar data set as the core of here master thesis. She learned a lot on such analyses during that time. As microbiome data analysis is not trivial and because I do not have any experience with that sort of data, I asked her to work for our project.
After her Master Graduation Maggie travelled back to Taiwan just to endorse for a trip with her parents through China and Japan. They are setting up agricultural partnerships throughout eastern Asia for their projects on heat-tolerant red and white flesh strawberries. White strawberries are as delicious as the red ones (that’s what Maggie told me; I have never tried;), but lack the protein responsible for the red color, to which many humans are allergic to. On her days off Maggie analyses the microbiome data from our field experiment. And when its late at night far east we discuss the findings and next steps in a Skype meeting and how we might get our head around the complexity of plant-microbe interactions and how agriculture could harness this untapped potential.
Different pea lines growing in the field.
ABOUT THE AUTHOR
Lukas Wille just finished his doctoral studies at ETH Zurich in the Molecular Plant Breeding group. His work centered around pathogen complexes causing pea root rot diseases. Understanding how different micro-organisms interact will help future resistance breeding and crop management and is a sustainable solution for supporting pea cultivation. Lukas combined experiments in the green house and in the field and used molecular tools to quantify root pathogens in diseased plants. Lukas now starts working at the Research Institute for Organic Agriculture (FiBL), where he will continue his work on pea root rot complexes and how this knowledge can be implemented in resistance breeding.