Embedded Files
A Month at Flakkebjerg, Aarhus University, Denmark, by DC4 Sarkal Jyakhwa
From November 4 to December 5, 2024, I had the privilege of visiting the AU Flakkebjerg Research Center, part of Aarhus University. Located in the countryside of Zealand, near Slagelse, the center offered an enriching and memorable experience, both professionally and personally.
I felt that the Flakkebjerg Research Center is small but surrounded by expansive research fields, giving it the charm of the countryside. The tranquil environment, coupled with the friendliness of the people there, made it a perfect setting for focused research. The team was always willing to help, creating a supportive atmosphere that I deeply appreciated.
My primary goal during this stay was to estimate the biomass of arbuscular mycorrhizal (AM) fungi in soil samples by extracting whole-cell fatty acids. The principle of fatty acid biomarkers is based on the knowledge that different kinds of fatty acids are found in different microorganisms. Specifically, I focused on analyzing the fatty acid marker 16:1ω5, a lipid found predominantly in AM fungal hyphae and spores. This marker serves as a reliable indicator of AM fungal biomass in soil.
The soil samples used for this study were collected from the Foulumgaard Research Center, another Aarhus University facility, during the first week of July 2024. Over the month, I worked tirelessly to process 96 soil samples, extracting and quantifying their lipid profiles to assess the fungal presence.
The beginning of my stay was both exciting and challenging. For the first two weeks, the sun seemed to vanish behind persistent clouds, creating a gloomy atmosphere. The workload was demanding, and the days were filled with challenges, but I adapted and found my rhythm. I managed to meet online with my supervisor, Ivika Ostonen, from the University of Tartu, a couple of times to discuss the progress and plans for the duration of my stay.
A huge shoutout to Associate Professor Sabine Ravnskov, for warmly welcoming me to Aarhus University, and to Bente Laursen, laboratory technician, who was an incredible mentor throughout the process. She guided me through the extraction procedures, answered my questions, and ensured everything ran smoothly.
One memorable moment was witnessing the first snowfall of the season on November 20, 2024. Although it melted quickly, it was a beautiful sight that broke the monotony of the grey days.
On November 21, I had the unique opportunity to present my research outside of the RootED Doctoral Network and my home institution, the University of Tartu in Estonia. During the seminar, I introduced the RootED Doctoral Network and shared my ongoing work on the interactions between AM fungi and root traits in an organic crop rotation experiment. The session was interactive, with thought-provoking questions from the audience. The discussions not only challenged my understanding but also broadened my perspective on the field.
By the end of my stay, I successfully extracted fatty acids from all 180 soil samples—96 planned samples plus additional ones. The initial results looked promising, which validated my efforts and precision throughout the month.
Despite the demanding schedule, I made time to explore the serene surroundings of Flakkebjerg. Weekends were for cycling along quiet roads lined with green fields of broccoli, wheat, and barley. The tranquility of the countryside provided a refreshing escape from the rigorous lab work.
My visit to Flakkebjerg was a transformative experience. From hands-on lab work to engaging discussions at the seminar, I gained valuable insights and skills while forming connections with passionate researchers. It was a month of learning, growth, and discovery—both in science and life. Finally, I confess that I missed Tartu during this visit.
Poster Presentation at the 22nd International Soil Tillage Research Organisation (ISTRO) Conference in Virginia Beach, USA by DC2 Maria Camila Herrera-Coy, Aarhus University
I am a PhD student in the RootEd doctoral network working at Aarhus University under the supervision of Prof. Lars Munkholm, Associate Prof. Sabine Ravnskov and Dr Loraine ten Damme. During the ISTRO conference, I presented the poster Towards a Methodology for Evaluating Subsoil Recovery by Single and Mixed Crops. The findings from this methodology quantify the soil recovery effect of potential bio-subsoiler species and crop mixtures. It contributes to a deeper comprehension of the soil structure-arbuscular mycorrhizal fungi-root interaction.
ISTRO 2024's theme was “Living Roots, Living Soil,” which focuses on regenerative agriculture, soil health, cover crops, residue systems, and sustainable crop production. The ISTRO conference promotes engagement among scientists and an opportunity to meet with other young researchers, share research, and stimulate new collaborations and ideas.
Poster Presenation at 12th International Society of Root Research (ISRR) by Pratikshya Joshi, INRAE
Poster Presenation at 12th International Society of Root Research (ISRR) by Pratikshya Joshi, INRAE
From June 2-7, I attended the 12th International Symposium by the International Society of Root Research (ISRR) with the theme Roots (and Roads) to a sustainable future in Leipzig, Germany. Thanks to the extensive network within the RootEd consortium, I arrived at the conference already familiar with several attendees, and connected with more researchers within the field as I attended with my supervisor and a doctoral student from my research team.
Presenting my doctoral project results through a poster titled “Impact of combined sulfur deficiency and water stress on nodulated pea root system architecture, water and nutrient uptake” helped improve my skills in scientific communication. This led to engaging discussions on sulfur deficiency and root phenotyping methods, and there was particular interest on Rhizotubes™ (cylindrical rhizotron systems which allow non-invasive root system imaging during cultivation). Our research on concurrent occurrence of sulfur deficiency and drought stress seemed new and relevant as multiple posters and presentations were focused on water stress and other key nutrients.
The plenary lectures, seminars and posters covered a large variety of topics ranging from water and nutrient uptake, root-microbe interaction to root traits phenotyping and root responses to environmental changes.
I found the lecture by Dr. Fieke Dijkstra on soil carbon dynamics interesting and learned how the activity between roots and microbes in the rhizosphere, the area around the roots, negatively influences carbon stabilisation through rhizosphere priming effect of accelerating soil organic matter decomposition, and also improves stabilise soil carbon by forming organo-mineral complexes called mineral associated organic matter (MAOMs). I was fascinated by Dr. Michael Bonkowski’s lecture on how plants select microbiome for its nutrient needs. For example, in the case of root bacteria called Rhizobia, the legume plant has to anticipate beforehand if the plant is worth the energy investment because it is only when the Rhizobia is established inside specialised organs called nodules, it starts to supply nitrogen to the plant in exchange for carbon. It helped me gain new perspectives on how plant is actively integrating information from the environment to decide on symbiotic relationships with soil microbiota. Finally, the panel discussion on the different cultivation methods, their advantages and drawbacks to answer different research questions within root research was stimulating and will be helpful when deciding on experimental setup. It was a great ending discussion to a week-long exchange of research and ideas, highlighting the diverse approaches and methodologies in the field.
I am grateful to my research group and to RootEd for this opportunity to be inspired by current root research direction and to establish contact with researchers for advice and future collaborations.
YouTube video by DC5 Denis Florentin Sfrangeu, University College Dublin
My research focuses on the 3D soil matrix and its impact on root-to-root interactions between wheat (Triticum aestivum L.) and blackgrass (Alopecurus myosuroides Huds.). I'm thrilled about the progress so far, and look forward to the discoveries ahead!
For more details, check out my YouTube video: https://lnkd.in/ewFqCbK6
Exploring Root Phenotyping Innovations at INRAE, Dijon: A Visit to 4pmi by Fengjiao Lu, Wageningen University & Research
In February, I had the opportunity to visit INRAE in Dijon, where I learned about the innovative root Phenotyping platform 4pmi. During the week, I visited the 4pmi platform in Dijon and spent most of my time with their engineer, Mikal. Through Mikal, I gained insight into their full pipeline of phenotyping, from data acquisition to machine learning for root traits calculation. During my trip, I discussed machine learning methods for root traits calculation such as root branching counting and root angle calculation. Additionally, I received valuable suggestions from them about our new rhizotron system.
A week at NIAB, Cambridge, by DC5 Denis Florentin Sfrangeu, University College Dublin
A week at NIAB, Cambridge, by DC5 Denis Florentin Sfrangeu, University College Dublin
My name is Denis-Florentin Sfrangeu, and I am a first year PhD student at University College Dublin, part of the RootED doctoral network under the supervision of Dr. Saoirse Tracy and Dr. Stéphanie Swarbreck (NIAB). My current research focuses on studying how the nutrient availability of the soil matrix affects root-to-root interactions between wheat and blackgrass, a notorious herbicide-resistant weed. The aims of my project are (i) to investigate how soil nutrient availability mediates the root-to-root interactions; (ii) to determine the blackgrass-susceptibility of agronomically important wheat cultivars; and (iii) to assess the role of different root architecture in the weed-crop interaction. In one of the experiments, my focus is to investigate how wheat is affected by neighbouring blackgrass under field conditions. This experiment will be conducted during my secondment at NIAB, under the supervision of Dr. Stéphanie Swarbreck.
Last week, I had the opportunity to conduct an experiment at NIAB, Cambridge. Founded in 1919 as the National Institute of Agricultural Botany and privatised in the 1990s, NIAB has grown into an internationally renowned crop science organization specializing in translational plant and soil sciences. It operates 10 regional centres across the UK, with its headquarters located in Cambridge. NIAB focuses on agronomy, data science, farming systems, and plant genetics, aiming to address climate change, food security, and sustainable development challenges. Its mission is to advance agriculture, arboriculture, and horticulture worldwide through services, training, and research in key areas such as agronomy, farming systems, and crop research.
Blackgrass (Alopecurus myosuroides Huds.) is a notorious herbicide-resistant weed, causing annual wheat yield reductions of 0.8 million tons and an estimated £0.4 billion loss in the UK. Its distribution is influenced by environmental factors (soil type, rainfall patterns), geographic factors (landforms, altitude), and biological factors (similar lifecycle to winter wheat). John Cussans is a Weed Biology and Management Specialist at NIAB working on the promotion and development of sustainable integrated weed management. One of his experiments, supported by the manufacturer Adama as part of their herbicide product support, is ongoing at a satellite near Hinxton, Cambridgeshire, UK. In the trial, John uses a randomized block design with factors such as wheat seed rate, herbicide application level, and drilling date to study the effect of neighbouring blackgrass on wheat plants. The wheat seed rate influences competition with blackgrass, crop yield, and herbicide effectiveness. The drilling date influences blackgrass density; later drilling allows more blackgrass to germinate and be destroyed before planting, reducing its density in the crop. These trials have shown that an autumn drilling date increases weed seedling control by enhancing soil-acting herbicide efficacy in colder, wetter conditions.
In our pilot experiment, we aimed to characterise the root architecture of wheat plants grown under different blackgrass densities in the field, more specifically three distinct herbicide application rates – untreated, low application rate, and medium application rate. Samples were collected using a technique known as shovelomics, which involves manually digging up plants with a spade to study their root systems. This method allows for the direct observation and measurement of root traits and biomass, providing valuable data on the interaction between wheat and blackgrass roots in their natural field environment.
After the samples were collected, they were placed in a sealable plastic bag and marked accordingly. Subsequently, root washing was performed, followed by photographing the samples, and performing both aboveground traits measurement (fresh and dry weight, number of plants, tallest tiller), and belowground traits measurement on scanned wheat plants (fresh and dry weight, root architecture traits). To ensure an accurate root quantification, the images of wheat roots were cropped (panel A), segmented using the Labkit plugin version 0.3.11 in Fiji version 1.54i (panel B), and then analysed using RhizoVision Explorer version 2.0.3 (panel C). An example of the root image analysis pipeline can be seen above.
During my one-week visit to NIAB, I had the opportunity to observe the current research, meet with the team members, and conduct a preliminary shovelomics experiment. This visit allowed me to better understand NIAB’s focus areas and missions, as well as to get hands-on experience with the shovelomics pipeline, from sample collection to data analysis. I look forward to my secondment at NIAB next year, when I will be able to collaborate with researchers and contribute to my ongoing research project to better understand how wheat and blackgrass interact at the root level.
Participation in Fascination of Plants day by DC3, Renaud Bulpa, University College Dublin
Participation in Fascination of Plants day by DC3, Renaud Bulpa, University College Dublin
On the 12th May 2024, I had the opportunity to take part in the 7th “Fascination of Plants day” as an invited researcher in the Université catholique de Louvain (UCLouvain) in Louvain – la – Neuve, Belgium. This international event aims at “lifting the veil on the fascinating world of plants” (UCLouvain - Fascination of plants day). To this end, researchers and technical staff members organised many different activities open to the public across the University, such as guided tours of the glasshouses facility, workshops on pollinators, on how to identify plants, on lichens, etc. and even a workshop for children to understand how plants work.
In this context, I hosted the workshop “Back to the roots : à la recherche de nos racines”, a workshop open to all and where I introduced and explained to the interested participants the concepts of root research. I showed them some simple techniques commonly used in root phenotyping, i.e., aeroponics, hydroponics, and rhizotrons, explaining their applications, advantages, and disadvantages. Furthermore, I showed how the data collected during experiments could be used to create models of root systems used in many studies.
For many attendees, this workshop highlighted for the first time the importance of roots in the functioning of a plant, and their fascinating dynamics and complexity, leading to several stimulating and invigorating conversations.
Page updated
Google Sites
Report abuse