Workshop “Scientific Writing” at the Thünen Institute for Biodiversity, Brunswick
(October 23-25 2023)
A scientific writing workshop for Ph.D. students of our SPP2322 was organized to support students to prepare scientific manuscripts for publication of results from their experimental work. The four tutors of this workshop shared their experience obtained over decades of their careers as authors, but also as editors of scientific journals (FEMS Microbiology Ecology, European Journal of Soil Biology, Soil Biology & Biochemistry) and as reviewers.
Different lectures addressed issues related to the overall structure and the requirements for each section to be written. Ph.D. students presented examples of their current results and ideas on how to incorporate those into a manuscript. Between lectures, there was time dedicated for more detailed discussion of specific problems to present and discuss results within small working groups and tutors. Many uncertainties about how to present and discuss results were addressed interactively and stimulating discussions continued even during the evening dinner at the Al Duomo restaurant located directly at the historical Burgplatz and the lion statue of Braunschweig.
Many thanks to the tutors (Damien Finn, Evgenia Blagodatskaya, Sergey Blagodatsky and Christoph Tebbe), to the technical staff of the Thünen Institute which supported a pleasant atmosphere, and to all participants for their curiosity and activity! Hopefully many high-quality publications in peer-reviewed journals to be followed.
2nd Summer school in Bad Urach – „Modeling in biothermodynamics and systems ecology” (June 5-7 2023)
A group of SoilSystems researchers came together at the “Haus auf der Alb” in Bad Urach to dive into the details of biogeochemical and bioenergetic process-based modeling.
The first “modeling exercise” started with finding out the distance of everyone’s place of birth from Bad Urach and a “peer-reviewed” presentation of each participant to the group. We followed then an intense schedule, which included daily lectures covering thermodynamic principles, microbial physiology and bioenergetics. In the exercises with R we started with a simple model to simulate aerobic microbial glucose utilization. We extended the model to account for temperature controls, microbial dormancy and finally also anaerobic glucose utilization. Model fitting was demonstrated with a data set on aerobic glucose decomposition in Dikopshof soil, which is one of the selected soils of the common experimental platform of the SPP.
On top of the modeling challenge, everyone successfully also mastered the physical challenge of a 12 km hike to the ruins of Bad Hohen Urach and the Urach Waterfalls followed by an evening research talk and intense scientific discussions at the well-deserved campfire.
Many thanks to the lecturers and organizers (Thomas Maskow, Søren Nors Nielsen, Thomas Wutzler, Sergey Blagodatsky, Martin Endress, Holger Pagel, Thilo Streck, and Arjun Chakrawal) and to all participants!
1st Training course “Determination of amino sugars in soils”
From 18th to 20th of April 2023, the training course “Determination of amino sugars in soils” was held at the Witzenhausen campus of the University of Kassel. Participants were able to get an in-depth look at how amino sugars in soils are measured using different methodologies.
The training course was opened by a lecture from Prof. Rainer Jörgensen, providing an introduction about the study of amino sugars and their role in soils. Subsequently, participants were conducted through two different amino sugar determination protocols: one to be read with High Performance Liquid Chromatography (HPLC) and another by Gas Chromatography (GC). On the first two days, the participants learnt how to perform hydrolysis, sample purification and derivatization. It was important for this course that they could ask specific questions and look up close at every step of the protocol, so they could implement it in their own universities.
On the last day of the course, Dr. Jens Dyckmans and Prof. Rainer Jörgensen gave lectures regarding specific aspects of GC and HPLC amino sugar measuring, respectively. There, participants got to see real outcomes (chromatograms) from previous measurements and have fruitful discussions regarding the challenges involved with the methodologies.
Our SPP participants were also welcomed by blooming cherry trees, typical of Witzenhausen!
Many thanks to Prof. Rainer Jörgensen, Dr. Jens Dyckmans, Ms. Rebeca Oliva and the Department of Soil Biology and Plant Nutrition of the University of Kassel.
2nd Annual Meeting in Hohenheim
We had the great pleasure of holding our 2nd annual conference from March 21st to 23rd in the beautiful castle of the University of Hohenheim. The Rector of the University of Hohenheim, Prof. Dr. Stephan Dabbert, warmly welcomed us with a talk on the tradition of agricultural and soil research in Hohenheim. Our first keynote speaker, Stefan Geisen from Wageningen University & Research, took us on a fascinating journey into the world of protists and nematodes, highlighting their role in microbial networks and interactions in soil systems.
On Tuesday afternoon and the whole of Wednesday, we received detailed insights into the progress of the 18 ongoing projects within our SPP SoilSystems in great presentations and a nice poster session. The fruitful discussion of the interesting results was deepened in several discussion rounds under the heading of our working groups, in which possible future activities beyond the project boundaries were also worked out. Many new ideas and collaborations also emerged at the convivial dinner on Tuesday evening in the Denkbar on the Hohenheim University campus.
The last day was opened by our second keynote speaker, Anke Herrmann from the Swedish University of Agricultural Sciences with a great talk about her pioneering work on the key topic of our research program: the energetic perspective of organic matter formation, turnover and its stabilization in soils. The 2nd annual meeting was closed with a general discussion round among all participants, where we tried to figure out where is a promising potential that has to be addressed in the second funding phase of the priority program. Overall, the 2nd annual meeting was a complete success.
Many thanks to our two keynote speakers Anke Herrmann and Stefan Geisen as well as to our local hosts from the University of Hohenheim under the leadership of Christian Poll and Sven Marhan.
1st Young Scientist Workshop in Trier
From 5th to 7th of December 2022 the first workshop for the young scientist in SPP2322 SoilSystems took place at University of Trier. It opened with a discussion round among the participants in which they gave updates on their project progress during their first PhD year, identified overarching challenges for the SPP and formed ideas on how to strengthen collaboration and communication with each other. The afternoon continued with a first introduction in the programming language R given by Dr. Mario Gilcher from Luxsense Geodata SARL who made sure that everyone could follow the course despite of very different experience levels to begin with. The day ended with a guided tour through the old town of Trier, which is considered to be the oldest city in Germany.
On the second day the young scientists continued their R training and were taught on key challenges using R such as data handling and different visualization options as well as applying basic statistic tests and testing their prerequisites. During the lessons, the participants could directly apply their new knowledge and in the last part of the course, they had the opportunity to independently test their skills working with a data set kindly provided by one of them. The workshop was also used to refresh the young scientists knowledge on Good Scientific Practice and they learned about the rights and duties in their scientific career highlighted with practical examples given by the presenter for this slot, Dr. Alexandra Krämer from the University of Bonn. During this, they also learned about the best practices for keeping a lab journal, their legal obligations regarding documentation and how to approach common challenges for lab journaling. The second day ended with a social evening at von Nell’s winery in the suburbs of Trier, where participants had the opportunity to see the winemaking process and taste locally brewed wine.
Many thanks again to Mario and Alexandra for sharing the knowledge on these important topics. Thanks also to Sören Thiele Bruhn, Denise Vonhoegen and Ubaida Yousaf who were the hosts of this workshop.
1st Summer school in Leipzig – „Methods on microbial substrate turnover”
After the first annual meeting in May, 15 participants came together again in Leipzig for the 1st summer school of the SPP SoilSystems (October 17-19) under the motto “Methods on microbial substrate turnover”.
The summer school opened with an introductory session for participants on how to use mass balances and thermodynamics in their projects. In the afternoon, Anja Miltner (UFZ Leipzig) gave a lecture on the background and basics of calculating isotope mass balances followed by an exercise session on that topic. The day ended with a common dinner in the Ratskeller. The second day opened with an online presentation on microbial ecology by Damien Finn and Christoph C. Tebbe (Thünen Institut für Biodiversität, Braunschweig). They provided an excellent overview of molecular methods and next-gen sequencing techniques that can be used to study microbial substrate turnover. Thomas Maskow (UFZ Leipzig) then gave two lectures as well as practical exercises (incl. thermodynamic calculations) on thermodynamics of compound transformation and calorimetric approaches. Finally, the day ended with an introductory lecture on the MTB – Microbial turnover to biomass – model by Stefan Trapp (Technical University of Denmark, Kongens Lyngby). The summer school ended on the third day with exercises on the MTB model and discussion rounds.
Many thanks to the lecturers Anja Miltner, Thomas Maskow, Matthias Kästner, Damien Finn, Christoph C. Tebbe and especially Stefan Trapp, who made the long journey from Denmark.
1st Annual Meeting in Leipzig
After our virtual kickoff-meeting (25th November 2021) we were very happy to came together in Leipzig for the first time in physical presence since the start of the SPP 2322 SoilSystems. The 1st annual meeting took place in the Leipziger KUBUS from 18th to 20th May 2022 and was hosted by colleagues from the UFZ (Department of Environmental Biotechnology & Department of Environmental Microbiology).
The meeting was opened with a joint presentation by the panel group, where general issues, a short scientific outline as well as a possible experimental approach of the SPP was presented. This was of special interest for the new Ph.D. students and colleagues, who did not attend the previous virtual meetings. Welcome to the SPP SoilSystems! A keynote was given by Matthias Kästner (UFZ Leipzig) afterwards with the title: How to estimate the theoretical energy release of a turnover reaction in soil? – an introduction into a dark area. At the poster and coffee session in the afternoon, all young scientists presented their projects and came in touch with all other SPP members. A scientific committee evaluated the posters and announced the winners of the first SPP SoilSystems poster prize:
- Martin Endress (University of Cologne) – P15: C-timing
- Marc Piecha (University of Greifswald) – P9: MYXED-UP & Guodong Shao (University of Tuebingen) – P14: EcoEnergeticS
Congratulation to the awardees!
On the second and third day of the meeting, the focus was on two different workshops. Thomas Maskow (UFZ Leipzig) and his group gave a hands-on workshop on calorespirometry including a theoretical background into soil thermodynamics, sample preparation, experimentation and data evaluation. Anja Miltner (UFZ Leipzig) introduced the SoilSystems community into mass balances using isotopes. Many thanks to Thomas, Anja and colleagues for giving these exciting workshops.
The first come together at the 1st annual meeting was also used to elect an Ombudsperson of the SPP as well as a Representative for the Young Scientist. Tessa Camenzind (Freie Universität Berlin) is the Ombudsperson from now on, while Alina Rupp (UFZ Leipzig) represents the Young Scientists in cooperation with Ubaida Yousaf (University of Trier). Congratulations and many thanks for volunteering.