Thomas Depaepe

Dr. Thomas Depaepe

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Research Focus & Metrics

Academic Career Length

10Years (2017-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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19 March 2018 in PLOS Genetics
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AZAxel De Zélicourt
Axel De Zélicourt
LSLukas Synek
Lukas Synek
MSMaged M. Saad
Maged M. Saad
HAHanin Alzubaidy
Hanin Alzubaidy
RJRewaa S. Jalal
Rewaa S. Jalal
Heribert HirtHeribert Hirt
Heribert Hirt
Several plant species require microbial associations for survival under different biotic and abiotic stresses. In this study, we show that Enterobacter sp. SA187, a desert plant endophytic bacterium, enhances yield of the crop plant alfalfa under field conditions as well as growth of the model plant Arabidopsis thaliana in vitro, revealing a high potential of SA187 as a biological solution for improving crop production. Studying the SA187 interaction with Arabidopsis, we uncovered a number of mechanisms related to the beneficial association of SA187 with plants. SA187 colonizes both the surface and inner tissues of Arabidopsis roots and shoots. SA187 induces salt stress tolerance by production of bacterial 2-keto-4-methylthiobutyric acid (KMBA), known to be converted into ethylene. By transcriptomic, genetic and pharmacological analyses, we show that the ethylene signaling pathway, but not plant ethylene production, is required for KMBA-induced plant salt stress tolerance. These results reveal a novel molecular communication process during the beneficial microbe-induced plant stress tolerance. Plants as sessile organisms are facing multiple stresses during their lifetime. Among them, abiotic stresses, such as salt stress, can cause severe crop yield reduction, leading to food security issues in many regions of the world. In order to respond to growing food demands, especially in the context of the global climate change and increasing world population, it then becomes urgent to develop new strategies to yield crops more tolerant to abiotic stresses. One way to overcome these challenges is to take advantage of plant beneficial microbes, defined as plant growth promoting bacteria (PGPB). In this study, we report the beneficial effect of Enterobacter sp. SA187 on plant growth under salt stress conditions. SA187 increased the yield of the forage crop alfalfa when submitted to different saline irrigations in field trials. Moreover, using the model plant Arabidopsis thaliana, we demonstrate that SA187 mediates its beneficial activity by producing 2-keto-4-methylthiobutyric acid (KMBA), which modulates the plant ethylene signaling pathway. This study highlights a novel mechanism involved in plant-PGPB interaction, and proves that endophytic bacteria can be efficiently used to enhance yield of current crops under salt stress conditions.

6 December 2019 in Frontiers in Plant Science
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LVLisa Vanderstraeten
Lisa Vanderstraeten
TDThomas Depaepe
Thomas Depaepe
SBSophie Bertrand
Sophie Bertrand
DSDominique Van Der Straeten
Dominique Van Der Straeten
The plant hormone ethylene plays a pivotal role in virtually every aspect of plant development, including vegetative growth, fruit ripening, senescence, and abscission. Moreover, it acts as a primary defense signal during plant stress. Being a volatile, its immediate biosynthetic precursor, 1-aminocyclopropane-1-carboxylic acid, ACC, is generally employed as a tool to provoke ethylene responses. However, several reports propose a role for ACC in parallel or independently of ethylene signaling. In this study, pharmacological experiments with ethylene biosynthesis and signaling inhibitors, 2-aminoisobutyric acid and 1-methylcyclopropene, as well as mutant analyses demonstrate ACC-specific but ethylene-independent growth responses in both dark- and light-grown Arabidopsis seedlings. Detection of ethylene emanation in ethylene-deficient seedlings by means of laser-based photoacoustic spectroscopy further supports a signaling role for ACC. In view of these results, future studies employing ACC as a proxy for ethylene should consider ethylene-independent effects as well. The use of multiple knockout lines of ethylene biosynthesis genes will aid in the elucidation of the physiological roles of ACC as a signaling molecule in addition to its function as an ethylene precursor.

8 May 2024 in Nature Communications
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VSVojtěch Schmidt
Vojtěch Schmidt
RSRoman Skokan
Roman Skokan
TDThomas Depaepe
Thomas Depaepe
KKKatarina Kurtović
Katarina Kurtović
SHSamuel Haluška
Samuel Haluška
JPJan Petrášek
Jan Petrášek
The genomes of charophyte green algae, close relatives of land plants, typically do not show signs of developmental regulation by phytohormones. However, scattered reports of endogenous phytohormone production in these organisms exist. We performed a comprehensive analysis of multiple phytohormones in Viridiplantae, focusing mainly on charophytes. We show that auxin, salicylic acid, ethylene and tRNA-derived cytokinins including cis-zeatin are found ubiquitously in Viridiplantae. By contrast, land plants but not green algae contain the trans-zeatin type cytokinins as well as auxin and cytokinin conjugates. Charophytes occasionally produce jasmonates and abscisic acid, whereas the latter is detected consistently in land plants. Several phytohormones are excreted into the culture medium, including auxin by charophytes and cytokinins and salicylic acid by Viridiplantae in general. We note that the conservation of phytohormone biosynthesis and signaling pathways known from angiosperms does not match the capacity for phytohormone biosynthesis in Viridiplantae. Our phylogenetically guided analysis of established algal cultures provides an important insight into phytohormone biosynthesis and metabolism across Streptophyta.

1 April 2021 in Trends in Plant Science
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TDThomas Depaepe
Thomas Depaepe
SHSophie Hendrix
Sophie Hendrix
HRHenry Christopher Janse van Rensburg
Henry Christopher Janse van Rensburg
Wim Van den EndeWim Van den Ende
Wim Van den Ende
ACAnn Cuypers
Ann Cuypers
DSDominique Van Der Straeten
Dominique Van Der Straeten
Upon stress, a trade-off between plant growth and defense responses defines the capacity for survival. Stress can result in accumulation of misfolded proteins in the endoplasmic reticulum (ER) and other organelles. To cope with these proteotoxic effects, plants rely on the unfolded protein response (UPR). The involvement of reactive oxygen species (ROS), ethylene (ETH), and sugars, as well as their crosstalk, in general stress responses is well established, yet their role in UPR deserves further scrutiny. Here, a synopsis of current evidence for ROS-ETH-sugar crosstalk in UPR is discussed. We propose that this triad acts as a major signaling hub at the crossroads of survival and death, integrating information from ER, chloroplasts, and mitochondria, thereby facilitating a coordinated stress response.

28 March 2017 in Journal of Plant Growth Regulation
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ARAmanda Rasmussen
Amanda Rasmussen
YHYuming Hu
Yuming Hu
TDThomas Depaepe
Thomas Depaepe
FVFilip Vandenbussche
Filip Vandenbussche
FBFrancois-Didier Boyer
Francois-Didier Boyer
Danny GeelenDanny Geelen
Danny Geelen
Adventitious root formation is essential for cutting propagation of diverse species; however, until recently little was known about its regulation. Strigolactones and ethylene have both been shown to inhibit adventitious roots and it has been suggested that ethylene interacts with strigolactones in root hair elongation. We have investigated the interaction between strigolactones and ethylene in regulating adventitious root formation in intact seedlings of Arabidopsis thaliana. We used strigolactone mutants together with 1-aminocyclopropane-1-carboxylic acid (ACC) (ethylene precursor) treatments and ethylene mutants together with GR24 (strigolactone agonist) treatments. Importantly, we conducted a detailed mapping of adventitious root initiation along the hypocotyl and measured ethylene production in strigolactone mutants. ACC treatments resulted in a slight increase in adventitious root formation at low doses and a decrease at higher doses, in both wild-type and strigolactone mutants. Furthermore, the distribution of adventitious roots dramatically changed to the top third of the hypocotyl in a dose-dependent manner with ACC treatments in both wild-type and strigolactone mutants. The ethylene mutants all responded to treatments with GR24. Wild type and max4 (strigolactone-deficient mutant) produced the same amount of ethylene, while emanation from max2 (strigolactone-insensitive mutant) was lower. We conclude that strigolactones and ethylene act largely independently in regulating adventitious root formation with ethylene controlling the distribution of root initiation sites. This role for ethylene may have implications for flood response because both ethylene and adventitious root development are crucial for flood tolerance.

1 April 2019 in Plant and Soil
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Journal Article
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LLLeandro Van Langenhove
Leandro Van Langenhove
TDThomas Depaepe
Thomas Depaepe
SVSara Vicca
Sara Vicca
JBJoke van Den Berge
Joke van Den Berge
CSClement Stahl
Clement Stahl
IJIvan A. Janssens
Ivan A. Janssens
Background and aims Biological fixation of atmospheric nitrogen (N2) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana. Methods We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates. Results Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites. Conclusions Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.