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4. Limited effects of crop foliar Si fertilization on a marginal soil under a future climate scenario

Author

Rineau, Francois, Groh, Jannis, Claes, Julie, Grosjean, Kristof, Mench, Michel, Moreno-Druet, Maria, Povilaitis, Virmantas, Pütz, Thomas, Rutkowska, Beata, Schröder, Peter, Soudzilovskaia, Nadejda A., Swinnen, Xander, Szulc, Wieslaw, Thijs, Sofie, Vanderborght, Jan, Vangronsveld, Jaco, Vereecken, Harry, Verhaege, Kasper, Žydelis, Renaldas, and Loit, Evelin

Published
2024
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5. Cable bacteria as long-range biological semiconductors

Author

Bonné, Robin, Hou, Ji-Ling, Hustings, Jeroen, Meert, Mathijs, Hidalgo-Martinez, Silvia, Cornelissen, Rob, D'Haen, Jan, Thijs, Sofie, Vangronsveld, Jaco, Valcke, Roland, Cleuren, Bart, Meysman, Filip J. R., and Manca, Jean V.

Subjects
Physics - Biological Physics, Condensed Matter - Materials Science
Abstract

Filamentous cable bacteria exhibit unprecedented long-range biological electron transport, which takes place in a parallel fibre structure that shows an extraordinary electrical conductivity for a biological material. Still, the underlying electron transport mechanism remains undisclosed. Here we determine the intrinsic electrical properties of individual cable bacterium filaments. We retrieve an equivalent electrical circuit model, characterising cable bacteria as resistive biological wires. Temperature dependent experiments reveal that the charge transport is thermally activated, and can be described with an Arrhenius-type relation over a broad temperature range (-196{\deg}C to +50{\deg}C), thus excluding metal-like electron transport. Furthermore, when cable bacterium filaments are utilized as the channel in a field-effect transistor, they show n-type transport, indicating that electrons rather than holes are the charge carriers. Electron mobilities are in the order of 10$^{-1}$ cm$^2$/Vs, comparable to many organic semiconductors. This new type of biological centimetre-range semiconductor with low resistivity offers new perspectives for both fundamental studies and applications in (bio)electronics., Comment: 19 pages, including supplementary information

Published
2019

24. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIR ON AGE Birth Cohort

Author

Van Pee, Thessa, primary, Hogervorst, Janneke, additional, Dockx, Yinthe, additional, Witters, Katrien, additional, Thijs, Sofie, additional, Wang, Congrong, additional, Bongaerts, Eva, additional, Van Hamme, Jonathan D., additional, Vangronsveld, Jaco, additional, Ameloot, Marcel, additional, Raes, Jeroen, additional, and Nawrot, Tim S., additional

Published
2023
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30. Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex

Author

Postiglione, Alessia, primary, Prigioniero, Antonello, additional, Zuzolo, Daniela, additional, Tartaglia, Maria, additional, Scarano, Pierpaolo, additional, Maisto, Maria, additional, Ranauda, Maria Antonietta, additional, Sciarrillo, Rosaria, additional, Thijs, Sofie, additional, Vangronsveld, Jaco, additional, and Guarino, Carmine, additional

Published
2022
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39. An Alliance of Trifolium repens—Rhizobium leguminosarum bv. trifolii—Mycorrhizal Fungi From an Old Zn-Pb-Cd Rich Waste Heap as a Promising Tripartite System for Phytostabilization of Metal Polluted Soils

Author

Oleńska, Ewa, primary, Małek, Wanda, additional, Sujkowska-Rybkowska, Marzena, additional, Szopa, Sebastian, additional, Włostowski, Tadeusz, additional, Aleksandrowicz, Olgierd, additional, Swiecicka, Izabela, additional, Wójcik, Małgorzata, additional, Thijs, Sofie, additional, and Vangronsveld, Jaco, additional

Published
2022
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41. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIRONAGE Birth Cohort.

Author

Van Pee, Thessa, Hogervorst, Janneke, Dockx, Yinthe, Witters, Katrien, Thijs, Sofie, Congrong Wang, Bongaerts, Eva, Van Hamme, Jonathan D., Vangronsveld, Jaco, Ameloot, Marcel, Raes, Jeroen, and Nawrot, Tim S.

Subjects
RNA analysis, FECAL analysis, CARBON analysis, AIR pollution, PARTICULATE matter, STATISTICS, LIFESTYLES, MOTHERS, CONFIDENCE intervals, SEQUENCE analysis, GUT microbiome, MULTIVARIATE analysis, MULTIPLE regression analysis, PRENATAL exposure delayed effects, CORD blood, SOCIOECONOMIC factors, ENVIRONMENTAL health, PLACENTA, RESEARCH funding, DESCRIPTIVE statistics, URINALYSIS, DATA analysis software, DATA analysis, PREGNANCY
Abstract

BACKGROUND: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce. OBJECTIVES: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families. METHODS: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI). RESULTS: Two diversity indices were negatively associated with placental black carbon [Shannon: -4.38% (95% CI: -8.31%, -0.28%); Simpson: -0.90% (95% CI: -1.76%, -0.04%)], cord blood black carbon [Shannon: -3.38% (95% CI: -5.66%, -0:84%); Simpson: -0.91 (95% CI: -1.66%, -0.16%)], and urinary black carbon [Shannon: -3.39% (95% CI: -5.77%, -0.94%); Simpson: -0.89% (95% CI: -1.37%, -0.40%)]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae, and urinary black carbon with Christensenellaceae and Coriobacteriaceae; associations with cord blood black carbon were not statistically significant after correction. CONCLUSION: Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. [ABSTRACT FROM AUTHOR]

Published
2023
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42. How Important Are the Relations between Vegetation Diversity and Bacterial Functional Diversity for the Functioning of Novel Ecosystems?

Author

Woźniak, Gabriela, Malicka, Monika, Kasztowski, Jacek, Radosz, Łukasz, Czarnecka, Joanna, Vangronsveld, Jaco, and Prostański, Dariusz

Abstract

Understanding ecosystem development of post-mining areas requires observing the development of the plant and microbial communities. It is widely known that mutual interaction is important for both of these groups, and both benefit significantly. The aim of this study was to broaden the knowledge about the relation between the vegetation and functional diversity of bacterial communities in novel ecosystems of post-mining areas and to discuss the potential applicability of methods of studies of bacterial functional diversity in these ecosystems with special attention paid to the BIOLOG method. The functional diversity of microbial communities of five types of microhabitats of post-coal mining heap (Upper Silesia, Poland) was studied using the BIOLOG method. Four of them were covered by spontaneously developed vegetation (two dominated by grasses Calamagrostis epigejos and Poa compressa and two others by dicotyledonous species Daucus carota and Tussilago farfara). The results obtained for vegetated microhabitats were compared with the diversity of microbial communities from non-vegetated types of microhabitat. Our study confirmed that microbial functional diversity measured by the summed area under the curve for all substrates, the richness index, the Shannon-Wiener index and the evenness index mirrors aboveground vegetation diversity. All of these measures differ, especially between non-vegetated patches and grassland patches dominated by C. epigejos and P. compressa. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Exploring the Microbiome Analysis and Visualization Landscape

Author

PEETERS, Jannes, THAS, Olivier, SHKEDY, Ziv, KODALCI, Leyla, MUSISI, Connie, OWOKOTOMO, Olajumoke Evangelina, DYCZKO, Aleksandra, HAMAD, Ibrahim, VANGRONSVELD, Jaco, KLEINEWIETFELD, Markus, THIJS, Sofie, AERTS, Jan, PEETERS, Jannes, THAS, Olivier, SHKEDY, Ziv, KODALCI, Leyla, MUSISI, Connie, OWOKOTOMO, Olajumoke Evangelina, DYCZKO, Aleksandra, HAMAD, Ibrahim, VANGRONSVELD, Jaco, KLEINEWIETFELD, Markus, THIJS, Sofie, and AERTS, Jan

Subjects
data analysis, microbiome, data visualization, biostatistics, visual analytics, bioinformatcs
Abstract

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.

Published
2021

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