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Pot S, Tender CD, Ommeslag S, Delcour I, Ceusters J, Vandecasteele B, Debode J, Vancampenhout K. Elucidating the microbiome of the sustainable peat replacers composts and nature management residues. Front Microbiol 2022; 13:983855. [PMID: 36246232 PMCID: PMC9555241 DOI: 10.3389/fmicb.2022.983855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sustainable peat alternatives, such as composts and management residues, are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. This study examined if and how microbiological characteristics of subtypes of composts and management residues differ from peat-based substrates, and how feedstock and (bio)chemical characteristics drive these characteristics. In addition, microbiome characteristics were evaluated that may contribute to plant growth and health. These characteristics include: genera associated with known beneficial or harmful microorganisms, microbial diversity, functional diversity/activity, microbial biomass, fungal to bacterial ratio and inoculation efficiency with the biocontrol fungus Trichoderma harzianum. Bacterial and fungal communities were studied using 16S rRNA and ITS2 gene metabarcoding, community-level physiological profiling (Biolog EcoPlates) and PLFA analysis. Inoculation with T. harzianum was assessed using qPCR. Samples of feedstock-based subtypes of composts and peat-based substrates showed similar microbial community compositions, while subtypes based on management residues were more variable in their microbial community composition. For management residues, a classification based on pH and hemicellulose content may be relevant for bacterial and fungal communities, respectively. Green composts, vegetable, fruit and garden composts and woody composts show the most potential to enhance plant growth or to suppress pathogens for non-acidophilic plants, while grass clippings, chopped heath and woody fractions of compost show the most potential for blends for calcifuge plants. Fungal biomass was a suitable predictor for inoculation efficiency of composts and management residues.
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Affiliation(s)
- Steffi Pot
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- *Correspondence: Steffi Pot,
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Zwijnaarde, Belgium
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Ilse Delcour
- PCS Ornamental Plant Research, Destelbergen, Belgium
| | - Johan Ceusters
- Division of Crop Biotechnics, Department of Biosystems, Research Group for Sustainable Crop Production & Protection, KU Leuven, Geel, Belgium
- Centre for Environmental Sciences, Environmental Biology, UHasselt, Diepenbeek, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Karen Vancampenhout
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium
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Oltean T, Lippens L, Lemeire K, De Tender C, Vuylsteke M, Denys H, Vandecasteele K, Vandenabeele P, Adjemian S. Association of Cell Death Markers With Tumor Immune Cell Infiltrates After Chemo-Radiation in Cervical Cancer. Front Oncol 2022; 12:892813. [PMID: 35903697 PMCID: PMC9316180 DOI: 10.3389/fonc.2022.892813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022] Open
Abstract
Irradiation induces distinct cellular responses such as apoptosis, necroptosis, iron-dependent cell death (a feature of ferroptosis), senescence, and mitotic catastrophe. Several of these outcomes are immunostimulatory and may represent a potential for immunogenic type of cell death (ICD) induced by radiotherapy triggering abscopal effects. The purpose of this study is to determine whether intra-tumoral ICD markers can serve as biomarkers for the prediction of patient's outcomes defined as the metastasis status and survival over a 5-year period. Thirty-eight patients with locally advanced cervical cancer, treated with neoadjuvant chemoradiotherapy using cisplatin were included in this study. Pre-treatment tumor biopsy and post-treatment hysterectomy samples were stained for cell death markers and danger associated molecular patterns (DAMPs): cleaved caspase-3 (apoptosis), phosphorylated mixed lineage kinase domain like pseudokinase (pMLKL; necroptosis), glutathione peroxidase 4 (GPX4; ferroptosis) and 4-hydroxy-2-noneal (4-HNE; ferroptosis), high mobility group box 1 (HMGB1) and calreticulin. Although these markers could not predict the patient's outcome in terms of relapse or survival, many significantly correlated with immune cell infiltration. For instance, inducing ferroptosis post-treatment seems to negatively impact immune cell recruitment. Measuring ICD markers could reflect the impact of treatment on the tumor microenvironment with regard to immune cell recruitment and infiltration. One Sentence Summary Cell death readouts during neoadjuvant chemoradiation in cervical cancer.
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Affiliation(s)
- Teodora Oltean
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Lippens
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Medical Oncology, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC) Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Hannelore Denys
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Medical Oncology, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Katrien Vandecasteele
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Peter Vandenabeele
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Methusalem Program, Ghent University, Ghent, Belgium
| | - Sandy Adjemian
- Cell Death and Inflammation Unit, Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Van der Jeugt F, Maertens R, Steyaert A, Verschaffelt P, De Tender C, Dawyndt P, Mesuere B. UMGAP: the Unipept MetaGenomics Analysis Pipeline. BMC Genomics 2022; 23:433. [PMID: 35689184 PMCID: PMC9188040 DOI: 10.1186/s12864-022-08542-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools. Results Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools. Conclusions UMGAP’s protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08542-4).
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Affiliation(s)
- Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
| | - Rien Maertens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Aranka Steyaert
- Department of Information Technology, IDLab, imec, Ghent, Belgium
| | - Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
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De Tender C, Vandecasteele B, Verstraeten B, Ommeslag S, Kyndt T, Debode J. Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome. Front Plant Sci 2021; 12:700479. [PMID: 34497619 PMCID: PMC8419269 DOI: 10.3389/fpls.2021.700479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Biochar has been reported to play a positive role in disease suppression against airborne pathogens in plants. The mechanisms behind this positive trait are not well-understood. In this study, we hypothesized that the attraction of plant growth-promoting rhizobacteria (PGPR) or fungi (PGPF) underlies the mechanism of biochar in plant protection. The attraction of PGPR and PGPF may either activate the innate immune system of plants or help the plants with nutrient uptake. We studied the effect of biochar in peat substrate (PS) on the susceptibility of strawberry, both on leaves and fruits, against the airborne fungal pathogen Botrytis cinerea. Biochar had a positive impact on the resistance of strawberry fruits but not the plant leaves. On leaves, the infection was more severe compared with plants without biochar in the PS. The different effects on fruits and plant leaves may indicate a trade-off between plant parts. Future studies should focus on monitoring gene expression and metabolites of strawberry fruits to investigate this potential trade-off effect. A change in the microbial community in the rhizosphere was also observed, with increased fungal diversity and higher abundances of amplicon sequence variants classified into Granulicella, Mucilaginibacter, and Byssochlamys surrounding the plant root, where the latter two were reported as biocontrol agents. The change in the microbial community was not correlated with a change in nutrient uptake by the plant in either the leaves or the fruits. A decrease in the defense gene expression in the leaves was observed. In conclusion, the decreased infection of B. cinerea in strawberry fruits mediated by the addition of biochar in the PS is most likely regulated by the changes in the microbial community.
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Affiliation(s)
- Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Bruno Verstraeten
- Epigenetics and Defence Research Group, Department Biotechnology, Ghent University, Ghent, Belgium
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Tina Kyndt
- Epigenetics and Defence Research Group, Department Biotechnology, Ghent University, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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5
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Vanhoutte I, De Tender C, Demeyere K, Abdallah MF, Ommeslag S, Vermeir P, Saeger SD, Debode J, Meyer E, Croubels S, Audenaert K, De Gelder L. Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells. Toxins (Basel) 2021; 13:toxins13080552. [PMID: 34437423 PMCID: PMC8402469 DOI: 10.3390/toxins13080552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH2O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.
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Affiliation(s)
- Ilse Vanhoutte
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
- Computer Science and Statistics, Department of Applied Mathematics, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kristel Demeyere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Mohamed F. Abdallah
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA), Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Evelyne Meyer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Leen De Gelder
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
- Correspondence: ; Tel.: +32-9-243-24-75
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De Zutter N, Ameye M, Debode J, De Tender C, Ommeslag S, Verwaeren J, Vermeir P, Audenaert K, De Gelder L. Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status. Microb Biotechnol 2021; 14:1594-1612. [PMID: 34021699 PMCID: PMC8313256 DOI: 10.1111/1751-7915.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants' P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize's P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.
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Affiliation(s)
- Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Jane Debode
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Caroline De Tender
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityKrijgslaan 281 S9GhentB‐9000Belgium
| | - Sarah Ommeslag
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Jan Verwaeren
- Research Unit Knowledge‐based Systems (KERMIT)Department of Data Analysis and Mathematical ModelingGhent UniversityCoupure links 653GhentB‐9000Belgium
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA)Faculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Leen De Gelder
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
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7
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Vandecasteele B, Amery F, Ommeslag S, Vanhoutte K, Visser R, Robbens J, De Tender C, Debode J. Chemically versus thermally processed brown shrimp shells or Chinese mitten crab as a source of chitin, nutrients or salts and as microbial stimulant in soilless strawberry cultivation. Sci Total Environ 2021; 771:145263. [PMID: 33545468 DOI: 10.1016/j.scitotenv.2021.145263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Brown shrimp (Crangon crangon) shells and Chinese mitten crab (Eriocheir sinensis) were chemically demineralized and deproteinized (denoted as M1 to M4 for the shrimp shells and M5 to M7 for the Chinese mitten crab), and shrimp shells were torrefied at 200 to 300 °C (denoted as R200, R255, R300), and were compared with a commercially available chitin source (denoted as reference chitin). Based on their chemical characteristics, a selection of chitin sources was tested for their N mineralization capacity. The N release was high for the chemically treated shrimp shells and Chinese mitten crab, but not for the torrefied shrimp shells with or without acid treatment, indicating that treatment at 200 °C or higher resulted in low N availability. Interaction with nutrients was tested in a leaching experiment with limed peat for three thermally and two chemically processed shrimp shells and the reference chitin source. The K concentrations in the leachate for the chemically treated shrimp shells and the reference chitin were lower than for limed peat during fertigation. Irreversible K retention was observed for one source of chemically treated shrimp shells, and the reference chitin. The thermally treated shrimp shells had a significantly higher net release of P, Na and Cl than the treatment without chitin source. Three shrimp shell based materials (M4, R200 and R300) and the reference chitin were tested in a greenhouse trial with strawberry at a dose of 2 g/L limed peat. A very positive and significant effect on Botrytis cinerea disease suppression in the leaves was found for the reference chitin, M4 and R200 compared to the unamended control. The disease suppression of the 3 chitin sources was linked with an increase of the microbial biomass in the limed peat with 24% to 28% due to chitin decomposition and a 9-44% higher N uptake in the plants.
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Affiliation(s)
- Bart Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium.
| | - Fien Amery
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
| | - Sarah Ommeslag
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
| | - Kaitlyn Vanhoutte
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ankerstraat 1, 8400, Oostende, Belgium
| | - Rian Visser
- ECN part of TNO, Westerduinweg 3, 1755 ZG, Petten, the Netherlands
| | - Johan Robbens
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ankerstraat 1, 8400, Oostende, Belgium
| | - Caroline De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - Jane Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
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Pot S, De Tender C, Ommeslag S, Delcour I, Ceusters J, Gorrens E, Debode J, Vandecasteele B, Vancampenhout K. Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media. Front Microbiol 2021; 12:643679. [PMID: 33897654 PMCID: PMC8059793 DOI: 10.3389/fmicb.2021.643679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Three characteristics are considered key for optimal use of composts in growing media: maturity, pH and organic matter content. Maturation is a critical step in the processing of composts contributing to compost quality. Blending of composts with chopped heath biomass, sieving out the larger fraction of composts and acidification of composts by adding elemental sulfur may be used either to increase organic matter content or to reduce pH for a better fit in growing media. While several studies have shown the effectiveness of these treatments to improve the use of composts in growing media, the effect of these treatments on the compost microbiome has merely been assessed before. In the present study, five immature composts were allowed to mature, and were subsequently acidified, blended or sieved. Bacterial and fungal communities of the composts were characterized and quantified using 16S rRNA and ITS2 gene metabarcoding and phospholipid fatty acid analysis. Metabolic biodiversity and activity were analyzed using Biolog EcoPlates. Compost batch was shown to be more important than maturation or optimization treatments to determine the compost microbiome. Compost maturation increased microbial diversity and favored beneficial microorganisms, which may be positive for the use of composts in growing media. Blending of composts increased microbial diversity, metabolic diversity, and metabolic activity, which may have a positive effect in growing media. Blending may be used to modify the microbiome to a certain degree in order to optimize microbiological characteristics. Acidification caused a decrease in bacterial diversity and microbial activity, which may be negative for the use in growing media, although the changes are limited. Sieving had limited effect on the microbiome of composts. Because of the limited effect on the microbiome, sieving of composts may be used flexible to improve (bio)chemical characteristics. This is the first study to assess the effects of maturation and optimization treatments to either increase organic matter content or lower pH in composts on the compost microbiome.
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Affiliation(s)
- Steffi Pot
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium
| | - Caroline De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Sarah Ommeslag
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium
| | - Ilse Delcour
- PCS Ornamental Plant Research, Destelbergen, Belgium
| | - Johan Ceusters
- Research Group for Sustainable Crop Production & Protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Geel, Belgium.,Centre for Environmental Sciences, Environmental Biology, UHasselt, Diepenbeek, Belgium
| | - Ellen Gorrens
- Lab4Food, Department of Microbial and Molecular Systems, KU Leuven, Geel, Belgium
| | - Jane Debode
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium
| | - Bart Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium
| | - Karen Vancampenhout
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Geel, Belgium
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9
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Joos L, Beirinckx S, Haegeman A, Debode J, Vandecasteele B, Baeyen S, Goormachtig S, Clement L, De Tender C. Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units. BMC Genomics 2020; 21:733. [PMID: 33092529 PMCID: PMC7579973 DOI: 10.1186/s12864-020-07126-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022] Open
Abstract
Background Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has increased exponentially due to advances in sequencing technologies, but the large amount of data generated remains difficult to analyze and interpret. Recently, metabarcoding analysis has shifted from clustering reads using Operational Taxonomical Units (OTUs) to Amplicon Sequence Variants (ASVs). Differences between these methods can seriously affect the biological interpretation of metabarcoding data, especially in ecosystems with high microbial diversity, as the methods are benchmarked based on low diversity datasets. Results In this work we have thoroughly examined the differences in community diversity, structure, and complexity between the OTU and ASV methods. We have examined culture-based mock and simulated datasets as well as soil- and plant-associated bacterial and fungal environmental communities. Four key findings were revealed. First, analysis of microbial datasets at family level guaranteed both consistency and adequate coverage when using either method. Second, the performance of both methods used are related to community diversity and sample sequencing depth. Third, differences in the method used affected sample diversity and number of detected differentially abundant families upon treatment; this may lead researchers to draw different biological conclusions. Fourth, the observed differences can mostly be attributed to low abundant (relative abundance < 0.1%) families, thus extra care is recommended when studying rare species using metabarcoding. The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity. Conclusions Investigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering.
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Affiliation(s)
- Lisa Joos
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Stien Beirinckx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Technologiepark 71, 9052, Ghent, Belgium
| | - Annelies Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - Jane Debode
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - Bart Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Technologiepark 71, 9052, Ghent, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Caroline De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium. .,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.
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10
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Venneman J, De Tender C, Debode J, Audenaert K, Baert G, Vermeir P, Cremelie P, Bekaert B, Landschoot S, Thienpondt B, Djailo BD, Vereecke D, Haesaert G. Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack. FEMS Microbiol Ecol 2020; 95:5524361. [PMID: 31247636 DOI: 10.1093/femsec/fiz101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
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Affiliation(s)
- Jolien Venneman
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281, S9, BE-9000, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Baert
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Laboratory of Chemical Analysis (LCA), Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Bert Thienpondt
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Benoît Dhed'a Djailo
- Faculty of Science and Agriculture, Kisangani University, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
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11
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Verschaffelt P, Van Thienen P, Van Den Bossche T, Van der Jeugt F, De Tender C, Martens L, Dawyndt P, Mesuere B. Unipept CLI 2.0: adding support for visualizations and functional annotations. Bioinformatics 2020; 36:4220-4221. [DOI: 10.1093/bioinformatics/btaa553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Accepted: 05/28/2020] [Indexed: 11/12/2022] Open
Abstract
Abstract
Summary
Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept’s powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users.
Availability and implementation
The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license.
Contact
pieter.verschaffelt@ugent.be
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Philippe Van Thienen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Tim Van Den Bossche
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
- CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Merelbeke 9820, Belgium
| | - Lennart Martens
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
- CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
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12
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Beirinckx S, Viaene T, Haegeman A, Debode J, Amery F, Vandenabeele S, Nelissen H, Inzé D, Tito R, Raes J, De Tender C, Goormachtig S. Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions. Microbiome 2020; 8:54. [PMID: 32305066 PMCID: PMC7166315 DOI: 10.1186/s40168-020-00833-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/19/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. RESULTS We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. CONCLUSIONS Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions. Video abstract.
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Affiliation(s)
- Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Fien Amery
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Raul Tito
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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13
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Debode J, De Tender C, Cremelie P, Lee AS, Kyndt T, Muylle H, De Swaef T, Vandecasteele B. Trichoderma-Inoculated Miscanthus Straw Can Replace Peat in Strawberry Cultivation, with Beneficial Effects on Disease Control. Front Plant Sci 2018; 9:213. [PMID: 29515613 PMCID: PMC5826379 DOI: 10.3389/fpls.2018.00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 05/30/2023]
Abstract
Peat based growing media are not ecologically sustainable and often fail to support biological control. Miscanthus straw was (1) tested to partially replace peat; and (2) pre-colonized with a Trichoderma strain to increase the biological control capacity of the growing media. In two strawberry pot trials (denoted as experiment I & II), extruded and non-extruded miscanthus straw, with or without pre-colonization with T. harzianum T22, was used to partially (20% v/v) replace peat. We tested the performance of each mixture by monitoring strawberry plant development, nutrient content in the leaves and growing media, sensitivity of the fruit to the fungal pathogen Botrytis cinerea, rhizosphere community and strawberry defense responses. N immobilization by miscanthus straw reduced strawberry growth and yield in experiment II but not in I. The pre-colonization of the straw with Trichoderma increased the post-harvest disease suppressiveness against B. cinerea and changed the rhizosphere fungal microbiome in both experiments. In addition, defense-related genes were induced in experiment II. The use of miscanthus straw in growing media will reduce the demand for peat and close resource loops. Successful pre-colonization of this straw with biological control fungi will optimize crop cultivation, requiring fewer pesticide applications, which will benefit the environment and human health.
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Affiliation(s)
- Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Ana S. Lee
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Epigenetics & Defence Research Group, Department Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Epigenetics & Defence Research Group, Department Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Hilde Muylle
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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14
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De Mulder T, Goossens K, Peiren N, Vandaele L, Haegeman A, De Tender C, Ruttink T, de Wiele TV, De Campeneere S. Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural. FEMS Microbiol Ecol 2017; 93:fiw251. [PMID: 28011597 DOI: 10.1093/femsec/fiw251] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid-adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid-adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep). The bacterial and methanogen communities of these sample types were analysed using 16S metabarcoding and qPCR. The results indicate that the liquid and solid-adherent environments are distinguished mainly by the differential abundance of specific taxonomic groups. Cellulolytic bacteria that pioneer biofilm formation, together with secondary colonisers are prevalent in solid-adherent samples, while dominant species in the fluid samples are primarily identified as consumers of soluble nutrients. Also, methanogen species are found to have a preference for either a solid-adherent or free-living occurrence. The epimural environment is characterised by a different microbial profile. Ten bacterial families and two methanogen genera are almost exclusively found in this environment.
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Affiliation(s)
- Thijs De Mulder
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Karen Goossens
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Nico Peiren
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Leen Vandaele
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Annelies Haegeman
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Caroline De Tender
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Tom Ruttink
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure 653, 9000 Ghent, Belgium
| | - Sam De Campeneere
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
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15
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De Tender C, Devriese LI, Haegeman A, Maes S, Vangeyte J, Cattrijsse A, Dawyndt P, Ruttink T. Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea. Environ Sci Technol 2017; 51:7350-7360. [PMID: 28562015 DOI: 10.1021/acs.est.7b00697/suppl_file/es7b00697_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.
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Affiliation(s)
- Caroline De Tender
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Lisa I Devriese
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Department of Environment and Health, Vrije Universiteit Amsterdam , De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Annelies Haegeman
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Sara Maes
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Jürgen Vangeyte
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - André Cattrijsse
- Flanders Marine Institute , InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Peter Dawyndt
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Tom Ruttink
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
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16
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De Tender C, Devriese LI, Haegeman A, Maes S, Vangeyte J, Cattrijsse A, Dawyndt P, Ruttink T. Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea. Environ Sci Technol 2017; 51:7350-7360. [PMID: 28562015 DOI: 10.1021/acs.est.7b00697] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.
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Affiliation(s)
- Caroline De Tender
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Lisa I Devriese
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Department of Environment and Health, Vrije Universiteit Amsterdam , De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Annelies Haegeman
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Sara Maes
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Jürgen Vangeyte
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - André Cattrijsse
- Flanders Marine Institute , InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Peter Dawyndt
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Tom Ruttink
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
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De Tender C, Haegeman A, Vandecasteele B, Clement L, Cremelie P, Dawyndt P, Maes M, Debode J. Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection. Front Microbiol 2016; 7:2062. [PMID: 28066380 PMCID: PMC5177642 DOI: 10.3389/fmicb.2016.02062] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/07/2016] [Indexed: 01/18/2023] Open
Abstract
Adding biochar, the solid coproduct of biofuel production, to peat can enhance strawberry growth, and disease resistance against the airborne fungal pathogen Botrytis cinerea. Additionally, biochar can induce shifts in the strawberry rhizosphere microbiome. However, the moment that this biochar-mediated shift occurs in the rhizosphere is not known. Further, the effect of an above-ground infection on the strawberry rhizosphere microbiome is unknown. In the present study we established two experiments in which strawberry transplants (cv. Elsanta) were planted either in peat or in peat amended with 3% biochar. First, we established a time course experiment to measure the effect of biochar on the rhizosphere bacterial and fungal communities over time. In a second experiment, we inoculated the strawberry leaves with B. cinerea, and studied the impact of the infection on the rhizosphere bacterial community. The fungal rhizosphere community was stabilized after 1 week, except for the upcoming Auriculariales, whereas the bacterial community shifted till 6 weeks. An effect of the addition of biochar to the peat on the rhizosphere microbiome was solely measured for the bacterial community from week 6 of plant growth onwards. When scoring the plant development, biochar addition was associated with enhanced root formation, fruit production, and postharvest resistance of the fruits against B. cinerea. We hypothesize that the bacterial rhizosphere microbiome, but also biochar-mediated changes in chemical substrate composition could be involved in these events. Infection of the strawberry leaves with B. cinerea induced shifts in the bacterial rhizosphere community, with an increased bacterial richness. This disease-induced effect was not observed in the rhizospheres of the B. cinerea-infected plants grown in the biochar-amended peat. The results show that an above-ground infection has its effect on the strawberry rhizosphere microbiome, changing the bacterial interactions in the root-substrate interface. This infection effect on the bacterial rhizosphere microbiome seems to be comparable to, but less pronounced than the effect of biochar-addition to the peat. The biological meaning of these observations needs further research, but this study indicates that biochar and an above-ground pathogen attack help the plant to recruit rhizosphere microbes that may aid them in their plant growth and health.
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Affiliation(s)
- Caroline De Tender
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium; Department of Applied Mathematics Computer Sciences and Statistics, Ghent UniversityGhent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Crop Husbandry and Environment, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Lieven Clement
- Department of Applied Mathematics Computer Sciences and Statistics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent UniversityGhent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium; Plant Sciences Unit, Crop Husbandry and Environment, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics Computer Sciences and Statistics, Ghent University Ghent, Belgium
| | - Martine Maes
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
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Debode J, De Tender C, Soltaninejad S, Van Malderghem C, Haegeman A, Van der Linden I, Cottyn B, Heyndrickx M, Maes M. Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology. Front Microbiol 2016; 7:565. [PMID: 27148242 PMCID: PMC4838818 DOI: 10.3389/fmicb.2016.00565] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/04/2016] [Indexed: 11/13/2022] Open
Abstract
Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia coli O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves.
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Affiliation(s)
- Jane Debode
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Saman Soltaninejad
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Inge Van der Linden
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
- Department of Food Safety and Food Quality, Ghent UniversityGhent, Belgium
| | - Bart Cottyn
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Marc Heyndrickx
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
- Department of Pathology, Bacteriology, and Poultry Diseases, Faculty of Veterinary Sciences, Ghent UniversityMerelbeke, Belgium
| | - Martine Maes
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
- Department of Biochemistry and Microbiology, Ghent UniversityGhent, Belgium
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