Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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RG-I galactan side-chains are involved in the regulation of the water-binding capacity of potato cell walls
Klaassen, Michiel T. ; Trindade, Luisa M. - \ 2020
Carbohydrate Polymers 227 (2020). - ISSN 0144-8617
Pectin - Potato cell walls (PCW) - Rhamnogalacturonan I (RG-I)β-(1→4)-D-galactan - Rhamnogalacturonan I, β-(1→4)-D-galactan - Water-binding capacity (WBC) - β-galactosidase

Potato cell walls (PCW) are a low value by-product from the potato starch industry. Valorisation of PCW is hindered by its high water-binding capacity (WBC). The composition of polysaccharides and interactions between these entities, play important roles in regulating the WBC in the cell wall matrix. Here, we show that in vivo exo-truncation of RG-I β-(1→4)-D-galactan side-chains decreased the WBC by 6–9%. In contrast, exo-truncation of these side-chains increased the WBC by 13% in vitro. We propose that degradation of RG-I galactan side-chains altered the WBC of PCW, due to cell wall remodelling and loosening that affected the porosity. Our findings reinforce the view that RG-I galactan side-chains play a role in modulating WBC, presumably by affecting polysaccharide architecture (spacing) and interactions in the matrix. Better understanding of structure-function relationships of pectin macromolecules is needed before cell wall by-products may be tailored to render added-value in food and biobased products.

Cell wall disruption: An effective strategy to improve the nutritive quality of microalgae in African catfish (Clarias gariepinus)
Agboola, Jeleel O. ; Teuling, Emma ; Wierenga, Peter A. ; Gruppen, Harry ; Schrama, Johan W. - \ 2019
Aquaculture Nutrition 25 (2019)4. - ISSN 1353-5773 - p. 783 - 797.
accessibility - algae - digestibility - disruption treatments - nutrient utilization - rigid cell wall

The rigid cell walls of microalgae may hinder their utilization in fish feeds. The current experiment assessed the correlation between the accessibility of microalgae nutrients and their in vivo digestibility in African catfish. Nannochloropsis gaditana biomass was subjected to physical or mechanical treatments to weaken its cell wall; untreated—no disruption treatment (UNT), pasteurization (PAS), freezing (FRO), freeze-drying (FRD), cold pasteurization (L40) and bead milling (BEM). Six experimental diets formulated from differently treated and untreated microalgae (at 30% diet inclusion level) were tested on growth performance and apparent nutrient digestibility (ADCs) in juvenile African catfish. A basal diet (REF) containing no microalgae was used as reference diet. Results showed that biomass gain and feed conversion ratio of fish fed L40 and BEM diets increased by 13% and 11%, respectively, relative to the UNT diet. Additionally, FRD, FRO, L40 and BEM cell wall disruption treatments improved protein digestibility by 0.5%, 5.9%, 8.4% and 16.3%, respectively, compared to the UNT treatment. There was a positive correlation between accessibility of microalgal nutrients and their digestibility in African catfish. Nutrient digestibility of microalgae was dependent on extent of cell disruption. Also, the impact of cell disruption on nutrient digestibility of microalgae differs between African catfish and Nile tilapia.

Fungal artillery of zombie flies: infectious spore dispersal using a soft water cannon
Ruiter, Jolet de; Arnbjerg-Nielsen, Sif Fink ; Herren, Pascal ; Høier, Freja ; Fine Licht, Henrik H. De; Jensen, Kaare H. - \ 2019
Journal of the Royal Society, Interface 16 (2019)159. - ISSN 1742-5689 - 10 p.
biomimetic soft cannon - dispersal range - Entomophthora muscae - force-balance model - fungal spore ejection - high-speed videography

Dead sporulating female fly cadavers infected by the house fly-pathogenic fungus Entomophthora muscae are attractive to healthy male flies, which by their physical inspection may mechanically trigger spore release and by their movement create whirlwind airflows that covers them in infectious conidia. The fungal artillery of E. muscae protrudes outward from the fly cadaver, and consists of a plethora of micrometric stalks that each uses a liquid-based turgor pressure build-up to eject a jet of protoplasm and the initially attached spore. The biophysical processes that regulate the release and range of spores, however, are unknown. To study the physics of ejection, we design a biomimetic 'soft cannon' that consists of a millimetric elastomeric barrel filled with fluid and plugged with a projectile. We precisely control the maximum pressure leading up to the ejection, and study the cannon efficiency as a function of its geometry and wall elasticity. In particular, we predict that ejection velocity decreases with spore size. The calculated flight trajectories under aerodynamic drag predict that the minimum spore size required to traverse a quiescent layer of a few millimetres around the fly cadaver is approximately 10 µm. This corroborates with the natural size of E. muscae conidia (approx. 27 µm) being large enough to traverse the boundary layer but small enough (less than 40 µm) to be lifted by air currents. Based on this understanding, we show how the fungal spores are able to reach a new host.

A conserved GH17 glycosyl hydrolase from plant pathogenic Dothideomycetes releases a DAMP causing cell death in tomato
Ökmen, Bilal ; Bachmann, Daniel ; Wit, Pierre J.G.M. de - \ 2019
Molecular Plant Pathology (2019). - ISSN 1464-6722
cell death-inducing - Cladosporium fulvum - DAMP - effectors - GH17

To facilitate infection, pathogens deploy a plethora of effectors to suppress basal host immunity induced by exogenous microbe-associated or endogenous damage-associated molecular patterns (DAMPs). In this study, we have characterized family 17 glycosyl hydrolases of the tomato pathogen Cladosporium fulvum (CfGH17) and studied their role in infection. Heterologous expression of CfGH17-1 to 5 by potato virus X in different tomato cultivars showed that CfGH17-1 and CfGH17-5 enzymes induce cell death in Cf-0, Cf-1 and Cf-5 but not in Cf-Ecp3 tomato cultivars or tobacco. Moreover, CfGH17-1 orthologues from other phytopathogens, including Dothistroma septosporum and Mycosphaerella fijiensis, also trigger cell death in tomato. CfGH17-1 and CfGH17-5 are predicted to be β-1,3-glucanases and their enzymatic activity is required for the induction of cell death. CfGH17-1 hydrolyses laminarin, a linear 1,3-β-glucan with 1,6-β linkages. CfGH17-1 expression is down-regulated during the biotrophic phase of infection and up-regulated during the necrotrophic phase. Deletion of CfGH17-1 in C. fulvum did not reduce virulence on tomato, while constitutive expression of CfGH17-1 decreased virulence, suggesting that abundant presence of CfGH17-1 during biotrophic growth may release a DAMP that activates plant defence responses. Under natural conditions CfGH17-1 is suggested to play a role during saprophytic growth when the fungus thrives on dead host tissue, which is in line with its high levels of expression at late stages of infection when host tissues have become necrotic. We suggest that CfGH17-1 releases a DAMP from the host cell wall that is recognized by a yet unknown host plant receptor.

Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Relationships between chemical composition and in vitro gas production parameters of maize leaves and stems
He, Yuan ; Cone, John W. ; Hendriks, Wouter H. ; Dijkstra, Jan - \ 2019
Journal of Animal Physiology and Animal Nutrition (2019). - ISSN 0931-2439
cell wall degradation - in vitro gas production - maize leaves - maize stems

This study investigated the chemical composition (proximate and Van Soest analysis) and in vitro gas production parameters of maize leaves and stems separately, and related the in vitro gas production parameters with the chemical composition, of thirteen maize cultivars. After harvest in September 2016, all plants were separated into two morphological fractions: leaves and stems. The crude protein (CP) content was greater, and the ratio of acid detergent lignin (ADL) to potentially rumen degradable fibre (calculated as the difference between neutral detergent fibre and ADL; ADL:pRDF) was lower in the leaves than in the stems in all 13 cultivars. For the leaves, the cumulative gas production between 3 and 20 hr (A2), representing cell wall fermentation in the rumen fluid, and the cumulative 72-hr gas production (GP72), representing total organic matter (OM) degradation, were moderately to weakly correlated with the chemical composition, including hemicellulose, cellulose, ADL and CP content (R2 < 0.40), whilst the best relationship between the half-time value (B2), representing the rate of cell wall degradation, and chemical composition had an R2 of 0.63. For the stems, the best relationship between A2, B2 and GP72 with chemical composition was greater (R2 ≥ 0.74) and the best relationship included hemicellulose (A2 only), cellulose and ADL (GP72 and A2 only) contents. In conclusion, maize leaves and stems differed in chemical composition, in particular CP content and ADL:pRDF. The A2 and GP72 of the stems, but not of the leaves, were highly correlated with the chemical composition, indicating that the cell wall and OM degradation of maize stems can be better predicted by its chemical composition.

Bioprocessing of common pulses changed seed microstructures, and improved dipeptidyl peptidase-IV and α-glucosidase inhibitory activities
Stefano, Elisa Di; Tsopmo, Apollinaire ; Oliviero, Teresa ; Fogliano, Vincenzo ; Udenigwe, Chibuike C. - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Type 2 diabetes mellitus (T2DM) is a leading cause of death globally. T2DM patients experience glucose intolerance, and inhibitors of dipeptidyl peptidase IV (DPP-IV) and α-glucosidase are used as drugs for T2DM management. DPP-IV and α-glucosidase inhibitors are also naturally contained in foods, but their potency can be affected by the food matrix and processing methods. In this study, germination and solid-state fermentation (SSF) were used to alter pulse seed microstructures, to convert compounds into more bioactive forms, and to improve their bioaccessibility. Germination substantially modified the seed microstructure, protein digestibility, contents and profiles of phenolic compounds in all the pulses. It also increased DPP-IV and α-glucosidase inhibitory activities in chickpeas, faba beans and yellow peas. Compared to germination, SSF with Lactobacillus plantarum changed the content and the profile of phenolic compounds mainly in yellow peas and green lentils because of greater disruption of the seed cell wall. In the same pulses, heat treatment and SSF of flour increased DPP-IV and α-glucosidase inhibitory activities. The results of this study suggest that germination and SSF with L. plantarum are effective and simple methods for modulating phenolic and protein profiles of common pulses and improve the action on DPP-IV and α-glucosidase.

Blackleg Detection in Potato Plants using Convolutional Neural Networks
Afonso, M.V. ; Blok, P.M. ; Polder, G. ; Wolf, J.M. van der; Kamp, J.A.L.M. - \ 2019
- 6 p.
Potato blackleg is a tuber-borne bacterial disease caused by species within the genera Dickeya and Pectobacterium that can cause decay of plant tissue and wilting through the action of cell wall degrading enzymes released by the pathogen. In case of serious infections, tubers may rot before emergence. Management is largely based on the use of pathogen-free seed potato tubers. For this, fields are visually monitored both for certification and also to take out diseased plants to avoid spread to neighboring plants. Imaging potentially offers a quick and non-destructive way to inspect the health of potato plants in a field. Early detection of blackleg diseased plants with modern vision techniques can significantly reduce costs. In this paper, we studied the use of deep learning for detecting blackleg diseased potato plants. Two deep convolutional neural networks were trained on RGB images with healthy and diseased plants. One of these networks (ResNet18) was experimentally found to produce a precision of 95 % and recall of 91 % for the disease class. These results show that convolutional neural networks can be used to detect blackleg diseased potato plants.
Distribution maps of cetacean and seabird populations in the North‐East Atlantic
Waggitt, J.J. ; Evans, P.G.H. ; Andrade, J. ; Banks, A.N. ; Boisseau, O. ; Bolton, M. ; Bradbury, G. ; Brereton, T. ; Camphuysen, C.J. ; Durinck, J. ; Felce, T. ; Fijn, R.C. ; Garcia‐baron, I. ; Garthe, S. ; Geelhoed, S.C.V. ; Gilles, A. ; Goodall, M. ; Haelters, J. ; Hamilton, S. ; Hartny‐mills, L. ; Hodgins, N. ; James, K. ; Jessopp, M. ; Kavanagh, A.S. ; Leopold, M. ; Lohrengel, K. ; Louzao, M. ; Markones, N. ; Martinez‐cediera, J. ; O’cadhla, O. ; Perry, S.I. ; Pierce, G.J. ; Ridoux, V. ; Robinson, K.P. ; Santos, M.B. ; Saavedra, C. ; Skov, H. ; Stienen, E.W.M. ; Sveegaard, S. ; Thompson, P. ; Vanermen, N. ; Wall, D. ; Webb, A. ; Wilson, J. ; Wanless, S. ; Hiddink, J.G. - \ 2019
Journal of Applied Ecology (2019). - ISSN 0021-8901 - 45 p.
Chitin-Binding Protein of Verticillium nonalfalfae Disguises Fungus from Plant Chitinases and Suppresses Chitin-Triggered Host Immunity
Volk, Helena ; Marton, Kristina ; Flajšman, Marko ; Radišek, Sebastjan ; Tian, Hui ; Hein, Ingo ; Podlipnik, Črtomir ; Thomma, Bart P.H.J. ; Košmelj, Katarina ; Javornik, Branka ; Berne, Sabina - \ 2019
Molecular Plant-Microbe Interactions 32 (2019)10. - ISSN 0894-0282 - p. 1378 - 1390.
Fungal effectors - Fungus–plant interactions - Mechanisms of pathogenicity

During fungal infections, plant cells secrete chitinases, which digest chitin in the fungal cell walls. The recognition of released chitin oligomers via lysin motif (LysM)-containing immune host receptors results in the activation of defense signaling pathways. We report here that Verticillium nonalfalfae, a hemibiotrophic xylem-invading fungus, prevents these digestion and recognition processes by secreting a carbohydrate-binding motif 18 (CBM18)-chitin-binding protein, VnaChtBP, which is transcriptionally activated specifically during the parasitic life stages. VnaChtBP is encoded by the Vna8.213 gene, which is highly conserved within the species, suggesting high evolutionary stability and importance for the fungal lifestyle. In a pathogenicity assay, however, Vna8.213 knockout mutants exhibited wilting symptoms similar to the wild-type fungus, suggesting that Vna8.213 activity is functionally redundant during fungal infection of hop. In a binding assay, recombinant VnaChtBP bound chitin and chitin oligomers in vitro with submicromolar affinity and protected fungal hyphae from degradation by plant chitinases. Moreover, the chitin-triggered production of reactive oxygen species from hop suspension cells was abolished in the presence of VnaChtBP, indicating that VnaChtBP also acts as a suppressor of chitin-triggered immunity. Using a yeast-two-hybrid assay, circular dichroism, homology modeling, and molecular docking, we demonstrated that VnaChtBP forms dimers in the absence of ligands and that this interaction is stabilized by the binding of chitin hexamers with a similar preference in the two binding sites. Our data suggest that, in addition to chitin-binding LysM (CBM50) and Avr4 (CBM14) fungal effectors, structurally unrelated CBM18 effectors have convergently evolved to prevent hydrolysis of the fungal cell wall against plant chitinases and to interfere with chitin-triggered host immunity.

Challenges and Opportunities for Soil Biodiversity in the Anthropocene
Geisen, Stefan ; Wall, Diana H. ; Putten, Wim H. van der - \ 2019
Current Biology 29 (2019)19. - ISSN 0960-9822 - p. R1036 - R1044.

In this review, Geisen et al. provide an overview of soil biodiversity and highlight the direct and indirect anthropogenic factors affecting it. They discuss the valuable ecosystem services provided by a diverse soil biota and highlight the need to protect soil diversity in the face of anthropogenic changes.

Phenotypic Variation of Cell Wall Composition and Stem Morphology in Hemp (Cannabis sativa L.): Optimization of Methods
Petit, Jordi ; Gulisano, Agata ; Dechesne, Annemarie ; Trindade, Luisa M. - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Cannabis sativa - cell wall - fiber quality - genetic diversity - hemp - phenotyping methods - stem morphology

The growing demands for sustainable fibers have stimulated the study of genetic diversity in the quality of hemp fiber (Cannabis sativa L.). Nevertheless, the lack of high-throughput phenotyping methods that are suited for the analysis of hemp fiber, hampers the analysis of many accessions, and consequently the breeding for this complex trait. In the present report, we developed and optimized the throughput of five methods to study the diversity in hemp fiber quality including cell wall extraction, biochemical composition of cell wall polysaccharides, quantification of lignin, quantification of crystalline polysaccharides and morphology of the stems. Six hemp accessions contrasting for cell wall properties were used to assess the throughput and suitability of these methods for genetic studies. The methods presented revealed to be highly repeatable, with low coefficients of variation between technical replicates. With these methods we were able to detect significant phenotypic variation in cell wall composition and stem morphology between the six accessions. In addition, the throughput of the methods has been upgraded to a level that enables their use for phenotyping cell wall traits in breeding programs. The cell wall extraction was optimized to extract enough material for the complete characterization of the cell wall of hemp while reducing the time for the entire analysis. The throughput of the stem morphological analysis was improved by decreasing the timing of fixation, infiltration, and embedding of mature and dry hemp stems. Notwithstanding, our methods already have the potential to phenotype large number of accessions in a relatively short period of time. Our methods will enable exploration of genetic diversity of fiber quality and will contribute to the development of new hemp varieties with advanced quality of fibers.

Livestock-Associated meticillin-resistant Staphylococcus aureus in a young harbour seal (Phoca vitulina) with endocarditis
Rubio-Garcia, Ana ; Rossen, John W.A. ; Wagenaar, Jaap A. ; Friedrich, Alex W. ; Zeijl, Jan H. Van - \ 2019
Veterinary Record Case Reports 7 (2019)3. - ISSN 2052-6121
Bacterial diseases - Endocarditis - Infection - Marine mammals - MRSA - Phoca vitulina

A five-month-old male harbour seal was admitted for rehabilitation to the Sealcentre Pieterburen on November 16, 2015. During initial veterinary examination parasitic pneumonia and secondary bacterial pneumonia were suspected. Therefore, the seal received antiparasitic and antimicrobial treatment and appeared to recover but died unexpectedly after several weeks. Postmortem examination revealed a perforation in the aortic wall and histopathological examination of the aorta revealed mural necrosis with haemorrhage and suppurative to mixed inflammation. Bacterial culture resulted in isolation of a meticillin-resistant Staphylococcus aureus (MRSA) from the pericardial effusion. Subsequent culture of rectal swabs collected at arrival and during rehabilitation showed that the animal was already colonised with MRSA when admitted to the Sealcentre. MRSA has been isolated from marine mammals before, however, to our knowledge this is the first report of MRSA-Associated endocarditis in seals and the first time that livestock-Associated MRSA is reported in seals.

FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum
Kong, Xiangjiu ; Zhang, Hao ; Wang, Xiaoliang ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Brankovics, Balázs ; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH- 1 and 1FgPex3 knock-out strains. The GFP and RFP transformants in the 1FgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The 1FgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid b-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the 1FgPex3 mutant was sensitive to osmotic stressors
as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of 1FgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
Correction to: Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment
Engelsdorf, Timo ; Kjaer, Lars ; Gigli-Bisceglia, Nora ; Vaahtera, Lauri ; Bauer, Stefan ; Miedes, Eva ; Wormit, Alexandra ; James, Lucinda ; Chairam, Issariya ; Molina, Antonio ; Hamann, Thorsten - \ 2019
BMC Plant Biology 19 (2019)1. - ISSN 1471-2229 - 1 p.

Following publication of the original article [1], the author reported that the two curves in the sub-diagram WSR4 in Fig. 2a should be the other way round.

Asymmetric redundancy of ZERZAUST and ZERZAUST HOMOLOG in different accessions of arabidopsis thaliana
Vaddepalli, Prasad ; Fulton, Lynette ; Schneitz, Kay - \ 2019
G3 : Genes Genomes Genetics 9 (2019)7. - ISSN 2160-1836 - p. 2245 - 2252.
Arabidopsis accessions genetic - Expression ZERZAUST ZERZAUST - HOMOLOG - Redundancy asymmetric gene

Divergence among duplicate genes is one of the important sources of evolutionary innovation. But, the contribution of duplicate divergence to variation in Arabidopsis accessions is sparsely known. Recently, we studied the role of a cell wall localized protein, ZERZAUST (ZET), in Landsberg erecta (Ler) accession, lack of which results in aberrant plant morphology. Here, we present the study of ZET in Columbia (Col) accession, which not only showed differential expression patterns in comparison to Ler, but also revealed its close homolog, ZERZAUST HOMOLOG (ZETH). Although, genetic analysis implied redundancy, expression analysis revealed divergence, with ZETH showing minimal expression in both Col and Ler. In addition, ZETH shows relatively higher expression levels in Col compared to Ler. Our data also reveal compensatory up-regulation of ZETH in Col, but not in Ler, implying it is perhaps dispensable in Ler. However, a novel CRISPR/Cas9-induced zeth allele confirmed that ZETH has residual activity in Ler. Finally, the synergistic interaction of the receptor-like kinase gene, ERECTA with ZET in ameliorating morphological defects suggests crucial role of modifiers on plant phenotype. The results provide genetic evidence for accession-specific differences in compensation mechanism and asymmetric gene contribution. Thus, our work reveals a novel example for how weakly expressed homologs contribute to diversity among accessions.

A Field-Scale Decision Support System for Assessment and Management of Soil Functions
Debeljak, Marko ; Trajanov, Aneta ; Kuzmanovski, Vladimir ; Schroder, J.J. ; Sandén, Taru ; Spiegel, Heide ; Wall, David ; Broek, Marijn van de; Rutgers, Michiel ; Bampa, Francesca ; Creamer, Rachel ; Henriksen, Christian Bugge - \ 2019
Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X
Agricultural decision support systems (DSS) are mostly focused on increasing the supply of individual soil functions such as e.g. primary productivity or nutrient cycling, while neglecting other important soil functions, such as e.g. water purification and regulation, climate regulation and carbon sequestration, soil biodiversity and habitat provision. Making right management decisions for long-term sustainability is therefore challenging, and farmers and farm advisors would greatly benefit from an evidence-based DSS targeted for assessing and improving the supply of several soil functions simultaneously. To address this, need we designed the Soil Navigator DSS by applying a qualitative approach to multi criteria decision modelling using Decision Expert (DEX) integrative methodology. Multi-criteria decision models for the five main soil functions were developed, calibrated and validated using knowledge of involved domain experts and knowledge extracted from existing datasets by data mining. Subsequently, the five DEX models were integrated into a DSS to assess the soil functions simultaneously, and to provide management advises for improving the performance of prioritized soil functions. To enable communication between the users and the DSS, we developed a user-friendly computer-based graphical user interface, which enables users to provide the required data regarding their field to the DSS and to get textual and graphical results about the performance of each of the five soil functions in a qualitative way. The final output from the DSS is a list of soil mitigation measures that the end-users could easily apply in the field in order to achieve the desired soil function performance. The Soil Navigator DSS has a great potential to complement the Farm Sustainability Tools for Nutrients included in the Common Agricultural Policy 2021-2027 proposal adopted by the European Commission. The Soil Navigator has also a potential to be spatially upgraded to assist decisions on which soil functions to prioritize in a specific region or member state. Furthermore, the Soil Navigator DSS could be used as an educational tool for farmers, farm advisors and students, and its potential should be further exploited for the benefit of farmers and the society as a whole.
Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment
Engelsdorf, Timo ; Kjaer, Lars ; Gigli-Bisceglia, Nora ; Vaahtera, Lauri ; Bauer, Stefan ; Miedes, Eva ; Wormit, Alexandra ; James, Lucinda ; Chairam, Issariya ; Molina, Antonio ; Hamann, Thorsten - \ 2019
BMC Plant Biology 19 (2019). - ISSN 1471-2229 - 15 p.
Bioenergy production - Cell wall - Cell wall integrity - Cell wall metabolism - Cell wall signalling - Plant pathogen-interaction

BACKGROUND: Plant cell walls participate in all plant-environment interactions. Maintaining cell wall integrity (CWI) during these interactions is essential. This realization led to increased interest in CWI and resulted in knowledge regarding early perception and signalling mechanisms active during CWI maintenance. By contrast, knowledge regarding processes mediating changes in cell wall metabolism upon CWI impairment is very limited. RESULTS: To identify genes involved and to investigate their contributions to the processes we selected 23 genes with altered expression in response to CWI impairment and characterized the impact of T-DNA insertions in these genes on cell wall composition using Fourier-Transform Infrared Spectroscopy (FTIR) in Arabidopsis thaliana seedlings. Insertions in 14 genes led to cell wall phenotypes detectable by FTIR. A detailed analysis of four genes found that their altered expression upon CWI impairment is dependent on THE1 activity, a key component of CWI maintenance. Phenotypic characterizations of insertion lines suggest that the four genes are required for particular aspects of CWI maintenance, cell wall composition or resistance to Plectosphaerella cucumerina infection in adult plants. CONCLUSION: Taken together, the results implicate the genes in responses to CWI impairment, cell wall metabolism and/or pathogen defence, thus identifying new molecular components and processes relevant for CWI maintenance.

A methodological framework to embrace soil biodiversity
Geisen, Stefan ; Briones, Maria J.I. ; Gan, Huijie ; Behan-Pelletier, Valerie M. ; Friman, Ville Petri ; Groot, G.A. de; Hannula, S.E. ; Lindo, Zoë ; Philippot, Laurent ; Tiunov, Alexei V. ; Wall, Diana H. - \ 2019
Soil Biology and Biochemistry 136 (2019). - ISSN 0038-0717
Biodiversity - Fauna - Food-webs - Microorganisms - Molecular methods - Soil functions and health

Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.

Maternal antibiotic use in sows affects microbiota and gut development in offspring
Schokker, D. ; Greeff, A. de - \ 2019
Sus scrofa - GSE115178 - PRJNA474010
We demonstrated that a maternal antibiotic treatment can change intestinal development of the offspring piglets permanently by showing that maternal gestational antibiotic treatment affects intestinal development in offspring piglets for a period of at least seven weeks after the antibiotic treatment in the sows was finished. It was shown that immediately after birth the piglets from amoxicillin treated sows, showed upregulation of genes involved in processes related to ‘tight junctions’ and ‘immunoglobulins’. In addition, these piglets had significantly lower number of goblet cells. Together, this may lead to a gut wall that is more rapidly closed in piglets from amoxicillin treated sows, affecting the uptake of immunoglobulins and the intestinal development. Later in life, around weaning, gene expression and morphological data indicate that the crypts of piglets from amoxicillin treated sows deepen around weaning as an effect of the amoxicillin treatment which in combination with the upregulation of genes involved in cell cycle processes, ribosomal activity and protein degradation might imply that the intestinal development, the subsequent differentiation of cells or the timing of these processes was delayed by the maternal antibiotic treatment
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