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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Warming enhances sedimentation and decomposition of organic carbon in shallow macrophyte-dominated systems with zero net effect on carbon burial
Velthuis, Mandy ; Kosten, Sarian ; Aben, Ralf ; Kazanjian, Garabet ; Hilt, Sabine ; Peeters, Edwin T.H.M. ; Donk, Ellen van; Bakker, Elisabeth S. - \ 2018
Global Change Biology (2018). - ISSN 1354-1013
carbon cycle - decomposition - global warming - mineralization - phenology - primary production - sedimentation - submerged aquatic plant

Temperatures have been rising throughout recent decades and are predicted to rise further in the coming century. Global warming affects carbon cycling in freshwater ecosystems, which both emit and bury substantial amounts of carbon on a global scale. Currently, most studies focus on the effect of warming on overall carbon emissions from freshwater ecosystems, while net effects on carbon budgets may strongly depend on burial in sediments. Here, we tested whether year-round warming increases the production, sedimentation, or decomposition of particulate organic carbon and eventually alters the carbon burial in a typical shallow freshwater system. We performed an indoor experiment in eight mesocosms dominated by the common submerged aquatic plant Myriophyllum spicatum testing two temperature treatments: a temperate seasonal temperature control and a warmed (+4°C) treatment (n = 4). During a full experimental year, the carbon stock in plant biomass, dissolved organic carbon in the water column, sedimented organic matter, and decomposition of plant detritus were measured. Our results showed that year-round warming nearly doubled the final carbon stock in plant biomass from 6.9 ± 1.1 g C in the control treatment to 12.8 ± 0.6 g C (mean ± SE), mainly due to a prolonged growing season in autumn. DOC concentrations did not differ between the treatments, but organic carbon sedimentation increased by 60% from 96 ± 9.6 to 152 ± 16 g C m−2 yaer−1 (mean ± SE) from control to warm treatments. Enhanced decomposition of plant detritus in the warm treatment, however, compensated for the increased sedimentation. As a result, net carbon burial was 40 ± 5.7 g C m−2 year−1 in both temperature treatments when fluxes were combined into a carbon budget model. These results indicate that warming can increase the turnover of organic carbon in shallow macrophyte-dominated systems, while not necessarily affecting net carbon burial on a system scale.

Agreement between four commercial diagnostic tests and routine bacteriological culture of milk to determine the udder infection status of dairy cows
Griffioen, Karien ; Velthuis, Annet G.J. ; Lagerwerf, Lotte A. ; Heuvelink, Annet E. ; Lam, Theo J.G.M. - \ 2018
Preventive Veterinary Medicine 157 (2018). - ISSN 0167-5877 - p. 162 - 173.
Agreement - Culture-based tests - Dairy cattle - Mastitis - On-farm - Target treatment

Mastitis is usually treated based on clinical signs or somatic cell count information rather than on results of bacteriological culture of milk. In many countries an optimal mastitis treatment is considered important from the perspective of therapy efficacy, prudent antimicrobial use and farm economics. Farmers can optimize their mastitis treatment decisions if they know whether and which mastitis pathogen is involved. Information on the mastitis pathogen involved can be acquired from diagnostic mastitis tests such as culture-based tests. This study aimed to determine the agreement of four commercial culture-based mastitis tests with routine bacteriological culture of milk to determine the intramammary infection status of a quarter or cow. The commercial culture-based tests evaluated in this study were CHROMagar Mastitis (CHROMagar, France), Hardy Diagnostics Mastitis Triplate (Hardy Diagnostics, USA), Minnesota Easy Culture System II Tri-plate (University of Minnesota, USA), and VétoRapid (Vetoquinol, the Netherlands). We used 866 prospectively collected milk samples, routinely submitted to the bacteriological laboratory of GD Animal Health for routine bacteriological culture of milk from April to June 2016. Samples were cultured on routine bacteriological culture of milk and on the commercial culture-based tests. We calculated the agreement beyond chance of each commercial culture-based test result with the result of routine bacteriological culture using 2x2 contingency tables. Furthermore, inter-reader agreement was determined for 597 samples read by two masked readers. The agreement of the four commercial culture-based mastitis tests with routine bacteriological culture of milk for Gram-positive bacteria ranged from 0.14 (95% CI 0.11-0.16) using Hardy Diagnostics Mastitis Triplate to 0.25 (95% CI 0.22-0.28) using Minnesota Easy Culture System II Tri-plate. The agreement for Gram-negative bacteria was approximately 0.70 (95% CI 0.66-0.74) for all four commercial culture-based tests. The agreement for no growth ranged from 0.22 (95% CI 0.19-0.25) using Hardy Diagnostics Mastitis Triplate to 0.34 (95% CI 0.31-0.38) using VétoRapid. This category was affected by prevalence and bias as the prevalence adjusted and bias adjusted kappa ranged from 0.63 (95% CI 0.56-0.69) using CHROMagar Mastitis to 0.68 (95% CI 0.62-0.74) using Hardy Diagnostic Mastitis Triplate. Agreement between readers was almost perfect. Although only for Gram-negative bacteria a good agreement was found between commercial culture-based tests and routine bacteriological culture of milk, and further on-farm evaluations are needed to determine the effect of these findings on udder health, commercial culture-based tests are of added value to support decisions whether and how to treat cows with mastitis.

Impacts of warming on top-down and bottom-up controls of periphyton production
Kazanjian, Garabet ; Velthuis, Mandy ; Aben, Ralf ; Stephan, Susanne ; Peeters, Edwin T.H.M. ; Frenken, Thijs ; Touwen, Jelle ; Xue, Fei ; Kosten, Sarian ; De Waal, Dedmer B. Van; Senerpont Domis, Lisette N. De; Donk, Ellen van; Hilt, Sabine - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Global warming profoundly impacts the functioning of aquatic ecosystems. Nonetheless, the effect of warming on primary producers is poorly understood, especially periphyton production, which is affected both directly and indirectly by temperature-sensitive top-down and bottom-up controls. Here, we study the impact of warming on gross primary production in experimental ecosystems with near-realistic foodwebs during spring and early summer. We used indoor mesocosms following a temperate temperature regime (control) and a warmed (+4 °C) treatment to measure biomass and production of phytoplankton and periphyton. The mesocosms' primary production was dominated by periphyton (>82%) during the studied period (April-June). Until May, periphyton production and biomass were significantly higher in the warm treatment (up to 98% greater biomass compared to the control) due to direct temperature effects on growth and indirect effects resulting from higher sediment phosphorus release. Subsequently, enhanced grazer abundances seem to have counteracted the positive temperature effect causing a decline in periphyton biomass and production in June. We thus show, within our studied period, seasonally distinct effects of warming on periphyton, which can significantly affect overall ecosystem primary production and functioning.

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment : a pooled analysis
Dorado-Garcia, Alejandro ; Smid, J.H. ; Pelt, Wilfrid Van; Bonten, M.J.M. ; Fluit, A.C. ; Bunt, Gerrita van den; Wagenaar, J.A. ; Hordijk, J. ; Dierikx, C.M. ; Veldman, K.T. ; Koeijer, A.A. de; Dohmen, W. ; Schmitt, H. ; Liakopoulos, A. ; Pacholewicz, Ewa ; Lam, T.J.G.M. ; Velthuis, Annet ; Heuvelink, A. ; Gonggrijp, Maaike ; Duijkeren, E. van; Hoek, A.H.A.M. van; Roda Husman, A.N. de; Blaak, H. ; Havelaar, A.H. ; Mevius, D.J. ; Heederik, D.J.J. - \ 2018
Journal of Antimicrobial Chemotherapy 73 (2018)2. - ISSN 0305-7453 - p. 339 - 347.
Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.
Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.
Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).
Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.
Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.
Samenvatting ESBL-Attributieanalyse (ESBLAT) : Op zoek naar de bronnen van antibioticaresistentie bij de mens
Mevius, Dik ; Heederik, Dick ; Duijkeren, Engeline ; Veldman, Kees ; Essen, Alieda van; Kant, Arie ; Liakopoulos, Apostolos ; Geurts, Yvon ; Pelt, Wilfrid van; Mughini Gras, Lapo ; Schmitt, Heike ; Dierikx, Cindy ; Hoek, Angela van; Evers, Eric ; Roda Husman, Annemaria de; Blaak, Hetty ; Dissel, Jaap van; Smid, Joost ; Dohmen, Wietske ; Dorado-Garcia, Alejandro ; Havelaar, Arie ; Hordijk, Joost ; Wagenaar, Jaap ; Fluit, Ad ; Bunt, Gerrita van den; Bonten, Marc ; Velthuis, Annet ; Heuvelink, Annet ; Buter, Rianne ; Gonggrijp, Maaike ; Santman-Berends, Inge ; Lam, Theo ; Urlings, Bert ; Heres, Lourens ; Bouwknecht, Martijn ; Groot, Jacques de - \ 2018
Netherlands : De Stichting TKI Agri&Food (TKI) - 11 p.
Rapport ESBL-Attributieanalyse (ESBLAT) : Op zoek naar de bronnen van antibioticaresistentie bij de mens
Mevius, Dik ; Heederik, Dick ; Duijkeren, Engeline ; Veldman, Kees ; Essen, Alieda van; Kant, Arie ; Liakopoulos, Apostolos ; Geurts, Yvon ; Pelt, Wilfrid van; Mughini Gras, Lapo ; Schmitt, Heike ; Dierikx, Cindy ; Hoek, Angela van; Evers, Eric ; Roda Husman, Annemaria de; Blaak, Hetty ; Dissel, Jaap van; Smid, Joost ; Dohmen, Wietske ; Dorado-Garcia, Alejandro ; Havelaar, Arie ; Hordijk, Joost ; Wagenaar, Jaap ; Fluit, Ad ; Bunt, Gerrita van den; Bonten, Marc ; Velthuis, Annet ; Heuvelink, Annet ; Buter, Rianne ; Gonggrijp, Maaike ; Santman-Berends, Inge ; Lam, Theo ; Urlings, Bert ; Heres, Lourens ; Bouwknecht, Martijn ; Groot, Jacques de - \ 2018
Netherlands : De Stichting TKI Agri&Food (TKI) - 73
Initiation, elongation, and realignment during influenza virus mRNA synthesis
Velthuis, Aartjan J.W. te; Oymans, Judith - \ 2018
Journal of Virology 92 (2018)3. - ISSN 0022-538X
Influenza A virus - Priming loop - Realignment - Replication - RNA-dependent RNA polymerase - Transcription - Viral transcription
The RNA-dependent RNA polymerase (RdRp) of the influenza A virus replicates and transcribes the viral genome segments in the nucleus of the host cell. To transcribe these viral genome segments, the RdRp "snatches" capped RNA oligonucleotides from nascent host cell mRNAs and aligns these primers to the ultimate or penultimate nucleotide of the segments for the initiation of viral mRNA synthesis. It has been proposed that this initiation process is not processive and that the RdRp uses a prime-realign mechanism during transcription. Here we provide in vitro evidence for the existence of this transcriptional prime-realign mechanism but show that it functions efficiently only for primers that are short or cannot stably base pair with the template. In addition, we demonstrate that transcriptional elongation is dependent on the priming loop of the PB1 subunit of the RdRp. We propose that the prime-realign mechanism may be used to rescue abortive transcription initiation events or cope with sequence variation among primers. Overall, these observations advance our mechanistic understanding of how influenza A virus initiates transcription correctly and efficiently.
A mechanism for priming and realignment during influenza A virus replication
Oymans, Judith ; Velthuis, Aartjan J.W. te - \ 2018
Journal of Virology 92 (2018)3. - ISSN 0022-538X
ApG - Influenza A virus - Priming loop - Realignment - RNA-dependent RNA polymerase - Viral replication
The influenza A virus genome consists of eight segments of singlestranded RNA. These segments are replicated and transcribed by a viral RNA-dependent RNA polymerase (RdRp) that is made up of the influenza virus proteins PB1, PB2, and PA. To copy the viral RNA (vRNA) genome segments and the cRNA segments, the replicative intermediate of viral replication, the RdRp must use two promoters and two different de novo initiation mechanisms. On the vRNA promoter, the RdRp initiates on the 3' terminus, while on the cRNA promoter, the RdRp initiates internally and subsequently realigns the nascent vRNA product to ensure that the template is copied in full. In particular, the latter process, which is also used by other RNA viruses, is not understood. Here we provide mechanistic insight into priming and realignment during influenza virus replication and show that it is controlled by the priming loop and a helix-loop-helix motif of the PB1 subunit of the RdRp. Overall, these observations advance our understanding of how the influenza A virus initiates viral replication and amplifies the genome correctly.
Identification and characterization of the Verticillium dahliae effector that is responsible for cotton defoliation
Li, J. ; Faino, L. ; Berg-Velthuis, G.C.M. van den; Liu, Tingli ; Zhang, Baolong ; Zhu, Longfu ; Thomma, B.P.H.J. - \ 2017
In: Abstract Book 5th International Conference on Biotic Plant Interaction, Xiamen, China 17-21 August 2017 - p. 227 - 227.
Plant pathogens from diverse taxonomic origins have been shown to secrete effector proteins into host plants to manipulate host physiology and establish infection. Verticillium dahliae is a soil-born fungus that causes Verticillium wilt disease in a wide range of crops, including cotton and olive. V. dahliae strains have previously been characterized as defoliating and non-defoliating strains based on their ability to cause defoliation on cotton, but the V. dahliae gene(s) that are involved in cotton defoliation remain unknown thus far. Here, we present a comparative genomics study defoliating and non-defoliating strains of V. dahliae that enabled us to identify a region of about 20 kb that specifically occurs in multiple defoliating strains. In this region, we were subsequently able to uncover a single highly-expressed gene that encodes a putative effector protein. Currently, we are performing experiments to confirm the role of this effector in cotton defoliation.
Cross continental increase in methane ebullition under climate change
Aben, Ralf C.H. ; Barros, Nathan ; Donk, Ellen Van; Frenken, Thijs ; Hilt, Sabine ; Kazanjian, Garabet ; Lamers, Leon P.M. ; Peeters, Edwin T.H.M. ; Roelofs, Jan G.M. ; Senerpont Domis, Lisette N. De; Stephan, Susanne ; Velthuis, Mandy ; De Waal, Dedmer B. Van; Wik, Martin ; Thornton, Brett F. ; Wilkinson, Jeremy ; Delsontro, Tonya ; Kosten, Sarian - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 °C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 °C increase), contributing to global warming.
A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape
Depotter, Jasper R.L. ; Seidl, Michael F. ; Berg-Velthuis, Grardy van den; Thomma, Bart P.H.J. ; Wood, Thomas A. - \ 2017
Environmental Microbiology 19 (2017)10. - ISSN 1462-2912 - p. 3997 - 4009.

Population genetic structures illustrate evolutionary trajectories of organisms adapting to differential environmental conditions. Verticillium stem striping disease on oilseed rape was mainly observed in continental Europe, but has recently emerged in the United Kingdom. The disease is caused by the hybrid fungal species Verticillium longisporum that originates from at least three separate hybridization events, yet hybrids between Verticillium progenitor species A1 and D1 are mainly responsible for Verticillium stem striping. We reveal a hitherto un-described dichotomy within V. longisporum lineage A1/D1 that correlates with the geographic distribution of the isolates with an 'A1/D1 West' and an 'A1/D1 East' cluster. Genome comparison between representatives of the A1/D1 West and East clusters excluded population distinctiveness through separate hybridization events. Remarkably, the A1/D1 West population that is genetically more diverse than the entire A1/D1 East cluster caused the sudden emergence of Verticillium stem striping in the UK, whereas in continental Europe Verticillium stem striping is predominantly caused by the more genetically uniform A1/D1 East population. The observed genetic diversity of the A1/D1 West population argues against a recent introduction of the pathogen into the UK, but rather suggests that the pathogen previously established in the UK and remained latent or unnoticed as oilseed rape pathogen until recently.

Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium
Seidl, M.F. ; Faino, L. ; Cook III, D.E. ; Kramer, H.M. ; Shi-Kunne, X. ; Berg-Velthuis, G.C.M. van den; Thomma, B.P.H.J. - \ 2017
In: Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - Genetics Society of America - p. 80 - 81.
Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.
The two-speed genome of Verticillium dahliae mediates emergence of potent virulence factors
Thomma, B.P.H.J. ; Faino, L. ; Li, J. ; Shi-Kunne, X. ; Depotter, J.R.L. ; Kramer, H.M. ; Berg-Velthuis, G.C.M. van den; Cook III, David ; Rövenich, H.J. ; Seidl, M.F. - \ 2017
In: Book of Abstracts 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - - p. 4 - 4.
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, virulence genes reside in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of such compartments, and the role of transposons therein, remains limited. We show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae, and that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. Remarkably, LS regions are enriched in active transposons, which may contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of V. dahliae virulence. Based on this knowledge, we are now able to identify crucial virulence factors of V. dahliae, which also allows investigating causal relationships between particular effectors and pathotypes.
Warming advances top-down control and reduces producer biomass in a freshwater plankton community
Velthuis, Mandy ; Senerpont Domis, Lisette N. De; Frenken, Thijs ; Stephan, Susanne ; Kazanjian, Garabet ; Aben, Ralf ; Hilt, Sabine ; Kosten, Sarian ; Donk, Ellen Van; De Waal, Dedmer B. Van - \ 2017
Ecosphere 8 (2017)1. - ISSN 2150-8925
Global warming has been shown to affect ecosystems worldwide. Warming may, for instance, disrupt plant herbivore synchrony and bird phenology in terrestrial systems, reduce primary production in oceans, and promote toxic cyanobacterial blooms in freshwater lakes. Responses of communities will not only depend on direct species-specific temperature effects, but also on indirect effects related to bottom-up and top-down processes. Here, we investigated the impact of warming on freshwater phytoplankton community dynamics, and assessed the relative contribution of nutrient availability, fungal parasitism, and grazing therein. For this purpose, we performed an indoor mesocosm experiment following seasonal temperature dynamics of temperate lakes and a warmed (+4°C) scenario from early spring to late summer. We assessed phytoplankton biomass, C:N:P stoichiometry and community composition, dissolved nutrient availabilities, fungal parasite (i.e., chytrid) prevalence, and zooplankton abundance. Warming led to an overall reduction in phytoplankton biomass as well as lower C:P and N:P ratios, while phytoplankton community composition remained largely unaltered. Warming resulted in an earlier termination of the diatom spring bloom, and an epidemic of its fungal parasite ended earlier as well. Furthermore, warming advanced zooplankton phenology, leading to an earlier top-down control on phytoplankton in the period after the spring bloom. Linear model analysis showed that most of the observed variance in phytoplankton biomass was related to seasonal temperature dynamics in combination with zooplankton abundance. Our findings showed that warming advanced grazer phenology and reduced phytoplankton biomass, thereby demonstrating how bottom-up and top-down related processes may shape future phytoplankton dynamics.
Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts
Kombrink, Anja ; Rovenich, Hanna ; Shi, Xiaoqian ; Rojas-Padilla, Eduardo ; Berg-Velthuis, Grardy van den; Domazakis, Emmanouil ; Jonge, Ronnie De; Valkenburg, Dirk-Jan ; Sánchez-Vallet, Andrea ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2017
Molecular Plant Pathology 18 (2017)4. - ISSN 1464-6722 - p. 596 - 608.
Chitin-binding LysM effectors contribute to virulence of various plant pathogenic fungi that are causal agents of foliar diseases. Here, we report on LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast to the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17 but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or on N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses, and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast to the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.
Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae
Santhanam, Partha ; Boshoven, Jordi C. ; Salas, Omar ; Bowler, Kyle ; Islam, M.T. ; Saber, Mojtaba Keykha ; Berg-Velthuis, Grardy van den; Bar-Peled, Maor ; Thomma, Bart P.H.J. - \ 2017
Molecular Plant Pathology 18 (2017)3. - ISSN 1464-6722 - p. 347 - 362.
Agrobacterium tumefaciens-mediated transformation (ATMT) - Attachment - Carbohydrate - Root colonization - Tomato - UDP-rhamnose - Vascular wilt
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.
Inventarisatie diagnostiek Diagnostiek Ontwikkeling en Toepassing voor het optimaliseren van uiergezondheid
Wal, F.J. van der; Heuvelink, A. ; Cornelissen, J.B.W.J. ; Achterberg, R.P. ; Griffioen, K. ; Mevius, D.J. ; Lam, T. ; Velthuis, A. ; Hop, G. ; Scherpenzeel, C. ; Dijkman, R. - \ 2016
1Health4Food DOT
Arabidopsis miRNA boosts host immunity against Verticillium via repression of plant target gene transcript
Berg-Velthuis, G.C.M. van den; Damme, M.M.A. van; Faino, L. ; Thomma, B.P.H.J. - \ 2016
Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
Faino, Luigi ; Seidl, Michael F. ; Shi, Xiaoqian ; Pauper, Marc ; Berg-Velthuis, Grardy van den; Wittenberg, A.H.J. ; Thomma, Bart P.H.J. - \ 2016
Genome Research 26 (2016)8. - ISSN 1088-9051 - p. 1091 - 1100.

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in "arms races" with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.

Warming accelerates termination of a phytoplankton spring bloom by fungal parasites
Frenken, Thijs ; Velthuis, Mandy ; Senerpont Domis, L.N. de; Stephan, Susanne ; Aben, Ralf ; Kosten, Sarian ; Donk, Ellen van; Waal, D.B. Van de - \ 2016
Global Change Biology 22 (2016)1. - ISSN 1354-1013 - p. 299 - 309.
Bacteria - Chytrid - Climate change - Ecological stoichiometry - Epidemic - Rotifer phenology - Synedra - Zoospores

Climate change is expected to favour infectious diseases across ecosystems worldwide. In freshwater and marine environments, parasites play a crucial role in controlling plankton population dynamics. Infection of phytoplankton populations will cause a transfer of carbon and nutrients into parasites, which may change the type of food available for higher trophic levels. Some phytoplankton species are inedible to zooplankton, and the termination of their population by parasites may liberate otherwise unavailable carbon and nutrients. Phytoplankton spring blooms often consist of large diatoms inedible for zooplankton, but the zoospores of their fungal parasites may serve as a food source for this higher trophic level. Here, we investigated the impact of warming on the fungal infection of a natural phytoplankton spring bloom and followed the response of a zooplankton community. Experiments were performed in ca. 1000 L indoor mesocosms exposed to a controlled seasonal temperature cycle and a warm (+4 °C) treatment in the period from March to June 2014. The spring bloom was dominated by the diatom Synedra. At the peak of infection over 40% of the Synedra population was infected by a fungal parasite (i.e. a chytrid) in both treatments. Warming did not affect the onset of the Synedra bloom, but accelerated its termination. Peak population density of Synedra tended to be lower in the warm treatments. Furthermore, Synedra carbon: phosphorus stoichiometry increased during the bloom, particularly in the control treatments. This indicates enhanced phosphorus limitation in the control treatments, which may have constrained chytrid development. Timing of the rotifer Keratella advanced in the warm treatments and closely followed chytrid infections. The chytrids' zoospores may thus have served as an alternative food source to Keratella. Our study thus emphasizes the importance of incorporating not only nutrient limitation and grazing, but also parasitism in understanding the response of plankton communities towards global warming.

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