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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    Symbiotic interactions between chickpea (Cicer arietinum L.) genotypes and Mesorhizobium strains
    Gunnabo, A.H. ; Heerwaarden, J. van; Geurts, R. ; Wolde-meskel, E. ; Degefu, T. ; Giller, K.E. - \ 2020
    Symbiosis (2020). - ISSN 0334-5114
    AMMI - Genotype-strain combinations - Rhizobium genotypes - Symbiotic effectiveness
    Legume genotype (GL) x rhizobium genotype (GR) interaction in chickpea was studied using a genetically diverse set of accessions and rhizobium strains in modified Leonard Jars. A subset of effective GL x GR combinations was subsequently evaluated in a pot experiment to identify combinations of chickpea genotypes and rhizobium strains with stable and superior symbiotic performance. A linear mixed model was employed to analyse the occurrence of GL x GR interaction and an additive main effects and multiplicative interaction (AMMI) model was used to study patterns in the performance of genotype-strain combinations. We found statistically significant interaction in jars in terms of symbiotic effectiveness that was entirely due to the inclusion of one of the genotypes, ICC6263. No interaction was found in a subsequent pot experiment. The presence of two genetic groups (Kabuli and Desi genepools) did not affect interaction with Mesorhizobium strains. With the exception of a negative interaction with genotype ICC6263 in the jar experiment, the type strain Mesorhizobium ciceri LMG 14989 outperformed or equalled other strains on all chickpea genotypes in both jar and pot experiments. Similar to earlier reports in common bean, our results suggest that efforts to find more effective strains may be more rewarding than aiming for identification of superior combinations of strains and genotypes.
    Pectobacterium parvum sp. nov., having a salmonella SPI-1-like type iii secretion system and low virulence
    Pasanen, Miia ; Waleron, Malgorzata ; Schott, Thomas ; Cleenwerck, Ilse ; Misztak, Agnieszka ; Waleron, Krzysztof ; Pritchard, Leighton ; Bakr, Ramadan ; Degefu, Yeshitila ; Wolf, Jan van der; Vandamme, Peter ; Pirhonen, Minna - \ 2020
    International Journal of Systematic and Evolutionary Microbiology 70 (2020)4. - ISSN 1466-5026 - 1 p.

    There was an error in the Supplementary Material of the published article. Supplementary Table 8 entitled ‘Genome comparisons with GET_HOMOLOGUES. Unique genes identified in P. parvum/P. polaris isolates’ was previously missing from the published Supplementary Material file. Supplementary Table 8 is available with the online version of this article. The author apologizes for any inconvenience caused.

    Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence
    Pasanen, M. ; Waleron, M. ; Schott, Thomas ; Cleenwerck, I. ; Misztak, Agieszka ; Waleron, Krzysztof ; Pritchard, L. ; Bakr, Ramadan ; Degefu, Yeshtila ; Wolf, J.M. van der; Vandamme, Peter ; Pirhonen, M. - \ 2020
    International Journal of Systematic and Evolutionary Microbiology 70 (2020)4. - ISSN 1466-5026 - p. 2440 - 2448.
    Pectobacterium - Pectobacterium parvum - Salmonella SPI-1 T3SS - potato - soft rot - virulence
    Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
    Assessment of Dickeya and Pectobacterium spp. on vegetables and ornamentals (Soft rot)
    Wolf, J.M. van der; Bergsma-Vlami, M. ; Saddler, G. ; Hélias, V. ; Tsror, L. ; Yedida, Iris ; Pirhonen, M. ; Degefu, Yeshtila ; Tuomisto, J.T. ; Lojkowska, Ewa ; Li, Sean - \ 2020
    Zenodo - 109 p.
    Euphresco - Plant health - Dickeya - Pectobacterium - soft rot - vegetables - ornamentals - diagnostics - surveys - epidemiology - management
    Dickeya and Pectobacterium belonging to the group of soft rot Pectobacteriaceae (SRP) are causing emerging problems in a wide range of vegetable and ornamental crops in Europe, including potato, carrot, cabbage, Chinese cabbage, celery, leek, pepper, parsley, Zantedeschia, hyacinth, Dahlia, Chrysanthemum, Philodendron, Freesia, Saintpaulia, Iris, Aglaonema, Crocus, Campanula and Phalaenopsis. The phytopathogens in both genera are genetically and phenotypically highly diverse. Disease problems in the different hosts are associated with the introduction of new variants or by spread of groups already present in Europe. Within this Euphresco project we aimed to identify and assess the risks of these new variants, and to develop management strategies, including reliable diagnostic methods to prevent introductions and further spread of SRP. To reach our goals, meetings were organized and collaborations were established with specialists worldwide. All information on meetings, protocols and activities of the Euphresco group are published on the Dickeya/Pectobacterium website, conveyed by the James Hutton Institute in Invergowrie (Scotland) (https://engage.hutton.ac.uk, contact person Dr I. Toth/Dr J. Fairly).

    During the project, 1.5 days meetings were held in 2015 in Gdansk (Poland), in 2016 in Helsinki (Finland), in 2017 in Edinburgh (Scotland) and in 2018 in Emmeloord (The Netherlands). Meetings were attended by an average of 30 participants from organizations in EU member states, North- and Latin America, Africa, Asia and Australia.

    One project’s objective was to develop methods for the detection and identification of Pectobacterium and Dickeya species in different matrices. For this, a panel of reference strains has been compiled for Dickeya and Pectobacterium species. Most strains have been deposited in international collections. For most strains also whole genome sequence data are available. During the course of this project, several diagnostic tests were developed and evaluated, often based on the TaqMan technology.

    In several countries, surveys in potato and ornamental crops were conducted, but also in other matrices of the potato ecosystem, including water used for irrigation. In addition, new taxonomic groups that have been identified, are now new species including: P. versatile, P. aquaticum, P. fontis and P. polonicum. In potato, P. brasiliense became dominant as blackleg causing organism and has largely outcompeted D. solani in the last five years. In surface water in Europe, D. zeae was found to be the dominant SRP. In other continents, serious outbreaks of potato blackleg with other SRP has been reported, such as D. dianthicola in the USA and Australia. Various new SRP have been described, namely P. punjabense, P. peruviense, P. polaris, D. lacustris and D. zantedeschia. For the first time, D. fangzhongdai was described in Phalaenopsis. Not all species can cause potato blackleg.

    Studies on various virulence factors were conducted for SRP, such as on chemoreceptors, small phenolic plant compounds interacting with signal molecules of Pectobacterium involved in the quorum sensing mechanism of the pathogen. A Tn-seq approach was developed and used to identify new virulence factors.

    Information was exchanged on disease management strategies which include cultivation practices, resistance breeding, hygiene and the use of (bio-) control agents. A strict hygiene and an intensive monitoring of seed lots was found to be associated with a significant reduction of infections with blackleg causing SRP. A phage therapy has been developed to protect (seed) potato tubers against soft rot during storage. Various bacteriophages and bacterial antagonists were characterized and some evaluated for control of potato soft rot and/or blackleg. Steam treatments for seed tubers were found to decrease the blackleg incidence. Cold plasma treatment was found to kill SRP grown in vitro. Similarly, stabilized silver nanostructures killed SRP. It was found that seed potato lots can differ in suppressiveness against D. solani. Indications were found that the microbiome in tuber tissue plays a role in this.
    Genetic Interaction Studies Reveal Superior Performance of Rhizobium tropici CIAT899 on a Range of Diverse East African Common Bean (Phaseolus vulgaris L.) Genotypes
    Gunnabo, A.H. ; Geurts, R. ; Wolde-Meskel, E. ; Degefu, T. ; Giller, K.E. ; Heerwaarden, J. van - \ 2019
    Applied and Environmental Microbiology 85 (2019)24. - ISSN 0099-2240
    bean genotypes - genotype-by-strain interaction - N2 fixation - nodulation - Rhizobium strains

    We studied symbiotic performance of factorial combinations of diverse rhizobial genotypes (GR) and East African common bean varieties (GL) that comprise Andean and Mesoamerican genetic groups. An initial wide screening in modified Leonard jars (LJ) was followed by evaluation of a subset of strains and genotypes in pots (contained the same, sterile medium) in which fixed nitrogen was also quantified. An additive main effect and multiplicative interaction (AMMI) model was used to identify the contribution of individual strains and plant genotypes to the GL × GR interaction. Strong and highly significant GL × GR interaction was found in the LJ experiment but with little evidence of a relation to genetic background or growth habits. The interaction was much weaker in the pot experiment, with all bean genotypes and Rhizobium strains having relatively stable performance. We found that R. etli strain CFN42 and R. tropici strains CIAT899 and NAK91 were effective across bean genotypes but with the latter showing evidence of positive interaction with two specific bean genotypes. This suggests that selection of bean varieties based on their response to inoculation is possible. On the other hand, we show that symbiotic performance is not predicted by any a priori grouping, limiting the scope for more general recommendations. The fact that the strength and pattern of GL × GR depended on growing conditions provides an important cautionary message for future studies.IMPORTANCE The existence of genotype-by-strain (GL × GR) interaction has implications for the expected stability of performance of legume inoculants and could represent both challenges and opportunities for improvement of nitrogen fixation. We find that significant genotype-by-strain interaction exists in common bean (Phaseolus vulgaris L.) but that the strength and direction of this interaction depends on the growing environment used to evaluate biomass. Strong genotype and strain main effects, combined with a lack of predictable patterns in GL × GR, suggests that at best individual bean genotypes and strains can be selected for superior additive performance. The observation that the screening environment may affect experimental outcome of GL × GR means that identified patterns should be corroborated under more realistic conditions.

    Additive yield response of chickpea (Cicer arietinum L.) to rhizobium inoculation and phosphorus fertilizer across smallholder farms in Ethiopia
    Wolde-meskel, Endalkachew ; Heerwaarden, Joost van; Abdulkadir, Birhan ; Kassa, Sofia ; Aliyi, Ibsa ; Degefu, Tulu ; Wakweya, Kissi ; Kanampiu, Fred ; Giller, Ken E. - \ 2018
    Agriculture, Ecosystems and Environment 261 (2018). - ISSN 0167-8809 - p. 144 - 152.
    Grain legume - Mesorhizobium - Nitrogen fixation - Yield gaps - Yield variability
    The impacts of rhizobium inoculation on growth and yield of chickpea have mainly been tested in experiments conducted in greenhouses or on research stations. We report the response of the crop to inoculation (I) and phosphorus fertilizer (P) application across a large number of smallholder's farms over four regions of Ethiopia, covering diverse soil fertility and agro-ecological conditions. Increased grain yields due to the soil fertility treatments was evident for 99% target farmers. On average, I and P increased grain yield by 21% and 25% respectively, while the combined application of I and P resulted in a 38% increase. However, observed grain yields on control plots and responses to the treatments on individual farms varied greatly, and relative yield responses (%; yield of P and/I minus control yield, divided by control yield) ranged from 3% to 138%. With the exception of a few extremely poorly yielding locations, average responses to P and I were high across a wide range of control yields, indicating the possibility of boosting chickpea productivity for smallholders with P fertilizer and inoculant technology. Variation in response to rhizobium inoculation was mostly independent of agro-ecology and soil type although it was found to be low on a number of farms with extremely high N contents (%). Assuming that a relative yield increase of 10% due to treatment effects is required to be visible, 71%, 73% and 92% of the farmers observed a yield benefit by applying P, I, and P + I, respectively. The results are discussed with respect to the additive benefits of P fertilizers and rhizobial inoculation and their implications for wide scale promotion of inoculant technology to smallholders.
    Screening for New Rhizobium Strains for Studying Legume Genotype x Strain Interaction in Chickpea and Common Bean in Ethiopia
    Gunnabo, A.H. ; Giller, K.E. ; Wolde-Meskel, E. ; Geurts, R. ; Heerwaarden, J. van; Degefu, T. - \ 2016
    - p. 35 - 35.
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