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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Sensor-based management of container nursery crops irrigated with fresh or saline water
Incrocci, Luca ; Marzialetti, Paolo ; Incrocci, Giorgio ; Vita, Andrea Di; Balendonck, Jos ; Bibbiani, Carlo ; Spagnol, Serafino ; Pardossi, Alberto - \ 2019
Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 49 - 61.
The objective of this study was to design and test a prototype fertigation controller for the management of container ornamental nursery stocks irrigated with different water sources, including saline water or reclaimed municipal/industrial wastewater. The prototype could schedule irrigation in various ways, i.e. as a time clock, or by means of a soil moisture dielectric sensor, or using a crop evapotranspiration (ET) model. The prototype also monitored the salinity in the root zone using a dielectric sensor that measured both substrate moisture and electrical conductivity (EC), or a probe measuring the EC of the water draining out of the containers. Excessive substrate salinization of the containers irrigated with saline water (containing 10 mM of sodium chloride) was prevented by the automated adoption of a series of measures: irrigation with fresh water or a mixture of fresh water and saline water; progressive increase of irrigation dose for each event, and progressive reduction of fertilizer concentration in the nutrient solution delivered to the crop. The system was tested in three experiments conducted in Pistoia (Italy) between 2008 and 2010 with two ornamental species: Photinia × fraseri Dress (a salt-medium tolerant species) and Prunus laurocerasus L. (a salt-sensitive species). When irrigation with fresh water was controlled with a dielectric sensor or an ET model, total irrigation water use and the loss of both N and P were reduced by 17% to 84% compared with the time-controlled irrigation. The sensor-based control of saline water irrigation reduced the salinity effects on dry matter accumulation in both species; however, it did not prevent the occurrence of leaf damages (leaf scorch) on Prunus plants, which were unmarketable by the end of growing season. On the contrary, no leaf damages were visible on Photinia plants irrigated with saline and/or fresh water, such that all were classified in the top quality market category. The controller developed in this work could be used in commercial nurseries to improve profitability and sustainability of container hardy ornamental nursery stock production.
Genera of phytopathogenic fungi : GOPHY 2
Marin-Felix, Y. ; Hernández-Restrepo, Margarita ; Wingfield, M.J. ; Akulov, A. ; Carnegie, A.J. ; Cheewangkoon, R. ; Gramaje, D. ; Groenewald, J.Z. ; Guarnaccia, V. ; Halleen, F. ; Lombard, L. ; Luangsa-ard, J. ; Marincowitz, S. ; Moslemi, A. ; Mostert, L. ; Quaedvlieg, W. ; Schumacher, R.K. ; Spies, C.F.J. ; Thangavel, R. ; Taylor, P.W.J. ; Wilson, A.M. ; Wingfield, B.D. ; Wood, A.R. ; Crous, P.W. - \ 2019
Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 47 - 133.
26 new taxa - DNA barcodes - Fungal systematics - Six new typifications

This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella, Utrechtiana and Wojnowiciella. This study includes the new genus Pyriculariomyces, 20 new species, five new combinations, and six typifications for older names.

Nils Foss Excellence Price
Hall, Robert - \ 2018
Robert David Hall is awarded the Nils Foss Excellence Prize Robert David Hall is Professor of Plant Metabolomics at Wageningen University & Research. Robert David Hall is a pioneer in developing and establishing metabolomics technologies to study the metabolic profiles of plants, with a particular emphasis on crop species. The aim of the research is to provide us with a better understanding of the biochemical composition of plant and food materials and to design new strategies for the development of improved food products of a higher quality.
Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition
Cochran, Alyssa T. ; Bauer, Jemma ; Metcalf, Jessica L. ; Lovecka, Petra ; Jong, Martina S. de; Warris, S. ; Mooijman, P.J.W. ; Meer, I.M. van der; Knight, Rob ; Pilon-Smits, E.A.H. - \ 2018
- p. 82 - 91.
Little is known about the microbiomes associated with plants with unusual properties, including plants that hyperaccumulate toxic elements such as selenium (Se). Se hyperaccumulators contain up to 1.5% of their dry weight in Se, concentrations shown to affect ecological interactions with herbivores, fungal pathogens and neighboring plants. Hyperaccumulators also enrich their surrounding soil with Se, which may alter the rhizobiome. To investigate whether plant Se affects rhizobacterial diversity and composition, we used a combination of culture-independent and culture-based approaches. Sequencing of 16S rRNA gene amplicons using the Illumina platform revealed that the rhizosphere microbiomes of Se hyperaccumulators were significantly different from nonaccumulators from the same site, with a higher average relative abundance of Pedobacter and Deviosa. Additionally, hyperaccumulators harbored a higher rhizobacterial species richness when compared with nonaccumulators from the same family on the same site. Independent from Se present at the site or in the host plant, the bacterial isolates were extremely resistant to selenate and selenite (up to 200 mM) and could reduce selenite to elemental Se. In conclusion, Se hyperaccumulation does not appear to negatively affect rhizobacterial diversity, and may select for certain taxa in the rhizosphere microbiome. Additionally, Se resistance in hyperaccumulator-associated bacteria and archaea may be widespread and not under selection by the host plant.
Scientific Opinion on the state of the art of Toxicokinetic/Toxicodynamic (TKTD) effect models for regulatory risk assessment of pesticides for aquatic organisms
Ockleford, Colin ; Adriaanse, Paulien ; Berny, Philippe ; Brock, Theodorus ; Duquesne, Sabine ; Grilli, Sandro ; Hernandez‐Jerez, Antonio F. ; Bennekou, Susanne Hougaard ; Klein, Michael ; Kuhl, Thomas ; Laskowski, Ryszard ; Machera, Kyriaki ; Pelkonen, Olavi ; Pieper, Silvia ; Smith, Robert H. ; Stemmer, Michael ; Sundh, Ingvar ; Tiktak, Aaldrik ; Topping, Christopher J. ; Wolterink, Gerrit ; Cedergreen, Nina ; Charles, Sandrine ; Focks, Andreas ; Reed, Melissa ; Arena, Maria ; Ippolito, Alessio ; Byers, Harry ; Teodorovic, Ivana - \ 2018
EFSA Journal 16 (2018)8. - ISSN 1831-4732
Following a request from EFSA, the Panel on Plant Protection Products and their Residues (PPR) developed an opinion on the state of the art of Toxicokinetic/Toxicodynamic (TKTD) models and their use in prospective environmental risk assessment (ERA) for pesticides and aquatic organisms. TKTD models are species‐ and compound‐specific and can be used to predict (sub)lethal effects of pesticides under untested (time‐variable) exposure conditions. Three different types of TKTD models are described, viz., (i) the ‘General Unified Threshold models of Survival’ (GUTS), (ii) those based on the Dynamic Energy Budget theory (DEBtox models), and (iii) models for primary producers. All these TKTD models follow the principle that the processes influencing internal exposure of an organism, (TK), are separated from the processes that lead to damage and effects/mortality (TD). GUTS models can be used to predict survival rate under untested exposure conditions. DEBtox models explore the effects on growth and reproduction of toxicants over time, even over the entire life cycle. TKTD model for primary producers and pesticides have been developed for algae, Lemna and Myriophyllum. For all TKTD model calibration, both toxicity data on standard test species and/or additional species can be used. For validation, substance and species‐specific data sets from independent refined‐exposure experiments are required. Based on the current state of the art (e.g. lack of documented and evaluated examples), the DEBtox modelling approach is currently limited to research applications. However, its great potential for future use in prospective ERA for pesticides is recognised. The GUTS model and the Lemna model are considered ready to be used in risk assessment.
A retrospective analysis to identify the contribution of the breeder on health and performance of broiler chickens
Jong, I.C. de; Riel, J.W. van - \ 2018
In: The XVth European Poultry Conference: Conference Information and Proceedings. - Zagreb : - ISBN 9789082915709 - p. 146 - 146.
Broiler, Data analysis, Health, Performance
Data on performance and health are routinely collected in the various stages of the broiler production chain. In The Netherlands, routinely collected data are usually stored and solely used by the owner(s), and the various databases are not connected. Connecting databases may however provide insight to improve the quality of the chain. We were interested in the contribution of the parent stock to the performance of the broiler flock, as transgenerational effects have been reported and variation in performance and health between breeder farms and flocks exist. Broiler flock data at depopulation, collected by the slaughter plant (growth, uniformity, rejections, first week and total mortality) and from a national database (antibiotic treatments) were linked to breeder flocks and farms by unique identifiers for the period between 2011-2016.
This resulted in 2174 broiler flock records (at house level). Within these records, 74 broiler farms, 88 breeder farms, and 209 breeder flocks were identified. A mixed model analysis was used to simultaneously estimate effects of season, parent flock age, time, and the variance components that determine the contribution of the chain phase to the broiler performance parameters. Results showed no systematic effects of the breeder farm on the various parameters at broiler level. Systematic effects of breeder flock were relatively small; the largest effect was found on rejections in the broiler flock (estimated contribution to the variance component: 7%). The largest contributions to the variance
component were found for broiler farm: 14% (antibiotic treatment) to 59% (growth index). Also the phase between egg laying at the breeder farm and chick placement at the broiler farm (here called: chick delivery) had a large contribution to the variance component: rejections: 27%, first week mortality: 52%). Negligible effects were found for house at broiler farm and specific breeder-broiler farm combinations. A moderate effect of broiler house within a chick delivery was found. It can be concluded that systematic effects of breeder flock and farm on broiler performance and health could not be found, and that broiler farm and chick delivery had a large contribution on the variation in broiler performance and health. This does not exclude that transgenerational
effects exist, but these may be relatively short lasting, and thus could not be found in the present analysis, or might be overruled by more influential factors after egg laying at the breeder farm.
Identification of risk factors and prevalence of injuries at different stages of the broiler slaughter process
Jong, I.C. de; Gerritzen, Marien ; Reimert, H.G.M. ; Lohman, T. - \ 2018
In: The XVth European Poultry Conference: Conference Information and Proceedings / Prukner-Radovčić, Estella, Medić, Helga, Zagreb : - ISBN 9789082915709 - p. 240 - 240.
Broiler, Handling, Injuries, Slaughter, Welfare
Transport and handling of broilers during the (pre)slaughter process are risk factors for welfare. The impact of preslaughter treatments on injuries and thus the effect on welfare is poorly known. Moreover, it is unclear which proportion of carcass damage can be attributed to the conscious phase, and affects welfare, and which proportion of carcass damage can be attributed to handling after stunning and killing of birds and is related to product quality. We first analysed routinely collected data of a Dutch slaughter plant to identify risk factors for carcass damage. It was included whether or not prevalence of carcass damage was related to flock welfare status. Data collected in 2014-2016 from five farms with low foot pad dermatitis (FPD) score (<40 points) and five farms with high FPD score (>80 points) were analysed (N=771 flocks), assuming that FPD score was indicative of flock welfare status. A regression model was applied. The model showed positive associations between live body weight (P=0.000; B=0.001), number of dead-on-arrival (P=0.001; B=0.004), and wing damage. A negative association was found between wing damage and number of broilers per tray (P=0.037; B=-0.015). No relation between FPD score and carcass damage was found. Second, prevalence of injuries or damage during the slaughter process was determined in 20 flocks. Wing, leg and breast bruises, wing dislocations, and wing and leg fractures were scored between lairage and post-plucking. An increase in wing fractures from lairage (0,99%), post-shackling (1.67%), post-stunning (2.73%) and post-plucking (5.02%) was found (P=0.000 between all stages). Medium and large breast bruises increased between lairage and post-plucking (P=0.000). Small wing bruises decreased between lairage and post-plucking (P=0.047). This study showed that flock welfare status was not related to injuries, and that weight and crate density could be identified as risk factors for wing damage. Injuries and damage do mainly occur during the slaughter process. However, it was difficult to determine whether or not carcass damage originated from handling live animals, and thus is an animal welfare problem, or after stunning and therefore is a product quality issue. It is advised to develop an accuratebruise and damage scoring system that can be used to determine whether or not carcassdamage was caused in live animals.
Modeling the Effect of Nutritional Strategies for Dairy Cows on the Composition of Excreta Nitrogen
Dijkstra, J. ; Bannink, A. ; Bosma, Pieter M. ; Lantinga, E.A. ; Reijs, J.W. - \ 2018
models - Dairy cattle - Feces - Urine - diet composition - Manure composition
For an integrated evaluation of the effect of nutritional strategies on the utilization and losses of N at dairy farms, reliable estimates of excreta production and composition are indispensable. An extant, dynamic, mechanistic model of rumen functioning was extended with static equations that describe intestinal digestion to simulate the composition of dairy cow feces and urine as a function of diet composition. The extended model predicts organic matter (OM), carbon (C), and nitrogen (N) output of both feces and urine, classified in different components. Total N excretion was partitioned in three fractions based on the C:N ratio of individual components representing their availability of N following manure application to crops, viz. NM (immediately available), NE (easily decomposable), and NR (resistant). Forty nutritional strategies for stall-fed dairy cows, covering diets with a wide range in protein content and OM digestibility, were evaluated. The simulated ranges in fecal and urinary composition were largely in line with values reported in literature. Diet intake and composition had a substantial effect on simulated total N excretion and excreta composition, mainly because of differences in the level of NM excretion and the C:N ratio of the NR fraction. Furthermore, it was shown that the type of OM excreted varies considerably between different diets. A simplified simulation of degradation processes during the first 4 months of excreta storage produced average values and ranges of slurry characteristics that were in line with values reported in literature. The simulated variation in slurry characteristics suggested a strong variability in ammonia N losses from the slurry pit and a moderate variability in plant availability of slurry N. Further efforts are required to integrate effects of manure storage conditions on the storage processes. In conclusion, the model can be a tool to predict fecal and urinary composition of cattle, and ultimately to improve the utilization of N from field applied manure as well as to evaluate the effects of different nutritional strategies on the whole-farm N balance.
Removal of soil biota alters soil feedback effects on plant growth and defense chemistry
Wang, Minggang ; Ruan, Weibin ; Kostenko, Olga ; Carvalho, Sabrina ; Hannula, S.E. ; Mulder, Patrick P.J. ; Bu, Fengjiao ; Putten, Wim H. van der; Bezemer, T.M. - \ 2018
New Phytologist (2018). - ISSN 0028-646X
fractionation - Jacobaea vulgaris - plant–soil feedback (PSF) - pyrrolizidine alkaloids (PAs) - soil biota - spectral reflectance

We examined how the removal of soil biota affects plant–soil feedback (PSF) and defense chemistry of Jacobaea vulgaris, an outbreak plant species in Europe containing the defense compounds pyrrolizidine alkaloids (PAs). Macrofauna and mesofauna, as well as fungi and bacteria, were removed size selectively from unplanted soil or soil planted with J. vulgaris exposed or not to above- or belowground insect herbivores. Wet-sieved fractions, using 1000-, 20-, 5- and 0.2-μm mesh sizes, were added to sterilized soil and new plants were grown. Sieving treatments were verified by molecular analysis of the inocula. In the feedback phase, plant biomass was lowest in soils with 1000- and 20-μm inocula, and soils conditioned with plants gave more negative feedback than without plants. Remarkably, part of this negative PSF effect remained present in the 0.2-μm inoculum where no bacteria were present. PA concentration and composition of plants with 1000- or 20-μm inocula differed from those with 5- or 0.2-μm inocula, but only if soils had been conditioned by undamaged plants or plants damaged by aboveground herbivores. These effects correlated with leaf hyperspectral reflectance. We conclude that size-selective removal of soil biota altered PSFs, but that these PSFs were also influenced by herbivory during the conditioning phase.

Post-thaw variability in litter decomposition best explained by microtopography at an ice-rich permafrost peatland
Malhotra, Avni ; Moore, Tim R. ; Limpens, Juul ; Roulet, Nigel T. - \ 2018
Arctic, Antarctic and Alpine Research 50 (2018)1. - ISSN 1523-0430
Discontinuous permafrost zone - litter decomposition - microtopography - peatland - permafrost thaw

Litter decomposition, a key process by which recently fixed carbon is lost from ecosystems, is a function of environmental conditions and plant community characteristics. In ice-rich peatlands, permafrost thaw introduces high variability in both abiotic and biotic factors, both of which may affect litter decomposition rates in different ways. Can the existing conceptual frameworks of litter decomposition and its controls be applied across a structurally heterogeneous thaw gradient? We investigated the variability in litter decomposition and its predictors at the Stordalen subarctic peatland in northern Sweden. We measured in situ decomposition of representative litter and environments using litter bags throughout two years. We found highly variable litter decomposition rates with turnover times ranging from five months to four years. Surface elevation was a strong correlate of litter decomposition across the landscape, likely as it integrates multiple environmental and plant community changes brought about by thaw. There was faster decomposition but also more mass remaining after two years in thawed areas relative to permafrost areas, suggesting faster initial loss of carbon but more storage into the slow-decomposing carbon pool. Our results highlight mechanisms and predictors of carbon cycle changes in ice-rich peatlands following permafrost thaw.

Small RNA molecules and their role in plant disease
Rose, Laura E. ; Overdijk, Elysa J.R. ; Damme, Mireille van - \ 2018
European Journal of Plant Pathology (2018). - ISSN 0929-1873 - 14 p.
Epigenetics - Plant immunity - Plant-pathogen interaction - RNA silencing

All plant species are subject to disease. Plant diseases are caused by parasites, e.g. viruses, bacteria, oomycetes, parasitic plants, fungi, or nematodes. In all organisms, gene expression is tightly regulated and underpins essential functions and physiology. The coordination and regulation of both host and pathogen gene expression is essential for pathogens to infect and cause disease. One mode of gene regulation is RNA silencing. This biological process is widespread in the natural world, present in plants, animals and several pathogens. In RNA silencing, small (20–40 nucleotides) non-coding RNAs (small-RNAs, sRNAs) accumulate and regulate gene expression transcriptionally or post-transcriptionally in a sequence-specific manner. Regulation of sRNA molecules provides a fast mode to alter gene activity of multiple gene transcripts. RNA silencing is an ancient mechanism that protects the most sensitive part of an organism: its genetic code. sRNA molecules emerged as regulators of plant development, growth and plant immunity. sRNA based RNA silencing functions both within and between organisms. Here we present the described sRNAs from plants and pathogens and discuss how they regulate host immunity and pathogen virulence. We speculate on how sRNA molecules can be exploited to develop disease resistant plants. Finally, the activity of sRNA molecules can be prevented by proteins that suppress RNA silencing. This counter silencing response completes the dialog between plants and pathogens controlling plant disease or resistance outcome on the RNA (controlling gene expression) and protein level.

Distinct Roles of Non-Overlapping Surface Regions of the Coiled-Coil Domain in the Potato Immune Receptor Rx1
Slootweg, Erik J. ; Spiridon, Laurentiu N. ; Martin, Eliza C. ; Tameling, Wladimir I.L. ; Townsend, Philip D. ; Pomp, Rikus ; Roosien, Jan ; Drawska, Olga ; Sukarta, Octavina C.A. ; Schots, Arjen ; Borst, Jan Willem ; Joosten, Matthieu H.A.J. ; Bakker, Jaap ; Smant, Geert ; Cann, Martin J. ; Petrescu, Andrei-Jose ; Goverse, Aska - \ 2018
Plant Physiology 178 (2018)3. - ISSN 0032-0889 - p. 1310 - 1331.
The intracellular immune receptor Rx1 of potato (Solanum tuberosum), which confers effector-triggered immunity to Potato virus X, consists of a central nucleotide-binding domain (NB-ARC) flanked by a carboxyl-terminal leucine-rich repeat (LRR) domain and an amino-terminal coiled-coil (CC) domain. Rx1 activity is strictly regulated by interdomain interactions between the NB-ARC and LRR, but the contribution of the CC domain in regulating Rx1 activity or immune signaling is not fully understood. Therefore, we used a structure-informed approach to investigate the role of the CC domain in Rx1 functionality.
Targeted mutagenesis of CC surface residues revealed separate regions required for the intramolecular and intermolecular interaction of the CC with the NB-ARC-LRR and the cofactor Ran GTPase-activating protein2 (RanGAP2), respectively. None of the mutant Rx1 proteins was constitutively active, indicating that the CC does not contribute to the autoinhibition of Rx1 activity. Instead, the CC domain acted as a modulator of downstream responses involved in effector-triggered immunity. Systematic disruption of the hydrophobic interface between the four helices of the CC enabled the uncoupling of cell death and disease resistance responses. Moreover, a strong dominant negative effect on Rx1-mediated resistance and cell death was observed upon coexpression of the CC alone with full-length Rx1 protein, which depended on the RanGAP2-binding surface of the CC. Surprisingly, coexpression of the N-terminal half of the CC enhanced Rx1-mediated resistance, which further indicated that the CC functions as a scaffold for downstream components involved in the modulation of disease resistance or cell death signaling.
A Resurrected Scenario : Single Gain and Massive Loss of Nitrogen-Fixing Nodulation
Velzen, Robin van; Doyle, Jeff J. ; Geurts, Rene - \ 2018
Trends in Plant Science (2018). - ISSN 1360-1385
evolution - Frankia - nitrogen-fixing root nodules - rhizobia

Root nodule endosymbiosis with nitrogen-fixing bacteria provides plants with unlimited access to fixed nitrogen, but at a significant energetic cost. Nodulation is generally considered to have originated in parallel in different lineages, but this hypothesis downplays the genetic complexity of nodulation and requires independent recruitment of many common features across lineages. Recent phylogenomic studies revealed that genes that function in establishing or maintaining nitrogen-fixing nodules are independently lost in non-nodulating relatives of nitrogen-fixing plants. In our opinion, these data are best explained by a scenario of a single gain followed by massively parallel loss of nitrogen-fixing root nodules triggered by events at geological scale.

Genome-wide identification, classification and expression of lipoxygenase gene family in pepper
Sarde, Sandeep J. ; Kumar, Abhishek ; Remme, Rahima N. ; Dicke, Marcel - \ 2018
Plant Molecular Biology (2018). - ISSN 0167-4412 - 13 p.
Defence - Gene transcription - Lipoxygenases (LOXs) - Pepper - Phylogenetic analysis - Sequence analyses

Key message: Lipoxygenases mediate important biological processes. Through comparative genomics, domain-scan analysis, sequence analysis, phylogenetic analysis, homology modelling and transcriptional analysis the lipoxygenase gene family of pepper (Capsicum annuum) has been identified. Abstract: Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases playing a pivotal role in diverse biological processes in plants, including defence and development. Here, we exploited the recent sequencing of the pepper genome to investigate the LOX gene family in pepper. Two LOX classes are recognized, the 9- and 13-LOXs that oxygenate lipids at the 9th and 13th carbon atom, respectively. Using two main in-silico approaches, we identified a total of eight LOXs in pepper. Phylogenetic analysis classified four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Furthermore, sequence similarity/identity and subcellular localization analysis strengthen the classification predicted by phylogenetic analysis. Pivotal amino acids together with all domains and motifs are highly conserved in all pepper LOXs. Expression of 13-LOXs appeared to be more dynamic compared to 9-LOXs both in response to exogenous JA application and to thrips feeding. Bioinformatic and expression analyses predict the putative functions of two 13-LOXs, CaLOX6 and CaLOX7, in the biosynthesis of Green Leaf Volatiles, involved in indirect defence. The data are discussed in the context of LOX families in solanaceous plants and plants of other families.

Phenotypic plasticity as a clue for invasion success of the submerged aquatic plant Elodea nuttallii
Szabó, S. ; Peeters, E.T.H.M. ; Várbíró, G. ; Borics, G. ; Lukács, B.A. - \ 2018
Plant Biology (2018). - ISSN 1435-8603
Alien - aquatic plant - competition - light - macrophyte - nitrogen

Two closely related alien submerged aquatic plants were introduced into Europe. The new invader (Elodea nuttallii) gradually displaced E. canadensis even at sites where the latter was well established. The aim of the study was to evaluate the combined effects of environmental factors on several phenotypic characteristics of the two Elodea species, and to relate these phenotypic characteristics to the invasion success of E. nuttallii over E. canadensis. In a factorial design, Elodea plants were grown in aquaria containing five different nitrogen concentrations and incubated at five different light intensities. We used six functional traits (apical shoot RGR), total shoot RGR, relative elongation, root length, lateral spread, branching degree) to measure the environmental response of the species. We calculated plasticity indices to express the phenotypic differences between species. Light and nitrogen jointly triggered the development of phenotypic characteristics that make E. nuttallii a more successful invader in eutrophic waters than E. canadensis. The stronger invader showed a wider range of phenotypic plasticity. The apical elongation was the main difference between the two species, with E. nuttallii being more than two times longer than E. canadensis. E. canadensis formed dense side shoots even under high shade and low nitrogen levels, whereas E. nuttallii required higher light and nitrogen levels. We found that under more eutrophic conditions, E. nuttallii reach the water surface sooner than E. canadensis and through intensive branching outcompetes all other plants including E. canadensis. Our findings support the theory that more successful invaders have wider phenotypic plasticity.

Legacy of land use history determines reprogramming of plant physiology by soil microbiome
Li, Xiaogang ; Jousset, Alexandre ; Boer, Wietse de; Carrión, Víctor J. ; Zhang, Taolin ; Wang, Xingxiang ; Kuramae, Eiko E. - \ 2018
ISME Journal (2018). - ISSN 1751-7362

Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.

Metabolite variation in the lettuce gene pool : towards healthier crop varieties and food
Treuren, Rob van; Eekelen, Henriette D.L.M. van; Wehrens, Ron ; Vos, Ric C.H. de - \ 2018
Metabolomics 14 (2018)11. - ISSN 1573-3882
Crop improvement - Genetic resources - Lettuce - Phytochemical variation - Untargeted metabolomics - Vitamin C

Introduction: Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. Objectives: We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties. Methods: Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information. Results: A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types. Conclusion: Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

Costs of persisting unreliable memory : Reduced foraging efficiency for free-flying parasitic wasps in a wind tunnel
Bruijn, Jessica A.C. de; Vet, Louise E.M. ; Smid, Hans M. - \ 2018
Frontiers in Ecology and Evolution 6 (2018)OCT. - ISSN 2296-701X
Cotesia glomerata - Foraging efficiency - Learning - Memory - Non-host - Oviposition - Prediction error - Unreliable information

Parasitic wasps are known to improve their foraging efficiency after learning of herbivore-induced plant volatiles (HIPVs) upon encountering their hosts on these plants. However, due to spatial and temporal variation of herbivore communities, learned HIPV cues can become unreliable, no longer correctly predicting host presence. Little is known about the potential fitness costs when memories holding such unreliable information persist. Here we studied how persistent memory, containing unreliable information, affects the foraging efficiency for hosts in Cotesia glomerata. Wasps were conditioned to associate one of two types of HIPVs with either P. brassicae frass, 1 single oviposition in P. brassicae, 3 ovipositions in P. brassicae spaced in time or they were kept unconditioned. The following day, wasps were allowed to forage in a wind tunnel, in an environment that either conflicted or was congruent with their learned plant experience. The foraging environment consisted of host (P. brassicae) and non-host (Mamestra brassicae) infested plants. The conflicting environment had non-hosts on the conditioned plant species and hosts on the non-conditioned plant species, whereas the congruent environment had hosts on the conditioned plant species and non-hosts on the unconditioned plant species. Wasps had to navigate through five non-host infested plants to reach the host-infested plant. Since C. glomerata wasps do not distinguish between HIPVs induced by host and non-host caterpillars, the conflicting foraging situation caused a prediction error, by guiding wasps to non-host infested plants. Especially wasps given 3 spaced oviposition experiences, tested in a conflicting situation, spent significantly more time on non-host infested plants and showed a high tendency to oviposit in the non-hosts. As a result, they took significantly more time to find their hosts. Conditioned wasps, which were tested in a congruent situation, were more responsive than unconditioned wasps, but there was no difference in foraging efficiency between these two groups in the wasps that showed a response. We conclude that persistent memories, such as formed after 3 experiences spaced in time, can lead to maladaptive foraging behavior if the contained information becomes unreliable.

Identification and characterization of a new class of Tomato spotted wilt virus isolates that break Tsw-based resistance in a temperature-dependent manner
Ronde, D. de; Lohuis, D. ; Kormelink, R. - \ 2018
Plant Pathology (2018). - ISSN 0032-0862
Capsicum - NSs protein - RNA-silencing suppressor - temperature-sensitive resistance-breaking - Tomato spotted wilt virus - Tsw-based resistance

The single dominant Tsw resistance gene from Capsicum chinense against the Tomato spotted wilt orthotospovirus (TSWV) is temperature sensitive, i.e. the resistance fails to function at or above 32 °C. This study describes a new class of temperature-sensitive resistance-breaking TSWV isolates that induce Tsw-mediated resistance at T < 28 °C but at T ≥ 28 °C break this resistance. The NSs genes from these isolates were cloned and expressed to be analysed for RNA silencing suppressor (RSS) activity and the ability to induce a Tsw-mediated hypersensitive response (HR) in C. chinense and Capsicum annuum (Tsw+). Unlike in viral infection, transient expression of some of the NSs proteins at standard temperatures (22 °C) did not induce Tsw-mediated HR, although varying degrees of RSS activity were observed. Attempts to express and test the NSs proteins for functionality at an elevated temperature through agroinfiltration remained unsuccessful. The NSs proteins of some TSWV resistance-breaking (RB) isolates were analysed and found to lack amino acid residues that were previously shown to be important for RNA silencing suppression and avirulence. This study describes a new class of resistance-breaking TSWV isolates that may be of importance for breeders and growers and for which the underlying mechanism still remains unknown.

Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties
Dinh, Quy Dung ; Finkers, Richard ; Westphal, Adrie H. ; Dongen, Walter M.A.M. van; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2018
PLoS One 13 (2018)10. - ISSN 1932-6203 - p. e0206636 - e0206636.

Sucrose synthase (SuSy) is one key enzyme directly hydrolyzing sucrose to supply substrates for plant metabolism, and is considered to be a biomarker for plant sink strength. Improvement in plant sink strength could lead to enhanced plant growth and yield. Cultivated tomatoes are known to have a narrow genetic diversity, which hampers further breeding for novel and improved traits in new cultivars. In this study, we observed limited genetic variation in SuSy1, SuSy3 and SuSy4 in 53 accessions of cultivated tomato and landraces, but identified a wealth of genetic diversity in 32 accessions of related wild species. The variation in the deduced amino acid sequences was grouped into 23, 22, and 17 distinct haplotypes for SuSy1/3/4, respectively. Strikingly, all known substrate binding sites were highly conserved, as well as most of the phosphorylation sites except in SuSy1. Two SuSy1 and three SuSy3 protein variants were heterologously expressed to study the effect of the amino acid changes on enzyme kinetic properties, i.e. maximal sucrose hydrolyzing capacity (Vmax), affinity for sucrose (Km), and catalytic efficiency (Vmax/Km) at 25°C and 16°C. SuSy1-haplotype#3 containing phosphorylation site Ser-16 did not have an improvement in the kinetic properties compared to the reference SuSy1-haplotype#1 containing Arg-16. Meanwhile SuSy3-haplotype#9 from a wild accession, containing four amino acid changes S53A, S106I, E727D and K741E, showed an increase in Vmax/Km at 16°C compared to the reference SuSy3-haplotype#1. This study demonstrates that SuSy kinetic properties can be enhanced by exploiting natural variation, and the potential of this enzyme to improve sucrose metabolism and eventually sink strength in planta.

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