Suppression of soil-borne plant pathogens

Soil borne plant pathogens considerably reduce crop yields worldwide and are difficult to control due to their ”masked” occurrence in the heterogeneous soil environment. This hampers the efficacy of chemical - and microbiological control agents. Outbreaks of crop diseases are not only dependent on the presence of pathogen propagules in the soil, but are also influenced by soil-related properties like physico-chemical characteristics, microbial activity and community composition. Strong competition for limited available carbon substrates restricts or prevents germination and pre-infective growth of pathogens. This competition can occur directly by rapid exploitation of substrates, so called resource competition, or indirectly via inhibitory secondary metabolites, called interference competition The overall effect of all competition based mechanisms and the abiotic environment on disease development is known as “general disease suppression” and is the sum of all factors that reduce disease. The aim of this thesis was to study different aspects of general disease suppression, in order to get more insight into the interplay between microbial communities, pathogen dynamics, and substrate availability in different agricultural soils. The first objective was to study the role of microbial volatile organic compounds in natural disease suppression in agricultural soils. In chapter 2 a series of simultaneous experiments were performed on a agricultural soil that received different management practises. We showed a strong correlation between root infection and -biomass production in a bioassay and the suppressive effects of microbial volatiles on the in vitro growth of the pathogen Pythium intermedium. No or weak volatile suppression coincided with significant lower root biomass and a higher disease index, whereas a strong volatile suppression related to high biomass and a low disease index. Furthermore, the composition of the original soil bacterial community showed a drastic shift due to the legacy effects of management practices, coinciding with the loss of volatile suppression. By comparing the emission profiles and the bacterial community composition of the differently managed soils, candidate inhibitory compounds and volatile producing bacterial groups could be identified. Altogether these results indicate that volatile organic compounds can have an important role in general disease suppression. To follow up on volatile suppression chapter 3 investigates the influence of soil-related (abiotic and biotic) variables on volatile mediated in vitro growth inhibition of different plant pathogens via an extensive soil survey including 50 Dutch arable agricultural fields. The volatile mediated suppression of three phylogenetic different soil borne pathogens (Rhizoctonia solani, Fusarium oxysporum and Pythium intermedium) was linked to a wide range of soil-related variables with univariate and multivariate regression models. The overall suppression of different pathogens was linked to microbial activity and organic substrates. However, different pathogens showed different sensitivity to volatile suppression. Furthermore, the soil-related factors corresponding to volatile mediated suppression were pathogen specific. In total, the results described in this chapter show that part of volatile suppression for a particular pathogen is based on general microbial activity, but our data shows as well that the individual response is pathogen specific. Chapter 4 explores the reservoir of potential plant pathogens harboring agricultural soils before the start of the growth season, together with the environmental drivers of this pool of pathogens. By investigating the pathogenic seedbank in relation to its environment we assessed which soil-related variables could explain differences among site pathogen community composition. Pathogens differing in phylogeny or mode of infection were related to different soil variables. For example the among-site differences in the presence of oomycetes could not be related to their environmental context. On the other hand the variation in root and shoot fungal pathogen community composition was linked to soil physico-chemical properties and non-pathogen microbial community composition, with potentially a significant role of litter saprophytes therein. As the presence of pathogen propagules in soil is not necessarily related to disease incidence, chapter 5 investigates the dynamics of root pathogens in the presence of a root in a model rhizosphere. We developed a qPCR based assay to test the growth response of a pathogen (Pythium intermedium) to the presence of root exudates over time. This exposure to root exudates showed soil specific pathogen dynamics. This finding may indicate that in situ (microbial) processes can successfully prevent pathogen development in some of the soils but not in others. Thus this method has the potential to provide an alternative way to assess the susceptibility of a soil to certain soil-borne diseases. The results of this thesis gave new insights into different aspects of disease suppression in agricultural soils which could serve as a fundament to develop environmentally-friendly control methods based on natural occurring ecological processes. Ideas for the implementation of this study and future research are discussed in chapter 6. </p

CRISPR/Cas9-induced (CTG⋅CAG)n repeat instability in the myotonic dystrophy type 1 locus: implications for therapeutic genome editing

Myotonic dystrophy type 1 (DM1) is caused by (CTG⋅CAG)n-repeat expansion within the DMPK gene and thought to be mediated by a toxic RNA gain of function. Current attempts to develop therapy for this disease mainly aim at destroying or blocking abnormal properties of mutant DMPK (CUG)n RNA. Here, we explored a DNA-directed strategy and demonstrate that single clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-cleavage in either its 5′ or 3′ unique flank promotes uncontrollable deletion of large segments from the expanded trinucleotide repeat, rather than formation of short indels usually seen after double-strand break repair. Complete and precise excision of the repeat tract from normal and large expanded DMPK alleles in myoblasts from unaffected individuals, DM1 patients, and a DM1 mouse model could be achieved at high frequency by dual CRISPR/Cas9-cleavage at either side of the (CTG⋅CAG)n sequence. Importantly, removal of the repeat appeared to have no detrimental effects on the expression of genes in the DM1 locus. Moreover, myogenic capacity, nucleocytoplasmic distribution, and abnormal RNP-binding behavior of transcripts from the edited DMPK gene were normalized. Dual sgRNA-guided excision of the (CTG⋅CAG)n tract by CRISPR/Cas9 technology is applicable for developing isogenic cell lines for research and may provide new therapeutic opportunities for patients with DM1

Quantifying continental collision dynamics for Alpine-style orogens

When continents collide, the arrival of positively buoyant continental crust slows down subduction. This collision often leads to the detachment of earlier subducted oceanic lithosphere, which changes the subsequent dynamics of the orogenic system. Recent studies of continental collision infer that the remaining slab may drive convergence through slab roll-back even after detachment. Here we use two-dimensional visco-elasto-plastic thermo-mechanical models to explore the conditions for post-collisional slab steepening versus shallowing by quantifying the dynamics of continental collision for a wide range of parameters. We monitor the evolution of horizontal mantle drag beneath the overriding plate and vertical slab pull to show that these forces have similar magnitudes and interact continuously with each other. We do not observe slab rollback or steepening after slab detachment within our investigated parameter space. Instead, we observe a two-stage elastic and viscous slab rebound process lasting tens of millions of years, which is associated with slab unbending and eduction that together generate orogenic widening and trench shift towards the foreland. Our parametric studies show that the initial length of the oceanic plate and the stratified lithospheric rheology exert a key control on the orogenic evolution. When correlated with previous studies our results suggest that post-detachment slab rollback may only be possible when minor amounts of continental crust subduct. Among the wide variety of natural scenarios, our modelling applies best to the evolution of the Central European Alps. Furthermore, the mantle drag force may play a more important role in continental dynamics than previously thought. Finally, our study illustrates that dynamic analysis is a useful quantitative framework that also intuitively explains observed model kinematics

Pilot Investigation of Coal Chemical Wastewater Containing Phenol by Pervaporation Process

Coal chemical wastewater contains a large number of industrial raw materials, such as phenol, resulting in difficulty as target to be treated and the resource waste as industrial raw materials. A pilot pervaporation process is investigated to separate and recycle phenols from coal chemical wastewater to reduce the follow-up biochemical processing load. Operation parameters which affect removing and recovering efficiency are studied, such as temperature, flow rate and downstream pressure. Phenol removal efficiency could reach 50% under the conditions of 70o C, 210 L/h and 3000 Pa. The system could continuously run for 20 cycles. Furthermore, the pervaporation procedure could be enhanced when pumped with gas which made the removal efficiency up to 66%

Biomechanical evaluation of different semi-rigid junctional fixation techniques using finite element analysis

BACKGROUND: Proximal junctional failure is a common complication attributed to the rigidity of long pedicle screw fixation constructs used for surgical correction of adult spinal deformity. Semi-rigid junctional fixation achieves a gradual transition in range of motion at the ends of spinal instrumentation, which could lead to reduced junctional stresses, and ultimately reduce the incidence of proximal junctional failure. This study investigates the biomechanical effect of different semi-rigid junctional fixation techniques in a T8-L3 finite element spine segment model.METHODS: First, degeneration of the intervertebral disc was successfully implemented by altering the height. Second, transverse process hooks, one- and two-level clamped tapes, and one- and two-level knotted tapes instrumented proximally to three-level pedicle screw fixation were validated against ex vivo range of motion data of a previous study. Finally, the posterior ligament complex forces and nucleus pulposus stresses were quantified.FINDINGS: Simulated range of motions demonstrated the fidelity of the general model and modelling of semi-rigid junctional fixation techniques. All semi-rigid junctional fixation techniques reduced the posterior ligament complex forces at the junctional zone compared to pedicle screw fixation. Transverse process hooks and knotted tapes reduced nucleus pulposus stresses, whereas clamped tapes increased nucleus pulposus stresses at the junctional zone.INTERPRETATION: The relationship between the range of motion transition and the reductions in posterior ligament complex and nucleus pulposus stresses was complex and dependent on the fixation techniques. Clinical trials are required to compare the effectiveness of semi-rigid junctional fixation techniques in terms of reducing proximal junctional failure incidence rates.</p

Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer

There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host. In a greenhouse experiment, we tested how different levels of soil organic matter (SOM) and fertilizer addition influence the interactions between plants and aphids. To examine the influence of the existing soil microbiome on the pathogen effects, we used both unsterilized field soil and sterilized field soil. In unsterilized soil with low SOM content, R. solani addition had a negative effect on aphid biomass, whereas it enhanced aphid biomass in soil with high SOM content. In sterilized soil, however, aphid biomass was enhanced by R. solani addition and by high SOM content. Plant biomass was enhanced by fertilizer addition, but only when SOM content was low, or in the absence of R. solani. We conclude that belowground pathogens influence aphid performance and that the effect of soil pathogens on aphids can be more positive in the absence of a soil microbiome. This implies that experiments studying the effect of pathogens under sterile conditions might not represent realistic interactions. Moreover, pathogen-plant-aphid interactions can be more positive for aphids under high SOM conditions. We recommend that soil conditions should be taken into account in the study of microbe-plant-insect interactions

Cost of fouling in full-scale reverse osmosis and nanofiltration installations in the Netherlands

The economic impact of fouling in spiral wound membranes is not yet well explored. There has been an established assumption that the cost of fouling in membrane processes is significant, but this hypothesis has not been thoroughly evaluated. We conducted an economic analysis on seven full-scale installations, four nano filtration (NF) and three reverse osmosis (RO), to estimate the cost of fouling in industrial plants. The cost of fouling was calculated in detail, including costs of increase in feed channel pressure drop, water permeability reduction, early membrane replacement, and extensive cleaning-in-place (CIP). The estimated cost of fouling was expressed as a fraction of operational expenses (OPEX) for each plant and the major cost factors in fouling and CIP costs were identified. The selected NF plants were fed with anoxic ground water, while the feed water to RO plants was either surface water or municipal wastewater effluent. All the NF plants produce drinking water, while the RO plants produce demineralized water for industrial applications. We found that the cost of fouling in the RO plants was around 24% of OPEX, while the fouling related costs in NF cases was only around 11% due to the low biofouling potential of the anoxic ground water. The major factor in the cost of fouling is the early membrane replacement cost, followed by additional energy and with only a minor contribution from the cleaning costs. The down-time cost (caused by the interruption of water production during a CIP event) can be the major CIP cost factor for the plants with frequent cleaning events, while the cost of chemicals dominates in the plants with non-frequent CIP. In case of manual cleaning-in-place, the cost of fouling is increased by around 2% for the RO plants with frequent CIP. The manual execution of CIP cleaning is an attention point to reconsider, as the reviewed plants hold an automated CIP cleaning, providing membrane productivity advantages

Detection and quantification of vitamins in microliter volumes of biological samples by LC‐MS for clinical screening

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146352/1/aic16345_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146352/2/aic16345.pd

Operating Conditions of Hollow Fiber Supported Liquid Membrane for Phenol Extraction from Coal Gasification Wastewater

The extraction and recycling of phenol from high concentration coal gasification wastewater has been studied using polypropylene (PP) hollow fiber membrane and polyvinylidene fluoride (PVDF) hollow fiber membrane as liquid membrane support, the mixture of tributyl phosphate (TBP) and kerosene as liquid membrane phase, and sodium hydroxide as stripping agent in the process of extraction. The experiments investigated the effect of the operating conditions of the hollow fiber supported liquid membrane, such as aqueous phase temperature and the connection forms of membrane modules, on the extraction efficiency of phenol from high concentration coal gasification wastewater. The conclusions obtained from lab scale experiments provided guidance for scale-up experiments. So, in the scale-up experiments, three membrane modules connected in parallel, then three membrane modules connected in series were used to increase the treatment capacity and improve the treatment effect, under the operating conditions of wastewater temperature 20 ˚C, PH 7.5~8.1, flow rate 100 L/h and the concentration of stripping phase 0.1 mol/L, stripping phase flow rate 50 L/h, the extraction efficiency of the PP-TBP supported liquid membrane system was 87.02% and the phenol concentration of effluent was 218.14mg/L. And the phenol concentration of effluent met the requirements of further biodegradation treatment