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Vanderschuren, H.

Publications and source records attributed to Vanderschuren, H..

11 recordsLinked to original sources

Teatime for Triticum: (how) can the presence of plants slow down decomposition?

Decomposition of organic matter is a key process in soils contributing to carbon and nutrient cycling. To identify management strategies for agroecosystems that reduce nutrient losses while maximizing plant growth, it is important to understand which parameters determine decomposition rates. This study therefore investigated how the presence of winter wheat (Triticum aestivum var. Asory) affects decomposition in a controlled Ecotron setup with two soil types with varying organic matter content across three simulated climates (2013, 2068, 2085). Using the tea bag index, interstitial soil pore water analyses, microbial biomass quantification, bacterial and fungal gene abundance, and soil respiration measurements, we tested the hypotheses that plant exudates would enhance decomposition rate and microbial biomass, while plant nitrogen uptake would deplete soil nitrate, potentially mitigated by fertilization. Contrary to expectations, decomposition rates were lower in planted than in unplanted soils, suggesting resource competition between plants and microbes. No significant differences were observed in microbial biomass or respiration due to plant presence, and fertilization effects on nitrate or microbial mineralization were undetectable, likely due to rapid turnover of organic molecules including uptake by plants and microbes. Mechanistically, fungi and soil humidity were more important for decomposition than bacteria or temperature. The findings corroborate climate impacts on decomposition but also indicate microbial resilience and highlight the potential of management strategies like cover crops, adjusted planting dates and crop residual management which can contribute to healthy soils by sustaining carbon and nutrient cycling.

ecology↗

From Synthetic to Biological Nitrification Inhibition: Advancing Stabilization of Organic Fertilizers

Fertilizer type plays a critical role in nitrogen (N) cycling, influencing nitrous oxide (N2O) emissions, soil mineral N dynamics, and microbial communities. Understanding these interactions is essential for developing sustainable fertilization strategies that balance agricultural productivity with environmental protection. This study examined the effects of mineral and organic fertilizers (OFs) on N transformations and evaluated the efficiency of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) in mitigating N2O losses. Results showed that OFs exhibited variable impacts on N2O emissions depending on their composition and C/N ratio. DMPP effectively reduced nitrification-driven N2O emissions, particularly in treatments with high ammoniacal N content. However, its efficiency was limited with animal-based OFs, suggesting a complex interaction between fertilizer properties and inhibitor effectiveness. DMPP had not direct impact on soil microbial diversity but specifically targeted the Nitrosomonaceae family and Nitrospira class. Beyond synthetic inhibitors, biological nitrification inhibition (BNI) emerged as a promising alternative, which we explored using rhizospheric soils from wheat landrace Persia 44 and white mustard (cv. Pole Position, Verdi). These soils significantly reduced N2O emissions, particularly when combined with OFs. The integration of BNI with organic fertilizers, especially liquid digestate, represents a promising strategy for reducing N losses while maintaining soil fertility. This study underscores the need for tailored fertilization strategies that combine chemical and biological tools to optimize N use efficiency and support environmentally sustainable agriculture.

plant biology↗

Tensions in tillage: Reduction in tillage intensity associates with lower wheat growth and nutritional grain quality despite enhanced soil biological indicators

Dryland ecosystems are particularly susceptible to the adverse effects of intensive agriculture, with intensive tillage exerting a major impact on soil health and its biotic components. The implementation of less disturbing soil management practices can be essential for preserving the soil environment and maintaining the diverse communities of microorganisms, micro- and mesofauna, which are essential contributors to soil fertility. In this study, we assessed soil chemical properties, soil biodiversity and functionality, and wheat crop growth across a tillage gradient encompassing no-tillage (NT), minimum tillage (MT), and standard tillage (ST). Results showed that NT resulted in increased soil macronutrient levels compared to MT and ST. In general, reduced tillage increased the abundance of soil biota, with significantly higher levels of bacterial and fungal marker genes observed in MT and NT compared to ST. Nematode abundance increased by 25% in MT and 50% in NT, compared to ST and predatory acari were significantly more abundant in NT, while numbers of total acari were higher in both NT and ST compared to MT. Community structure analysis revealed that tillage strongly influenced bacterial, fungal and acari community composition, reflecting a gradient of soil disturbance intensity. Corresponding to the increased abundance of soil biota, reduced tillage increased microbial activity and soil functionality along the disturbance gradient. This was evident in the potential activity of carbon, nitrogen and phosphorus cycling enzymes, as well as the microbial capacity for carbon utilisation. In addition, evidence of the formation of biocrust as a possible source of carbon input was found. Furthermore, we observed important wheat pathogens to decrease and fungal antagonists to increase in NT compared to ST. Despite enhanced soil biological indicators under reduced tillage, wheat growth, nitrogen uptake and grain B vitamin contents were higher in ST compared to NT. In addition, we observed a shift in technological grain properties across tillage practices. The higher root:shoot ratio (an indicator of nitrogen deficiency) and median root diameter (hormone-driven lateral expansion) in NT suggest that soil compaction could be a potential cause of reduced wheat performance. These results suggest that despite improved soil biological indicators, other factors such as a low rates of N mineralization potential and prevalence of soil compaction may be limiting wheat performance in NT systems. HighlightsO_LIEnhanced microbial activity and functionality under reduced tillage C_LIO_LITillage intensity shaped community structure of microbes, nematodes and acari C_LIO_LISoil biocrust development under NT may increase soil organic carbon C_LIO_LIRoot traits revealed soil compaction and nutrient limitation in NT systems C_LIO_LIReduced tillage impaired wheat quality and changed technological grain properties C_LI

ecology↗

Low-input soil management increases yield and decreases CO2-emissions but aggravates risk of nitrate leaching and diseases in winter wheat cropping systems under climate change

Empirical data is key to anticipate the impact of climate change on cropping systems and develop land management strategies that are sustainable while ensuring food security. Here, the combined effects of projected increases in temperature, atmospheric CO2-concentrations, solar irradiation and altered precipitation patterns on winter wheat cropping systems were investigated using an Ecotron. Experimental plant-soil systems were subjected to three different climatic conditions representing a gradient of ongoing climate change implementing the weather patterns of the years 2013, 2068, and 2085 respectively. The wheat plants were grown in two differentially manged agricultural soil types: one with long-term low organic matter (OM) inputs and the other one with long-term high OM inputs. In the low OM system, the risk for plant diseases and nitrate leaching was increased, but it outperformed the high OM system with higher yields and lower CO2-emissions. Developing high-yielding cropping systems leveraging the CO2-fertilisation effect without sacrificing environmental health will therefore require further refined of management practices to improve nutrient cycling and reduce greenhouse gas emissions. One possibility is adapting crop rotations and cover crops to the shorter wheat cycle observed in the future climates to replenish soil nutrients and break disease cycles. Further, in both here studied soil types the wheat plants developed natural coping mechanisms against environmental stressors, such as enhanced root growth and increased levels of proline and silicon. Unravelling the molecular mechanisms that trigger such inherent plant defences is a further interesting target for breeding future crops. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/626142v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@fefc32org.highwire.dtl.DTLVardef@5f6757org.highwire.dtl.DTLVardef@1799ca4org.highwire.dtl.DTLVardef@11aec5c_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava

Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging. In the present study, we generated BAC libraries of the CMD- susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identified and sequenced BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequenced and assembled the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps revealed discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC guided approach to assess cassava genome assemblies significantly improved the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identified 81 stress resistance proteins present in the CMD2 region, amongst which 31 were previously not reported in publicly available CMD2 sequences.

genomics↗

Mutation of the VInv 5' UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards

Protein-coding regions of genes have so far been the preferred targets for trait improvement using CRISPR-Cas9 genome editing in plants. Alteration of the reading frame can result in termination of transcription or translation, hence, loss of function of the encoded protein. 5 UTR sequences also represent a practical target region to alter gene expression and protein abundance. However, editing of 5 UTRs has so far been scarcely used to engineer trait in crop plants. Here, we demonstrate that insertion of a single adenine nucleotide mediated by Cas9 in the 5 UTR region of two alleles from the Vacuolar invertase gene (VInv) of the tetraploid potato variety Lady Rosetta (LaRo) is sufficient to substantially lower the content of reducing sugars in the potato under cold-storage conditions. Moreover, the acrylamide content generated during processing of the edited potato lines into crisps was more than three folds lower than the current EU-regulated maximum level of 750 g/kg in crisps. This gene-editing approach represents a durable strategy to improve food safety of potatoes in varieties widely preferred by the consumers and the industry.

plant biology↗

Differential DNA methylation in the Vinv promoter region controls Cold Induced Sweetening in potato

Control of potato sprouting is important to ensure constant supply of high-quality potato to the industry. Efficient control of sprouting can be achieved by chemical treatment or cold temperature. Recent bans on anti-sprouting molecules are prompting the use of cold storage in the potato value chain. Unfortunately, storage of potato at low temperatures is associated with cold induced sweetening (CIS) due to the induction of the vacuolar invertase gene under low temperatures. Because CIS is associated with the production of the potentially carcinogenic acrylamide in processed potatoes, concise knowledge on the regulatory mechanisms controlling the CIS-phenotype in potatoes is expected to help pave the way for the production of CIS-resistant potato varieties. Here, we dissect the promoters of the Vacuolar invertase (Vinv) genes from CIS-susceptible and CIS-resistant varieties to investigate their implication in CIS-phenotype determination. Using bisulfite sequencing and CRISPR-dCas9-DRM2-mediated de novo DNA methylation, we show that the CIS-resistant phenotype of Verdi, is in part due to hypermethylation of its Vinv promoter, more specifically in the 1.0-1.7kb region. Those findings open new perspectives to engineer CIS-resistant potatoes by genome and epigenome modifications.

plant biology↗

Asparagine accumulation in chicory storage roots is controlled by translocation and feedback regulation of asparagine biosynthesis in leaves

O_LIThe presence of acrylamide (AA), a potentially carcinogenic and neurotoxic compound, in food has become a major concern for public health. AA in plant-derived food mainly arises from the reaction of the amino acid asparagine (Asn) and reducing sugars during processing of foodstuffs at high temperature. C_LIO_LIUsing a selection of genotypes from the chicory germplasm we performed Asn measurements in storage roots and leaves to identify genotypes contrasting for Asn accumulation. We combined molecular analysis and grafting experiments to show that leaf to root translocation controls asparagine biosynthesis and accumulation in chicory storage roots. C_LIO_LIWe could demonstrate that Asn accumulation in storage roots depends on Asn biosynthesis and transport from the leaf, and that a negative feedback loop by Asn on CiASN1 expression impacts Asn biosynthesis in leaves. C_LIO_LIOur results provide a new model for asparagine biosynthesis in root crop species and highlight the importance of characterizing and manipulating asparagine transport to reduce AA content in processed plant-based foodstuffs. C_LI

plant biology↗

CRISPR-Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses

We used CRISPR-Cas9 in the staple food crop cassava with the aim of engineering resistance to African cassava mosaic virus, a member of a widespread and important family of plant-pathogenic DNA viruses. We found that between 33 and 48% of edited virus genomes evolved a conserved single-nucleotide mutation that confers resistance to CRISPR-Cas9 cleavage. Our study highlights the potential for virus escape from this technology. Care should be taken to design CRISPR-Cas9 experiments that minimize the risk of virus escape.

plant biology↗

CIDER-Seq: unbiased virus enrichment and single-read, full length genome sequencing

Deep-sequencing of virus isolates using short-read sequencing technologies is problematic since viruses are often present in complexes sharing a high-degree of sequence identity. The full-length genomes of such highly-similar viruses cannot be assembled accurately from short sequencing reads. We present a new method, CIDER-Seq (Circular DNA Enrichment Sequencing) which successfully generates accurate full-length virus genomes from individual sequencing reads with no sequence assembly required. CIDER-Seq operates by combining a PCR-free, circular DNA enrichment protocol with Single Molecule Real Time sequencing and a new sequence deconcatenation algorithm. We apply our technique to produce more than 1,200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral doublestranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our results show that CIDER-seq is a powerful, cost-effective tool for accurately sequencing circular DNA viruses, with future applications in deep-sequencing other forms of circular DNA such as transposons and plasmids.

genomics↗

Early transcriptome response to brown streak virus infection in susceptible and resistant cassava varieties

Cassava brown streak viruses (CBSVs) are responsible for significant cassava yield losses in eastern sub-Saharan Africa. In the present work, we inoculated CBSV-susceptible and -resistant cassava varieties with a mixed infection of CBSVs using top-cleft grafting. Virus titres in grafted scions were monitored in a time course experiment in both varieties. We performed RNA-seq of the two cassava varieties at the earliest time-point of full infection in the susceptible scions. Genes encoding proteins in RNA silencing and salicylic acid pathways were regulated in the susceptible cassava variety but transcriptional changes were limited in the resistant variety. After infection, genes related to callose deposition at plasmodesmata were regulated and callose deposition was significantly reduced in the susceptible cassava variety. We also show that {beta}-1,3-glucanase enzymatic activity is differentially regulated in the susceptible and resistant varieties. The differences in transcriptional responses to CBSV infection indicate that resistance involves callose deposition at plasmodesmata but does not trigger typical anti-viral defence responses. A meta-analysis of the current RNA-seq dataset and selected, previously reported, host-potyvirus and virus-cassava RNA-seq datasets revealed comparable host responses across pathosystems only at similar time points after infection or infection of a common host.\n\nHIGHLIGHTOur results suggest that resistance to CBSV in cassava involves callose deposition at the plasmodesmata and our meta-analysis of multiple virus-crop RNA-seq studies suggests that conserved responses across different host-virus systems are limited and depend greatly on time after infection.

plant biology↗