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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Simulating long-term effects of bioenergy extraction on dead wood availability at a landscape scale in Sweden
Hof, Anouschka R. ; Löfroth, Therese ; Rudolphi, Jörgen ; Work, Timothy ; Hjältén, Joakim - \ 2018
Forests 9 (2018)8. - ISSN 1999-4907
Biodiversity - Biofuel - Boreal forest - Modelling - Saproxylic species

Wood bioenergy may decrease the reliance on fossil carbon and mitigate anticipated increases in temperature. However, increased use of wood bioenergy may have large impacts on forest biodiversity primarily through the loss of dead wood habitats. We evaluated both the large-scale and long-term effects of different bioenergy extraction scenarios on the availability of dead wood and the suitability of the resulting habitat for saproxylic species, using a spatially explicit forest landscape simulation framework applied in the Swedish boreal forest. We demonstrate that bioenergy extraction scenarios, differing in the level of removal of biomass, can have significant effects on dead wood volumes. Although all of the scenarios led to decreasing levels of dead wood, the scenario aimed at species conservation led to highest volumes of dead wood (about 10 m3 ha-1) and highest connectivity of dead wood patches (mean proximity index of 78), whilst the scenario aimed at reaching zero fossil fuel targets led to the lowest levels (about 8 m3 ha-1) and least connectivity (mean proximity index of 7). Our simulations stress that further exploitation of dead wood from sites where volumes are already below suggested habitat thresholds for saproxylic species will very likely have further negative effects on dead wood dependent species.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii
Sambles, Christine ; Moore, Karen ; Lux, Thomas M. ; Jones, Katy ; Littlejohn, George R. ; Gouveia, João D. ; Aves, Stephen J. ; Studholme, David J. ; Lee, Rob ; Love, John - \ 2017
MicrobiologyOpen 6 (2017)4. - ISSN 2045-8827
Botryococcus braunii - Biofuel - Consortium - Metagenomics - Microcosm
Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30-C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.
De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock
Evangelistella, Chiara ; Valentini, Alessio ; Ludovisi, Riccardo ; Firrincieli, Andrea ; Fabbrini, Francesco ; Scalabrin, Simone ; Cattonaro, Federica ; Morgante, Michele ; Mugnozza, Giuseppe Scarascia ; Keurentjes, Joost J.B. ; Harfouche, Antoine - \ 2017
Biotechnology for Biofuels 10 (2017). - ISSN 1754-6834 - 24 p.
Arundo donax - Biofuel - Carbon fixation - De novo leaf transcriptome - Genic-SSRs - Phenylpropanoid - Purine and thiamine metabolism - RNA-Seq - SAPs - Stomata

Background: Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited. Results: We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes. Conclusions: This study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.

Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels
Weijde, Tim van der; Lessa Alvim Kamei, Claire ; Severing, Eduard ; Torres Salvador, Andres Francisco ; Gomez, Leonardo D. ; Dolstra, Oene ; Maliepaard, Chris A. ; McQueen-Mason, Simon J. ; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2017
BMC Genomics 18 (2017). - ISSN 1471-2164 - 15 p.
Biofuel - Biomass quality - Cell wall composition - Conversion efficiency - Genetic map - Miscanthus - Quantitative trait loci (QTL) - Saccharification efficiency - Yield

Background: Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. Results: To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. Conclusion: In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.

A novel bioenergy feedstock in Latin America? Cultivation potential of Acrocomia aculeata under current and future climate conditions
Plath, Mirco ; Moser, Christine ; Bailis, Rob ; Brandt, Patric ; Hirsch, Heidi ; Klein, Alexandra Maria ; Walmsley, David ; Wehrden, Henrik von - \ 2016
Biomass and Bioenergy 91 (2016). - ISSN 0961-9534 - p. 186 - 195.
Biofuel - Ecological niche modeling - Macaw palm - Macaúba - Sustainability

Plant oil is a key commodity in the global economy, particularly for food and bioenergy markets. However, current production practices often impair smallholder livelihoods, cause land use changes, and compete for food production. The neotropical palm Acrocomia aculeata is currently being promoted as a novel sustainable biomass feedstock, particularly for bioenergy, but only little is known about the palm's ecological requirements. Based on a comprehensive literature and database search for recorded occurrences of A. aculeata in Latin America, we computed an ecological niche modeling to determine the palm's potential distribution area based on climatic and soil variables. We subsequently considered current land cover and predicted future climate change scenarios to discuss the cultivation potential of A. aculeata within its possible distribution area. The results revealed a large potential to cultivate A. aculeata in Latin America under current abiotic environmental conditions. The two core distribution regions identified were (1) Central America including the Caribbean, northern Colombia and Venezuela, and (2) southern Brazil and eastern Paraguay. A considerable proportion of the medium to highly suitable growing areas were found to be currently used for agricultural production or covered by land types with high conservation and carbon sequestration value. Applying the model under the IPCC's A2A 'business as usual' emission scenario suggested that by 2080 the vast majority of suitable growing areas severely decline in extent or disappear entirely. Our ecological niche modeling thus shows that despite the palm's high cultivation potential, a sustainable deployment of A. aculeata requires a precautious, evidence-based approach.

What can and can't we say about indirect land-use change in Brazil using an integrated economic - land-use change model?
Verstegen, J.A. ; Hilst, Floor van der; Woltjer, Geert ; Karssenberg, Derek ; Jong, S.M. de; Faaij, André P.C. - \ 2016
Global change biology Bioenergy (2016). - ISSN 1757-1693 - p. 561 - 578.
Biofuel - Brazil - Error propagation - Indirect land-use change - Land-use change - Modelling - Monte Carlo - Spatio-temporal - Sugar cane - Uncertainty

It is commonly recognized that large uncertainties exist in modelled biofuel-induced indirect land-use change, but until now, spatially explicit quantification of such uncertainties by means of error propagation modelling has never been performed. In this study, we demonstrate a general methodology to stochastically calculate direct and indirect land-use change (dLUC and iLUC) caused by an increasing demand for biofuels, with an integrated economic - land-use change model. We use the global Computable General Equilibrium model MAGNET, connected to the spatially explicit land-use change model PLUC. We quantify important uncertainties in the modelling chain. Next, dLUC and iLUC projections for Brazil up to 2030 at different spatial scales and the uncertainty herein are assessed. Our results show that cell-based (5 × 5 km2) probabilities of dLUC range from 0 to 0.77, and of iLUC from 0 to 0.43, indicating that it is difficult to project exactly where dLUC and iLUC will occur, with more difficulties for iLUC than for dLUC. At country level, dLUC area can be projected with high certainty, having a coefficient of variation (cv) of only 0.02, while iLUC area is still uncertain, having a cv of 0.72. The latter means that, considering the 95% confidence interval, the iLUC area in Brazil might be 2.4 times as high or as low as the projected mean. Because this confidence interval is so wide that it is likely to straddle any legislation threshold, our opinion is that threshold evaluation for iLUC indicators should not be implemented in legislation. For future studies, we emphasize the need for provision of quantitative uncertainty estimates together with the calculated LUC indicators, to allow users to evaluate the reliability of these indicators and the effects of their uncertainty on the impacts of land-use change, such as greenhouse gas emissions.

Cell Wall Diversity in Forage Maize : Genetic Complexity and Bioenergy Potential
Torres, A.F. ; Noordam-Boot, C.M.M. ; Dolstra, Oene ; Weijde, Tim van der; Combes, Eliette ; Dufour, Philippe ; Vlaswinkel, Louis ; Visser, R.G.F. ; Trindade, L.M. - \ 2015
Bio Energy Research 8 (2015)1. - ISSN 1939-1234 - p. 187 - 202.
Biofuel - Cell wall composition - Maize - Pretreatment - QTL - Saccharification

Genetic studies are ideal platforms for assessing the extent of genetic diversity, inferring the genetic architecture, and evaluating complex trait interrelations for cell wall compositional and bioconversion traits relevant to bioenergy applications. Through the characterization of a forage maize doubled haploid (DH) population, we indicate the substantial degree of highly heritable (h2 > ~65 %) diversity in cell wall composition and bioconversion potential available within this important agronomic species. In addition to variation in lignin content, extensive genotypic diversity was found for the concentration and composition of hemicelluloses, the latter found to exert an influence on the recalcitrance of maize cell walls. Our results also demonstrate that forage maize harbors considerable variation for the release of cell wall glucose following pretreatment and enzymatic saccharification. In fact, the extent of variability observed for bioconversion efficiency (nearly 30 % between population extremes) greatly exceeded ranges reported in previous studies. In our population, a total of 52 quantitative trait loci (QTL) were detected for biomass compositional and bioconversion characters across 8 chromosomes. Noteworthy, from eight QTL related to bioconversion properties, five were previously unidentified and warrant further investigation. Ultimately, our results substantiate forage maize germplasm as a valid genetic resource for advancing cell wall degradability traits in bioenergy maize-breeding programs. However, since useful variation for cell wall traits is defined by QTL with “minor” effects (R2 = ~10 %), cultivar development for bio-based applications will rely on advanced marker-assisted selection procedures centered on detecting and increasing the frequency of favorable QTL alleles in elite flint and dent germplasm.

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