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.

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Alpha diversity of vascular plants in European forests
Večeřa, Martin ; Divíšek, Jan ; Lenoir, Jonathan ; Jiménez-Alfaro, Borja ; Biurrun, Idoia ; Knollová, Ilona ; Agrillo, Emiliano ; Campos, Juan Antonio ; Čarni, Andraž ; Crespo Jiménez, Guillermo ; Ćuk, Mirjana ; Dimopoulos, Panayotis ; Ewald, Jörg ; Fernández-González, Federico ; Gégout, Jean Claude ; Indreica, Adrian ; Jandt, Ute ; Jansen, Florian ; Kącki, Zygmunt ; Rašomavičius, Valerijus ; Řezníčková, Marcela ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Svenning, Jens Christian ; Swacha, Grzegorz ; Vassilev, Kiril ; Venanzoni, Roberto ; Willner, Wolfgang ; Wohlgemuth, Thomas ; Chytrý, Milan - \ 2019
Journal of Biogeography 46 (2019)9. - ISSN 0305-0270 - p. 1919 - 1935.
diversity - Europe - European Vegetation Archive (EVA) - forest vegetation - plant community - predictive modelling - Random Forests - species-richness patterns - vascular plants - vegetation-plot database

Aim: The former continental-scale studies modelled coarse-grained plant species-richness patterns (gamma diversity). Here we aim to refine this information for European forests by (a) modelling the number of vascular plant species that co-occur in local communities (alpha diversity) within spatial units of 400 m2; and (b) assessing the factors likely determining the observed spatial patterns in alpha diversity. Location: Europe roughly within 12°W–30°E and 35–60°N. Taxon: Vascular plants. Methods: The numbers of co-occurring vascular plant species were counted in 73,134 georeferenced vegetation plots. Each plot was classified by an expert system into deciduous broadleaf, coniferous or sclerophyllous forest. Random Forest models were used to map and explain spatial patterns in alpha diversity for each forest type separately using 19 environmental, land-use and historical variables. Results: Our models explained from 51.0% to 70.9% of the variation in forest alpha diversity. The modelled alpha-diversity pattern was dominated by a marked gradient from species-poor north-western to species-rich south-eastern Europe. The most prominent richness hotspots were identified in the Calcareous Alps and adjacent north-western Dinarides, the Carpathian foothills in Romania and the Western Carpathians in Slovakia. Energy-related factors, bedrock types and terrain ruggedness were identified as the main variables underlying the observed richness patterns. Alpha diversity increases especially with temperature seasonality in deciduous broadleaf forests, on limestone bedrock in coniferous forests and in areas with low annual actual evapotranspiration in sclerophyllous forests. Main conclusions: We provide the first predictive maps and analyses of environmental factors driving the alpha diversity of vascular plants across European forests. Such information is important for the general understanding of European biodiversity. This study also demonstrates a high potential of vegetation-plot databases as sources for robust estimation of the number of vascular plant species that co-occur at fine spatial grains across large areas.

sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Discovering novel hydrolases from hot environments
Wohlgemuth, Roland ; Littlechild, Jennifer ; Monti, Daniela ; Schnorr, Kirk ; Rossum, Teunke van; Siebers, Bettina ; Menzel, Peter ; Kublanov, Ilya V. ; Rike, Anne Gunn ; Skretas, Georgios ; Szabo, Zalan ; Peng, Xu ; Young, Mark J. - \ 2018
Biotechnology Advances 36 (2018)8. - ISSN 0734-9750 - p. 2077 - 2100.
Biocatalysis - Enrichment - Enzyme characterization - Enzyme screening - Gene expression - Genomics - Hydrolases - Metagenomics - Sequencing - Thermophiles

Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.

Alien plant invasions in European woodlands
Wagner, Viktoria ; Chytrý, Milan ; Jiménez-Alfaro, Borja ; Pergl, Jan ; Hennekens, Stephan ; Biurrun, Idoia ; Knollová, Ilona ; Berg, Christian ; Vassilev, Kiril ; Rodwell, John S. ; Škvorc, Željko ; Jandt, Ute ; Ewald, Jörg ; Jansen, Florian ; Tsiripidis, Ioannis ; Botta-Dukát, Zoltán ; Casella, Laura ; Attorre, Fabio ; Rašomavičius, Valerijus ; Ćušterevska, Renata ; Schaminée, Joop H.J. ; Brunet, Jörg ; Lenoir, Jonathan ; Svenning, Jens Christian ; Kącki, Zygmunt ; Petrášová-Šibíková, Mária ; Šilc, Urban ; García-Mijangos, Itziar ; Campos, Juan Antonio ; Fernández-González, Federico ; Wohlgemuth, Thomas ; Onyshchenko, Viktor ; Pyšek, Petr - \ 2017
Diversity and Distributions 23 (2017)9. - ISSN 1366-9516 - p. 969 - 981.
EUNIS - exotic - forest - invasive plants - life-form - neophyte - non-native - origin - tree
Aim: Woodlands make up a third of European territory and carry out important ecosystem functions, yet a comprehensive overview of their invasion by alien plants has never been undertaken across this continent. Location: Europe. Methods: We extracted data from 251,740 vegetation plots stored in the recently compiled European Vegetation Archive. After filtering (resulting in 83,396 plots; 39 regions; 1970–2015 time period), we analysed the species pool and frequency of alien vascular plants with respect to geographic origin and life-forms, and the levels of invasion across the European Nature Information System (EUNIS) woodland habitats. Results: We found a total of 386 alien plant species (comprising 7% of all recorded vascular plants). Aliens originating from outside of and from within Europe were almost equally represented in the species pool (192 vs. 181 species) but relative frequency was skewed towards the former group (77% vs. 22%) due, to some extent, to the frequent occurrence of Impatiens parviflora (21% frequency among alien plants). Phanerophytes were the most species-rich life-form (148 species) and had the highest representation in terms of relative frequency (39%) among aliens in the dataset. Apart from Europe (181 species), North America was the most important source of alien plants (109 species). At the local scale, temperate and boreal softwood riparian woodland (5%) and mire and mountain coniferous woodland (<1%) had the highest and lowest mean relative alien species richness (percentage of alien species per plot), respectively. Main conclusions: Our results indicate that European woodlands are prone to alien plant invasions especially when exposed to disturbance, fragmentation, alien propagule pressure and high soil nutrient levels. Given the persistence of these factors in the landscape, competitive alien plant species with a broad niche, including alien trees and shrubs, are likely to persist and spread further into European woodlands.
Classification of European beech forests : a Gordian Knot?
Willner, Wolfgang ; Jiménez-Alfaro, Borja ; Agrillo, Emiliano ; Biurrun, Idoia ; Campos, Juan Antonio ; Čarni, Andraž ; Casella, Laura ; Csiky, János ; Ćušterevska, Renata ; Didukh, Yakiv P. ; Ewald, Jörg ; Jandt, Ute ; Jansen, Florian ; Kącki, Zygmunt ; Kavgacı, Ali ; Lenoir, Jonathan ; Marinšek, Aleksander ; Onyshchenko, Viktor ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šibík, Jozef ; Škvorc, Željko ; Svenning, Jens Christian ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Tzonev, Rossen ; Vassilev, Kiril ; Venanzoni, Roberto ; Wohlgemuth, Thomas ; Chytrý, Milan - \ 2017
Applied Vegetation Science 20 (2017)3. - ISSN 1402-2001 - p. 494 - 512.
Beech forest - Europe - Fagetalia sylvaticae - Fagion sylvaticae - Fagus sylvatica - Luzulo-Fagion sylvaticae - Syntaxonomy - TWINSPAN - Vegetation plot database

Questions: What are the main floristic patterns in European beech forests? Which classification at the alliance and suballiance level is the most convincing?. Location: Europe and Asia Minor. Methods: We applied a TWINSPAN classification to a data set of 24 605 relevés covering the whole range of Fagus sylvatica forests and the western part of Fagus orientalis forests. We identified 24 ‘operational phytosociological units’ (OPUs), which were used for further analysis. The position of each OPU along the soil pH and temperature gradient was evaluated using Ellenberg Indicator Values. Fidelity of species to OPUs was calculated using the phi coefficient and constancy ratio. We compared alternative alliance concepts, corresponding to groups of OPUs, in terms of number and frequency of diagnostic species. We also established formal definitions for the various alliance concepts based on comparison of the total cover of the diagnostic species groups, and evaluated alternative geographical subdivisions of beech forests. Results: The first and second division levels of TWINSPAN followed the temperature and soil pH gradients, while lower divisions were mainly geographical. We grouped the 22 OPUs of Fagus sylvatica forests into acidophytic, meso-basiphytic and thermo-basiphytic beech forests, and separated two OPUs of F. orientalis forests. However, a solution with only two ecologically defined alliances of F. sylvatica forests (acidophytic vs basiphytic) was clearly superior with regard to number and frequency of diagnostic species. In contrast, when comparing groupings with three to six geographical alliances of basiphytic beech forests, respectively, we did not find a strongly superior solution. Conclusions: We propose to classify F. sylvatica forests into 15 suballiances – three acidophytic and 12 basiphytic ones. Separating these two groups at alliance or order level was clearly supported by our results. Concerning the grouping of the 12 basiphytic suballiances into ecological or geographical alliances, as advocated by many authors, we failed to find an optimal solution. Therefore, we propose a multi-dimensional classification of basiphytic beech forests, including both ecological and geographical groups as equally valid concepts which may be used alternatively depending on the purpose and context of the classification.

Towards an air pollution health study data management system - A case study from a smoky Swiss railway
Papoutsoglou, Evangelia ; Samourkasidis, Argyrios ; Tsai, Ming-Yi ; Davey, Mark ; Ineichen, Alex ; Athanasiadis, Ioannis N. - \ 2015
In: Building the knowledge base for environmental action and sustainability. - University of Copenhagen - ISBN 9788779037120 - p. 65 - 74.
In air pollution health studies, measurements are conducted intensively but only periodically at numerous locations in a variety of environments (indoors, outdoors, personal). Often a variety of instruments are used to measure various pollutants ranging from gases (eg, CO, NO2, O3, VOCs, PAHs) to particulate matter (eg, particles smaller than 2.5um: PM2.5, PM10, ultrafine particles: UFP), and including other environmental parameters such as temperature, relative humidity, GPS position. As a result it is always a significant challenge for researchers to effectively QA/QC, combine, and archive these data so as to reliably assess people’s exposure to poor air quality. With the CEDAR system presented here we aim to provide a solution to this problem by employing a platform using templates for easily reading custom formatted files, apply rules for filtering and quality checking measurements, and ultimately publishing them as services on the web. The system is demonstrated for the case an air quality project conducted in a Swiss railway station where smoking is allowed.
Biocatalytic asymmetric phosphorylation of mevalonate
Matsumi, R. ; Hellriegel, C. ; Schoenenberger, B. ; Milesi, T. ; Oost, J. van der; Wohlgemuth, R. - \ 2014
RSC Advances : An international journal to further the chemical sciences 4 (2014)25. - ISSN 2046-2069 - p. 12989 - 12994.
liver phosphomevalonate kinase - substrate-specificity - zur biosynthese - pig-liver - isopentenyl pyrophosphate - quantitative nmr - acid - cholesterol - purification - terpene
The excellent selectivity of the mevalonate kinase-catalyzed phosphorylation of mevalonate simplifies lengthy multi-step routes to (R)-mevalonate-5-phosphate to a one-step biocatalytic reaction, because the phosphate group can be transferred directly and without any additional reaction steps involving introduction and removal of protecting groups. By adjusting the required reaction time for complete conversion, the kinetic resolution of racemic mevalolactone can be easily used for the preparation of (S)-mevalonate and (R)-mevalonate-5-phosphate. A new recombinant mevalonate kinase has been prepared by the expression of the mevalonate kinase gene from the hyperthermophilic archaeon Thermococcus kodakarensis in Escherichia coli and by the subsequent purification. Direct quantitative 31P-NMR kinetic analysis has been utilized to characterize the enantioselectivity of the mevalonate kinase. This method is useful for determining the biocatalyst's utility for the synthesis of enantiomerically pure (R)-mevalonate-5-phosphate as well as for biocatalytic process development.
Spatial and temporal patterns of Ellenberg nutrient values in forests of Germany and adjacent regions - a survey based on phytosociological databases
Ewald, J. ; Hennekens, S.M. ; Conrad, S. ; Wohlgemuth, T. ; Jansen, F. ; Jenssen, M. ; Cornelis, J. ; Michiels, H.G. ; Kayser, J. ; Chytry, M. - \ 2013
Tuexenia 33 (2013). - ISSN 0722-494X - p. 93 - 109.
Within the last 30 years the role of nitrogen in Central European forests has changed fundamentally from limiting resource to environmental problem. As the retrospective tracking of nutrient availability by soil chemical and biogeochemical measurements faces serious problems, bioindication based on understorey species composition is indispensable for monitoring broad-scale eutrophication. Based on a broad survey of more than 100,000 forest vegetation plots accessible in electronic data-bases from Germany and adjacent countries, we calculated unweighted average Ellenberg nutrient values (mN) as a proxy of plant-available macronutrients. Based on the quantiles of the frequency distribution of mN in a regionally stratified sample, we define five trophic classes, which can be used to compare dimensionless mN values. We studied spatial patterns of average nutrient values within 17 regions and compared the periods from 1899 to 1975 and 1976 to 2006. After 1975 eutrophic (mN > 5.67) and hypertrophic (mN > 6.28) conditions were common everywhere except in the Alps and Saxony-Anhalt, but very oligotrophic conditions (mN <3.44) were still widespread in regions with nutrient-poor bedrock. Before 1975 mN of plots had been lower than after 1975 in all but the southeastern regions. Between the pre- and post-1975 data the proportion of hypertrophic plots increased from 5.7 to 11.8%, and that of very oligo-trophic plots decreased from 14.6 to 8.3%. To remove bias resulting from uneven distribution, the dataset was stratified by five tree layer dom-inance types, period and region and resampled. In pre-1975 plots medians of mN increased in the order Pinus sylvestris, Quercus spp., Picea abies, Fagus sylvatica and Alnus spp, whereas the increase of mN was highest in forest types with historically low nutrient values. Therefore, the widespread change in mN must be attributed to the pronounced vegetation changes in Quercus and Pinus stands, indicating the importance of land-use change, i.e. recovery of nutrient cycles after hundreds of years of exploita-tion through coppicing, grazing and litter use. The analysis confirms eutrophication as a megatrend of modern vegetation change and demonstrates the high research potential of linking vegetation plot databases across large regions. Keywords: bioindication, Central Europe, Ellenberg indicator values, eutrophication, nitrogen deposi-tion, soil nutrients, vegetation-plot data
Wald und Klimawandel in der inneralpinen Trockenregion Visp
Rigling, A. ; Elkin, C. ; Dobbertin, M. ; Eilmann, B. ; Ciuggiola, A. ; Wohlgemuth, T. ; Bugmann, H. - \ 2012
Schweizerische Zeitschrift für Forstwesen 163 (2012)12. - ISSN 0036-7818 - p. 481 - 492.
Over the past decades, observed increases in temperature have been particularly pronounced in mountain regions. If this trend should continue in the 21st Century, frequency and intensity of droughts will increase, and will pose major challenges for forest management. Under current conditions drought-related tree mortality is already an important factor of forest ecosystems in dry inner-Alpine valleys. Here we assess the sensitivity of forest ecosystems to climate change and evaluate alternative forest management strategies in the Visp region. We integrate data from forest monitoring plots, field experiments and dynamic forests models to evaluate how the forest ecosystem services timber production, protection against natural hazards, carbon storage and biodiversity will be impacted. Our results suggest that at dry low elevation sites the drought tolerance of native tree species will be exceeded so that in the longer term a transition to more drought-adapted species should be considered. At medium elevations, drought and insect disturbances as by bark beetles are projected to be important for forest development, while at high elevations forests are projected to expand and grow better. All of the ecosystem services that we considered are projected to be impacted by changing forest conditions, with the specific impacts often being elevation-dependent. In the medium term, forest management that aims to increase the resilience of forests to drought can help maintain forest ecosystem services temporarily. However, our results suggest that relatively rigid management interventions are required to achieve significant effects. By using a combination of environmental monitoring, field experiments and modeling, we are able to gain insight into how forest ecosystem, and the services they provide, will respond to future changes.
Industrial biotechnology in the chemical and pharmaceutical industry
Franssen, M.C.R. ; Kircher, M. ; Wohlgemuth, R. - \ 2010
In: Industrial Biotechnology. Sustainable Growth and Economic Success / Soeteart, W., Vandamme, E.J., Weinheim : Wiley-VCH - ISBN 9783527314423 - p. 323 - 350.
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