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    '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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    Classification of the European marsh vegetation (Phragmito-Magnocaricetea) to the association level
    Landucci, Flavia ; Šumberová, Kateřina ; Tichý, Lubomír ; Hennekens, Stephan ; Aunina, Liene ; Biță-Nicolae, Claudia ; Borsukevych, Lyubov ; Bobrov, Alexander ; Čarni, Andraž ; Bie, Els De ; Golub, Valentin ; Hrivnák, Richard ; Iemelianova, Svitlana ; Jandt, Ute ; Jansen, Florian ; Kącki, Zygmunt ; Lájer, Konrád ; Papastergiadou, Eva ; Šilc, Urban ; Sinkevičienė, Zofija ; Stančić, Zvjezdana ; Stepanovič, Jazep ; Teteryuk, Boris ; Tzonev, Rossen ; Venanzoni, Roberto ; Zelnik, Igor ; Chytrý, Milan - \ 2020
    Applied Vegetation Science 23 (2020)2. - ISSN 1402-2001 - p. 297 - 316.
    Association - cocktail method - consistency - discriminating species groups - functional species group - physiognomy - sociological species group - vegetation classification - vegetation database - wetland vegetation

    Aims: To create a comprehensive, consistent and unequivocal phytosociological classification of European marsh vegetation of the class Phragmito-Magnocaricetea. Location: Europe. Methods: We applied the Cocktail method to a European data set of 249,800 vegetation plots. We identified the main purposes and attributes on which to base the classification, defined assignment rules for vegetation plots, and prepared formal definitions for all the associations, alliances and orders of the class Phragmito-Magnocaricetea using formal logic. Each formula consists of the combination of “functional species groups”, cover values of individual species, and in the case of high-rank syntaxa also of “discriminating species groups” created using the Group Improvement (GRIMP) method. Results: The European Phragmito-Magnocaricetea vegetation was classified into 92 associations grouped in 11 alliances and six orders. New syntaxa (previously invalidly published according to the International Code of Phytosociological Nomenclature) were introduced: Bolboschoeno maritimi-Schoenoplection tabernaemontani, Glycerio maximae-Sietum latifolii, Glycerio notatae-Veronicetum beccabungae, Schoenoplectetum corymbosi and Thelypterido palustris-Caricetum elongatae. Based on a critical revision, some other syntaxa were rejected or excluded from the class Phragmito-Magnocaricetea. Conclusions: This work provides the first consistent classification of the class Phragmito-Magnocaricetea at the European scale, which is an important tool for nature conservation. Our classification largely respects previously existing concepts of syntaxa, but it also proposes modifications to the recently published EuroVegChecklist. This work also provides a protocol that can be used for extending the current classification to new syntaxa and geographical regions.

    Classification of European and Mediterranean coastal dune vegetation
    Marcenò, Corrado ; Guarino, Riccardo ; Loidi, Javier ; Herrera, Mercedes ; Isermann, Maike ; Knollová, Ilona ; Tichý, Lubomír ; Tzonev, Rossen T. ; Acosta, Alicia Teresa Rosario ; Fitzpatrick, Úna ; Iakushenko, Dmytro ; Janssen, John A.M. ; Jiménez-Alfaro, Borja ; Kacki, Zygmunt ; Keizer-Sedláková, Iva ; Kolomiychuk, Vitaliy ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Chytrý, Milan - \ 2018
    Applied Vegetation Science 21 (2018)3. - ISSN 1402-2001 - p. 533 - 559.
    Ammophiletea - Biogeography - Expert system - Honckenyo-Elymetea - Koelerio-Corynephoretea canescentis - Phytosociology - Sand dune - Vegetation classification

    Aims: Although many phytosociological studies have provided detailed local and regional descriptions of coastal dune vegetation, a unified classification of this vegetation in Europe and the Mediterranean Basin has been missing. Our aim is to produce a formalized classification of this vegetation and to identify the main factors driving its plant species composition at a continental scale. Location: Atlantic and Baltic coasts of Europe, Mediterranean Basin and the Black Sea region. Methods: We compiled a database of 30,759 plots of coastal vegetation, which were resampled to reduce unbalanced sampling effort, obtaining a data set of 11,769 plots. We classified these plots with TWINSPAN, interpreted the resulting clusters and used them for developing formal definitions of phytosociological alliances of coastal dune vegetation, which were included in an expert system for automatic vegetation classification. We related the alliances to climatic factors and described their biogeographic features and their position in the coastal vegetation zonation. We examined and visualized the floristic relationships among these alliances by means of DCA ordination. Results: We defined 18 alliances of coastal dune vegetation, including the newly described Centaureo cuneifoliae-Verbascion pinnatifidi from the Aegean region. The main factors underlying the differentiation of these alliances were biogeographic and macroclimatic contrasts between the Atlantic-Baltic, Mediterranean and Black Sea regions, along with ecological differences between shifting and stable dunes. The main difference in species composition was between the Atlantic-Baltic and Mediterranean-Black Sea regions. Within the former region, the main difference was driven by the different ecological conditions between shifting and stable dunes, whereas within the latter, the main difference was biogeographic between the Mediterranean and the Black Sea. Conclusions: The first formal classification of the European coastal dune vegetation was established, accompanied by an expert system containing the formal definitions of alliances, which can be applied to new data sets. The new classification system critically revised the previous concepts and integrated them into a consistent framework, which reflects the main gradients in species composition driven by biogeographic influences, macroclimate and the position of the sites in the coast-inland zonation of the dune systems. A revision of the class concept used in EuroVegChecklist is also proposed.

    Review of grassland habitats and development of distribution maps of heathland, scrub and tundra habitats of EUNIS habitats classification
    Schaminee, J.H.J. ; Chytrý, M. ; Hennekens, S.M. ; Janssen, J.A.M. ; Jimenez-Alfaro, B. ; Knollová, Ilona ; Marceno, L. ; Mucina, L. ; Rodwell, J.S. ; Tichý, L. - \ 2016
    EEA - European Environment Agency (Report EEA/NSV 15/005) - 372 p.
    Assessing vegetation change using vegetation-plot databases: a risky business
    Chytry, M. ; Tichý, L. ; Hennekens, S.M. ; Schaminee, J.H.J. - \ 2014
    Applied Vegetation Science 17 (2014)1. - ISSN 1402-2001 - p. 32 - 41.
    long-term changes - plant-communities - phytosociological databases - species richness - grassland - forests - netherlands - drivers - decades - index
    Aim Data from vegetation plots can be used for the assessment of past vegetation change in three ways: (1) comparison of old and new records from permanent plots established for vegetation monitoring; (2) revisiting historical phytosociological plots and subsequent comparison of old and new records; (3) comparison of large sets of old and new phytosociological records from the same area but different plots. Option (3) would be the cheapest in regions where large vegetation-plot databases are available, but there is a risk of incorrect results due to a spatial mismatch of old and new plots. Here we assess the accuracy of such analyses. Methods We used three data sets of permanent plots from Czech mountain bogs and Dutch oak forests and heathlands to quantify vegetation change. We selected subsets to simulate analyses based on (1) data from permanent plots or revisited phytosociological plots, i.e. containing old and new records from the same plots, (2) vegetation-plot databases with old and new records from different, randomly selected sites, and (3) vegetation-plot databases with old and new records from different but close sites. We repeated each subset selection 1000 times and analysed vegetation change in each of the three data sets and each variant of subset selection using permutational multivariate analysis of variance. Results For data sets with no actual vegetation change, analyses of some subsets simulating vegetation-plot databases incorrectly suggested significant changes. For a data set with real change, a change was detected in analyses of simulated vegetation-plot databases, but in several cases it had a different direction or magnitude to the real change. Conclusions The assessment of vegetation change using vegetation-plot databases should be either avoided or interpreted with extreme caution because of the risk of incorrect results. Analyses such as these may be used to propose hypotheses about past vegetation change, but their results should not be considered valid unless confirmed using more reliable data. In many contexts, re-visitation studies of historical phytosociological plots may be the best strategy to assess past vegetation change, while new networks of carefully stratified permanent plots are preferable for monitoring future change.
    Review of EUNIS forest habitat classification
    Schaminee, J.H.J. ; Chytry, M. ; Hennekens, S.M. ; Jiménez-Alfaro, B. ; Mucina, L. ; Rodwell, J.S. ; Tichy, R. - \ 2013
    Copenhagen : EEA (EEA Technical Report EEA/NSV/13/005) - 111 p.
    Development of vegetation syntaxa crosswalks to EUNIS habitat classification and related data sets
    Schaminee, J.H.J. ; Chytry, M. ; Hennekens, S.M. ; Mucina, L. ; Rodwell, J.S. ; Tichý, L. - \ 2012
    Wageningen : Alterra (EEA Report EEA/NSV/12/001) - 134 p.
    Sulfur Cycle
    Lens, P.N.L. ; Hulshoff Pol, L.W. ; Tichy, R. - \ 2000
    In: Encyclopedia of Microbiology 4 - p. 495 - 505.
    Bioleaching of metals from soils or sediments.
    Tichy, R. ; Rulkens, W.H. ; Grotenhuis, J.T.C. ; Nydl, V. ; Cuypers, C. ; Fajtl, J. - \ 1998
    Water Science and Technology 37 (1998). - ISSN 0273-1223 - p. 119 - 127.
    Oxidation of biologically-produced sulphur in a continuous mixed-suspension reactor.
    Tichy, R. ; Janssen, A. ; Grotenhuis, J.T.C. ; Abswoude, R. van; Lettinga, G. - \ 1998
    Water Research 32 (1998). - ISSN 0043-1354 - p. 701 - 710.
    Solid-state reduced sulfur compounds: environmental aspects and bioremediation.
    Tichy, R. ; Grotenhuis, J.T.C. ; Bos, P. ; Lens, P. - \ 1998
    Critical Reviews in Environmental Science and Technology 28 (1998). - ISSN 1064-3389 - p. 1 - 40.
    Remediation of polluted soil and sediment: perspectives and failures.
    Rulkens, W.H. ; Tichy, R. ; Grotenhuis, J.T.C. - \ 1998
    Water Science and Technology 37 (1998). - ISSN 0273-1223 - p. 27 - 35.
    Bioleaching of metals from soils or sediments using the microbial sulfur cycle
    Tichy, R. - \ 1998
    Agricultural University. Promotor(en): W.H. Rulkens; G. Lettinga; J.T.C. Grotenhuis. - S.l. : Tichy - ISBN 9789054859673 - 138
    zware metalen - bodemverontreiniging - bioremediëring - microbiële activiteiten - zwavel - heavy metals - soil pollution - bioremediation - microbial activities - sulfur

    Reduced inorganic sulfur species like elemental sulfur or sulfide are sensitive to changes in oxidative environments. Generally, inorganic reduced sulfur exists in natural environments in a solid phase, whereas its oxidation leads to sulfur solubilization and a production of acidity. This oxidation occurs spontaneously, due to chemical mechanisms, however, its rate can be enhanced by microbes by several orders of magnitude. The acidification which accompanies the sulfur oxidation brings about rather extreme conditions for microbial growth, pH can drop below 2. The microbial oxidation of reduced inorganic sulfur causes several phenomena of environmental concern. The most substantial environmental aspects is the coupling of sulfur oxidative changes with mobility of toxic heavy metals. Oxidation of sulfur and subsequent production of acid leads to a release of cationic metals to the environment. This is happening e.g. in acid mine drainage, acidification and toxic metals release from sediments dredged for nautical reasons, contamination due to flood events, appearance of acid sulfate soils at sites rich in sulfide minerals or at metals-polluted sites which receive acidic leachates.

    The microbial sulfur oxidation can be also applied in specific technologies. Its use for biohydrometallurgy, i.e. microbial mining of metals from low-grade ores is well known and applied in practise. Another application is microbial desulfurization of coal containing inorganic sulfur inclusions. Recently, its use for decontamination of solid wastes containing toxic metals has been proposed. The bioleaching of heavy metals from anaerobically digested sewage sludge was successfully demonstrated at technological scale.

    This thesis deals with the microbial leaching of toxic cationic heavy metals from contaminated soils or sediments. The bioleaching of metals from these materials provides a direct advantage if it contains a sufficient amount of reduced sulfur. This applies for freshwater sediments which can accumulate substantial amounts of reduced sulfur in anoxic conditions at bottom of freshwater bodies. Metal sulfides, important form of heavy metals in these materials, are directly attacked by microbial oxidation. Metals in other forms are solubilized by the effects of lowering pH. Therefore, bioleaching is the most natural attempt to solubilize metals in the sediments, since the oxidative changes always occur. However, when the amount of reduced sulfur is insufficient or negligible, like in most aerobic soils, additional sulfur substrate or direct addition of sulfuric acid must be considered to achieve sufficiently low pH.

    The advantage of using bioleaching or sulfuric acid is particularly in the possible application of other processes of microbial sulfur cycle, i.e. sulfate reduction resulting in a sulfide production and precipitation of heavy metals in the spent leaching liquor and a partial sulfide oxidation leading to the recovery of elemental sulfur. The elemental sulfur can be supplied back to the bioleaching step.

    Experiments were done to compare the feasibility of microbially produced elemental sulfur (from partial sulfide oxidation) with sulfur flower as a substrate for bioleaching. The results proved that the microbially produced elemental sulfur is a feasible substrate and it seems better available for thiobacilli, than the sulfur flower. This effect is caused by two phenomena: (1) the surface of microbially produced sulfur is more hydrophillic than the orthorhombic sulfur flower and (2) the microbially produced sulfur consists of much smaller particles and provides thus higher specific surface area (2.5 m 2.g -1) than the commercially available orthorhombic sulfur flower (0.1 m 2.g -1). However, the mutual relevance of these two aspects is not fully understood and it may be speculated to which extent would be sulfur oxidation increased, when sulfur flower is pulverized to particles of similar size as the microbially produced sulfur.

    The growth yields on the two types of sulfur were nearly identical during batch experiments, however, the final biomass and sulfate concentrations with microbially produced sulfur were about twice as high as with the sulfur flower. The maximum sulfur specific oxidation rate in batch cultivation was also about two-times higher with microbially produced sulfur than with the sulfur flower. During microbial sulfur oxidation, the first was consumed the finest fraction, which forms typically up to 40% of the microbially produced sulfur. Subsequently, the larger aggregates are oxidized, however, at lower rate. The lowest pH achieved by thiobacilli in a continuous cultivation on microbially produced sulfur was 1.7. This was observed at a dilution rate of 0.04 h -1. Maximum production rate of sulfuric acid was 1 mmol.L -1.h -1at a sulfur loading of ca. 4 mmol.L -1.h -1. When compared to the maximum conversion rates of the other process of microbial sulfur cycle, i.e. sulfate reduction and partial sulfide oxidation, the production of sulfuric acid proceeds at the lowest rate.

    Three experimental studies were accomplished to demonstrate the bioleaching of metals from soil and sediments. The first study involved artificially zinc-contaminated clay, silt, and sandy soil, and the leaching behaviour was studied at varying additions of sulfuric acid between pH 1.5-6. The measurement of aluminium solubilization was used to quantify the extent of soil matrix damage at extreme acidity. Zinc solubilization followed a monotonous increase with decreasing pH, being 17-43% at pH 7 and 72-95% at pH 1.5. However, the aluminium solubilization revealed a sharp edge at pH=4. Below this pH, Al-concentrations increased exponentially, indicating major damage to the soil mineral matrix. The study revealed two different possible strategies in leaching: the first, called here intensive, uses high concentrations of sulfuric acid to achieve satisfactory extraction efficiency and high soil/solution ratio. However, a considerable damage of the soil matrix can be expected. The second strategy, called extensive, uses lower concentrations of acid, however, the soil/solution ratio must be properly decreased.

    The second leaching study aimed at the possible use of sulfur oxidation in-situ, i.e. within the soil profile after artificial contamination of the soil with cadmium. Microbially produced elemental sulfur and orthorhombic sulfur flower were supplied to the soil prior to its placement into the soil pots and the velocity of soil acidification and cadmium solubilization were observed. The microbially produced sulfur proved faster oxidation and acidification than the orthorhombic sulfur flower: immediately after addition of microbially produced sulfur, pH started to decrease. pH-decrease in sulfur flower treatments was observed only after 55 days lag. The solubilization of cadmium into the pore water followed directly the changes of pH. In this study, a vegetative uptake of solubilized cadmium was tested using a common mustard ( Sinapis alba ). With decreasing soil pH, the concentrations of cadmium in biomass increased, however, the biomass yields decreased. When Cd concentrations and biomass yield were combined, an optimum soil pH of 5-5.5 was found for the vegetative removal. However, the overall efficiency of the vegetative removal was rather low.

    In the third leaching study, a sediment from a wetland receiving mine drainage was used, since this sediment was expected to contain high amounts of reduced sulfur. 150-hours aeration of the sediment resulted in acidification down to pH 4.2, accompanied by the increase in redox-potential from -150 meV to +300 meV and an increase of sulfate concentration to ca. 6 mmol.L -1. At the same time, the solubilization of Cd, Cu and Zn was recorded. Total soluble iron revealed initial increase up to 48 mg.L -1within 50 hours of aeration, followed by decrease below detection limit. This was explained by initial desorption of soluble Fe 2+followed by its oxidation and precipitation of the resulting Fe 3+ion. The minimum pH achieved by aeration of the sediment was not sufficient to achieve satisfiable extraction efficiency for the studied metals. Therefore, addition of sulfuric acid or elemental sulfur was investigated.

    The study firstly involved the leaching after exposition to varying concentrations of sulfuric acid. Two different processes were observed in the sediment slurry after acid addition: (1) the monotonous pH decrease with time, caused by oxidation of reduced compounds, which was observed at low acid additions, and (2) delayed pH increase at high acid additions due to the scavenging of acidity by various processes of pH-buffering, solubilization of minerals, diffusion etc. Solubility of Cd, Cu, Pb, and Zn was controlled by exposure intensity defined as actual activity of acid multiplied by the time of exposition. Similar to the first leaching study, intensive and extensive leaching strategies could have been distinguished, where intensive leaching involved high concentrations of H 2 SO 4 and short extraction times, and the extensive leaching used no or low amendments of acid, however, at prolonged extraction times. In the second step of experiments, the bioleaching tests were performed. According to the previous studies, microbially produced sulfur proved faster acidification compared to the orthorhombic sulfur flower.

    The use of microbial sulfur oxidation for the enhancement of toxic metals removal from contaminated soils or sediments is technically feasible. When integrated with the other processes of microbial sulfur cycle, i.e. sulfate reduction and partial sulfide oxidation, it may strongly benefit from relatively easy processing of the spent liquor and sulfur regeneration and re-use. Compared to these processes, the bioleaching is a rate-limiting step.

    It is possible to perform bioleaching both in fully agitated soil slurries, as well as in heap-leaching or in-situ configurations, using an intensive or extensive leaching strategies. The use of processes with different intensity may be the main advantage of the partial or full use of microbial sulfur cycle to control the toxic metals in the environment. Example of the integration of processes of microbial sulfur cycle is e.g. a wetland or anaerobic pond using sulfate reduction in an extensive and sustainable way to control the pollution of voluminous metals and sulfate containing aqueous stream, followed by a more intensive bioleaching. Other example is the introduction of elemental sulfur in the soil to promote its slow acidification and release of metals into the pore water. The collected water can be further treated by intensive or extensive sulfate reduction.

    Bioleaching of metals from soils or sediments.
    Tichy, R. ; Rulkens, W.H. ; Grotenhuis, J.T.C. ; Nydl, V. ; Cuypers, C. ; Fajtl, J. - \ 1997
    In: Proc. First int. conf. on env. restoration, Ed. M. Ros. IAWQ and Slovenian Water Poll. Contr Ass. (SCDZV) Ljublana - p. 124 - 131.
    Remediation of polluted soil and sediment: perspectives and failures.
    Rulkens, W.H. ; Tichy, R. ; Grotenhuis, J.T.C. - \ 1997
    In: Proc. First int. conf. on env. restoration, Ed. M. Ros. IAWQ and Slovenian Water Poll. Contr. Ass. (SCDZV) Ljublana - p. 29 - 36.
    Strategy for leaching zinc from artificially contaminated soil.
    Tichy, R. ; Grotenhuis, J.T.C. ; Rulkens, W.H. ; Nydl, V. - \ 1996
    Environmental Technology 17 (1996). - ISSN 0959-3330 - p. 1181 - 1192.
    The large extrinsic loop of the CP47 protein in Photosystem II Analysis of domains necessary for photoautotrophic growth
    Tichy, M. ; Leguijt, T. ; Vermaas, W.F.J. - \ 1995
    In: Proceedings 3rd workshop on photosynthesis, Asilomar, USA, January
    Sites polluted with heavy metals: current techniques for clean-up and desirable future developments.
    Rulkens, W.H. ; Tichy, R. ; Grotenhuis, J.T.C. - \ 1995
    In: Proc. Int. Conf. on Heavy metals in the environment. Duitsland. Vol 1 - p. 10 - 19.
    Possibilities for using biologically-produced sulphur for cultivation of Thiobacilli with respect to bioleaching processes.
    Tichy, R. ; Janssen, A. ; Grotenhuis, J.T.C. ; Lettinga, G. ; Rulkens, W.H. - \ 1994
    Bioresource Technology 48 (1994). - ISSN 0960-8524 - p. 221 - 227.
    Bioleaching of zinc contaminated soils with Thiobacilli.
    Tichy, R. ; Grotenhuis, J.T.C. ; Rulkens, W.H. - \ 1993
    In: Integrated soil and sediment research: a basis for proper protection / Eijsackers, H., Hamers, T., Dordrecht : Kluwer Academic Publishers - p. 686 - 687.
    Application of the sulphur cycle for bioremediation of soils polluted with heavy metals.
    Tichy, R. ; Grotenhuis, J.T.C. ; Janssen, A. ; Houten, R. van; Rulkens, W.H. ; Lettinga, G. - \ 1993
    In: Contaminated Soil '93 / Arendt, F., Dordrecht : Kluwer Academic Publishers - p. 1459 - 1462.
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