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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The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes
Damm, U. ; Sato, T. ; Alizadeh, A. ; Groenewald, J.Z. ; Crous, P.W. - \ 2019
Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 1 - 46.
Anthracnose - Ascomycota - Colletotrichum - Gloeosporium - Glomerella - Phylogeny - Systematics

Although Glomerella glycines, Colletotrichum magnum and C. orchidearum are known as causal agents of anthracnose of soybean, Cucurbitaceae and Orchidaceae, respectively, their taxonomy remains unresolved. In preliminary analyses based on ITS, strains of these species appear basal in Colletotrichum phylogenies, clustering close to C. cliviae, C. brevisporum and other recently described species from tropical or subtropical regions. Phylogenetic analyses (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 102 strains previously identified as Ga. glycines, C. magnum and C. orchidearum as well as other related strains from different culture collections and studies placed these taxa in three species complexes, and distinguished at least 24 species, including 11 new species. In this study, C. magnum, C. orchidearum and C. piperis were epitypified and their taxonomy resolved, while C. cliviicola was proposed as a new name for C. cliviae. Furthermore, a sexual morph was observed for C. yunnanense, while C. brevisporum, C. cliviicola and C. tropicicola were reported from new hosts or countries. Regarding their conidial morphology, species in the C. dracaenophilum, C. magnum and C. orchidearum species complexes are reminiscent of C. gloeosporioides or C. boninense s. lat., and were likely to be confused with them in the past.

Sea ice biology and biogeochemistry
Peeken, I. ; Castellani, Giula ; Flores, Hauke ; Ehrlich, Julia ; Lange, Benjamin ; Schaafsma, F.L. ; Gradinger, Rolf ; Hassett, Brandon ; Kunisch, Erin ; Damm, Ellen ; Verdugo, Josefa ; Kohlbach, Doreen ; Graeve, Martin ; Blum, Bodil - \ 2018
In: The expeditions PS106/1 and 2 of the research vessel Polarstern to the Arctic Ocean in 2017 / Macke, Andreas, Flores, Hauke, Helmholtz : AWI Alfred-Wegener-Institut (Berichte zur Polar-und Meeresforschung ) - p. 99 - 119.
Climate Impacts in Europe Under +1.5°C Global Warming
Jacob, Daniela ; Kotova, Lola ; Teichmann, Claas ; Sobolowski, Stefan P. ; Vautard, Robert ; Donnelly, Chantal ; Koutroulis, Aristeidis G. ; Grillakis, Manolis G. ; Tsanis, Ioannis K. ; Damm, Andrea ; Sakalli, Abdulla ; Vliet, Michelle T.H. van - \ 2018
Earth's Future 6 (2018)2. - ISSN 2328-4277 - p. 264 - 285.
+1.5oC and +2oC global warming - Climate Change - Climate Change Impacts - Europe - IMPACT2C project
The Paris Agreement of the United Nations Framework Convention on Climate Change aims not only at avoiding +2°C warming (and even limit the temperature increase further to +1.5°C), but also sets long-term goals to guide mitigation. Therefore, the best available science is required to inform policymakers on the importance of and the adaptation needs in a +1.5°C warmer world. Seven research institutes from Europe and Turkey integrated their competencies to provide a cross-sectoral assessment of the potential impacts at a pan-European scale. The initial findings of this initiative are presented and key messages communicated. The approach is to select periods based on global warming thresholds rather than the more typical approach of selecting time periods (e.g., end of century). The results indicate that the world is likely to pass the +1.5°C threshold in the coming decades. Cross-sectoral dimensions are taken into account to show the impacts of global warming that occur in parallel in more than one sector. Also, impacts differ across sectors and regions. Alongside the negative impacts for certain sectors and regions, some positive impacts are projected. Summer tourism in parts of Western Europe may be favored by climate change; electricity demand decreases outweigh increases over most of Europe and catchment yields in hydropower regions will increase. However, such positive findings should be interpreted carefully as we do not take into account exogenous factors that can and will influence Europe such as migration patterns, food production, and economic and political instability.
Spatio-temporal trends and trade-offs in ecosystem services : An Earth observation based assessment for Switzerland between 2004 and 2014
Braun, Daniela ; Damm, Alexander ; Hein, Lars ; Petchey, Owen L. ; Schaepman, Michael E. - \ 2018
Ecological Indicators 89 (2018). - ISSN 1470-160X - p. 828 - 839.
Cultural services - MODIS - Regulating services - Remote sensing - Synergies - Time series
Understanding and monitoring pressures on ecosystems and their consequences for ecosystem services (ES) is essential for management decisions and verification of progress towards national and international policies (e.g. Aichi Biodiversity Targets, Sustainable Development Goals). Remote sensing (RS) offers a unique capability to assess ES systematically and regularly across spatial and temporal scales. We aim to evaluate the benefits of RS to monitor spatio-temporal variations of ES by assessing several ES in Switzerland between 2004 and 2014. We coupled mechanistic ES models and RS data to estimate time series of three regulating (i.e. carbon dioxide regulation (CO2R), soil erosion prevention (SEP), and air quality regulation (AQR)) and one cultural ES (recreational hiking (RH)). The resulting ES were used to assess spatial and temporal changes, trade-offs and synergies of ES potential supply and flow in Switzerland between 2004 and 2014. Resulting ES trends showed diverse spatial patterns across Switzerland with largest changes in CO2R and AQR. ES interactions revealed a scale and elevation dependency. We identified weak to strong synergies between all ES combinations except for trade-offs between CO2R-AQR and AQR-RH at Swiss scale. Spatially, all ES interactions revealed a heterogeneous mix of synergies and trade-offs within Switzerland.Our results demonstrate the strength of RS for systematic and regular spatio-temporal ES monitoring and contribute insights to the large potential of RS, which will be extended with future Earth observation missions. Derived spatially explicit ES information will facilitate decision-making in landscape planning and conservation and will allow examining progress towards environmental policies.
Impacts of +2 °C global warming on winter tourism demand in Europe
Damm, Andrea ; Greuell, Wouter ; Landgren, Oskar ; Prettenthaler, Franz - \ 2017
Climate Services 7 (2017). - ISSN 2405-8807 - p. 31 - 46.
Climate change impacts - Overnight stays - Weather-Value at Risk - Winter tourism demand
Increasing temperatures and snow scarce winter seasons challenge the winter tourism industry. In this study the impacts of +2 °C global warming on winter tourism demand in Europe's ski tourism related NUTS-3 regions are quantified. Using time series regression models, the relationship between natural snow conditions and monthly overnight stays is estimated. Based on these model results, we quantify the risk of tourism demand losses due to weather variability and assess the potential impacts of climate change. Hereby, the concept of Weather-Value at Risk (0.95) is applied. Snow data are provided by the hydrological model VIC, which is forced by E-OBS data to obtain historical snow values for tourism model calibration and forced by EURO-CORDEX climate simulations to obtain snow projections until 2100. Under +2 °C warming, the weather-induced risk of losses in winter overnight stays related to skiing tourism in Europe amounts to up to 10.1 million nights per winter season, which is +7.3 million overnight stays additionally at risk compared to the reference period (1971–2000). Among the top four European skiing tourism nations – Austria, France, Italy and Switzerland – France and Switzerland show the lowest increase in risk of losses in winter overnight stays. The highest weather-induced risk of losses in winter overnight stays – in the reference period as well as in the +2 °C scenarios – is found in Austria, followed by Italy. These two countries account for the largest fraction of winter overnight stays in skiing related NUTS-3 regions.
From instantaneous to continuous : Using imaging spectroscopy and in situ data to map two productivity-related ecosystem services
Braun, Daniela ; Damm, Alexander ; Paul-Limoges, Eugénie ; Revill, Andrew ; Buchmann, Nina ; Petchey, Owen L. ; Hein, Lars ; Schaepman, Michael E. - \ 2017
Ecological Indicators 82 (2017). - ISSN 1470-160X - p. 409 - 419.
APEX - Carbon dioxide regulation - Ecosystem functions - Ecosystem services - Food supply - Gross primary production - Remote sensing - Sun-induced chlorophyll fluorescence

Spatially well-informed decisions are essential to sustain and regulate processes and ecosystem services (ES), and to maintain the capacity of ecosystems to supply services. However, spatially explicit ES information is often lacking in decision-making, or exists only as ES maps based on categorical land cover data. Remote sensing (RS) opens new pathways to map ES, in particular biophysical ES supply. We developed an observation-based concept for spatially explicit and continuous ES mapping at landscape scale following the biophysical part of the ES cascade. We used Earth observations in combination with in situ data to map ecosystem properties, functions, and biophysical ES supply. We applied this concept in a case study to map two ES: carbon dioxide regulation and food supply. Based on Earth observations and in situ data, we determined the ecosystem property Sun-Induced chlorophyll Fluorescence (SIF) to indicate ecosystem state and applied scaling models to estimate gross primary production (GPP) as indicator for ecosystem functioning and consequently carbon dioxide regulation and food supply as ES. Resulting ES maps showed heterogeneous patterns in ES supply within and among ecosystems, which were particularly evident within forests and grasslands. All investigated land cover classes were sources of CO2, with averages ranging from ‐66 to ‐748 g C m‐2 yr‐1, after considering the harvest of total above ground biomass of crops and the storage organ, except for forest being a sink of CO2 with an average of 105 g C m‐2 yr‐1. Estimated annual GPP was related to food supply with a maize grain yield average of 9.5 t ha‐1 yr‐1 and a sugar beet root yield of 110 t ha‐1 yr‐1. Validation with in situ measurements from flux towers and literature values revealed a good performance of our approach for food supply (relative RMSE of less than 23%), but also some over- and underestimations for carbon dioxide regulation. Our approach demonstrated how RS can contribute to spatially explicit and continuous ES cascade mapping and suggest that this information could be useful for environmental assessments and decision-making in spatial planning and conservation.

Sea ice biology and biogeochemistry
Peeken, I. ; Castellani, G. ; Flores, H. ; J., Ehrlich ; Lange, B. ; Kohlbach, D. ; Graeve, M. ; Schaafsma, F.L. ; Gradinger, R. ; Bluhm, B. ; Hassett, B. ; Kunisch, E. ; Damm, E. ; Verdugo, J. - \ 2017
In: Expedition Programme Polarstern PS106 / Knust, Rainer, Macke, Andrea, Flores, Hauke, AWI Alfred-Wegener-Institut - p. 27 - 32.
Multifunctional floodplain management and biodiversity effects : a knowledge synthesis for six European countries
Schindler, Stefan ; O’Neill, Fionnuala H. ; Biró, Marianna ; Damm, Christian ; Gasso, Viktor ; Kanka, Robert ; Sluis, Theo van der; Krug, Andreas ; Lauwaars, Sophie G. ; Sebesvari, Zita ; Pusch, Martin ; Baranovsky, Boris ; Ehlert, Thomas ; Neukirchen, Bernd ; Martin, James R. ; Euller, Katrin ; Mauerhofer, Volker ; Wrbka, Thomas - \ 2016
Biodiversity and Conservation 25 (2016)7. - ISSN 0960-3115 - p. 1349 - 1382.
Ecosystem services - Flood protection - Green infrastructure - River Regulation - River restoration - Water framework directive

Floodplain ecosystems are biodiversity hotspots and supply multiple ecosystem services. At the same time they are often prone to human pressures that increasingly impact their intactness. Multifunctional floodplain management can be defined as a management approach aimed at a balanced supply of multiple ecosystem services that serve the needs of the local residents, but also those of off-site populations that are directly or indirectly impacted by floodplain management and policies. Multifunctional floodplain management has been recently proposed as a key concept to reconcile biodiversity and ecosystem services with the various human pressures and their driving forces. In this paper we present biophysics and management history of floodplains and review recent multifunctional management approaches and evidence for their biodiversity effects for the six European countries Ireland, the Netherlands, Germany, Slovakia, Hungary and the Ukraine. Multifunctional use of floodplains is an increasingly important strategy in some countries, for instance in the Netherlands and Hungary, and management of floodplains goes hand in hand with sustainable economic activities resulting in flood safety and biodiversity conservation. As a result, biodiversity is increasing in some of the areas where multifunctional floodplain management approaches are implemented. We conclude that for efficient use of management resources and ecosystem services, consensual solutions need to be realized and biodiversity needs to be mainstreamed into management activities to maximize ecosystem service provision and potential human benefits. Multifunctionality is more successful where a broad range of stakeholders with diverse expertise and interests are involved in all stages of planning and implementation.

First report of Colletotrichum godetiae causing bitter rot on ‘Golden Delicious’ apples in the Netherlands
Wenneker, M. ; Pham, K.T.K. ; Lemmers, M.E.C. ; Boer, F.A. de; Lans, A.M. van der; Leeuwen, P.J. van; Hollinger, T.C. - \ 2016
Plant Disease 100 (2016)1. - ISSN 0191-2917 - p. 218 - 218.
Apple (Malus domestica) is an important fruit crop in the Netherlands, with a total production of 418,000 tons in 2011. Symptoms of apple bitter rot were observed on ‘Golden Delicious’ apples in the Netherlands in July 2013 after 9 months of storage in a packing house at controlled atmosphere. Lesions were round, 1 to 5 cm in diameter, gray and dry with acervuli, producing orange spore masses in concentric rings. Fruit were rinsed with sterile water, and lesions were sprayed with 70% ethanol until droplet runoff. The skin was removed aseptically with a scalpel, and tissue under the lesion was isolated and placed onto Potato Dextrose Agar (PDA). The PDA plates were incubated at 20°C in the dark, and single-spore isolates were propagated on PDA. The isolates were identified as Colletotrichum sp. based on culture morphology, having light gray to pale orange mycelium and, when viewed from the reverse side, ranged from pink to reddish orange. The cultures carried yellowish spore masses and dark melanized structures similar to acervuli that oozed orange conidia. Conidia were cylindrical to fusiform, pointed at one or both ends, and measured 8.0 to 17.0 μm × 3.5 to 5.0 μm. Both cultural and morphological characteristics of the pathogen were similar to those described for C. acutatum, causal agent of bitter rot of apple. A representative isolate (PPO-44377) was used for multilocus gene sequencing (Damm et al. 2012). Genomic DNA was extracted using the LGC Mag Plant Kit (Berlin, Germany) in combination with the KingFisher method (Waltham, USA) and six loci were amplified and sequenced. Primer pairs ACT-512F + ACT-783R, CHS-354R + CHS-79F, GDF1 + GDR1, CYLH3F + CYLH3R, BT2Fd + BT4R, and ITS1 and ITS4 (White et al. 1990) were used for amplification of parts of the actin (ACT), chitin synthase (CHS-1) gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), beta-tubulin (TUB2) and ITS region of the rDNA gene, respectively. One sequence for each locus has been deposited in GenBank under Accession Nos. KR180290 (ACT), KR180292 (CHS-1), KR180293 (GAPDH), KR180294 (HIS3), KR180295 (TUB2), and KR180296 (ITS). MegaBLAST analysis revealed that the ITS sequences matched with 98.9 to 100% identity to Colletotrichum spp. belonging to C. acutatum species complex (including C. godetiae). The phylogenetic trees constructed using sequences of ACT, CHS-1, GAPDH, HIS3, and TUB2 of our strain (PPO-44377), and available sequences from GenBank confirmed the identity of this strain as C. godetiae. Koch’s postulates were performed on 15 ‘Golden Delicious’ apples. Surface-sterilized fruit were inoculated with 20 μl of a spore suspension (105 conidia/ml) prepared from a 15-day-old PDA culture after wounding with a needle. Inoculated fruits were sealed in a plastic bag and were incubated in darkness at 20°C. Symptoms appeared after 4 to 6 days on 80% of the fruits while mock-inoculated controls with water remained symptomless. Fungal colonies isolated from the lesions and cultured on PDA had morphological characteristics that resembled the original isolate from the infected apples. There are few reports of symptoms associated with C. godetiae on apple in Europe (Baroncelli et al. 2014; Ivic et al. 2013; Munda 2014). This is the first report of bitter rot caused by C. godetiae on apple fruit in the Netherlands. Currently, bitter rot is not an important disease in apples in the Netherlands. However, it is ranges worldwide and is considered one of the most important diseases, causing considerable crop losses, and may become an emerging problem in the Netherlands in the near future.
Multifunctionality of floodplain landscapes: relating management options to ecosystem services
Schindler, S. ; Sebesvari, Z. ; Damm, C. ; Sluis, T. van der - \ 2014
Landscape Ecology 29 (2014)2. - ISSN 0921-2973 - p. 229 - 244.
biodiversity conservation - restoration - indicators - ecology - scales - assessments - knowledge - policy - rivers - reach
The concept of green infrastructure has been recently taken up by the European Commission for ensuring the provision of ecosystem services (ESS). It aims at the supply of multiple ESS in a given landscape, however, the effects of a full suite of management options on multiple ESS and landscape multifunctionality have rarely been assessed. In this paper we use European floodplain landscapes as example to develop an expert based qualitative conceptual model for the assessment of impacts of landscape scale interventions on multifunctionality. European floodplain landscapes are particularly useful for such approach as they originally provided a high variety and quantity of ESS that has declined due to the strong human impact these landscapes have experienced. We provide an overview of the effects of floodplain management options on landscape multifunctionality by assessing the effects of 38 floodplain management interventions on 21 relevant ESS, as well as on overall ESS supply. We found that restoration and rehabilitation consistently increased the multifunctionality of the landscape by enhancing supply of provisioning, regulation/maintenance, and cultural services. In contrast, conventional technical regulation measures and interventions related to extraction, infrastructure and intensive land use cause decrease in multifunctionality and negative effects for the supply of all three aspects of ESS. The overview of the effects of interventions shall provide guidance for decision makers at multiple governance levels. The presented conceptual model could be effectively applied for other landscapes that have potential for a supply of a high diversity of ESS.
The Colletotrichum gigasporum species complex
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2014
Persoonia 33 (2014). - ISSN 0031-5850 - p. 83 - 97.
sp-nov - primer sets - endophytes - pathogens - china - gloeosporioides - anthracnose - diversity - sequences - acutatum
In a preliminary analysis, 21 Colletotrichum strains with large conidia preserved in the CBS culture collection clustered with a recently described species, C. gigasporum, forming a clade distinct from other currently known Colletotrichum species complexes. Multi-locus phylogenetic analyses (ITS, ACT, TUB2, CHS-1, GAPDH) as well as each of the single-locus analyses resolved seven distinct species, one of them being C. gigasporum. Colletotrichum gigasporum and its close allies thus constitute a previously unknown species complex with shared morphological features. Five of the seven species accepted in the C. gigasporum species complex are described here as novel species, namely C. arxii, C. magnisporum, C. pseudomajus, C. radicis and C. vietnamense. A species represented by a single sterile strain, namely CBS 159.50, was not described as novel species, and is treated as Colletotrichum sp. CBS 159.50. Furthermore, C. thailandicum is reduced to synonymy with C. gigasporum.
The Colletotrichum destructivum species complex - hemibiotrophic pathogens of forage and field crops
Damm, U. ; O'Connell, R.J. ; Groenewald, J.Z. ; Crous, P.W. - \ 2014
Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 49 - 84.
random insertional mutagenesis - cowpea vigna-unguiculata - infection process - 1st report - host-specificity - anthracnose disease - glomerella-truncata - nicotiana-tabacum - sequence-analysis - primer sets
Colletotrichum destructivum is an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. Several Colletotrichum isolates, previously reported as closely related to C. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates of C. destructivum and related species revealed 16 clades that are recognised as separate species in the C. destructivum complex, which includes C. destructivum, C. fuscum, C. higginsianum, C. lini and C. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namely C. americae-borealis, C. antirrhinicola, C. bryoniicola, C. lentis, C. ocimi, C. pisicola, C. utrechtense and C. vignae are newly described.
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
The genera of Fungi: fixing the application of type species of generic names
Crous, P.W. ; Giraldo, A. ; Hawksworth, D.L. ; Robert, V. ; Kirk, P.M. ; Guarro, J. ; Robbertse, B. ; Schoch, C.L. ; Damm, U. ; Trakunyingcharoen, T. ; Groenewald, J.Z. - \ 2014
IMA fungus 5 (2014)1. - ISSN 2210-6340 - p. 141 - 160.
To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the “Without-prejudice List of Protected Generic Names of Fungi” (see IMA Fungus 4 (2): 381–443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.
Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae
Liu, F. ; Damm, U. ; Cai, L. ; Crous, P.W. - \ 2013
Fungal Diversity 61 (2013)1. - ISSN 1560-2745 - p. 89 - 105.
yunnan provinces - fungal pathogens - primer sets - sp-nov - china - guizhou - hosts
Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C. acutatum, C. boninense and C. gloeosporioides. In the present study, a multi-locus phylogenetic analysis (ACT, CAL, CHS-1, GAPDH, GS, ITS, TUB2) revealed that strains of the C. gloeosporioides complex associated with Proteaceae belong to at least six species. These include C. alienum, C. aotearoa, C. kahawae (subsp. ciggaro), C. siamense, and two new taxa, C. proteae and C. grevilleae. The most economically important pathogen of Proteaceae seems to be C. alienum, and not C. gloeosporioides as previously reported. All taxa associated with Proteaceae are morphologically described on different media in culture, except strains of C. siamense, which proved to be sterile. Furthermore, C. populi is synonymised with C. aenigma.
The Colletotrichum orbiculare species complex: Important pathogens of field crops and weeds
Damm, U. ; Cannon, P.F. ; Liu, F. ; Barreto, R.W. ; Guatimosim, E. ; Crous, P.W. - \ 2013
Fungal Diversity 61 (2013)1. - ISSN 1560-2745 - p. 29 - 59.
f-sp malvae - round-leaved mallow - protein-kinase - xanthium-spinosum - anthracnose fungus - sequence-analysis - infection process - parasitic fungi - north india - primer sets
Colletotrichum orbiculare causes anthracnose of Cucurbitaceae and is phylogenetically closely related to pathogens of several other herbaceous hosts belonging to the Asteraceae, Fabaceae and Malvaceae. Most of them are known for their hemibiotrophic infection strategy and as destructive pathogens either of field crops or weeds. In order to study the phylogenetic relationships of these fungi, a multilocus analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2, GS) of 42 strains of C. orbiculare and related species was conducted. The analysis resulted in nine clades that confirmed the four species previously known as belonging to this species complex, C. lindemuthianum, C. malvarum, C. orbiculare and C. trifolii, and recognised four new species from weeds, namely C. bidentis, C. sidae, C. spinosum and C. tebeestii. The name C. orbiculare itself is widely used in plant pathology and science, but is invalid according to current nomenclatural rules. Therefore we described a new species with the same epithet and a type specimen that agrees with our current understanding of this species, and is linked to a living culture. Following the recent epitypification of C. lindemuthianum, we chose appropriate specimens with associated strains to serve as epitypes of C. malvarum and C. trifolii, and selected an authentic specimen of C. trifolii as lectotype.
Fungal Planet description sheets: 154–213
Crous, P.W. ; Wingfield, M.J. ; Guarro, J. ; Cheewangkoon, R. ; Bank, M. van der; Swart, W.J. ; Stchigel, A.M. ; Cano-Lira, J.F. ; Roux, J. ; Madrid, H. ; Damm, U. ; Wood, A.R. ; Shuttleworth, L.A. ; Hodges, C.S. ; Munster, M. ; Jesús Yáñez-Morales, M. de; Zúñiga-Estrada, L. ; Cruywagen, E.M. ; Hoog, G.S. de; Silvera, C. ; Najafzadeh, J. ; Davison, E.M. ; Davison, P.J.N. ; Barrett, M.D. ; Barrett, R.L. ; Manamgoda, D.S. ; Minnis, A.M. ; Kleczewski, N.M. ; Flory, S.L. ; Castlebury, L.A. ; Clay, K. ; Hyde, K.D. ; Maússe-Sitoe, S.N.D. ; Chen, S. ; Lechat, C. ; Hairaud, M. ; Lesage-Meessen, L. ; Pawlowska, J. ; Wilk, M. ; Sliwinska-Wyrzychowska, A. ; Metrak, M. ; Wrzosek, M. ; Pavlic-Zupanc, D. ; Maleme, H.M. ; Slippers, B. ; Mac Cormack, W.P. ; Archuby, D.I. ; Grünwald, N.J. ; Tellería, M.T. ; Dueñas, M. ; Martín, M.P. ; Marincowitz, S. ; Beer, Z.W. de; Perez, C.A. ; Gené, J. ; Marin-Felix, Y. ; Groenewald, J.Z. - \ 2013
Persoonia 31 (2013). - ISSN 0031-5850 - p. 188 - 296.
sp-nov - colletotrichum-sansevieriae - anamorph genus - south-africa - 1st report - phytophthora-ipomoeae - leaf-blight - genera - phylogeny - botryosphaeriaceae
Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Circumscription of the anthracnose pathogens Colletotrichum lindemuthianum and C. nigrum
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2013
Mycologia 105 (2013)4. - ISSN 0027-5514 - p. 844 - 860.
molecular diversity - differential cultivars - genetic-variability - sequence-analysis - host-specificity - primer sets - sp-nov - glomerella - resistance - identification
The anthracnose pathogen of common bean (Phaseolus vulgaris) is usually identified as Colletotrichum lindemuthianum, while anthracnose of potato (Solanum tuberosum), peppers (Capsicum annuum), tomato (S. lycopersicum) and several other crop plants is often attributed to C. coccodes. In order to study the phylogenetic relationships of these important pathogens, we conducted a multigene analysis (ITS, ACT, TUB2, CHS-1, GAPDH) of strains previously identified as C. lindemuthianum, C. coccodes and other related species, as well as representative species of the major Colletotrichum species complexes. Strains of C. lindemuthianum belonged to a single clade; we selected an authentic specimen as lectotype, and an appropriate specimen and culture from the CBS collection to serve as epitype. Two clades were resolved within C. coccodes s. lat. One clade included the ex-neotype strain of C. coccodes on Solanum, while an epitype was selected for C. nigrum, which represents the oldest name of the second clade, which occurs on Capsicum, Solanum, as well as several other host plants. Furthermore, we recognized C. lycopersici as a synonym of C. nigrum, and C. biologicum as a synonym of C. coccodes.
A Bayesian object-based approach for estimating vegetation biophysical and biochemical variables from APEX at-sensor radiance data
Laurent, V.C.E. ; Verhoef, W. ; Damm, A. ; Schaepman, M.E. ; Clevers, J.G.P.W. - \ 2013
Remote Sensing of Environment 139 (2013). - ISSN 0034-4257 - p. 6 - 17.
radiative-transfer models - leaf-area index - sun-induced fluorescence - remote-sensing data - reflectance data - global products - brdf model - inversion - canopy - lai
Vegetation variables such as leaf area index (LAI) and leaf chlorophyll content (Cab) are important inputs for vegetation growth models. LAI and Cab can be estimated from remote sensing data using either empirical or physically-based approaches. The latter are more generally applicable because they can easily be adapted to different sensors, acquisition geometries, and vegetation types. They estimate vegetation variables through inversion of radiative transfer models. Such inversions are ill-posed but can be regularized by coupling models, by using a priori information, and spatial and/or temporal constraints. Striving to improve the accuracy of LAI and Cab estimates from single remote sensing images, this contribution proposes a Bayesian object-based approach to invert at-sensor radiance data, combining the strengths of regularization by model coupling, as well as using a priori data and object-level spatial constraints. The approach was applied to a study area consisting of homogeneous agricultural fields, which were used as objects for applying the spatial constraints. LAI and Cab were estimated from at-sensor radiance data of the Airborne Prism EXperiment (APEX) imaging spectrometer by inverting the coupled SLC-MODTRAN4 canopy-atmosphere model. The estimation was implemented in two steps. In the first step, up to six variables were estimated for each object using a Bayesian optimization algorithm. In the second step, a look-up-table (WT) was built for each object with only LAI and Cab as free variables, constraining the values of all other variables to the values obtained in the first step. The results indicated that the Bayesian object-based approach estimated LAI more accurately (R-2 = 0.45 and RMSE = 1.0) than a LUT with a Bayesian cost function (LUT-BCF) approach (R-2 = 022 and RMSE = 2.1), and Cab with a smaller absolute bias (-9 versus -23 mu g/cm(2)). The results of this study are an important contribution to further improve the regularization of ill-posed RT model inversions. The proposed approach allows reducing uncertainties of estimated vegetation variables, which is essential to support various environmental applications. The definition of objects and a priori data in cases where less extensive ground data are available, as well as the definition of the observation covariance matrix, are critical issues which require further research. (C) 2013 Elsevier Inc All rights reserved.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Schoch, C.L. ; Seifert, K.A. ; Huhndorf, S. ; Robert, V. ; Spouge, J.L. ; Levesque, C.A. ; Chen, W. ; Crous, P.W. ; Boekhout, T. ; Damm, U. ; Hoog, G.S. de; Eberhardt, U. ; Groenewald, J.Z. ; Groenewald, M. ; Hagen, F. ; Houbraken, J. ; Quaedvlieg, W. ; Stielow, B. ; Vu, T.D. ; Walther, G. - \ 2012
Proceedings of the National Academy of Sciences of the United States of America 109 (2012)16. - ISSN 0027-8424 - p. 6241 - 6246.
arbuscular mycorrhizal fungi - phylogenetic-relationships - basidiomycetous yeasts - intragenomic variation - ectomycorrhizal fungi - species recognition - sequence-analysis - rpb1 sequences - rdna - subunit
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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