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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    Author Correction: Global status and conservation potential of reef sharks
    MacNeil, M.A. ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, C.S. ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, M.S. ; Ali, Khadeeja ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; Barcia, Laura García ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcy ; Brooks, Edd ; Brown, J.J. ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabaugh, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, B.M. ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Sjamsul Quamar, L.M. ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature (2020). - ISSN 0028-0836

    An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Global status and conservation potential of reef sharks
    MacNeil, Aaron ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, Samantha ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, Shiham ; Khadeeja, Ali ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; García Barcia, Laura ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcey ; Brooks, Edd ; Brown, Jed ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabough, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, Mabel ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Quamar, Sjamsul ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature 583 (2020). - ISSN 0028-0836 - p. 801 - 806.

    Decades of overexploitation have devastated shark populations, leaving considerable doubt as to their ecological status1,2. Yet much of what is known about sharks has been inferred from catch records in industrial fisheries, whereas far less information is available about sharks that live in coastal habitats3. Here we address this knowledge gap using data from more than 15,000 standardized baited remote underwater video stations that were deployed on 371 reefs in 58 nations to estimate the conservation status of reef sharks globally. Our results reveal the profound impact that fishing has had on reef shark populations: we observed no sharks on almost 20% of the surveyed reefs. Reef sharks were almost completely absent from reefs in several nations, and shark depletion was strongly related to socio-economic conditions such as the size and proximity of the nearest market, poor governance and the density of the human population. However, opportunities for the conservation of reef sharks remain: shark sanctuaries, closed areas, catch limits and an absence of gillnets and longlines were associated with a substantially higher relative abundance of reef sharks. These results reveal several policy pathways for the restoration and management of reef shark populations, from direct top-down management of fishing to indirect improvement of governance conditions. Reef shark populations will only have a high chance of recovery by engaging key socio-economic aspects of tropical fisheries.

    Carbon-nitrogen interactions in European forests and semi-natural vegetation - Part 1 : Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling
    Sutton, Mark A. ; Flechard, Chris R. ; Ibrom, Andreas ; Skiba, Ute M. ; Vries, Wim De; Oijen, Marcel Van; Cameron, David R. ; DIse, Nancy B. ; Korhonen, Janne F.J. ; Buchmann, Nina ; Legout, Arnaud ; Simpson, David ; Sanz, Maria J. ; Aubinet, Marc ; Loustau, Denis ; Montagnani, Leonardo ; Neirynck, Johan ; Janssens, Ivan A. ; Pihlatie, Mari ; Kiese, Ralf ; Siemens, Jan ; Francez, Andre Jean ; Augustin, Jurgen ; Varlagin, Andrej ; Olejnik, Janusz ; Juszczak, Radoslaw ; Aurela, Mika ; Berveiller, Daniel ; Chojnicki, Bogdan H. ; Dämmgen, Ulrich ; Delpierre, Nicolas ; Djuricic, Vesna ; Drewer, Julia ; Dufrêne, Eric ; Eugster, Werner ; Fauvel, Yannick ; Fowler, David ; Frumau, Arnoud ; Granier, André ; Gross, Patrick ; Hamon, Yannick ; Helfter, Carole ; Hensen, Arjan ; Horvath, Laszlo ; Kitzler, Barbara ; Kruijt, Bart ; Kutsch, Werner L. ; Lobo-Do-Vale, Raquel ; Lohila, Annalea ; Longdoz, Bernard ; Marek, Michal V. ; Matteucci, Giorgio ; Mitosinkova, Marta ; Moreaux, Virginie ; Neftel, Albrecht ; Ourcival, Jean Marc ; Pilegaard, Kim ; Pita, Gabriel ; Sanz, Francisco ; Schjoerring, Jan K. ; Sebastià, Maria Teresa ; Sim Tang, Y. ; Uggerud, Hilde ; Urbaniak, Marek ; DIjk, Netty Van; Vesala, Timo ; Vidic, Sonja ; Vincke, Caroline ; Weidinger, Tamas ; Zechmeister-Boltenstern, Sophie ; Butterbach-Bahl, Klaus ; Nemitz, Eiko - \ 2020
    Biogeosciences 17 (2020)6. - ISSN 1726-4170 - p. 1583 - 1620.

    The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC=dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3 leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from 70 to 826 gCm2 yr1 at total wetCdry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 gNm2 yr1 and from 4 to 361 g Cm2 yr1 at Ndep rates of 0.1 to 3.1 gNm2 yr1 in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated Ndep where Nr leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3 were on average 27%(range 6 % 54 %) of Ndep at sites with Ndep < 1 gNm2 yr1 versus 65% (range 35 % 85 %) for Ndep > 3 gNm2 yr1. Such large levels of Nr loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with Nr deposition up to 2 2.5 gNm2 yr1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP = GPP ratio). At elevated Ndep levels (> 2.5 gNm2 yr1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC=dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.

    Pesticides decrease bacterial diversity and abundance of irrigated rice fields
    Onwona‐Kwakye, Michael ; Plants‐paris, Kimberly ; Keita, Kadiatou ; Lee, Jessica ; Brink, Paul J. van den; Hogarh, Jonathan N. ; Darkoh, Charles - \ 2020
    Microorganisms 8 (2020)3. - ISSN 2076-2607
    Irrigated fields - Pesticides - Pesticides and bacteria - Soil bacteria - Soil microbiota and diversity

    Bacteria play an important role in soil ecosystems and their activities are crucial in nutrient composition and recycling. Pesticides are extensively used in agriculture to control pests and improve yield. However, increased use of pesticides on agricultural lands results in soil contamination, which could have adverse effect on its bacterial communities. Here, we investigated the effect of pesticides commonly used on irrigated rice fields on bacterial abundance and diversity. Irrigated soil samples collected from unexposed, pesticide‐exposed, and residual exposure areas were cultured under aerobic and anaerobic conditions. DNA was extracted and analysed by 16S rRNA sequencing. The results showed overall decrease in bacterial abundance and diversity in areas exposed to pesticides. Operational taxonomic units of the genera Enterobacter, Aeromonas, Comamonas, Stenotrophomonas, Bordetella, and Staphylococcus decreased in areas exposed to pesticides. Conversely, Domibacillus, Acinetobacter, Pseudomonas, and Bacillus increased in abundance in pesticide‐exposed areas. Simpson and Shannon diversity indices and canonical correspondence analysis demonstrated a decrease in bacterial diversity and composition in areas exposed to pesticides. These results suggest bacteria genera unaffected by pesticides that could be further evaluated to identify species for bioremediation. Moreover, there is a need for alternative ways of improving agricultural productivity and to educate farmers to adopt innovative integrated pest management strategies to reduce deleterious impacts of pesticides on soil ecosystems.

    Nitrogen deposition is the most important environmental driver of growth of pure, even-aged and managed European forests
    Etzold, Sophia ; Ferretti, Marco ; Reinds, Gert Jan ; Solberg, Svein ; Gessler, Arthur ; Waldner, Peter ; Schaub, Marcus ; Simpson, David ; Benham, Sue ; Hansen, Karin ; Ingerslev, Morten ; Jonard, Mathieu ; Karlsson, Per Erik ; Lindroos, Antti Jussi ; Marchetto, Aldo ; Manninger, Miklos ; Meesenburg, Henning ; Merilä, Päivi ; Nöjd, Pekka ; Rautio, Pasi ; Sanders, Tanja G.M. ; Seidling, Walter ; Skudnik, Mitja ; Thimonier, Anne ; Verstraeten, Arne ; Vesterdal, Lars ; Vejpustkova, Monika ; Vries, Wim de - \ 2020
    Forest Ecology and Management 458 (2020). - ISSN 0378-1127
    Air pollution - Climate change - Forest management - ICP Forests - Observational study - Ozone - Statistical modelling

    Changing environmental conditions may substantially interact with site quality and forest stand characteristics, and impact forest growth and carbon sequestration. Understanding the impact of the various drivers of forest growth is therefore critical to predict how forest ecosystems can respond to climate change. We conducted a continental-scale analysis of recent (1995–2010) forest volume increment data (ΔVol, m3 ha−1 yr−1), obtained from ca. 100,000 coniferous and broadleaved trees in 442 even-aged, single-species stands across 23 European countries. We used multivariate statistical approaches, such as mixed effects models and structural equation modelling to investigate how European forest growth respond to changes in 11 predictors, including stand characteristics, climate conditions, air and site quality, as well as their interactions. We found that, despite the large environmental gradients encompassed by the forests examined, stand density and age were key drivers of forest growth. We further detected a positive, in some cases non-linear effect of N deposition, most pronounced for beech forests, with a tipping point at ca. 30 kg N ha−1 yr−1. With the exception of a consistent temperature signal on Norway spruce, climate-related predictors and ground-level ozone showed much less generalized relationships with ΔVol. Our results show that, together with the driving forces exerted by stand density and age, N deposition is at least as important as climate to modulate forest growth at continental scale in Europe, with a potential negative effect at sites with high N deposition.

    Impact of the invasive alien topmouth gudgeon (Pseudorasbora parva) and its associated parasite Sphaerothecum destruens on native fish species
    Spikmans, Frank ; Lemmers, Pim ; Camp, Huub J.M. op den; Haren, Emiel van; Kappen, Florian ; Blaakmeer, Anko ; Velde, Gerard van der; Langevelde, Frank van; Leuven, Rob S.E.W. ; Alen, Theo A. van - \ 2020
    Biological Invasions 22 (2020)2. - ISSN 1387-3547 - p. 587 - 601.
    Biodiversity threat - eDNA - Gasterosteus aculeatus - Leucaspius delineatus - Pathogen - Pungitius pungitius

    The Asian cyprinid Pseudorasbora parva is considered to be a major threat to native fish communities and listed as an invasive alien species of European Union concern. Our study aims to gain evidence-based knowledge on the impact of both P. parva and its parasite Sphaerothecum destruens on native fish populations by analysing fish assemblages and body condition of individuals of native fish species in floodplain water bodies that were invaded and uninvaded by P. parva. We explored the use of environmental DNA (eDNA) techniques to detect S. destruens. Prevalence of S. destruens in native fish species was assessed. Fish samplings showed significantly negative correlations between the abundance of P. parva and the native Leucaspius delineatus, and Pungitius pungitius and three biodiversity indices of the fish assemblages (Simpson’s diversity index, Shannon–Wiener index and evenness). Contrastingly, the abundances of the native Gasterosteus aculeatus and P. parva were positively related. In nearly all isolated water bodies with P. parva, this species is outnumbering native fish species. No effect of P. parva presence was found on body condition of native fish species. Sphaerothecum destruens was demonstrated to occur in both P. parva and G. aculeatus. Gasterosteus aculeatus is suggested to be an asymptomatic carrier that can aid the further spread of S. destruens. Analysis of eDNA proved to be a promising method for early detection of S. destruens, here showing that S. destruens presence coincided with P. parva presence. The ongoing invasion of both P. parva and S. destruens is predicted to pose a significant risk to native fish communities.

    Illiberalism and Energy Transitions in Myanmar and Thailand
    Simpson, A. ; Smits, M. - \ 2019
    Georgetown Journal of Asian Affairs 4 (2019)2. - ISSN 2376-8002 - 13 p.
    Over the next century most states are likely to face momentous and potentially catastrophic environmental impacts due to climate change. This has made managing energy policy – traditionally focused on delivering energy security and equitable access – much more strenuous. Governments now face an energy policy trilemma: delivering both traditional energy goals while also minimizing greenhouse gas emissions. Most governments have found it difficult to achieve high levels of all three goals at any one time, particularly within the developing countries of Southeast Asia.
    Undervalued potential of crassulacean acid metabolism for current and future agricultural production
    Davis, Sarah C. ; Simpson, June ; Gil-Vega, Katia Del Carmen ; Niechayev, Nicholas A. ; Tongerlo, Evelien van; Castano, Natalia Hurtado ; Dever, Louisa V. ; Búrquez, Alberto - \ 2019
    Journal of Experimental Botany 70 (2019)22. - ISSN 0022-0957 - p. 6521 - 6537.
    Agave - Opuntia - agroecosystems - aloe - cacti - crops - drought - orchid - pineapple - vanilla - water use efficiency

    The potential for crassulacean acid metabolism (CAM) to support resilient crops that meet demands for food, fiber, fuel, and pharmaceutical products far exceeds current production levels. This review provides background on five families of plants that express CAM, including examples of many species within these families that have potential agricultural uses. We summarize traditional uses, current developments, management practices, environmental tolerance ranges, and economic values of CAM species with potential commercial applications. The primary benefit of CAM in agriculture is high water use efficiency that allows for reliable crop yields even in drought conditions. Agave species, for example, grow in arid conditions and have been exploited for agricultural products in North and South America for centuries. Yet, there has been very little investment in agricultural improvement for most useful Agave varieties. Other CAM species that are already traded globally include Ananas comosus (pineapple), Aloe spp., Vanilla spp., and Opuntia spp., but there are far more with agronomic uses that are less well known and not yet developed commercially. Recent advances in technology and genomic resources provide tools to understand and realize the tremendous potential for using CAM crops to produce climate-resilient agricultural commodities in the future.

    A synthesis of ecosystem management strategies for forests in the face of chronic nitrogen deposition
    Clark, Christopher M. ; Richkus, Jennifer ; Jones, Phillip W. ; Phelan, Jennifer ; Burns, Douglas A. ; Vries, Wim de; Du, Enzai ; Fenn, Mark E. ; Jones, Laurence ; Watmough, Shaun A. - \ 2019
    Environmental Pollution 248 (2019). - ISSN 0269-7491 - p. 1046 - 1058.
    Forest management - Nitrogen deposition - Plant diversity - Soil acidity - Soil nitrogen availability

    Total nitrogen (N) deposition has declined in many parts of the U.S. and Europe since the 1990s. Even so, it appears that decreased N deposition alone may be insufficient to induce recovery from the impacts of decades of elevated deposition, suggesting that management interventions may be necessary to promote recovery. Here we review the effectiveness of four remediation approaches (prescribed burning, thinning, liming, carbon addition) on three indicators of recovery from N deposition (decreased soil N availability, increased soil alkalinity, increased plant diversity), focusing on literature from the U.S. We reviewed papers indexed in the Web of Science since 1996 using specific key words, extracted data on the responses to treatment along with ancillary data, and conducted a meta-analysis using a three-level variance model structure. We found 69 publications (and 2158 responses) that focused on one of these remediation treatments in the context of N deposition, but only 29 publications (and 408 responses) reported results appropriate for our meta-analysis. We found that carbon addition was the only treatment that decreased N availability (effect size: −1.80 to −1.84 across metrics), while liming, thinning, and prescribed burning all tended to increase N availability (effect sizes: +0.4 to +1.2). Only liming had a significant positive effect on soil alkalinity (+10.5%–82.2% across metrics). Only prescribed burning and thinning affected plant diversity, but with opposing and often statistically marginal effects across metrics (i.e., increased richness, decreased Shannon or Simpson diversity). Thus, it appears that no single treatment is effective in promoting recovery from N deposition, and combinations of treatments should be explored. These conclusions are based on the limited published data available, underscoring the need for more studies in forested areas and more consistent reporting suitable for meta-analyses across studies.

    Spatial variation of modelled total, dry and wet nitrogen deposition to forests at global scale
    Schwede, Donna B. ; Simpson, David ; Tan, Jiani ; Fu, Joshua S. ; Dentener, Frank ; Du, Enzai ; Vries, Wim de - \ 2018
    Environmental Pollution 243 (2018)B. - ISSN 0269-7491 - p. 1287 - 1301.
    Dry deposition - Forest biomes - Modelling approach - Nitrogen deposition - Wet deposition

    Forests are an important biome that covers about one third of the global land surface and provides important ecosystem services. Since atmospheric deposition of nitrogen (N) can have both beneficial and deleterious effects, it is important to quantify the amount of N deposition to forest ecosystems. Measurements of N deposition to the numerous forest biomes across the globe are scarce, so chemical transport models are often used to provide estimates of atmospheric N inputs to these ecosystems. We provide an overview of approaches used to calculate N deposition in commonly used chemical transport models. The Task Force on Hemispheric Transport of Air Pollution (HTAP2) study intercompared N deposition values from a number of global chemical transport models. Using a multi-model mean calculated from the HTAP2 deposition values, we map N deposition to global forests to examine spatial variations in total, dry and wet deposition. Highest total N deposition occurs in eastern and southern China, Japan, Eastern U.S. and Europe while the highest dry deposition occurs in tropical forests. The European Monitoring and Evaluation Program (EMEP) model predicts grid-average deposition, but also produces deposition by land use type allowing us to compare deposition specifically to forests with the grid-average value. We found that, for this study, differences between the grid-average and forest specific could be as much as a factor of two and up to more than a factor of five in extreme cases. This suggests that consideration should be given to using forest-specific deposition for input to ecosystem assessments such as critical loads determinations. Estimates of nitrogen deposition to global forests by global models may be a factor of 2 or more higher if the forest-specific deposition is used, compared to the grid cell average value and is on average 12% higher for all global forests.

    Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling
    Raju, Sajan C. ; Lagström, Sonja ; Ellonen, Pekka ; Vos, Willem M. de; Eriksson, Johan G. ; Weiderpass, Elisabete ; Rounge, Trine B. - \ 2018
    Journal of Microbiological Methods 147 (2018). - ISSN 0167-7012 - p. 76 - 86.
    Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.
    Transitions to Energy and Climate Security in Southeast Asia? Civil Society Encounters with Illiberalism in Thailand and Myanmar
    Simpson, Adam ; Smits, Mattijs - \ 2018
    Society & Natural Resources 31 (2018)5. - ISSN 0894-1920 - p. 580 - 598.
    Climate - energy - illiberalism - Myanmar - Thailand
    All states, whether governed by liberal or illiberal regimes, face the prospect of momentous and potentially catastrophic environmental impacts due to climate change. Historically, energy policy has been directed towards simply achieving energy security. This goal has now been significantly complicated by the need to achieve it while minimizing greenhouse gas emissions. Environmental non governmental organizations (ENGOs) could play a crucial role in promoting the transition to energy and climate security but the relative (il)liberalism of the political regime they operate under influences their effectiveness. This article assesses how ENGOs have impacted on the transition to energy and climate security in Myanmar and Thailand, two Southeast Asian countries highly susceptible to climate impacts and characterized by illiberal rule. It finds that the impact of ENGOs was highly dependent on their strategies, tactics and operation, with community-level projects providing a key route to effect change under conditions of extreme illiberalism.
    Meander initiation of a laterally stable river during the Late Holocene
    Candel, J.H.J. ; Kleinhans, M.G. ; Makaske, A. ; Hoek, W.Z. ; Quik, C. ; Wallinga, J. - \ 2017
    In: Conference Programme and Abstract Volume 11th International Conference on Fluvial Sedimentology. - Calgary : University of Calgary - p. 135 - 135.
    Species richness and composition of arbuscular mycorrhizal fungi occurring on eucalypt trees (Eucalyptus camaldulensis Dehnh.) in rainy and dry season
    Khaekhum, S. ; Lumyong, S. ; Kuyper, T.W. ; Boonlue, Sophon - \ 2017
    Current Research in Environmental and Applied Mycology 7 (2017)4. - ISSN 2229-2225 - p. 282 - 292.
    Arbuscular mycorrhizal fungal - Colonization - Eucalyptus camaldulensis - Rhizosphere - Species diversity
    River red gum (Eucalyptus camaldulensis Dehnh.), the most commonly planted eucalypt species globally, has several advantages and is widely used for many purposes, which makes the tree important. Mycorrhizal establishment in eucalyptus has been known for many years, and the benefits of this symbiosis have been commercially explored. The main goal of this research was to assess the diversity and distribution of arbuscular mycorrhizal fungi (AMF) on eucalyptus planted in agricultural fields in the rainy and dry season. Fields were chosen in ten different sites located in four provinces in the northeast of Thailand. Rhizosphere soil and root samples were collected and the number of AMF spores and AMF root colonization were assessed. The number of AMF spores was higher in the rainy season than in the dry season, while AMF root colonization was higher in the dry season than in the rainy season. On the basis of morphological identification of AMF, a total of 35 AMF fungal taxa in eight genera were identified, ten belonging to Acaulospora, one to Dentiscutata, one to Entrophospora, 16 to Glomus, three to Gigaspora, one to Racocetra, two to Scutellospora, and one to Septoglomus. Glomus was the dominant genus followed by Acaulospora. Relative abundance, and frequency of occurrence were higher in the rainy season than in the dry season. Racocetra fulgida was the most common species with a frequency of occurrence of 90% in rainy season, and 80% in dry season. Species richness, Simpson's index of dominance and Shannon-Wiener index of diversity were not significantly different between both seasons.
    Biodiversity analyses for risk assessment of genetically modified potato
    Lazebnik, Jenny ; Dicke, Marcel ; Braak, Cajo J.F. ter; Loon, Joop J.A. van - \ 2017
    Agriculture, Ecosystems and Environment 249 (2017). - ISSN 0167-8809 - p. 196 - 205.
    Biodiversity - Biodiversity index - Environmental risk assessment - Functional groups - Genetically modified crops - Multivariate analysis
    An environmental risk assessment for the introduction of genetically modified crops includes assessing the consequences for biodiversity. In this study arthropod biodiversity was measured using pitfall traps in potato agro-ecosystems in Ireland and The Netherlands over two years. We tested the impact of site, year, potato genotype, and fungicide management regime on arthropod community composition. Three potato genotypes were compared: the cultivar Désirée, susceptible to the late blight pathogen Phytophthora infestans, a genetically modified cisgenic clone of Désirée resistant to P. infestans and the cultivar Sarpo Mira, also resistant to late blight. We aimed to test several ways to measure biodiversity in the context of risk assessment by using both univariate biodiversity indices and multivariate ordination methods, categorizing the pitfall trap catch by taxonomic or functional category. The Shannon-Wiener and Simpson biodiversity indices both showed strong differences between sites, years and potato genotypes, but showed no effects of the fungicide management regime. The effect of genotype was due to cultivar differences between Désirée and Sarpo Mira rather than between the GM-event (A15-31) and its isogenic comparator Désirée. Multivariate permutation analyses and RDA ordination confirmed these findings and also showed interactions between year, site and either genotype or treatment. The added value of the multivariate analysis was that it provided information on the specific arthropod groups or taxa that contributed to community structure. Multivariate analyses are recommended for use as a sensitive method to compare functionally important arthropod groups driving community structure within the framework of environmental risk assessments, or for the process of indicator species selection.
    Modelling long-term impacts of changes in climate, nitrogen deposition and ozone exposure on carbon sequestration of European forest ecosystems
    Vries, Wim de; Posch, Maximilian ; Simpson, David ; Reinds, Gert Jan - \ 2017
    Science of the Total Environment 605-606 (2017). - ISSN 0048-9697 - p. 1097 - 1116.
    Carbon sequestration - Climate change - CO - Forest - Nitrogen deposition - Ozone
    We modelled the effects of past and expected future changes in climate (temperature, precipitation), CO2 concentration, nitrogen deposition (N) and ozone (O3) exposure (phytotoxic ozone dose, POD) on carbon (C) sequestration by European forest ecosystems for the period 1900–2050. Tree C sequestration was assessed by using empirical response functions, while soil C sequestration was simulated with the process-based model VSD, combined with the RothC model. We evaluated two empirical growth responses to N deposition (linear and non-linear) and two O3 exposure relationships (linear function with total biomass or net annual increment). We further investigated an ‘interactive model’ with interactions between drivers and a ‘multiplicative model’, in which the combined effect is the product of individual drivers. A single deposition and climate scenario was used for the period 1900–2050. Contrary to expectations, growth observations at European level for the period 1950–2010 compared better with predictions by the multiplicative model than with the interactive model. This coincides with the fact that carbon responses in kg C ha− 1 yr− 1 per unit change in drivers, i.e. per °C, ppm CO2, kg N ha− 1 yr− 1 and mmol m− 2 yr− 1 POD, are more in line with literature data when using the multiplicative model. Compared to 1900, the estimated European average total C sequestration in both forests and forest soils between 1950 and 2000 increased by 21% in the interactive model and by 41% in the multiplicative model, but observed changes were even higher. This growth increase is expected to decline between 2000 and 2050. The simulated changes between 1950 and 2000 were mainly due to the increase in both N deposition and CO2, while the predicted increases between 2000 and 2050 were mainly caused by the increase in CO2 and temperature, and to lesser extent a decrease in POD, counteracted by reduced N deposition.
    How natural capital delivers ecosystem services : A typology derived from a systematic review
    Smith, A.C. ; Harrison, P.A. ; Pérez Soba, M. ; Archaux, F. ; Blicharska, M. ; Egoh, B.N. ; Erős, T. ; Fabrega Domenech, N. ; György, I. ; Haines-Young, R. ; Li, S. ; Lommelen, E. ; Meiresonne, L. ; Miguel Ayala, L. ; Mononen, L. ; Simpson, G. ; Stange, E. ; Turkelboom, F. ; Uiterwijk, M. ; Veerkamp, C.J. ; Wyllie de Echeverria, V. - \ 2017
    Ecosystem Services 26 (2017). - ISSN 2212-0416 - p. 111 - 126.
    Attribute - Biodiversity - Functional diversity - Land management - Trade-offs - Trait

    There is no unified evidence base to help decision-makers understand how the multiple components of natural capital interact to deliver ecosystem services. We systematically reviewed 780 papers, recording how natural capital attributes (29 biotic attributes and 11 abiotic factors) affect the delivery of 13 ecosystem services. We develop a simple typology based on the observation that five main attribute groups influence the capacity of natural capital to provide ecosystem services, related to: A) the physical amount of vegetation cover; B) presence of suitable habitat to support species or functional groups that provide a service; C) characteristics of particular species or functional groups; D) physical and biological diversity; and E) abiotic factors that interact with the biotic factors in groups A–D. ‘Bundles’ of services can be identified that are governed by different attribute groups. Management aimed at maximising only one service often has negative impacts on other services and on biological and physical diversity. Sustainable ecosystem management should aim to maintain healthy, diverse and resilient ecosystems that can deliver a wide range of ecosystem services in the long term. This can maximise the synergies and minimise the trade-offs between ecosystem services and is also compatible with the aim of conserving biodiversity.

    Transitions to Energy and Climate Security in Thailand
    Simpson, A. ; Smits, M. - \ 2017
    In: Handbook of Transitions to Energy and Climate Security / Looney, Robert E., Abingdon : Routledge - ISBN 9781857437454 - p. 296 - 311.
    Predicting bee community responses to land-use changes : Effects of geographic and taxonomic biases
    Palma, Adriana De; Abrahamczyk, Stefan ; Aizen, Marcelo A. ; Albrecht, Matthias ; Basset, Yves ; Bates, Adam ; Blake, Robin J. ; Boutin, Céline ; Bugter, Rob ; Connop, Stuart ; Cruz-López, Leopoldo ; Cunningham, Saul A. ; Darvill, Ben ; Diekötter, Tim ; Dorn, Silvia ; Downing, Nicola ; Entling, Martin H. ; Farwig, Nina ; Felicioli, Antonio ; Fonte, Steven J. ; Fowler, Robert ; Franzén, Markus ; Goulson, Dave ; Grass, Ingo ; Hanley, Mick E. ; Hendrix, Stephen D. ; Herrmann, Farina ; Herzog, Felix ; Holzschuh, Andrea ; Jauker, Birgit ; Kessler, Michael ; Knight, M.E. ; Kruess, Andreas ; Lavelle, Patrick ; Féon, Violette Le; Lentini, Pia ; Malone, Louise A. ; Marshall, Jon ; Pachón, Eliana Martínez ; McFrederick, Quinn S. ; Morales, Carolina L. ; Mudri-Stojnic, Sonja ; Nates-Parra, Guiomar ; Nilsson, Sven G. ; Öckinger, Erik ; Osgathorpe, Lynne ; Parra-H, Alejandro ; Peres, Carlos A. ; Persson, Anna S. ; Petanidou, Theodora ; Poveda, Katja ; Power, Eileen F. ; Quaranta, Marino ; Quintero, Carolina ; Rader, Romina ; Richards, Miriam H. ; Roulston, Tai ; Rousseau, Laurent ; Sadler, Jonathan P. ; Samnegård, Ulrika ; Schellhorn, Nancy A. ; Schüepp, Christof ; Schweiger, Oliver ; Smith-Pardo, Allan H. ; Steffan-Dewenter, Ingolf ; Stout, Jane C. ; Tonietto, Rebecca K. ; Tscharntke, Teja ; Tylianakis, Jason M. ; Verboven, Hans A.F. ; Vergara, Carlos H. ; Verhulst, Jort ; Westphal, Catrin ; Yoon, Hyung Joo ; Purvis, Andy - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 14 p.

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

    After mastery: Insights from practice theorizing
    Yanow, D. - \ 2015
    In: The emergence of novelty in organizations / Garud, Raghu, Simpson, Barbara, Langley, Ann, Tsoukas, Haridimos, Oxford Academic - ISBN 9780198728313 - p. 272 - 317.
    Much of the practice studies literature, especially in a phenomenological vein, focuses on novices learning, acquiring what the master “has.” This leaves two under-theorized areas: a “life-cyle” of practitioner and practicing phases, including pre-novice and post-mastery; and forms of practice-learning across these, including that characteristic of mastery itself. In conceiving of themselves as all-knowing and then “rushing to judgment” or making “premature diagnoses,” for instance, masters seem to lose their ability to inquire. Might learning to become a master contribute to some things being “unlearned” which are key to good practicing in being a master, thereby generating problems in the practice? This chapter elucidates the characteristics of novice-learning in organizational settings of various sorts. It then frames several problems in need of further theorizing, including the changing character of practitioners’ awareness of “tools” across the practice life-cycle and the need for work-practice studies to theorize about practices entailing human “tools.”
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