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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Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide
Willems, Lione ; Westerveld, Larissa Van; Roberts, Stefan ; Weitzhandler, Isaac ; Calcines Cruz, Carlos ; Hernandez-Garcia, Armando ; Chilkoti, Ashutosh ; Mastrobattista, Enrico ; Oost, John Van Der; Vries, Renko De - \ 2019
Biomacromolecules 20 (2019)10. - ISSN 1525-7797 - p. 3641 - 3647.

Consensus motifs for sequences of both crystallizable and amorphous blocks in silks and natural structural analogues of silks vary widely. To design novel silklike polypeptides, an important question is therefore how the nature of either the crystallizable or the amorphous block affects the self-assembly and resulting physical properties of silklike polypeptides. We address herein the influence of the amorphous block on the self-assembly of a silklike polypeptide that was previously designed to encapsulate single DNA molecules into rod-shaped viruslike particles. The polypeptide has a triblock architecture, with a long N-terminal amorphous block, a crystallizable midblock, and a C-terminal DNA-binding block. We compare the self-assembly behavior of a triblock with a very hydrophilic collagen-like amorphous block (GXaaYaa)132 to that of a triblock with a less hydrophilic elastin-like amorphous block (GSGVP)80. The amorphous blocks have similar lengths and both adopt a random coil structure in solution. Nevertheless, atomic force microscopy revealed significant differences in the self-assembly behavior of the triblocks. If collagen-like amorphous blocks are used, there is a clear distinction between very short polypeptide-only fibrils and much longer fibrils with encapsulated DNA. If elastin-like amorphous blocks are used, DNA is still encapsulated, but the polypeptide-only fibrils are now much longer and their size distribution partially overlaps with that of the encapsulated DNA fibrils. We attribute the difference to the more hydrophilic nature of the collagen-like amorphous block, which more strongly opposes the growth of polypeptide-only fibrils than the elastin-like amorphous blocks. Our work illustrates that differences in the chemical nature of amorphous blocks can strongly influence the self-assembly and hence the functionality of engineered silklike polypeptides.

Exploring the munchies: An online survey of users’ experiences of cannabis effects on appetite and the development of a Cannabinoid Eating Experience Questionnaire
Roberts, Carl A. ; Jager, Gerry ; Christiansen, Paul ; Kirkham, Tim C. - \ 2019
Journal of Psychopharmacology 33 (2019)9. - ISSN 0269-8811 - 11 p.
Appetite - cannabinoids - cannabis - munchies - survey

Background: Cannabis intoxication is commonly reported to increase appetite and enhance appreciation of food (the ‘munchies’). These effects are attributed to activation of the endocannabinoid system. However, the psychological changes that underlie these phenomena are under-researched. We report here the results of an extensive online survey of cannabis users with an exploratory Cannabinoid Eating Experience Questionnaire (CEEQ). Method: Frequent cannabis users completed a 46-item questionnaire about their eating behaviour under the influence of cannabis. An English-speaking sample (n=591) provided data for the initial exploratory validation of the scale. A second Dutch-language survey (n=163) was used for confirmatory factor analysis. Test-retest reliability was based on a third English-speaking sample (n=40) who completed the revised, 28-item CEEQ twice across 2 weeks. Results: Principal components analysis provided a two-factor solution. Factor 1 (hedonic) comprised 14 items that related primarily to the enjoyment and altered sensory aspects of eating. Factor 2 (appetitive) comprised a further 14 items related to motivational factors that instigate or promote eating. The two-factor structure was supported by confirmatory factor analysis. Both the hedonic and appetitive subscales had good internal reliability (α=0.92 for each subscale, in two independent samples). Good test-retest reliability was obtained for the revised 28-item questionnaire (ps<.01 for Total CEEQ and each subscale). Conclusion: The Cannabinoid Eating Experience Questionnaire provided a valid, reliable assessment of the psychological features of cannabis-induced alterations to appetite. Our data confirm that cannabis principally influences the motivational factors that lead to the initiation of eating and the hedonic factors implicated in maintaining eating.

Management of Malnutrition in Older Patients—Current Approaches, Evidence and Open Questions
Volkert, Dorothee ; Beck, Anne Marie ; Cederholm, Tommy ; Cereda, Emanuele ; Cruz-Jentoft, Alfonso ; Goisser, Sabine ; Groot, Lisette de; Großhauser, Franz ; Kiesswetter, Eva ; Norman, Kristina ; Pourhassan, Maryam ; Reinders, Ilse ; Roberts, Helen C. ; Rolland, Yves ; Schneider, Stéphane M. ; Sieber, Cornel C. ; Thiem, Ulrich ; Visser, Marjolein ; Wijnhoven, Hanneke A.H. ; Wirth, Rainer - \ 2019
Journal of Clinical Medicine 8 (2019)7. - ISSN 2077-0383 - 16 p.
Malnutrition is widespread in older people and represents a major geriatric syndrome with multifactorial etiology and severe consequences for health outcomes and quality of life. The aim of the present paper is to describe current approaches and evidence regarding malnutrition treatment and to highlight relevant knowledge gaps that need to be addressed. Recently published guidelines of the European Society for Clinical Nutrition and Metabolism (ESPEN) provide a summary of the available evidence and highlight the wide range of different measures that can be taken—from the identification and elimination of potential causes to enteral and parenteral nutrition—depending on the patient’s abilities and needs. However, more than half of the recommendations therein are based on expert consensus because of a lack of evidence, and only three are concern patient-centred outcomes. Future research should further clarify the etiology of malnutrition and identify the most relevant causes in order to prevent malnutrition. Based on limited and partly conflicting evidence and the limitations of existing studies, it remains unclear which interventions are most effective in which patient groups, and if specific situations, diseases or etiologies of malnutrition require specific approaches. Patient-relevant outcomes such as functionality and quality of life need more attention, and research methodology should be harmonised to allow for the comparability of studies.
Convergent evolution of hetero-oligomeric cellulose synthesis complexes in mosses and seed plants
Li, Xingxing ; Speicher, Tori L. ; Dees, Dianka C.T. ; Mansoori, Nasim ; McManus, John B. ; Tien, Ming ; Trindade, Luisa M. ; Wallace, Ian S. ; Roberts, Alison W. - \ 2019
The Plant Journal (2019). - ISSN 0960-7412
cell wall - cellulose - cellulose synthase - cellulose synthesis complex - convergent evolution - Physcomitrella patens

In seed plants, cellulose is synthesized by rosette-shaped cellulose synthesis complexes (CSCs) that are obligate hetero-oligomeric, comprising three non-interchangeable cellulose synthase (CESA) isoforms. The moss Physcomitrella patens has rosette CSCs and seven CESAs, but its common ancestor with seed plants had rosette CSCs and a single CESA gene. Therefore, if P. patens CSCs are hetero-oligomeric, then CSCs of this type evolved convergently in mosses and seed plants. Previous gene knockout and promoter swap experiments showed that PpCESAs from class A (PpCESA3 and PpCESA8) and class B (PpCESA6 and PpCESA7) have non-redundant functions in secondary cell wall cellulose deposition in leaf midribs, whereas the two members of each class are redundant. Based on these observations, we proposed the hypothesis that the secondary class A and class B PpCESAs associate to form hetero-oligomeric CSCs. Here we show that transcription of secondary class A PpCESAs is reduced when secondary class B PpCESAs are knocked out and vice versa, as expected for genes encoding isoforms that occupy distinct positions within the same CSC. The class A and class B isoforms co-accumulate in developing gametophores and co-immunoprecipitate, suggesting that they interact to form a complex in planta. Finally, secondary PpCESAs interact with each other, whereas three of four fail to self-interact when expressed in two different heterologous systems. These results are consistent with the hypothesis that obligate hetero-oligomeric CSCs evolved independently in mosses and seed plants and we propose the constructive neutral evolution hypothesis as a plausible explanation for convergent evolution of hetero-oligomeric CSCs.

Inducible Fibril Formation of Silk-Elastin Diblocks
Willems, Lione ; Roberts, Stefan ; Weitzhandler, Isaac ; Chilkoti, Ashutosh ; Mastrobattista, Enrico ; Oost, John Van Der; Vries, Renko De - \ 2019
ACS Omega 4 (2019)5. - ISSN 2470-1343 - p. 9135 - 9143.

Silk-elastin block copolymers have such physical and biological properties that make them attractive biomaterials for applications ranging from tissue regeneration to drug delivery. Silk-elastin block copolymers that only assemble into fibrils at high concentrations can be used for a template-induced fibril assembly. This can be achieved by additionally including template-binding blocks that promote high local concentrations of polymers on the template, leading to a template-induced fibril assembly. We hypothesize that template-inducible silk-fibril formation, and hence high critical concentrations for fibril formation, requires careful tuning of the block lengths, to be close to a critical set of block lengths that separates fibril forming from nonfibril forming polymer architectures. Therefore, we explore herein the impact of tuning block lengths for silk-elastin diblock polypeptides on fibril formation. For silk-elastin diblocks ESm-SQn, in which the elastin pentamer repeat is ES = GSGVP and the crystallizable silk octamer repeat is SQ = GAGAGAGQ, we find that no fibril formation occurs for n = 6 but that the n = 10 and 14 diblocks do show concentration-dependent fibril formation. For n = 14 diblocks, no effect is observed of the length m (with m = 40, 60, 80) of the amorphous block on the lengths of the fibrils. In contrast, for the n = 10 diblocks that are closest to the critical boundary for fibril formation, we find that long amorphous blocks (m = 80) oppose the growth of fibrils at low concentrations, making them suitable for engineering template-inducible fibril formation.

Improving environmental risk assessments of chemicals: Steps towards evidence-based ecotoxicology
Martin, Olwenn V. ; Adams, Julie ; Beasley, Amy ; Belanger, Scott ; Breton, Roger L. ; Brock, Theo C.M. ; Buonsante, Vito A. ; Galay Burgos, Malyka ; Green, John ; Guiney, Patrick D. ; Hall, Tilghman ; Hanson, Mark ; Harris, Meagan J. ; Henry, Tala R. ; Huggett, Duane ; Junghans, Marion ; Laskowski, Ryszard ; Maack, Gerd ; Moermond, Caroline T.A. ; Panter, Grace ; Pease, Anita ; Poulsen, Veronique ; Roberts, Mike ; Rudén, Christina ; Schlekat, Christian E. ; Schoeters, Ilse ; Solomon, Keith R. ; Staveley, Jane ; Stubblefield, Bill ; Sumpter, John P. ; Warne, Michael S.J. ; Wentsel, Randall ; Wheeler, James R. ; Wolff, Brian A. ; Yamazaki, Kunihiko ; Zahner, Holly ; Ågerstrand, Marlene - \ 2019
Environment International 128 (2019). - ISSN 0160-4120 - p. 210 - 217.
Chemical safety - Decision-making - Ecological risk assessment - Ecotoxicology - Environmental risk assessment - Evidence-based
Growth rings of Brazil nut trees (Bertholletia excelsa) as a living record of historical human disturbance in Central Amazonia
Caetano Andrade, Victor L. ; Flores, Bernardo M. ; Levis, Carolina ; Clement, Charles R. ; Roberts, Patrick ; Schöngart, Jochen - \ 2019
PLoS ONE 14 (2019)4. - ISSN 1932-6203

The Brazil nut tree (Bertholletia excelsa) is an iconic and economically valuable species that dominates vast swathes of the Amazon Basin. This species seems to have been an important part of human subsistence strategies in the region from at least the Early Holocene, and its current distribution may be a legacy of past human settlement. Because B. excelsa is a long-lived pioneer tree it requires natural or human disturbances to increase light availability in the understory for a successful establishment. However, it remains unclear how the long-term population dynamics of this species have been shaped by pre-colonial and post-colonial human practices. Here, we use tree-ring analyses to look at changes in growing conditions over the past 400 years in a Brazil nut tree population in Central Amazonia. We identify changes in tree recruitment and growth rates associated not only with regional climatic variability, but also major political and socio-economic activities recorded by historical documents in the vicinity of Manaus. We demonstrate that the expansion of a post-colonial political center (Manaus) from the middle of the 18 th century onwards coincided with a reduction in recruitment of B. excelsa. We argue that this hiatus suggests the interruption of indigenous management practices, probably due to the collapse of pre-Columbian societies. A second recruitment pulse, and unprecedented cycles of growth release and suppression, aligns with a shift to modern exploitation of the forest into the 20 th century. Our findings shed light on how past histories of human-forest interactions can be revealed by the growth rings of trees in Amazonia. Future interdisciplinary analysis of these trees should enable more detailed investigation of how human forest management has changed in this part of the world, through pre-colonial, colonial, and industrial periods of human activity, with potential implications for conservation.

The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions
Brouwer, Michael S.M. ; Jurburg, Stephanie D. ; Harders, Frank ; Kant, Arie ; Mevius, Dik J. ; Roberts, Adam P. ; Bossers, Alex - \ 2019
Plasmid 102 (2019). - ISSN 0147-619X - p. 51 - 55.

One of the factors that can affect conjugation of IncI1 plasmids, amongst others, is the genetic region known as the shufflon. This multiple inversion system modifies the pilus tip proteins used during conjugation, thus affecting the affinity for different recipient cells. Although recombination is known to occur in in vitro conditions, little is known about the regulation and the extent of recombination that occurs. To measure the recombination of the shufflon, we have amplified the entire shufflon region and sequenced the amplicons using nanopore long-read sequencing. This method was effective to determine the order of the segments of the shufflon and allow for the analysis of the shufflon variants that are present in a heterogeneous pool of templates. Analysis was performed over different growth phases and after addition of cefotaxime. Furthermore, analysis was performed in different E. coli host cells to determine if recombination is likely to be influenced. Recombination of the shufflon was constantly ongoing in all conditions that were measured, although no differences in the amount of different shufflon variants or the rate at which novel variants were formed could be found. As previously reported, some variants were abundant in the population while others were scarce. This leads to the conclusion that the shufflon is continuously recombining at a constant rate, or that the method used here was not sensitive enough to detect differences in this rate. For one of the plasmids, the host cell appeared to have an effect on the specific shufflon variants that were formed which were not predominant in another host, indicating that host factors may be involved. As previously reported, the pilV-A and pilV-A' ORFs are formed at higher frequencies than other pilV ORFs. These results demonstrate that the recombination that occurs within the shufflon is not random. While any regulation of the shufflon affected by these in vitro conditions could not be revealed, the method of amplifying large regions for long-read sequencing for the analysis of multiple inversion systems proved effective.

What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
Food and Energy Security 8 (2019)1. - ISSN 2048-3694

Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

The diverse economy: feminism, Capitalocentrism and postcapitalist futures
McKinnon, Katherine ; Dombroski, Kelly ; Morrow, Oona - \ 2018
In: Handbook on the International Political Economy of Gender / Elias, Juanita, Roberts, Adrienne, Edward Elgar (Social and Political Science 2018 ) - ISBN 9781783478835 - p. 335 - 350.
Feminist economic geography has been a rich site for exploring issues of political economy and gender. In this chapter the authors explore the contributions of feminist economic geographers to rethinking economy. Diverse economies thinking reveals diversity in existing economic practices, broadening our view of what is important and viable economic activity. This includes recognizing and valuing care work and the household, and recognizing diversity in forms of economic transactions, labour and enterprise through which people around the world secure their livelihoods. Alternative markets, unpaid work and noncapitalist enterprises all come into view as vital parts of our economy. Community economies scholarship begins by rethinking ‘the economy’ and the discourses that shape expectations of how globalization and capitalism function. Building on the work of J.K. Gibson-Graham, the diverse economies framework informs the work of others in the ‘Community Economies Collective’ and the ‘Community Economies Research Network’.
Risk assessment paradigm for glutamate
Roberts, Ashley ; Lynch, Barry ; Rietjens, Ivonne M.C.M. - \ 2018
Annals of Nutrition & Metabolism 73 (2018)Suppl 5. - ISSN 0250-6807 - p. 53 - 64.
Acceptable daily intake - Glutamate - Macronutrient - Risk assessment

Background: Re-evaluation of the use of glutamic acid and glutamate salts (referred to as glutamate hereafter) by the European Food Safety Authority (EFSA) proposed a group acceptable daily intake (ADI) of 30 mg/kg body weight (bw)/day. Summary: This ADI is below the normal dietary intake, while even intake of free glutamate by breast-fed babies can be above this ADI. In addition, the pre-natal developmental toxicity study selected by EFSA, has never been used by regulatory authorities worldwide for the safety assessment of glutamate despite it being available for nearly 40 years. Also, the EFSA ignored that toxicokinetic data provide support for eliminating the use of an uncertainty factor for interspecies differences in kinetics. Key Messages: A 3-generation reproductive toxicity study in mice that includes extensive brain histopathology, provides a better point of departure showing no effects up to the highest dose tested of 6,000 mg/kg bw/day. Furthermore, kinetic data support use of a compound-specific uncertainty factor of 25 instead of 100. Thus, an ADI of at least 240 mg/kg bw/day would be indicated. In fact, there is no compelling evidence to indicate that the previous ADI of "not specified" warrants any change.

Introduction and summary of the 2018 dietary glutamate workshop
Cynober, Luc ; Fernstrom, John D. ; Koletzko, Berthold ; Rietjens, Ivonne M.C.M. ; Roberts, Ashley ; Tennant, David R. ; Tomé, Daniel ; Vorhees, Charles V. - \ 2018
Annals of Nutrition & Metabolism 73 (2018)Suppl 5. - ISSN 0250-6807 - 4 p.
Amino acid - European food safety authority - Glutamate - Risk assessment - Toxicology

The 2018 Dietary Glutamate Workshop was organized and sponsored by the International Glutamate Technical Committee to provide a platform for a broad expert discussion on all relevant aspects of glutamate metabolism and safety in human nutrition. The participants reached a consensus with previous safety evaluations conducted by the global expert bodies, but contradicted the 2017 re-evaluation of dietary glutamates by the European Food Safety Authority, which proposed a group acceptable daily intake (ADI) of 30 mg/kg body weight per day. The participants of the Workshop concluded that the present knowledge on metabolism, kinetics, developmental and general toxicity of dietary glutamates did not warrant a change in the previous ADI of "not specified."

Negative hydrostatic pressure is an unnoticed but significant source of contamination in tissue culture
Askari, N. ; Klerk, G.J. de - \ 2018
In: Proceedings of the 2017 Annual Meeting of the International Plant Propagators' Society. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462612099 - p. 85 - 87.
Plants are characterized by a negative hydrostatic pressure, brought about by transpiration and by capillary activity of xylem vessels (Taiz and Zeiger, 2010). Because of this, a stem that is being cut sucks up what is nearby. Often this is air but it may also be liquid. The diameter of the xylem vessels is 50-100 μm, so when the liquid contains bacteria (that are typically 0.5-5.0 μm), they will enter deeply into the tissue (Askari et al., 2014; De Klerk et al., 2014). To our knowledge, this alleged source of contamination has never been examined.
Plant Desiccation Tolerance: A Survival Strategy with Exceptional Prospects for Climate‐Smart Agriculture
Hilhorst, H.W.M. ; Farrant, Jill M. - \ 2018
In: Annual Plant Reviews Online / Roberts, Jerry, Wiley - ISBN 9781119312994 - 27 p.
Drought is one of the main threats to agriculture worldwide because most of our staple crops are not very tolerant to dehydration stress. Some 135 species of angiosperms, however, are extremely tolerant of severe drought. These so‐called resurrection plants are desiccation tolerant because they can withstand drying to water contents below 0.1 gram water per gram dry weight and remain viable for extended periods of time, similar to most seeds. Indeed, recent research has shown that mechanisms of desiccation tolerance of different species, be it vegetative tissues or seeds, utilise the same basic ingredients, including anti‐oxidants, chaperone proteins, and specific carbohydrates. However, there is species‐specific behaviour, related to habitat, e.g. in cell wall properties and the manner in which photo‐oxidative damage is prevented upon drying. Crop plants produce desiccation‐tolerant seeds and, hence, possess the genomic information required for desiccation tolerance, but this is exclusively expressed in the seeds. Elucidation of the mechanisms of desiccation tolerance may enable the ‘release’ of this characteristic in the leaves, stems, and roots.
Plant domestication decreases both constitutive and induced chemical defences by direct selection against defensive traits
Moreira, Xoaquín ; Abdala-Roberts, Luis ; Gols, Rieta ; Francisco, Marta - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Studies reporting domestication effects on plant defences have focused on constitutive, but not on induced defences. However, theory predicts a trade-off between constitutive (CD) and induced defences (ID), which intrinsically links both defensive strategies and argues for their joint consideration in plant domestications studies. We measured constitutive and induced glucosinolates in wild cabbage (Brassica oleracea ssp. oleracea) and two domesticated varieties (B. oleracea var. acephala and B. oleracea var. capitata) in which the leaves have been selected to grow larger. We also estimated leaf area (proxy of leaf size) to assess size-defence trade-offs and whether domestication effects on defences are indirect via selection for larger leaves. Both CD and ID were lower in domesticated than in wild cabbage and they were negatively correlated (i.e. traded off) in all of the cabbage lines studied. Reductions in CD were similar in magnitude for leaves and stems, and CD and leaf size were uncorrelated. We conclude that domestication of cabbage has reduced levels not only constitutive defences but also their inducibility, and that reductions in CD may span organs not targeted by breeding. This reduction in defences in domesticated cabbage is presumably the result of direct selection rather than indirect effects via trade-offs between size and defences.

Development and analysis of the Soil Water Infiltration Global database
Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

Data challenges and opportunities for environmental management of North Sea oil and gas decommissioning in an era of blue growth
Murray, Fiona ; Needham, Katherine ; Gormley, Kate ; Rouse, Sally ; Coolen, Joop W.P. ; Billett, David ; Dannheim, Jennifer ; Birchenough, Silvana N.R. ; Hyder, Kieran ; Heard, Richard ; Ferris, Joseph S. ; Holstein, Jan M. ; Henry, Lea-Anne ; Mcmeel, Oonagh ; Calewaert, Jan-Bart ; Roberts, J.M. - \ 2018
Marine Policy 97 (2018). - ISSN 0308-597X - p. 130 - 138.
Maritime industries routinely collect critical environmental data needed for sustainable management of marine ecosystems, supporting both the blue economy and future growth. Collating this information would provide a valuable resource for all stakeholders. For the North Sea, the oil and gas industry has been a dominant presence for over 50 years that has contributed to a wealth of knowledge about the environment. As the industry begins to decommission its offshore structures, this information will be critical for avoiding duplication of effort in data collection and ensuring best environmental management of offshore activities. This paper summarises the outcomes of a Blue Growth Data Challenge Workshop held in 2017 with participants from: the oil and gas industry; the key UK regulatory and management bodies for oil and gas decommissioning; open access data facilitators; and academic and research institutes. Here, environmental data collection and archiving by oil and gas operators in the North Sea are described, alongside how this compares to other offshore industries; what the barriers and opportunities surrounding environmental data sharing are; and how wider data sharing from offshore industries could be achieved. Five primary barriers to data sharing were identified: 1) Incentives, 2) Risk Perception, 3) Working Cultures, 4) Financial Models, and 5) Data Ownership. Active and transparent communication and collaboration between stakeholders including industry, regulatory bodies, data portals andacademic institutions will be key to unlocking the data that will be critical to informing responsible decommissioning decisions for offshore oil and gas structures in the North Sea.
Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Analysing the impacts of air quality policies on ecosystem services; a case study for Telemark, Norway
Hein, L. ; White, L. ; Miles, A. ; Roberts, P. - \ 2018
Journal of Environmental Management 206 (2018). - ISSN 0301-4797 - p. 650 - 663.
Air pollution - Ecosystem services - Nitrogen deposition - Norway
There is an increasing interest in considering the effects of air pollution on ecosystem services supply in order to enhance cost-benefit analyses of air pollution policies. This paper presents a generic, conceptual approach that can be used to link atmospheric deposition of air pollutants to ecosystem services supply and societal benefits. The approach is applied in a case study in the Telemark county of Norway. First, we examine the potential effects of four European air quality policy scenarios on N deposition in the ecosystems of this county. Second, we analyse the subsequent impacts on the supply of three ecosystem services: carbon sequestration, timber production and biodiversity. Changes in the supply of the first two services are analysed in both physical and monetary units, biodiversity effects are only analysed in physical terms. The scenarios derive from work conducted in the context of the European National Emissions Ceilings Directive. In the 2010 base case the benefits of carbon sequestration are estimated at 13 million euro per year and the value of timber harvesting at 2.9 million euro per year. Under the examined policy scenarios aiming to reduce nitrogen emissions the societal benefits resulting from these two ecosystem services in Telemark are found to be reduced; the scenarios have little effect on terrestrial biodiversity. Such results cannot be scaled up, individual ecosystem services respond differently to changes in air pollution depending upon type of pollutant, type of ecosystem, type of service, and the magnitude of change. The paper further presents an analysis of the uncertainties that need to be considered in linking air pollution and ecosystem services including those in deposition rates, ecosystem responses, human responses and in the values of ecosystem services. Our conceptual approach is also useful for larger scale analysis of air pollution effects on ecosystem services, for example at national or potentially European scale.
Dimensions of biodiversity loss : Spatial mismatch in land-use impacts on species, functional and phylogenetic diversity of European bees
Palma, Adriana De; Kuhlmann, Michael ; Bugter, Rob ; Ferrier, Simon ; Hoskins, Andrew J. ; Potts, Simon G. ; Roberts, Stuart P.M. ; Schweiger, Oliver ; Purvis, Andy - \ 2017
Diversity and Distributions 23 (2017)12. - ISSN 1366-9516 - p. 1435 - 1446.
agricultural intensification - land-use conversion - non-random species loss - pollinator diversity
Aim: Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity. Location: One Thousand four hundred and forty six sites across Europe. Methods: We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land-use characteristics including land-use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map—at a scale of approximately 1 km2—the losses in diversity relative to semi-natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi-natural/natural vegetation). Results: We show that—relative to the predicted local diversity in uninhabited semi-natural/natural habitat—half of all EU27 countries have lost over 10% of their average local species diversity and two-thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher-intensity cropland than in semi-natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe. Main conclusions: These results highlight the importance of exploring multiple measures of diversity when prioritizing and evaluating conservation actions, as species-diverse assemblages may be phylogenetically and functionally impoverished, potentially threatening pollination service provision.
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