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Efficient inference of homologs in large eukaryotic pan-proteomes
Sheikhizadeh Anari, Siavash ; Ridder, Dick de; Schranz, M.E. ; Smit, Sandra - \ 2018
BMC Bioinformatics 19 (2018)1. - ISSN 1471-2105 - 11 p.
Homologous genes - k-mer - Orthology - Pan-genome - Protein similarity

BACKGROUND: Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data.

RESULTS: To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa.

CONCLUSIONS: We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at as an extension to our pan-genomic analysis tool, PanTools.

Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjancenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 1186 - 1186.

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

De duurzaamheid van de Nederlandse landbouw : 1950 – 2015 – 2040
Smit, Meino - \ 2018
University. Promotor(en): Jandouwe van der Ploeg. - Wageningen : Wageningen University - ISBN 9789463432894 - 214
Toward sustainable environmental quality : Priority research questions for Europe
Brink, Paul J. Van den; Boxall, Alistair B.A. ; Maltby, Lorraine ; Brooks, Bryan W. ; Rudd, Murray A. ; Backhaus, Thomas ; Spurgeon, David ; Verougstraete, Violaine ; Ajao, Charmaine ; Ankley, Gerald T. ; Apitz, Sabine E. ; Arnold, Kathryn ; Brodin, Tomas ; Cañedo-Argüelles, Miguel ; Chapman, Jennifer ; Corrales, Jone ; Coutellec, Marie Agnès ; Fernandes, Teresa F. ; Fick, Jerker ; Ford, Alex T. ; Giménez Papiol, Gemma ; Groh, Ksenia J. ; Hutchinson, Thomas H. ; Kruger, Hank ; Kukkonen, Jussi V.K. ; Loutseti, Stefania ; Marshall, Stuart ; Muir, Derek ; Ortiz-Santaliestra, Manuel E. ; Paul, Kai B. ; Rico, Andreu ; Rodea-Palomares, Ismael ; Römbke, Jörg ; Rydberg, Tomas ; Segner, Helmut ; Smit, Mathijs ; Gestel, Cornelis A.M. van; Vighi, Marco ; Werner, Inge ; Zimmer, Elke I. ; Wensem, Joke van - \ 2018
Environmental Toxicology and Chemistry 37 (2018)9. - ISSN 0730-7268 - p. 2281 - 2295.
Chemical management - Environmental risk assessment - Global megatrends - Key questions exercise - Sustainability

The United Nations' Sustainable Development Goals have been established to end poverty, protect the planet, and ensure prosperity for all. Delivery of the Sustainable Development Goals will require a healthy and productive environment. An understanding of the impacts of chemicals which can negatively impact environmental health is therefore essential to the delivery of the Sustainable Development Goals. However, current research on and regulation of chemicals in the environment tend to take a simplistic view and do not account for the complexity of the real world, which inhibits the way we manage chemicals. There is therefore an urgent need for a step change in the way we study and communicate the impacts and control of chemicals in the natural environment. To do this requires the major research questions to be identified so that resources are focused on questions that really matter. We present the findings of a horizon-scanning exercise to identify research priorities of the European environmental science community around chemicals in the environment. Using the key questions approach, we identified 22 questions of priority. These questions covered overarching questions about which chemicals we should be most concerned about and where, impacts of global megatrends, protection goals, and sustainability of chemicals; the development and parameterization of assessment and management frameworks; and mechanisms to maximize the impact of the research. The research questions identified provide a first-step in the path forward for the research, regulatory, and business communities to better assess and manage chemicals in the natural environment.

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. - \ 2018
Nature Microbiology 3 (2018)8. - ISSN 2058-5276 - p. 898 - 908.

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.

Associations between pneumonia and residential distance to livestock farms over a five-year period in a large population-based study
Kalkowska, Dominika A. ; Boender, Gert J. ; Smit, Lidwien A.M. ; Baliatsas, Christos ; Yzermans, Joris ; Heederik, Dick J.J. ; Hagenaars, Thomas J. - \ 2018
PLoS One 13 (2018)7. - ISSN 1932-6203

In a recent study of electronic health records (EHR) of general practitioners in a livestock-dense area in The Netherlands in 2009, associations were found between residential distance to poultry farms and the occurrence of community-acquired pneumonia (CAP). In addition, in a recent cross-sectional study in 2494 adults in 2014/2015 an association between CAP and proximity to goat farms was observed. Here, we extended the 2009 EHR analyses across a wider period of time (2009–2013), a wider set of health effects, and a wider set of farm types as potential risk sources. A spatial (transmission) kernel model was used to investigate associations between proximity to farms and CAP diagnosis for the period from 2009 to 2013, obtained from EHR of in total 140,059 GP patients. Also, associations between proximity to farms and upper respiratory infections, inflammatory bowel disease, and (as a control disease) lower back pain were analysed. Farm types included as potential risk sources in these analyses were cattle, (dairy) goats, mink, poultry, sheep, and swine. The previously found association between CAP occurrence and proximity to poultry farms was confirmed across the full 5-year study period. In addition, we found an association between increased risk for pneumonia and proximity to (dairy) goat farms, again consistently across all years from 2009 to 2013. No consistent associations were found for any of the other farm types (cattle, mink, sheep and swine), nor for the other health effects considered. On average, the proximity to poultry farms corresponds to approximately 119 extra patients with CAP each year per 100,000 people in the research area, which accounts for approximately 7.2% extra cases. The population attributable risk percentage of CAP cases in the research area attributable to proximity to goat farms is approximately 5.4% over the years 2009–2013. The most probable explanation for the association of CAP with proximity to poultry farms is thought to be that particulate matter and its components are making people more susceptible to respiratory infections. The causes of the association with proximity to goat farms is still unclear. Although the 2007–2010 Q-fever epidemic in the area probably contributed Q-fever related pneumonia cases to the observed additional cases in 2009 and 2010, it cannot explain the association found in later years 2011–2013.

Study on Producer Organisations and their activities in the olive oil, beef and veal and arable crops sectors
Cronin, E. ; Selten, M. ; Galen, M.A. van; Bijman, J. ; Viaggi, D. ; Arevalo, I. ; Smit, A.B. ; Ruijs, M.N.A. ; Meulen, B.M.J. van der; Vollaro, M. - \ 2018
Brussels : European Union - ISBN 9789279859038 - 163
The ‘Study on Producer Organisations and their activities in the olive oil, beef and veal and arable crops sectors’ aims to deliver an analysis of producer organisations from these three sectors. The analysis is mainly based on a survey conducted for a representative sample of 203 POs and 23 APOs. The sampling of the surveyed organisations builds on an inventory of existing organisations in the 28 Member States. The study reveals that there are many more non-recognised POs than recognised POs: there are estimated to be over five times as many non-recognised POs as there are recognised POs. The survey results confirm that producer organisations engaged in commercial activities also carry out other potentially “efficiency enhancing activities” (i.e. organisation of quality control, distribution and transport, input procurement, packaging, waste management etc.). The most important perceived benefits for the farmers include (i) market and price stability, (ii) reduced costs and economies of scale, (iii) higher price and ensuring a fair standard of living for the members and (iv) improved market access. The activities of producer organisations are widely perceived by survey respondents as contributing positively to CAP objectives.
Global-change effects on early-stage decomposition processes in tidal wetlands-implications from a global survey using standardized litter
Mueller, Peter ; Schile-Beers, Lisa M. ; Mozdzer, Thomas J. ; Chmura, Gail L. ; Dinter, Thomas ; Kuzyakov, Yakov ; Groot, Alma V. de; Esselink, Peter ; Smit, Christian ; Alpaos, Andrea D'; Ibáñez, Carles ; Lazarus, Magdalena ; Neumeier, Urs ; Johnson, Beverly J. ; Baldwin, Andrew H. ; Yarwood, Stephanie A. ; Montemayor, Diana I. ; Yang, Zaichao ; Wu, Jihua ; Jensen, Kai ; Nolte, Stefanie - \ 2018
Biogeosciences 15 (2018)10. - ISSN 1726-4170 - p. 3189 - 3202.

Tidal wetlands, such as tidal marshes and mangroves, are hotspots for carbon sequestration. The preservation of organic matter (OM) is a critical process by which tidal wetlands exert influence over the global carbon cycle and at the same time gain elevation to keep pace with sea-level rise (SLR). The present study assessed the effects of temperature and relative sea level on the decomposition rate and stabilization of OM in tidal wetlands worldwide, utilizing commercially available standardized litter. While effects on decomposition rate per se were minor, we show strong negative effects of temperature and relative sea level on stabilization, as based on the fraction of labile, rapidly hydrolyzable OM that becomes stabilized during deployment. Across study sites, OM stabilization was 29% lower in low, more frequently flooded vs. high, less frequently flooded zones. Stabilization declined by ∼ 75% over the studied temperature gradient from 10.9 to 28.5°C. Additionally, data from the Plum Island long-term ecological research site in Massachusetts, USA, show a pronounced reduction in OM stabilization by > 70% in response to simulated coastal eutrophication, confirming the potentially high sensitivity of OM stabilization to global change. We therefore provide evidence that rising temperature, accelerated SLR, and coastal eutrophication may decrease the future capacity of tidal wetlands to sequester carbon by affecting the initial transformations of recent OM inputs to soil OM.

Boeren in Beweging : Hoe boeren afwegingen maken over natuurinclusieve landbouw en hoe anderen hen kunnen helpen
Westerink, Judith ; Smit, Bert ; Dijkshoorn, Marijke ; Polman, Nico ; Vogelzang, Theo - \ 2018
Wageningen : Wageningen University & Research - ISBN 9789463433068 - 48
In de ‘Rijksnatuurvisie 2014 Natuurlijk verder’ is een nieuwe term
ontstaan: natuurinclusieve landbouw. Het Rijk zwengelde hiermee een
discussie aan over de mate waarin en de manier waarop natuur een
plek zou moeten hebben in alle facetten van het boerenbedrijf. Het zou
een transitie moeten worden: de hele Nederlandse landbouw zou zich
richting natuurinclusiviteit moeten bewegen.
Deze term is vervolgens opgepakt door onderzoekers, burgers, natuurorganisaties
en belangengroepen. Allerlei projecten werden de afgelopen
jaren opgezet of onder de noemer ‘natuurinclusief’ gebracht. In
bijeenkomsten werd het gesprek aangegaan met ketenpartijen en
Een transitie richting een natuurinclusieve landbouw gaat echter alleen
plaatsvinden als boeren zelf in beweging komen. Als overheid, burgers,
bedrijven en organisaties boeren willen helpen om die beweging te
maken, is het belangrijk om inzicht te krijgen in wat hen beweegt. Wat
speelt mee in de keuzes die zij maken om wel of niet de natuurinclusieve
kant op te gaan en welke rol heeft hun omgeving daarin?
Deze brochure is het resultaat van een onderzoek naar die vragen. Het
was een verkennend, kwalitatief onderzoek, beperkt tot de melkveehouderij
en de akkerbouw en uitgevoerd in 2016/2017. We spraken met
vijf melkveehouders in Eemland en vijf akkerbouwers in Flevoland;
eerst individueel en vervolgens als groep per gebied. Want: hoe voeren
boeren met elkaar het gesprek over natuurinclusieve landbouw? Ook
spraken we voor elke sector nog met drie erfbetreders, om te verkennen
hoe zij denken over de transitie naar natuurinclusieve landbouw.
Het onderzoek was niet opgezet voor een representatief beeld, maar
om inzicht te krijgen in wat meespeelt bij overwegingen van boeren om
te kiezen voor natuurinclusieve landbouw.
In het volgende hoofdstuk introduceren we het raamwerk
dat we gebruikt hebben om zicht te krijgen op de
totstandkoming van de keuzes van boeren op het gebied
van natuurinclusieve landbouw. We hebben dit gebruikt
om de interviews en focusgroepen voor te bereiden en
te analyseren. Vervolgens vatten we samen wat natuurinclusieve
landbouw betekent voor de melkveehouderij
in Eemland en voor de akkerbouw in Flevoland. Dit
moet niet gelezen worden als objectieve waarheid, maar
als de werkelijkheid zoals boeren die zien en zoals zij die
in hun keuzes meewegen. Ook is het belangrijk om te
beseffen dat de inhoud van elk hoofdstuk is samengesteld
op basis van de uitspraken van vijf verschillende
boeren, die niet per se door alle vijf zijn gezegd1. In
hoofdstuk 3 besteden we extra aandacht aan de rol van
de erfbetreders. In hoofdstuk 4 vertalen we de bevindingen
uit Eemland en Flevoland naar aanknopingspunten
om als politiek en maatschappij de keuze voor natuurinclusieve
landbouw voor boeren gemakkelijker te maken.
Ten slotte doen we gerichte aanbevelingen voor diverse
Deze brochure is dan ook bedoeld voor iedereen die bij
zou kunnen dragen aan een transitie richting natuurinclusieve
landbouw: overheden, ketenpartijen, natuurorganisaties,
agrarische collectieven, erfbetreders, burgers
etc. Voor boeren staat er waarschijnlijk weinig nieuws in
deze brochure, maar hopelijk wel veel herkenning! Als
onderzoekers hopen we dat meer mensen zich naar
aanleiding van deze brochure willen verdiepen in en
verbinden aan boeren die streven naar natuurinclusiviteit,
en daarmee medeverantwoordelijkheid gaan nemen
voor ons landschap, ons voedsel en onze natuur.
Prognoses CO2-emissie glastuinbouw 2030
Velden, N.J.A. van der; Smit, P.X. ; Buurma, J.S. - \ 2018
Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2018-056) - ISBN 9789463432832 - 76
The greenhouse horticulture sector needs a policy-driven interim goal for CO2 emissions in 2030. The prognosis for CO2 emissions in 2030 ranges from 2.7 to 3.3 megatonnes , based on three future scenarios for economic development. These CO2 emissions are substantially lower than they were in 2015 (5.8 megatonnes). In the optimistic scenario, the economy grows most strongly, and the greenhouse horticulture sector – with an equal acreage, many new greenhouses and more lighting has the strongest development. The opposite is the case in the pessimistic scenario. Energy demand and CO2 emissions are greater in the optimistic scenario than in the pessimistic scenario. However, we see greater difference in energy demand. In the optimistic scenario, the horticultural sector utilises more energy supply options without CO2 emissions. Realisation of each of the three scenarios requires strong policy input from both the government and the greenhouse horticultural sector concerning energy saving and energy supplies without CO2 emissions. The latter point makes cooperation with parties outside the greenhouse horticulture sector necessary
Verdienmodellen natuurinclusieve landbouw
Polman, Nico ; Dijkshoorn, Marijke ; Doorneweert, Bart ; Rijk, Piet ; Vogelzang, Theo ; Reinhard, Stijn ; Smit, Bert ; Splinter, Gerben ; Heideveld, Antoine ; Geerts, Rob ; Grin, John ; Korevaar, Hein ; Setten, Bert van; Vrolijk, Maarten - \ 2018
Wageningen : Wageningen Economic Research - 57
Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, Defeng ; Purwana Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Güngör, Berivan ; Hartog, M.V. ; Hontelez, J. ; Verver, Jan ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)20. - ISSN 0027-8424 - p. E4700 - E4709.
Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
Maatschappelijke opgaven voor de agrosector : perspectief op de ontwikkeling van de agrosector tot 2030
Berkhout, Petra ; Beldman, Alfons ; Bergevoet, Ron ; Dagevos, H. ; Hoste, Robert ; Poppe, Krijn ; Silvis, Huib ; Smit, Bert ; Terluin, Ida - \ 2018
Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2018-022) - ISBN 9789463432481 - 33
Dit rapport schetst de verwachte ontwikkeling van de Nederlandse agrosector en de onderliggendesubsectoren, uitgaande van bestaand beleid en bestaande beleidsvoornemens. Op basis van ditreferentiebeeld, maakt het rapport inzichtelijk of doelen op gebied van milieu en dierenwelzijn wordengehaald, of dat aanvullende maatregelen nodig zijn.---This report gives an overview of the expected developments of the Dutch agricultural sector and itsconstituent subsectors, based on existing policy and policy proposals. This overview clarifies whetherthe environmental and animal welfare policy goals will be achieved or whether extra measures arerequired.
Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity
Mommer, L. ; Cotton, Anne ; Raaijmakers, J.M. ; Termorshuizen, A.J. ; Ruijven, J. van; Hendriks, Marloes ; Rijssel, Sophie van; Mortel, J.E. van de; Paauw, J.W.M. van der; Schijlen, E.G.W.M. ; Smit-Tiekstra, Annemiek ; Berendse, F. ; Kroon, Hans de; Dumbrell, A.J. - \ 2018
New Phytologist 218 (2018)2. - ISSN 0028-646X - p. 542 - 553.
There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a 'black box' in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.
Subsidence of organic dredged sediments in an upland deposit in Wormer- en Jisperveld : North Holland, the Netherlands
Oliveira, Bruna R.F. ; Smit, Martijn P.J. ; Veld, Harry ; Paassen, Leon A. van; Rijnaarts, Huub H.M. ; Grotenhuis, Tim - \ 2018
Environmental Earth Sciences 77 (2018)4. - ISSN 1866-6280
Dredged sediments - Lowlands - Organic matter oxidation - Peatlands - Shrinkage - Subsidence - Upland deposit
Land subsidence in low-lying peatlands can be caused by shrinkage and organic matter oxidation. When these areas have networks of ditches and canals for drainage purposes, the sediments that accumulate in the waterways can be used to reverse the process of land subsidence. The objective of this study is to understand how dredged sediments can be used to reverse the process of land subsidence by analysing the contribution of shrinkage and organic matter mineralization to the subsidence observed in an upland deposit. A deposit of dredged sediments in the Wormer- en Jisperveld—North Holland, the Netherlands—was characterized during 17 months in terms of subsidence of the sediments, subsidence of the soil underlying the deposit, geotechnical water content, organic matter content, type of organic matter and nutrients. The deposit was filled to a height of 195 cm, and after 17 months, the subsidence of the sediments was 88 cm. In addition, a subsidence of 19.5 cm of the underlying soil was observed. Subsidence could be attributed to shrinkage since no significant changes in the organic matter content and total organic carbon were observed. The type of organic matter changed in the direction of humification until winter 2014, stabilized from winter 2014 to spring 2015 and changed in the direction of mineralization after the spring of 2015. Subsidence of dredged sediments in upland deposits is caused by shrinkage during the first 17 months. The solution of spreading thinner layers of sediments over the land to decrease the subsidence rates should be explored since the pressure of the deposit on the underlying soil caused an extra subsidence of 19.5 cm.
Exportgroei boomkwekerijproducten zet in 2017 door
Smit, P.X. - \ 2018
In: De Nederlandse landbouwexport 2017 / Raemakers, Pascal, Dolman, Mark, Jukema, Gerben, Den Haag : Centraal Bureau voor de Statistiek - ISBN 9789035724174 - p. 56 - 59.
Aardbevingen: de rek is eruit bij Groninger boeren
Smit, Bert - \ 2018

smit, bert

Below-ground complementarity effects in a grassland biodiversity experiment are related to deep-rooting species
Oram, Natalie J. ; Ravenek, Janneke M. ; Barry, Kathryn E. ; Weigelt, Alexandra ; Chen, Hongmei ; Gessler, Arthur ; Gockele, Annette ; Kroon, Hans de; Paauw, Jan Willem van der; Scherer-Lorenzen, Michael ; Smit-Tiekstra, Annemiek ; Ruijven, Jasper van; Mommer, Liesje - \ 2018
Journal of Ecology 106 (2018)1. - ISSN 0022-0477 - p. 265 - 277.
Additive partitioning - Diversity-productivity relationship - Jena Trait-Based Experiment - Molecular markers - Resource partitioning - Root distribution

Below-ground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. We determined species-specific root standing biomass over depth using molecular techniques (real-time qPCR) in a large grassland biodiversity experiment (one to eight plant species mixtures), in 2 years. Species-specific root biomass data were used to disentangle the effects of positive interactions between species (complementarity effects) and effects due to dominance of productive species (selection effects) on root biomass in mixtures. In a next step, these biodiversity effects were linked to the diversity of rooting depths and the averaged rooting depth of the community. Root biomass increased with species richness. This was mainly due to positive interactions (the complementarity effect), which increased with species richness below-ground. In contrast, the selection effect decreased with species richness. Although there was considerable variation in vertical root distribution between species in monocultures, the diversity of rooting strategies did not explain the complementarity effect. Rather, the abundance of deep-rooting species in mixtures (i.e. high community-weighted mean) was significantly related to the complementarity effect. Comparing the "predicted" root distribution (based on monocultures) to the actual distribution in mixtures, we found that mixtures rooted deeper than expected, but this did not better explain the complementarity effect. Synthesis. This study demonstrates that vertical root distributions of species provide only subtle evidence for resource partitioning. We found no evidence that functional diversity in vertical rooting patterns was important for the complementarity effect, in contrast to our expectation that the enhancement of productivity was due to resource partitioning. Alternatively, we found significant but weak relationships between the complementarity effect and deep-rooting communities, based on the community-weighted mean root distribution. This suggests that factors other than below-ground resource partitioning alone may drive the biodiversity-productivity relationship.

The operational context of care sport connectors in the Netherlands
Leenaars, K.E.F. ; Velden-Bollemaat, E.C. Van Der; Smit, E. ; Wagemakers, A. ; Molleman, G.R.M. ; Koelen, M.A. - \ 2018
Health Promotion International 33 (2018)4. - ISSN 0957-4824 - p. 622 - 634.
To stimulate physical activity (PA) and guide primary care patients towards local sport facilities, Care Sport Connectors (CSCs), to whom a broker role has been ascribed, were introduced in 2012 in the Netherlands. The aim of this study is to describe CSCs’ operational context. A theoretical framework was developed and used as the starting point for this study. Group interviews were held with policymakers in nine participating municipalities, and, when applicable, the CSC’s manager was also present. Prior to the interviews, a first outline of the operational context was mapped, based on the analysis of policy documents and a questionnaire completed by the policymakers. A deductive content analysis, based on the theoretical framework, was used to analyse the interviews. Differences were found in CSCs’ operational context in the different municipalities, especially the extent to which municipalities adopted an integral approach. An integral approach consists of an integral policy in combination
with an imbedding of this policy in partnerships at management level. This integral approach is reflected in the activities of other municipal operations, for example the implementation of health and PA programs by different organisations. Given the CSC mandate, we think that this integral approach
may be supportive of the CSCs’ work, because it is reflected in other operations of the municipalities and thus creates conditions for the CSCs’ work. Further study is required to ascertain whether this integral approach is actually supporting CSCs in their work to connect the primary care and the PA sector.
The role and impact of Care Sport Connectors in connecting the care and physical activity sector
Wagemakers, A. ; Molleman, G. ; Leenaars, K.E.F. ; Smit, E. - \ 2017
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