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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Disentangling microbial decomposition networks : linking detritus-based soil microbial food webs to ecosystem processes
Heijboer, Amber - \ 2018
University. Promotor(en): Peter de Ruiter; G.A. Kowalchuk, co-promotor(en): Jaap Bloem. - Wageningen : Wageningen University - ISBN 9789463437509 - 198
A Diurnal Rhythm in Brown Adipose Tissue Causes Rapid Clearance and Combustion of Plasma Lipids at Wakening
Berg, Rosa van den; Kooijman, Sander ; Noordam, Raymond ; Ramkisoensing, Ashna ; Abreu-Vieira, Gustavo ; Tambyrajah, Lauren L. ; Dijk, Wieneke ; Ruppert, Philip ; Mol, Isabel M. ; Kramar, Barbara ; Caputo, Rosanna ; Puig, Laura Sardón ; Ruiter, Evelien M. de; Kroon, Jan ; Hoekstra, Menno ; Sluis, Ronald J. van der; Meijer, Onno C. ; Willems van Dijk, Ko ; Kerkhof, Linda W.M. van; Christodoulides, Constantinos ; Karpe, Fredrik ; Gerhart-Hines, Zachary ; Kersten, Sander ; Meijer, Johanna H. ; Coomans, Claudia P. ; Heemst, Diana van; Biermasz, Nienke R. ; Rensen, Patrick C.N. - \ 2018
Cell Reports 22 (2018)13. - ISSN 2211-1247 - p. 3521 - 3533.
angiopoietin-like 4 - APOE3-Leiden.CETP mice - brown adipose tissue - circadian rhythm - diurnal rhythm - fatty acids - lipoprotein lipase - postprandial lipid response - triglycerides
Many favorable metabolic effects have been attributed to thermogenic activity of brown adipose tissue (BAT). Yet, time of day has rarely been considered in this field of research. Here, we show that a diurnal rhythm in BAT activity regulates plasma lipid metabolism. We observed a high-amplitude rhythm in fatty acid uptake by BAT that synchronized with the light/dark cycle. Highest uptake was found at the onset of the active period, which coincided with high lipoprotein lipase expression and low angiopoietin-like 4 expression by BAT. Diurnal rhythmicity in BAT activity determined the rate at which lipids were cleared from the circulation, thereby imposing the daily rhythm in plasma lipid concentrations. In mice as well as humans, postprandial lipid excursions were nearly absent at waking. We anticipate that diurnal BAT activity is an important factor to consider when studying the therapeutic potential of promoting BAT activity. van den Berg et al. show a strong circadian rhythm in fatty acid uptake by brown adipose tissue that peaks at wakening regardless of the light exposure period. Consequently, postprandial lipid handling by brown adipose tissue is highest at wakening, resulting in the lowest postprandial plasma lipid excursions.
Impact of prediagnostic smoking and smoking cessation on colorectal cancer prognosis : A meta-analysis of individual patient data from cohorts within the CHANCES consortium
Ordóñez-Mena, J.M. ; Walter, V. ; Schöttker, B. ; Jenab, M. ; O'Doherty, M.G. ; Kee, F. ; Bueno-de-Mesquita, B. ; Peeters, P.H.M. ; Stricker, B.H. ; Ruiter, R. ; Hofman, A. ; Söderberg, S. ; Jousilahti, P. ; Kuulasmaa, K. ; Freedman, N.D. ; Wilsgaard, T. ; Wolk, A. ; Nilsson, L.M. ; Tjønneland, A. ; Quirós, J.R. ; Duijnhoven, F.J.B. van; Siersema, P.D. ; Boffetta, P. ; Trichopoulou, A. ; Brenner, H. - \ 2018
Annals of Oncology 29 (2018)2. - ISSN 0923-7534 - p. 472 - 483.
Colorectal neoplasms - Meta-analysis - Smoking - Smoking cessation - Survival
Background: Smoking has been associated with colorectal cancer (CRC) incidence and mortality in previous studies and might also be associated with prognosis after CRC diagnosis. However, current evidence on smoking in association with CRC prognosis is limited. Patients and methods: For this individual patient data meta-analysis, sociodemographic and smoking behavior information of 12 414 incident CRC patients (median age at diagnosis: 64.3 years), recruited within 14 prospective cohort studies among previously cancer-free adults, was collected at baseline and harmonized across studies. Vital status and causes of death were collected for a mean follow-up time of 5.1 years following cancer diagnosis. Associations of smoking behavior with overall and CRC-specific survival were evaluated using Cox regression and standard meta-analysis methodology. Results: A total of 5229 participants died, 3194 from CRC. Cox regression revealed significant associations between former [hazard ratio (HR)=1.12; 95 % confidence interval (CI)=1.04-1.20] and current smoking (HR=1.29; 95% CI=1.04-1.60) and poorer overall survival compared with never smoking. Compared with current smoking, smoking cessation was associated with improved overall (HR<10 years=0.78; 95% CI=0.69-0.88; HR≥10 years=0.78; 95% CI=0.63-0.97) and CRC-specific survival (HR≥10 years=0.76; 95% CI=0.67-0.85). Conclusion: In this large meta-analysis including primary data of incident CRC patients from 14 prospective cohort studies on the association between smoking and CRC prognosis, former and current smoking were associated with poorer CRC prognosis compared with never smoking. Smoking cessation was associated with improved survival when compared with current smokers. Future studies should further quantify the benefits of nonsmoking, both for cancer prevention and for improving survival among CRC patients, in particular also in terms of treatment response.
Soil food web assembly and vegetation development in a glacial chronosequence in Iceland
Leeuwen, J.P. van; Lair, G.J. ; Gisladottir, G. ; Sanden, T.M. ; Bloem, J. ; Hemerik, A. ; Ruiter, P.C. de - \ 2017
In: Book of Abstracts Wageningen Soil Conference 2017. - Wageningen : Wageningen University & Research - ISBN 9789463430616 - p. 124 - 124.
Priorities for research in soil ecology
Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
Emergent facilitation promotes biological diversity in pelagic food webs
Ruiter, Peter C. de; Gaedke, Ursula - \ 2017
Food Webs 10 (2017). - ISSN 2352-2496 - p. 15 - 21.

Studies on the role of species interactions in community dynamics and diversity have mostly focused on competition and predator-prey interactions, but the possible role of positive interactions between species, i.e. facilitation, is increasingly recognised. A type of facilitation that received little attention is the one that arises indirectly via pathways of direct trophic and competitive interactions. Here we show that in pelagic food webs the positive effects from such ‘emergent’ facilitation can be sufficiently strong to dominate over direct negative effects, prevent competitive exclusion, promote co-existence and preserve biodiversity. We carried out a press perturbation experiment using a pelagic algae-ciliate food web model whose realism is based on extensive observations on the algae-ciliate community in Lake Constance. The model incorporated trait gradients regarding algal edibility and growth rate and ciliate selectivity and prey attack rate as commonly observed in pelagic food webs. Results of the press perturbation exercise showed that some ciliate groups did not persist alone, or only at very low biomass values, while they reached realistic biomass values in the presence of competing groups of ciliates. The mechanism behind this facilitation is that grazing by less selective ciliates protected the more edible and preferred prey for the selective ciliates. We argue that such emergent facilitation, and the positive consequences for co-existence and biodiversity, is likely to occur in real pelagic food webs. In this way, the present study revealed a potentially important mechanism in the preservation of biological diversity in pelagic food webs.

Effects of land use on soil microbial biomass, activity and community structure at different soil depths in the Danube floodplain
Leeuwen, J.P. van; Djukic, I. ; Bloem, J. ; Lehtinen, T. ; Hemerik, L. ; Ruiter, P.C. de; Lair, G.J. - \ 2017
European Journal of Soil Biology 79 (2017). - ISSN 1164-5563 - p. 14 - 20.
Land use - Microbial activity - PLFA - Soil depth - Soil ecosystem functioning - Soil microbial biomass
Human activities such as land use and -management may strongly affect the soil's ability to provide ecosystem services, in which microbes are playing a key role. Because sampling is usually restricted to the topsoil, little is known about effects of land use on ecosystem functioning down the soil profile. The present study assessed the effects of different land use types (arable, forest, grassland) on soil microbial biomass, activity and community structure at different soil depths (A, AC, C horizons), under the same climatic and pedological conditions, in the Danube Floodplain in Austria. Microbial biomass was 4–5 times lower in the arable field than in forest and grassland in the upper horizons. Additionally, both microbial biomass and activity decreased 3–4 fold with soil depth in forest and grassland. However, up to 30% of total microbial biomass was found in the C horizon in the arable field. We found a differentiation of microbial community structure between land use types and with soil depth: i.e. strong differences in the topsoil between land uses, whereas community structure in the C horizon was similar. This study confirms that land use exerts strong effects on soil microbes in the topsoil and that microbial biomass and activity decrease with soil depth. However, considerable microbial biomass and activity are found below 30 cm depth which is usually not included in samplings. In the deeper soil horizon effects of land use disappear, with microbial community structure and functioning becoming similar in similar pedological conditions.
Soil Functions in Earth's Critical Zone : Key Results and Conclusions
Banwart, S.A. ; Bernasconi, S.M. ; Blum, W.E.H. ; Souza, D.M. de; Chabaux, F. ; Duffy, C. ; Kercheva, M. ; Krám, P. ; Lair, G.J. ; Lundin, L. ; Menon, M. ; Nikolaidis, N. ; Novak, M. ; Panagos, P. ; Ragnarsdottir, K.V. ; Robinson, D.A. ; Rousseva, S. ; Ruiter, P. de; Gaans, P. van; Weng, L. ; White, T. ; Zhang, B. - \ 2017
Advances in Agronomy (2017). - ISSN 0065-2113
Critical zone - Ecosystem services - Soil - Soil functions - Water
This chapter summarizes the methods, results, and conclusions of a 5-year research project (SoilTrEC: Soil Transformations in European Catchments) on experimentation, process modeling, and computational simulation of soil functions and soil threats across a network of European, Chinese, and United States Critical Zone Observatories (CZOs). The study focused on the soil functions of biomass production, carbon storage, water storage and transmission, water filtration, transformation of nutrients, and maintaining habitat and genetic diversity.The principal results demonstrate that soil functions can be quantified as biophysical flows and transformations of material and energy. The functions can be simulated with mathematical models of soil processes within the soil profile and at the critical zone interfaces with vegetation and atmosphere, surface waters and the below-ground vadose zone and groundwater. A new dynamic model for soil structure development, together with data sets from the CZOs, demonstrate both seasonal fluctuations in soil structure dynamics related to vegetation dynamics and soil carbon inputs, and long-term trends (decadal) in soil carbon storage and soil structure development.Cross-site comparison for 20 soil profiles at seven field sites with variation in soil type, lithology, land cover, land use, and climate demonstrate that sites can be classified, using model parameter values for soil aggregation processes together with climatic conditions and soil physical properties, along a trajectory of soil structure development from incipient soil formation through productive land use to overly intensive land use with soil degradation.A new modeling code, the Integrated Critical Zone model, was applied with parameter sets developed from the CZO site data to simulate the biophysical flows and transformations that quantify multiple soil functions. Process simulations coupled the new model for soil structure dynamics with existing modeling approaches for soil carbon dynamics, nutrient transformations, vegetation dynamics, hydrological flow and transport, and geochemical equilibria and mineral weathering reactions. Successful calibration, testing, and application of the model with data sets from horticulture plot manipulation experiments demonstrate the potential to apply modeling and simulation to the scoping and design of new practices and policy options to enhance soil functions and reduce soil threats worldwide.
Data from: How habitat-modifying organisms structure the food web of two coastal ecosystems
Zee, Els M. van der; Angelini, Christine ; Govers, Laura L. ; Christianen, M.J.A. ; Altieri, Andrew H. ; Reijden, K.J. van der; Silliman, Brian R. ; Koppel, Johan van de; Geest, Matthijs van der; Gils, Jan A. van; Veer, Henk W. van der; Piersma, Theunis ; Ruiter, P.C. de; Olff, H. ; Heide, Tjisse van der - \ 2016
food web - non-trophic interactions - foundation species - ecological networks - ecosystem engineering - facilitation
The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and West African tropical seagrass meadows. Results reveal that habitat-modifying species, through non-trophic facilitation rather than their trophic role, enhance species richness across multiple trophic levels, increase the number of interactions per species (link density), but decrease the realized fraction of all possible links within the food web (connectance). Compared to the trophic role of the most highly connected species, we found this non-trophic effects to be more important for species richness and of more or similar importance for link density and connectance. Our findings demonstrate that food webs can be fundamentally shaped by interactions outside the trophic network, yet intrinsic to the species participating in it. Better integration of non-trophic interactions in food web analyses may therefore strongly contribute to their explanatory and predictive capacity.
How habitat-modifying organisms structure the food web of two coastal ecosystems
Zee, Els M. van der; Angelini, Christine ; Govers, Laura L. ; Christianen, Marjolijn J.A. ; Altieri, Andrew H. ; Reijden, Karin J. van der; Silliman, Brian R. ; Koppel, Johan van de; Geest, Matthijs van der; Gils, Jan A. van; Veer, Henk W. van der; Piersma, Theunis ; Ruiter, Peter C. de; Olff, Han ; Heide, Tjisse van der - \ 2016
Proceedings of the Royal Society. B: Biological Sciences 283 (2016)1826. - ISSN 0962-8452 - 9 p.
Consumer–resource interactions - Ecological networks - Ecosystem engineering - Facilitation - Foundation species - Non-trophic interactions
The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and West African tropical seagrass meadows. Results reveal that habitat-modifying species, through non-trophic facilitation rather than their trophic role, enhance species richness across multiple trophic levels, increase the number of interactions per species (link density), but decrease the realized fraction of all possible links within the food web (connectance). Compared to the trophic role of the most highly connected species, we found this non-trophic effects to be more important for species richness and of more or similar importance for link density and connectance. Our findings demonstrate that food webs can be fundamentally shaped by interactions outside the trophic network, yet intrinsic to the species participating in it. Better integration of non-trophic interactions in food web analyses may therefore strongly contribute to their explanatory and predictive capacity.
Staren naar potvisstaarten
Mul, Evert - \ 2016

Potvissen stranden al eeuwen op de Noordzeekust. Bioloog Evert Mul vergelijkt staartvinnen om de oorzaak te vinden.

Plant biomass, soil microbial community structure and nitrogen cycling under different organic amendment regimes; a 15N tracer-based approach
Heijboer, Amber ; Berge, Hein F.M. ten; Ruiter, Peter C. de; Jørgensen, Helene Bracht ; Kowalchuk, George A. ; Bloem, Jaap - \ 2016
Applied Soil Ecology 107 (2016). - ISSN 0929-1393 - p. 251 - 260.
Immobilization - Mineral fertilizer - Mineralization - Organic amendments - Phospholipid fatty acids - Soil microbial community

Sustainable agriculture requires nutrient management options that lead to a profitable crop yield with relatively low nitrogen (N) losses to the environment. We studied whether the addition of contrasting organic amendments together with inorganic fertilizer can promote both requirements simultaneously. In particular we studied how the chemical composition of organic amendments affects the biomass, activity and composition of the soil microbial community and subsequently carbon (C) and N mineralization, microbial N immobilization and plant growth and nutrient uptake. In a pot experiment, Brussels sprouts (Brassica oleracea, cvar. Cyrus) were grown on arable soil, mixed with 15N-labelled mineral fertilizer and different kinds of organic amendments (cattle manure solid fraction, maize silage, lucerne silage, wheat straw) differing in C:N ratio and lignin content. After 69 and 132 days, destructive sampling took place to assess the effects of the different treatments on soil microbial biomass (microscopic measurements), microbial community composition (phospholipid fatty acid profiles), soil microbial activity (14C-leucine incorporation), C and N mineralization, plant biomass and 15N retrieval in soil pools, microbial biomass and plant biomass. Addition of organic amendments increased soil microbial biomass, activity and fungal/bacterial ratio and created distinct microbial community compositions, whereby high C:N ratio organic amendments had stronger effects compared to low C:N ratio amendments. Structural equation modelling showed that higher values of soil microbial activity were associated with increased N mineralization rates, increased plant biomass and plant 15N uptake, while microbial 15N immobilization was associated with soil microbial community composition. The outcomes of this study highlight the importance of the chemical composition and the amount of the organic amendments for finding a balance between plant N uptake, microbial N immobilization and N retention in labile and stable soil pools through the effects on the composition and activity of the soil microbial community. The results provide insights that can be used in designing combined input (nutrient and organic) nutrient management strategies for a more sustainable agriculture.

Searching for balance : stability and equilibria of food webs
Altena, C. van - \ 2016
University. Promotor(en): Peter de Ruiter; J.A.P. Heesterbeek; Wolf Mooij, co-promotor(en): Lia Hemerik. - Wageningen : Wageningen University - ISBN 9789462576827 - 130 p.
food webs - models - interactions - ecology - biocoenosis - ecological balance - voedselwebben - modellen - interacties - ecologie - biocenose - ecologisch evenwicht

Abstract

How complexity of food webs relates to stability has been a subject of many studies. Often,

unweighted connectance is used to express complexity. Unweighted connectance is

measured as the proportion of realized links in the network. Weighted connectance, on the

other hand, takes link weights (fluxes or feeding rates) into account and captures the shape

of the flux distribution. Here, we used weighted connectance to revisit the relation between

complexity and stability. We used 15 real soil food webs and determined the feeding rates

and the interaction strength matrices. We calculated both versions of connectance, and

related these structural properties to food web stability. We also determined the skewness

of both flux and interaction strength distributions with the Gini coefficient. We found no

relation between unweighted connectance and food web stability, but weighted connectance

was positively correlated with stability. This finding challenges the notion that complexity

may constrain stability, and supports the ‘complexity begets stability’ notion. The positive

correlation between weighted connectance and stability implies that the more evenly flux

rates were distributed over links, the more stable the webs were. This was confirmed by the

Gini coefficients of both fluxes and interaction strengths. However, the most even

distributions of this dataset still were strongly skewed towards small fluxes or weak

interaction strengths. Thus, incorporating these distribution with many weak links via

weighted instead of unweighted food web measures can shed new light on classical

theories

Fire-induced pine woodland to shrubland transitions in Southern Europe may promote shifts in soil fertility
Garcia Mayor, Angeles ; Valdecantos, A. ; Vallejo, V.R. ; Keizer, J.J. ; Bloem, J. ; Baeza, J. ; González-Pelayo, O. ; Machado, A.I. ; Ruiter, P.C. de - \ 2016
Science of the Total Environment 573 (2016). - ISSN 0048-9697 - p. 1232 - 1241.
Early warning indicators - Fire frequency - Mediterranean region - Microsite - Mineral soil - Pinus spp. woodlands - Soil quality - Sudden shift

Since the mid of the last century, fire recurrence has increased in the Iberian Peninsula and in the overall Mediterranean basin due to changes in land use and climate. The warmer and drier climate projected for this region will further increase the risk of wildfire occurrence and recurrence. Although the impact of wildfires on soil nutrient content in this region has been extensively studied, still few works have assessed this impact on the basis of fire recurrence. This study assesses the changes in soil organic C and nutrient status of mineral soils in two Southern European areas, Várzea (Northern Portugal) and Valencia (Eastern Spain), affected by different levels of fire recurrence and where short fire intervals have promoted a transition from pine woodlands to shrublands. At the short-term ( 5. years), a decline in overall soil fertility with fire recurrence was also observed, with a drop between pine woodlands (one fire) and shrublands (two and three fires), particularly in the soil microsites between shrubs. Our results suggest that the current trend of increasing fire recurrence in Southern Europe may result in losses or alterations of soil organic matter, particularly when fire promotes a transition from pine woodland to shrubland. The results also point to labile organic matter fractions in the intershrub spaces as potential early warning indicators for shifts in soil fertility in response to fire recurrence.

Organische mestkwaliteit beïnvloedt bodemmicroben en bodemfuncties
Heijboer, A. ; Berge, H.F.M. ten; Ruiter, P.C. de; Kowalchuk, G.A. ; Jorgensen, H.B. ; Bloem, J. - \ 2016
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 27-29 (2016). - ISSN 0169-6300 - p. 27 - 29.
agro-ecosystemen - bemesting - bodembiologie - micro-organismen - bodemmicrobiologie - stikstofkringloop - fosfolipiden - veldproeven - brassica oleracea var. gemmifera - agroecosystems - fertilizer application - soil biology - microorganisms - soil microbiology - nitrogen cycle - phospholipids - field tests
Micro-organismen spelen een sleutelrol in bodemfuncties zoals de kringlopen van koolstof en stikstof. Voor een duurzame landbouw is het van belang dat deze kringlopen optimaal functioneren om verliezen van nutriënten zoveel mogelijk te voorkomen. Dit onderzoek geeft inzicht in de rol van bodemmicroben bij optimalisatie van de stikstofkringloop door toevoeging van zowel minerale kunstmest als verschillende kwaliteiten organisch materiaal.
Quantification of the smoking-associated cancer risk with rate advancement periods : Meta-analysis of individual participant data from cohorts of the CHANCES consortium
Ordóñez-Mena, José Manuel ; Schöttker, Ben ; Mons, Ute ; Jenab, Mazda ; Freisling, Heinz ; Bueno-de-Mesquita, Bas ; O'Doherty, Mark G. ; Scott, Angela ; Kee, Frank ; Stricker, Bruno H. ; Hofman, Albert ; Keyser, Catherine E. de; Ruiter, Rikje ; Söderberg, Stefan ; Jousilahti, Pekka ; Kuulasmaa, Kari ; Freedman, Neal D. ; Wilsgaard, Tom ; Groot, Lisette C.P.G.M. de; Kampman, Ellen ; Håkansson, Niclas ; Orsini, Nicola ; Wolk, Alicja ; Nilsson, Lena Maria ; Tjønneland, Anne ; Pajak, Andrzej ; Malyutina, Sofia ; Kubínová, Růžena ; Tamosiunas, Abdonas ; Bobak, Martin ; Katsoulis, Michail ; Orfanos, Philippos ; Boffetta, Paolo ; Trichopoulou, Antonia ; Brenner, Hermann - \ 2016
BMC Medicine 14 (2016)1. - ISSN 1741-7015
Cancer - Cohort - Incidence - Meta-analysis - Mortality - Smoking

Background: Smoking is the most important individual risk factor for many cancer sites but its association with breast and prostate cancer is not entirely clear. Rate advancement periods (RAPs) may enhance communication of smoking related risk to the general population. Thus, we estimated RAPs for the association of smoking exposure (smoking status, time since smoking cessation, smoking intensity, and duration) with total and site-specific (lung, breast, colorectal, prostate, gastric, head and neck, and pancreatic) cancer incidence and mortality. Methods: This is a meta-analysis of 19 population-based prospective cohort studies with individual participant data for 897,021 European and American adults. For each cohort we calculated hazard ratios (HRs) for the association of smoking exposure with cancer outcomes using Cox regression adjusted for a common set of the most important potential confounding variables. RAPs (in years) were calculated as the ratio of the logarithms of the HRs for a given smoking exposure variable and age. Meta-analyses were employed to summarize cohort-specific HRs and RAPs. Results: Overall, 140,205 subjects had a first incident cancer, and 53,164 died from cancer, during an average follow-up of 12 years. Current smoking advanced the overall risk of developing and dying from cancer by eight and ten years, respectively, compared with never smokers. The greatest advancements in cancer risk and mortality were seen for lung cancer and the least for breast cancer. Smoking cessation was statistically significantly associated with delays in the risk of cancer development and mortality compared with continued smoking. Conclusions: This investigation shows that smoking, even among older adults, considerably advances, and cessation delays, the risk of developing and dying from cancer. These findings may be helpful in more effectively communicating the harmful effects of smoking and the beneficial effect of smoking cessation.

The soil life cycle : food webs and ecosystem services during soil transformations
Leeuwen, J.P. van - \ 2016
University. Promotor(en): Peter de Ruiter; Jaap Bloem; Lia Hemerik. - Wageningen : Wageningen University - ISBN 9789462576261 - 166 p.
soil - food webs - ecosystem services - life cycle - soil biology - soil flora - soil fauna - bodem - voedselwebben - ecosysteemdiensten - levenscyclus - bodembiologie - bodemflora - bodemfauna

Soil is one of the most important natural resource for life on Earth and provides important ecosystem services, such as food production, carbon sequestration, water regulation and contaminant attenuation. Soil quality, defined as the soil’s ability to provide these services, is drastically reduced in many locations and regions worldwide due to human activities. This loss in soil quality ultimately leads to soil degradation, erosion and desertification, imposing a severe and increasing risk for the growing human population. It is therefore essential that we are aware of the importance of protecting soil, and at the same time understand processes that build up and regenerate soil. The key objective of the present study was to obtain a better understanding of soil food web structure and functioning, and how these develop in stages along the soil life cycle. Using field surveys, I investigated the soil food web structure and functioning in different sites along the soil life cycle, including soils developing in glacial chronosequences, productive soils under different land use and management, and soils under risk of degradation.

The soil food web was expected to build up in biomass and structure, be highest in the intermediate soils, and decrease in soils at or nearby degradation. This was indeed the case when comparing developing soils in the chronosequences, and comparing productive soils with degrading soils. But also land use type turned out to be very important for the structure of the soil food web. Biological measures such as biomass, activity and diversity of soil organisms, especially that of soil microarthropods, were found to be indicative for soil quality in all sites.

I also investigated the possible role of soil organisms in the soil ecosystem functioning, in terms of soil structure formation and C and N mineralisation. Although soil organisms are known to have an important role on soil structure formation, no clear indications of such a role were found for that function in the studied sites. However, soil microbial biomass and activity, and the biomass of other trophic groups, did play a crucial role in soil ecosystem process rates, especially the C and N mineralisation rates.

In conclusion, I have found that soil food webs assemble in a directive manner: organism biomass and activity increase with soil productivity. In productive soils, land use type and land management are the main drivers affecting soil food web structure and functioning, although this effect is limited to the topsoil. Under harsh conditions, soil organisms reach a relatively low biomass and are sensitive to aspects of intensive agricultural land use.

Food web stability and weighted connectance : the complexity-stability debate revisited
Altena, Cassandra van; Hemerik, Lia ; Ruiter, Peter C. de - \ 2016
Theoretical Ecology (2016). - ISSN 1874-1738 - p. 49 - 58.
Jacobian matrix - Link distribution - Weighted connectance

How the complexity of food webs relates to stability has been a subject of many studies. Often, unweighted connectance is used to express complexity. Unweighted connectance is measured as the proportion of realized links in the network. Weighted connectance, on the other hand, takes link weights (fluxes or feeding rates) into account and captures the shape of the flux distribution. Here, we used weighted connectance to revisit the relation between complexity and stability. We used 15 real soil food webs and determined the feeding rates and the interaction strength matrices. We calculated both versions of connectance, and related these structural properties to food web stability. We also determined the skewness of both flux and interaction strength distributions with the Gini coefficient. We found no relation between unweighted connectance and food web stability, but weighted connectance was positively correlated with stability. This finding challenges the notion that complexity may constrain stability, and supports the ‘complexity begets stability’ notion. The positive correlation between weighted connectance and stability implies that the more evenly flux rates were distributed over links, the more stable the webs were. This was confirmed by the Gini coefficients of both fluxes and interaction strengths. However, the most even distributions of this dataset still were strongly skewed towards small fluxes or weak interaction strengths. Thus, incorporating these distribution with many weak links via weighted instead of unweighted food web measures can shed new light on classical theories.

Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe
Creamer, R.C. ; Hannula, S.E. ; Leeuwen, J.P. van; Stone, D. ; Rutgers, M. ; Schmelz, R.M. ; Ruiter, P.C. de; Bohse Hendriksen, N. ; Bolger, T. ; Bouffaud, M.L. ; Buee, M. ; Calvalho, F. ; Costa, D. ; Dirilgen, T. ; Francisco, R. ; Griffiths, B.S. ; Griffiths, R. ; Martin, F. ; Martins da Silva, P. ; Mendes, S. ; Morais, P.V. ; Pereira, C. ; Philippot, L. ; Plassart, P. ; Redecker, D. ; Römbke, J. ; Sousa, J.P. ; Wouterse, M. ; Lemanceau, P. - \ 2016
Applied Soil Ecology 97 (2016). - ISSN 0929-1393 - p. 112 - 124.
Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.
Patterns in intraspecific interaction strengths and the stability of food webs
Altena, C. van; Hemerik, L. ; Heesterbeek, J.A.P. ; Ruiter, P.C. de - \ 2016
Theoretical Ecology 9 (2016)1. - ISSN 1874-1738 - p. 95 - 106.
A common approach to analyse stability of biological communities is to calculate the interaction strength matrix. Problematic in this approach is defining intraspecific interaction strengths, represented by diagonal elements in the matrix, due to a lack of empirical data for these strengths. Theoretical studies have shown that an overall increase in these strengths enhances stability. However, the way in which the pattern in intraspecific interaction strengths, i.e. the variation in these strengths between species, influences stability has received little attention. We constructed interaction strength matrices for 11 real soil food webs in which four patterns for intraspecific interaction strengths were chosen, based on the ecological literature. These patterns included strengths that were (1) similar for all species, (2) trophic level dependent, (3) biomass dependent, or (4) death rate dependent. These four patterns were analysed for their influence on (1) ranking food webs by their stability and (2) the response in stability to variation of single interspecific interaction strengths. The first analysis showed that ranking the 11 food webs by their stability was not strongly influenced by the choice of diagonal pattern. In contrast, the second analysis showed that the response of food web stability to variation in single interspecific interaction strengths was sensitive to the choice of diagonal pattern. Notably, stability could increase using one pattern and decrease using another. This result asks for deliberate approaches to choose diagonal element values in order to make predictions on how particular species, interactions, or other food web parameters affect food web stability.
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