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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A predictive strategy for mapping locations where future MOSSFA events are expected
Murk, A.J. ; Hollander, D.J. ; Chen, S. ; Hu, C. ; Liu, Y. ; Vonk, S.M. ; Schwing, Patrick T. ; Gilbert, S. ; Foekema, E.M. - \ 2019
In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 355 - 368.
A MOSSFA (marine oil snow sedimentation and flocculent accumulation) event was the reason that substantial amounts of the spilled oil were transported to the seafloor during the Deepwater Horizon (DWH) oil well blowout. The region-wide sinking and flocculent accumulation of marine oil snow on the sediment surface changed redox conditions, slowed down the biodegradation of the oil, and increased the spatial and temporal impacts on the benthic community and habitat suitability. Recent field research has confirmed that, in addition to the DWH MOSSFA event in the northern Gulf of Mexico (nGoM), another extensive MOSSFA event occurred in a biologically sensitive area in the southern Gulf of Mexico (sGoM) during the 1979 - 1980 Ixtoc I oil well blowout. Thus, MOSSFA events are not unexpected and have the potential to not only alter sediment chemical conditions but also to extend, expand, and intensify the ecological impact of an oil spill. Consequently this risk should be taken into consideration when preparing response...
Effect of marine snow on microbial oil degradation
Langenhoff, A.A.M. ; Rahsepar, S.A. ; Eenennaam, J.S. van; Radović, Jagoš R. ; Oldenburg, Thomas B.P. ; Foekema, E.M. ; Murk, A.J. - \ 2019
In: Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 301 - 311.
In the aftermath of an oil spill, a possible response is the addition of chemical dispersants to prevent further spreading of the spilled oil on the ocean surface. The main objective is to enhance the formation of smaller oil droplets by reducing the interfacial tension between oil and water, thus dispersing the oil into the water column. The resulting solubilized oil with microdroplets along with the associated toxic compounds will be swiftly incorporated into the seawater. The formation of smaller oil droplets and the dispersant enhanced solubilized oil will increase its availability for bacteria and thus the biodegradability. Subsequently, the number and activity of oil-degrading bacteria increases, and more oil will be degraded in a shorter period of time (Kessler et al., Science 331:312–315, 2011). However, during the immediate release of the dispersed oil, volatile hydrocarbons including some of the more toxic compounds of benzene, toluene, ethylbenzene, and xylenes (BTEX) can inhibit the oil degradation (Sherry et al., Front Microbiol 5:131, 2014).
Depending on the oceanic conditions, the addition of chemical dispersants can result in excessive formation of marine snow. It has been shown that the application of dispersants during phytoplankton blooms can trigger the formation of marine snow to which the sticky dispersed oil can bind. In the presence of mineral particles, oiled snow complexes are being formed that become negatively buoyant and sink to the ocean floor. As a result, oiled marine snow accumulates on the ocean floor where biodegradation is inhibited due to oxygen depletion.
The abovementioned two mechanisms of inhibition of oil biodegradation upon application of oil spill dispersants will be discussed in this chapter.
Testing the Effect of MOSSFA (Marine Oil Snow Sedimentation and Flocculent Accumulation) Events in Benthic Microcosms
Foekema, E.M. ; Eenennaam, Justine van; Hollander, D.J. ; Langenhoff, A.A.M. ; Oldenburg, Thomas B.P. ; Radović, Jagoš R. ; Rohal, Melissa ; Romero, Isabel C. ; Schwing, Patrick T. ; Murk, A.J. - \ 2019
In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 288 - 299.
In multispecies experiments performed in microcosms with natural sediment, it was investigated how the presence of marine snow affects the fate and ecological impact of deposited oil residues. The response of different taxonomic groups like nematodes, foraminifera, crustaceans and molluscs onto the presence of marine snow with or without oil was compared with the impact of deposited oil residues without marine snow. Also the effect of the presence of marine snow on oil biodegradation and transfer for oil-derived compounds to selected biota was studied. Although not designed to mimic the specific deep sea conditions in the Gulf of Mexico, the outcome of the experiments gave new insights in how a MOSSFA event can affect the benthic community. In general the experments indicated that at field realistic oil-derived compound concentrations, the adverse impact of the marine snow on the sediment surface has a stronger impact on the benthic ecosystem than...
Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants
Wilschut, Rutger A. ; Geisen, Stefan ; Martens, Henk ; Kostenko, Olga ; Hollander, Mattias de; Hooven, Freddy C. ten; Weser, Carolin ; Snoek, L.B. ; Bloem, Janneke ; Caković, Danka ; Čelik, Tatjana ; Koorem, Kadri ; Krigas, Nikos ; Manrubia, Marta ; Ramirez, Kelly S. ; Tsiafouli, Maria A. ; Vreš, Branko ; Putten, Wim H. van der - \ 2019
Global Change Biology 25 (2019)8. - ISSN 1354-1013 - p. 2714 - 2726.
Centaurea stoebe - enemy release hypothesis - plant-pathogenic nematodes - range expansion - range-expanding plant species - root-feeding nematodes

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change-driven intracontinental range-expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range-expanding and four congeneric native species along a 2,000 km latitudinal transect from South-Eastern to North-Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range-expanding plant species than in congeneric natives and that in their new range, range-expanding plant species accumulate fewest root-feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range-expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range-expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root-feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range-expanding and native plant species and that some range-expanding plant species may become released from root-feeding nematodes in the new range.

Non-fasting bioelectrical impedance analysis in cystic fibrosis: Implications for clinical practice and research
Hollander-Kraaijeveld, F.M. ; Lindeman, Y. ; Roos, N.M. de; Burghard, M. ; Graaf, E.A. van de; Heijerman, H.G.M. - \ 2019
Journal of Cystic Fibrosis (2019). - ISSN 1569-1993
Anthropometry - Body composition - Cystic fibrosis - FEV1%pred - Non-fasting - Single frequency bioelectrical impedance analysis

Background: Nutritional status affects pulmonary function in cystic fibrosis (CF) patients and can be monitored by using bioelectrical impedance analysis (BIA). BIA measurements are commonly performed in the fasting state, which is burdensome for patients. We investigated whether fasting is necessary for clinical practice and research. Methods: Fat free mass (FFM) and fat mass (FM) were determined in adult CF patients (n = 84) by whole body single frequency BIA (Bodystat 500) in a fasting and non-fasting state. Fasting and non-fasting BIA outcomes were compared with Bland-Altman plots. Pulmonary function was expressed as Forced Expiratory Volume at 1 s percentage predicted (FEV1%pred). Comparability of the associations between fasting and non-fasting body composition measurements with FEV1%pred was assessed by multiple linear regression. Results: Fasting FFM, its index (FFMI), and phase angle were significantly lower than non-fasting estimates (−0.23 kg, p = 0.006, −0.07 kg/m2, p = 0.002, −0.10°, p = 0.000, respectively). Fasting FM and its index (FMI) were significantly higher than non-fasting estimates (0.22 kg, p = 0.008) 0.32%, p = 0.005, and 0.07 kg/m2, (p = 0.005). Differences between fasting and non-fasting FFM and FM were <1 kg in 86% of the patients. FFMI percentile estimates remained similar in 83% of the patients when measured after nutritional intake. Fasting and non-fasting FFMI showed similar associations with FEV1%pred (β: 4.3%, 95% CL: 0.98, 7.70 and β: 4.6%, 95% CI: 1.22, 8.00, respectively). Conclusion: Differences between fasting and non-fasting FFM and FM were not clinically relevant, and associations with pulmonary function remained similar. Therefore, BIA measurements can be performed in a non-fasting state.

Voedingsexperts over listeria: voedingsindustrie laat steken vallen
Beumer, Rijkelt - \ 2018

Het aantal teruggeroepen voedingsproducten vanwege de ziekmakende listeriabacterie is de afgelopen tijd enorm toegenomen. In de afgelopen 365 dagen stond de teller op veertien, terwijl het jaar ervoor maar vier meldingen telde.

Balans van de Leefomgeving 2018 : Nederland duurzaam vernieuwen
Egmond, Petra van; Elzenga, Hans ; Buitelaar, Edwin ; Eerdt, Martha van; Eskinasi, Martijn ; Franken, Ron ; Gaalen, Frank van; Hanemaaijer, Aldert ; Hilbers, Hans ; Hollander, Guus de; Nijland, Hans ; Ritsema van Eck, Jan ; Ros, Jan ; Schilder, Frans ; Spoon, Martijn ; Uitbeijerse, Gabrielle ; Wouden, Ries van der; Vonk, Marijke ; Vugteveen, Pim ; Goossen, Martijn ; Blom, Wim ; Bredenoord, Hendrien ; Brink, Thelma van den; Evers, David ; Doren, Didi van; Grinsven, Hans van; Hinsberg, Arjen van; Muilwijk, Hanneke ; Oorschot, Mark van; Peeters, Jeroen ; Puijenbroek, Peter van; Raspe, Otto ; Rijn, Frank van; Schijndel, Marian van; Sluis, Sietske van der; Sorel, Niels ; Timmerhuis, Jacqueline ; Verwest, Femke ; Westhoek, Henk ; Sanders, Marlies ; Dirkx, Joep - \ 2018
Den Haag : Planbureau voor de Leefomgeving - 284
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.
Nederlandse en Franse vissers zijn verwikkeld in een visoorlog: 'Waar de Hollander vist, blijft voor ons niks over'
Rijnsdorp, Adriaan - \ 2017
Fungal diversity and potential tree pathogens in decaying logs and stumps
Wal, Annemieke van der; klein Gunnewiek, Paulien ; Hollander, Mattias de; Boer, Wietse de - \ 2017
Forest Ecology and Management 406 (2017). - ISSN 0378-1127 - p. 266 - 273.
Fungal diversity - Fungal tree pathogens - Heartwood - Illumina MiSeq sequencing of ITS - LOGLIFE - Wood decomposition
Different types of dead wood in forest ecosystems contribute to an increase of habitats for decomposer fungi. This may have a positive effect on fungal diversity but may also increase habitats for tree pathogens. In this study we investigate the fungal diversity and composition via high-throughput sequencing in decaying stumps and logs (three years after cutting) of two tree species (Larix kaempferi and Quercus rubra) in a forest site. Fungal diversity and composition in decaying wood was different between tree species, between stumps and logs of the same tree species, and between sapwood and heartwood. When different wood sources were combined, fungal species diversity increased. This indicates that different wood sources contribute to fungal diversity and, therefore, species conservation in forests. Potential fungal tree pathogens were found in L. kaempferi stumps and logs, whereas their occurrence was generally less in Q. rubra wood sources. No clear difference was found in the relative abundance of potential fungal tree pathogens between stumps and logs, but some potential tree pathogens were only found in either stumps or logs. This indicates that both logs and stumps can be habitats for potential fungal tree pathogens, and each wood type seems to harbor different fungal tree pathogens. In conclusion, forest management practices that aim at maintaining different types of dead wood seem to positively affect fungal diversity, but may additionally increase the risk of survival of potential tree pathogens. This potential risk seems to depend on the tree species.
The optimal approach to nutrition and cystic fibrosis : Latest evidence and recommendations
Hollander, Francis M. ; Roos, Nicole M. de; Heijerman, Harry G.M. - \ 2017
Current Opinion in Pulmonary Medicine 23 (2017)6. - ISSN 1070-5287 - p. 556 - 561.
cystic fibrosis - cystic fibrosis transmembrane conductance regulator - evidence-based guidelines - nutrition - pulmonary function

Purpose of review Cystic fibrosis (CF) is a progressive genetic disease that affects multiple organ systems. Therapy is directed to maintain and optimize nutritional status and pulmonary function, as these are key factors in survival. In this review, the most recent findings regarding nutritional management associated with pulmonary function and outcome will be explored. Recent findings Evidence-based and expert-based guidelines emphasize the need for adequate nutritional intake to improve nutritional status. For infants and young children, the aim is to achieve the 50th percentile of weight and length for a healthy same-age population up to age 2 years. For older children and adolescents 2-18 years, the target is a BMI of at or above the 50th percentile for healthy children. For CF adults of at least 18 years, the target is a BMI of at or above 22kg/m2 for women and at or above 23kg/m2 for men. Recently, new drugs are developed with the aim to treat the malfunction of the cystic fibrosis transmembrane conductance regulator gene. This potentiator/corrector therapy improves lung function and nutritional status and decreases the number of infective exacerbations. As survival is improving and the CF population is aging, it is important to focus on micronutrient and macronutrient intake of CF patients in different age and disease stages. Summary Recent evidence-based nutritional guidelines and improved medical treatment support the nutritional monitoring and interventions in CF patients. Nutritional care should be personalized and provided by a specialized CF dietitian because patients' care needs may change dramatically during their disease progress.

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture
Hannula, S.E. ; Morriën, Elly ; Hollander, Mattias de; Putten, Wim H. Van Der; Veen, Johannes A. van; Boer, Wietse De - \ 2017
ISME Journal 11 (2017)10. - ISSN 1751-7362 - p. 2294 - 2304.
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13 CO 2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13 C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13 C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
Pérez-Jaramillo, Juan E. ; Carrión, Víctor J. ; Bosse, Mirte ; Ferrão, Luiz F.V. ; Hollander, Mattias de; Garcia, Antonio Augusto Franco ; Ramírez, Camilo A. ; Mendes, Rodrigo ; Raaijmakers, Jos M. - \ 2017
ISME Journal 11 (2017)10. - ISSN 1751-7362 - p. 2244 - 2257.
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
Body Weight and Body Mass Index in Patients with End-Stage Cystic Fibrosis Stabilize After the Start of Enteral Tube Feeding
Hollander, Francis M. ; Roos, Nicole M. de; Belle-Van Meerkerk, Gerdien ; Teding van Berkhout, Ferdinand ; Heijerman, Harry G.M. ; Graaf, Ed A. van de - \ 2017
Journal of the Academy of Nutrition and Dietetics 117 (2017)11. - ISSN 2212-2672 - p. 1808 - 1815.
Body mass index - Cystic fibrosis-related diabetes - End-stage lung disease - Enteral tube feeding - Pulmonary function
Background: Enteral tube feeding (ETF) is widely used in patients with cystic fibrosis (CF) and end-stage lung disease, but previous studies have been limited to investigating whether ETF improves outcomes in patients with moderately or mildly impaired pulmonary function. Objective: This study investigated body weight, body mass index (BMI; calculated as kg/m2), pulmonary function, and the presence of CF-related diabetes before and after the start of ETF. Design: This was a retrospective observational study. Participants/setting: Data from 26 adult patients in an outpatient setting who had end-stage CF (19 women) and had been using ETF for at least 6 months between 2000 and 2014 were analyzed. Main outcome measures: Body weight, BMI, pulmonary function (forced expiratory volume in 1 second as percent of predicted) and incidence of CF-related diabetes from 6 months before to 6 months after starting ETF. Statistical analyses performed: Time effects were tested with one-way analysis of variance for data that were normally distributed and the Friedman test for non-parametric data. Correlations were tested with Pearson's r or Spearman's ρ, depending on the distribution of the data. Results: Mean body weight increased by 3.5 kg (95% CI 2.2 to 4.8 kg) after patients started ETF. In women, mean BMI decreased by 0.7 in the 6 months before the start of ETF (P<0.05) and increased by 1.4 in the 6 months thereafter (P<0.05). In men, BMI changes were similar (-0.8 and +1.1), but not statistically significant. Forced expiratory volume in 1 second as percent of predicted significantly decreased in time from a median of 28% to 26% at the start of ETF to 25% after 6 months (P=0.0013), with similar trends in women and men. There was no correlation between changes in weight and lung function. CF-related diabetes was already present in 12 patients and developed in 1 more patient after the start of ETF. Conclusions: ETF improved body weight and BMI but not pulmonary function in 26 patients with end-stage CF. Clinical outcomes were similar in women and men, but the sample size of men was too small to determine statistical significance.
Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity
Dassen, Sigrid ; Cortois, Roeland ; Martens, Henk ; Hollander, Mattias de; Kowalchuk, George A. ; Putten, Wim H. van der; Deyn, Gerlinde B. De - \ 2017
Molecular Ecology 26 (2017)15. - ISSN 0962-1083 - p. 4085 - 4098.
Arbuscular mycorrhizal fungi - Microbial diversity - Plant community diversity - Rhizobia - α-diversity - β-diversity
Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.
Quantification of simulated cow urine puddle areas using a thermal IR camera
Snoek, Dennis ; Hofstee, Jan Willem ; Dueren den Hollander, Arjen W. van; Vernooij, Roel E. ; Ogink, Nico W.M. ; Groot Koerkamp, Peter W.G. - \ 2017
Computers and Electronics in Agriculture 137 (2017). - ISSN 0168-1699 - p. 23 - 28.
Adaptive threshold - Ammonia emission - Cow urine - Infrared camera - Puddle area

In Europe, National Emission Ceilings (NEC) have been set to regulate the emissions of harmful gases, like ammonia (NH3). From NH3 emission models and a sensitivity analysis, it is known that one of the major variables that determines NH3 emission from dairy cow houses is the urine puddle area on the floor. However, puddle area data from cow houses is scarce. This is caused by the lack of appropriate measurement methods and the challenging measurement circumstances in the houses. In a preliminary study inside commercial dairy cow houses, an IR camera was successfully tested to distinguish a fresh urine puddle from its background to determine a puddle's area. The objective of this study was to further develop, improve and validate the IR camera method to determine the area of a warm fluid layer with a measurement uncertainty of <0.1 m2. In a laboratory set-up, 90 artificial, warm, blue puddles were created, and both an IR and a colour image of each puddle was taken within 5 s after puddle application. For the colour images, three annotators determined the ground truth puddle areas (Ap,GT). For the IR images, an adaptive IR threshold algorithm was developed, based on the mean background temperature and the standard deviation of all temperature values in an image. This IR algorithm was able to automatically determine the IR puddle area (Ap,IR) in each IR image. The agreement between the two methods was assessed. The Ap,IR underestimated the Ap,GT by 2.53% for which is compensated by the model Ap,GT=1.0253·Ap,IR. This regression model intercepted with zero and the noise was only 0.0651 m2, so the measurement uncertainty was <0.1 m2. In addition, the Ap,IR was not affected by the mean background temperature.

Successive DNA extractions improve characterization of soil microbial communities
Rocha Dimitrov, Mauricio ; Veraart, Annelies J. ; Hollander, Mattias de; Smidt, Hauke ; Veen, Johannes A. van; Kuramae, Eiko E. - \ 2017
PeerJ 5 (2017). - ISSN 2167-8359
454-pyrosequencing - Soil bacterial community - Soil DNA extractions - Soil fungal community - Soil microbial abundance - Soil microbial characterization - T-RFLP

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.

Prediction Equations Underestimate Resting Energy Expenditure in Patients with End-Stage Cystic Fibrosis
Hollander, Francis M. ; Kok, Annemieke ; Roos, Nicole M. de; Belle-Van Meerkerk, Gerdien ; Graaf, Ed A. van de - \ 2017
Nutrition in Clinical Practice 32 (2017)1. - ISSN 0884-5336 - p. 116 - 121.
calorie requirements - cystic fibrosis - end-stage lung disease - energy metabolism - energy prediction equations - indirect calorimetry - lung transplantation - resting energy expenditure

Background: Resting energy expenditure (REE) is increased in patients with cystic fibrosis (CF) with end-stage lung disease due to chronic inflammation and pulmonary infections. After lung transplantation (LTx), energy expenditure is expected to be lower because inflammation will decrease. We assessed the agreement between measured and predicted REE in pre-LTx CF and post-LTx patients with CF and differences in REE in pre-LTx CF and post-LTx patients with CF in a cross-sectional study. Methods: Included were 12 pre-LTx patients with CF (9 women; median age 31.6 years; interquartile range [IQR], 23.3-40.0) and 12 patients with CF within 2 years after LTx (6 women; median age 33.5 years; IQR, 22.3-40.3). REE was measured in a fasted state using indirect calorimetry. Values were compared with predicted REE calculated by formulas of Harris-Benedict (1919 and 1984), Schofield, and the World Health Organization (1985). A calculated REE between 90% and 110% of REE measured was considered adequate. Results: Prediction equations underestimate REE in at least 75% of pre-LTx and 33% of post-LTx patients with CF. Mean (SD) REE measured by indirect calorimetry was 1735 (251) kcal pre-LTx and 1650 (235) kcal post-LTx (P =.40). REE expressed per kilogram of fat-free mass (FFM) was 40.5 kcal/kg in pre-LTx patients with CF, which was higher than the 34.3 kcal/kg in post-LTx patients with CF (P =.01). Conclusions: Prediction equations underestimate REE in patients with end-stage CF. REE per kg of FFM is lower post-LTx than pre-LTx in patients with CF. Measurement of REE is recommended for patients with CF, especially pre-LTx, to optimize energy requirements for improving nutrition status.

Soil networks become more connected and take up more carbon as nature restoration progresses
Morriën, W.E. ; Hannula, S.E. ; Snoek, L.B. ; Helmsing, N.R. ; Zweers, Hans ; Hollander, M. de; Soto, Raquel Luján ; Bouffaud, Marie Lara ; Buée, M. ; Dimmers, W.J. ; Duyts, Henk ; Geisen, Stefan ; Girlanda, Mariangela ; Griffiths, R.I. ; Jorgensen, H.B. ; Jensen, J. ; Plassart, P. ; Redecker, Dirk ; Schmelz, R.M. ; Schmidt, Olaf ; Thomson, Bruce C. ; Tisserant, Emilie ; Uroz, Stephane ; Winding, Anne ; Bailey, M.J. ; Bonkowski, M. ; Faber, J.H. ; Martin, F. ; Lemanceau, Philippe ; Boer, W. de; Veen, J.A. van; Putten, W.H. van der - \ 2017
Nature Communications 8 (2017). - ISSN 2041-1723 - 10 p.
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
Beheer van Muskusratten in Nederland : Effectiviteit van bestrijding op grond van historie en een grootschalige veldproef: Deel I – Samenvatting tussenrapportage
Bos, D. ; Klop, E. ; Hemert, H. van; Haye, M.J.J. la; Hollander, H. ; Loon, E. van; Ydenberg, R. - \ 2016
Feanwâlden : Altenburg & Wymenga (A&amp;W-rapport 2191) - 46 p.
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