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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The importance of surface reflectance anisotropy for cloud and NO2 retrievals from GOME-2 and OMI
Lorente, Alba ; Boersma, K.F. ; Stammes, Piet ; Tilstra, L.G. ; Richter, Andreas ; Yu, Huan ; Kharbouche, Said ; Muller, Jan Peter - \ 2018
Atmospheric Measurement Techniques 11 (2018)7. - ISSN 1867-1381 - p. 4509 - 4529.

The angular distribution of the light reflected by the Earth's surface influences top-of-atmosphere (TOA) reflectance values. This surface reflectance anisotropy has implications for UV/Vis satellite retrievals of albedo, clouds, and trace gases such as nitrogen dioxide (NO2). These retrievals routinely assume the surface to reflect light isotropically. Here we show that cloud fractions retrieved from GOME-2A and OMI with the FRESCO and OMCLDO2 algorithms have an east-west bias of 10% to 50 %, which are highest over vegetation and forested areas, and that this bias originates from the assumption of isotropic surface reflection. To interpret the across-track bias with the DAK radiative transfer model, we implement the bidirectional reflectance distribution function (BRDF) from the Ross-Li semi-empirical model. Testing our implementation against state-of-the-art RTMs LIDORT and SCIATRAN, we find that simulated TOA reflectance generally agrees to within 1 %. We replace the assumption of isotropic surface reflection in the equations used to retrieve cloud fractions over forested scenes with scattering kernels and corresponding BRDF parameters from a daily high-resolution database derived from 16 years' worth of MODIS measurements. By doing this, the east-west bias in the simulated cloud fractions largely vanishes. We conclude that across-track biases in cloud fractions can be explained by cloud algorithms that do not adequately account for the effects of surface reflectance anisotropy. The implications for NO2 air mass factor (AMF) calculations are substantial. Under moderately polluted NO2 and backwardscattering conditions, clear-sky AMFs are up to 20% higher and cloud radiance fractions up to 40% lower if surface anisotropic reflection is accounted for. The combined effect of these changes is that NO2 total AMFs increase by up to 30% for backward-scattering geometries (and decrease by up to 35% for forward-scattering geometries), which is stronger than the effect of either contribution alone. In an unpolluted troposphere, surface BRDF effects on cloud fraction counteract (and largely cancel) the effect on the clearsky AMF. Our results emphasise that surface reflectance anisotropy needs to be taken into account in a coherent manner for more realistic and accurate retrievals of clouds and NO2 from UV/Vis satellite sensors. These improvements will be beneficial for current sensors, in particular for the recently launched TROPOMI instrument with a high spatial resolution.

Presence of anti-Müllerian hormone (AMH) during follicular development in the porcine ovary
Almeida, Fernanda R.C.L. ; Costermans, Natasja G.J. ; Soede, Nicoline M. ; Bunschoten, Annelies ; Keijer, Jaap ; Kemp, Bas ; Teerds, Katja J. - \ 2018
PLoS One 13 (2018)7. - ISSN 1932-6203

Background Anti-Müllerian hormone (AMH) is expressed by granulosa cells of developing follicles and plays an inhibiting role in the cyclic process of follicular recruitment by determining follicle-stimulating hormone threshold levels. Knowledge of AMH expression in the porcine ovary is important to understand the reproductive efficiency in female pigs. Research aim In the present study we investigated the expression of AMH during follicular development in prepubertal and adult female pigs by immunohistochemistry, laser capture micro-dissection and RT-qPCR. Results and conclusion Although in many aspects the immunohistochemical localization of AMH in the porcine ovary does not differ from other species, there are also some striking differences. As in most species, AMH appears for the first time during porcine follicular development in the fusiform granulosa cells of recruited primordial follicles and continues to be present in granulosa cells up to the antral stage. By the time follicles reach the pre-ovulatory stage, AMH staining intensity increases significantly, and both protein and gene expression is not restricted to granulosa cells; theca cells now also express AMH. AMH continues to be expressed after ovulation in the luteal cells of the corpus luteum, a phenomenon unique to the porcine ovary. The physiological function of AMH in the corpus luteum is at present not clear. One can speculate that it may contribute to the regulation of the cyclic recruitment of small antral follicles. By avoiding premature exhaustion of the ovarian follicular reserve, AMH may contribute to optimization of reproductive performance in female pigs.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity
Schurink, Anouk ; Silva, Vinicius H. da; Velie, Brandon D. ; Dibbits, Bert W. ; Crooijmans, Richard P.M.A. ; François, Liesbeth ; Janssens, Steven ; Stinckens, Anneleen ; Blott, Sarah ; Buys, Nadine ; Lindgren, Gabriella ; Ducro, Bart J. - \ 2018
BMC Genetics 19 (2018)1. - ISSN 1471-2156
Copy number variations - Friesian horse - Genome-wide association study - Insect bite hypersensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Continental-scale macrofungal assemblage patterns correlate with climate, soil carbon and nitrogen deposition
Andrew, Carrie ; Halvorsen, Rune ; Heegaard, Einar ; Kuijper, Thomas W. ; Heilmann-Clausen, Jacob ; Krisai-Greilhuber, Irmgard ; Bässler, Claus ; Egli, Simon ; Gange, Alan C. ; Høiland, Klaus ; Kirk, Paul M. ; Senn-Irlet, Beatrice ; Boddy, Lynne ; Büntgen, Ulf ; Kauserud, Håvard - \ 2018
Journal of Biogeography 45 (2018)8. - ISSN 0305-0270 - p. 1942 - 1953.
assemblage - biogeography - climate - ectomycorrhizal - Europe - fungi - macroecology - saprotrophic - temporal change

Aim: Macroecological scales of species compositional trends are well documented for a variety of plant and animal groups, but remain sparse for fungi, despite their ecological importance in carbon and nutrient cycling. It is, thus, essential to understand the composition of fungal assemblages across broad geographical scales and the underlying drivers. Our overall aim was to describe these patterns for fungi across two nutritional modes (saprotrophic and ectomycorrhizal). Furthermore, we aimed to elucidate the temporal component of fruiting patterns and to relate these to soil carbon and nitrogen deposition. Location: Central and Northern Europe. Methods: A total of 4.9 million fungal fruit body observations throughout Europe, collected between 1970 and 2010, were analysed to determine the two main environmental and geographical gradients structuring fungal assemblages for two main nutritional modes, saprotrophic and ectomycorrhizal fungi. Results: Two main gradients explaining the geography of compositional patterns were identified, for each nutritional mode. Mean annual temperature (and related collinear, seasonal measures) correlated most strongly with the first gradient for both nutritional modes. Soil organic carbon was the highest correlate of the second compositional gradient for ectomycorrhizal fungi, suspected as an indicator of vegetation- and pH-related covariates. In contrast, nitrogen deposition constituted a second gradient for saprotrophic fungi, likely a proxy for anthropogenic pollution. Compositional gradients and environmental conditions correlated similarly when the data were divided into two time intervals of 1970–1990 and 1991–2010. Evidence of compositional temporal change was highest with increasing elevation and latitude. Main conclusions: Fungal assemblage patterns demonstrate clear biogeographical patterns that relate the nutritional modes to their main environmental correlates of temperature, soil organic carbon and nitrogen deposition. With respect to global change impacts, the highest rates of compositional change by time suggest targeting higher latitudes and elevations for a better understanding of fungal dynamics. We, finally, suggest further examination of the ranges and dispersal abilities of fungi to better assess responses to global change.

Tradeoffs in the quest for climate smart agricultural intensification in Mato Grosso, Brazil
Gil, Juliana D.B. ; Garrett, Rachael D. ; Rotz, Alan ; Daioglou, Vassilis ; Valentim, Judson ; Pires, Gabrielle F. ; Costa, Marcos H. ; Lopes, Luciano ; Reis, Julio C. - \ 2018
Environmental Research Letters 13 (2018)6. - ISSN 1748-9318
climate scenarios - integrated crop-livestock systems - low carbon agriculture - pasture intensification - sustainability

Low productivity cattle ranching, with its linkages to rural poverty, deforestation and greenhouse gas (GHG) emissions, remains one of the largest sustainability challenges in Brazil and has impacts worldwide. There is a nearly universal call to intensify extensive beef cattle production systems to spare land for crop production and nature and to meet Brazil's Intended Nationally Determined Contribution to reducing global climate change. However, different interventions aimed at the intensification of livestock systems in Brazil may involve substantial social and environmental tradeoffs. Here we examine these tradeoffs using a whole-farm model calibrated for the Brazilian agricultural frontier state of Mato Grosso, one of the largest soybean and beef cattle production regions in the world. Specifically, we compare the costs and benefits of a typical extensive, continuously grazed cattle system relative to a specialized soybean production system and two improved cattle management strategies (rotational grazing and integrated soybean-cattle) under different climate scenarios. We found clear tradeoffs in GHG and nitrogen emissions, climate resilience, and water and energy use across these systems. Relative to continuously grazed or rotationally grazed cattle systems, the integreated soybean-cattle system showed higher food production and lower GHG emissions per unit of human digestible protein, as well as increased resilience under climate change (both in terms of productivity and financial returns). All systems suffered productivity and profitability losses under severe climate change, highlighting the need for climate smart agricultural development strategies in the region. By underscoring the economic feasibility of improving the performance of cattle systems, and by quantifying the tradeoffs of each option, our results are useful for directing agricultural and climate policy.

Influence of stocking density on growth, digestive enzyme activities, immune responses, antioxidant of Oreochromis niloticus fingerlings in biofloc systems
Liu, Gang ; Ye, Zhangying ; Liu, Dezhao ; Zhao, Jian ; Sivaramasamy, Elayaraja ; Deng, Yale ; Zhu, Songming - \ 2018
Fish and Shellfish Immunology 81 (2018). - ISSN 1050-4648 - p. 416 - 422.
Antioxidant - Biofloc - Digestive enzyme activities - Immune responses - Stocking density - Tilapia

A 120-day feeding trial was conducted to evaluate the effect of different stocking densities on growth, the non-specific immunities, antioxidant status and digestive enzyme activities of Oreochromis niloticus fingerlings under a zero-water exchange biofloc system. Tilapias (0.51 ± 0.05 g) were randomly distributed in twelve tanks, each with 300 L water. The experimental design was completely randomized using three replications with four treatments 166 orgs m−3 (LD, low density), 333 orgs m−3 (MD, middle density) and 600 orgs m−3 (HD, high density) with glucose added as biofloc groups, and a clear water group without glucose added as a control 333 orgs m−3. The fish cultured in LD and MD group showed higher final body weight. For the digestive enzymes, the lipase, trypsin, and amylase activities were all depressed in HD group and control group. Regarding the immune and antioxidant abilities, significantly lower values (P < 0.05) of the lysozyme, complement 3, and glutathione were observed for the fish that reared in the control group and HD group. The stress indicator, the cortisol, 5-hydroxytryptamine, and glucose concentrations were also depressed in HD group and control group, meanwhile the alanine aminotransferase, aspartate transaminase and alkaline phosphatase were all higher in HD group and control group. The significant higher survival was observed in the LD and MD group after Vibrio harveyi challenge test. The results of the experiment indicated that the biofloc in situ had the effects of anti-crowding stress.

Effect of low concentrations of dissolved oxygen on the activity of denitrifying methanotrophic bacteria
Kampman, Christel ; Piai, Laura ; Temmink, Hardy ; Hendrickx, Tim L.G. ; Zeeman, Grietje ; Buisman, Cees J.N. - \ 2018
Water Science and Technology 77 (2018)11. - ISSN 0273-1223 - p. 2589 - 2597.
Anaerobic methane oxidation - Anaerobic wastewater treatment - Denitrification - Methylomirabilis oxyfera - Oxygen

Chemical energy can be recovered from municipal wastewater as biogas through anaerobic treatment. However, effluent from direct anaerobic wastewater treatment at low temperatures still contains ammonium and substantial amounts of dissolved CH4. After nitritation, CH4 can be used as electron donor for denitrification by the anaerobic bacterium Candidatus Methylomirabilis oxyfera. The effect of 0.7% (0.35 mg dissolved O2/L), 1.1% (0.49 mg dissolved O2/L), and 2.0% (1.0 mg dissolved O2/L), on denitrifying activity was tested. Results demonstrated that at 0.7% O2, denitrifying methanotrophic activity slightly increased and returned to its original level after O2 had been removed. At 1.1% O2, CH4 consumption rate increased 118%, nitrite consumption rate increased 58%. After removal of O2, CH4 consumption rate fully recovered, and nitrite consumption rate returned to 88%. These indicate that traces of O2 that bacteria are likely to be exposed to in wastewater treatment are not expected to negatively affect the denitrifying methanotrophic process. The presence of 2.0% O2 inhibited denitrifying activity. Nitrite consumption rate decreased 60% and did not recover after removal of O2. No clear effect on CH4 consumption was observed.

Soil Physical Quality of Citrus Orchards Under Tillage, Herbicide, and Organic Managements
Prima, Simone di; Rodrigo-Comino, Jesús ; Novara, Agata ; Iovino, Massimo ; Pirastru, Mario ; Keesstra, Saskia ; Cerdà, Artemi - \ 2018
Pedosphere 28 (2018)3. - ISSN 1002-0160 - p. 463 - 477.
Beerkan estimation of soil transfer parameter - capacitive indicator - organic farming - soil management - soil quality assessment - structural stability index

Soil capacity to support life and to produce economic goods and services is strongly linked to the maintenance of good soil physical quality (SPQ). In this study, the SPQ of citrus orchards was assessed under three different soil managements, namely no-tillage using herbicides, tillage under chemical farming, and no-tillage under organic farming. Commonly used indicators, such as soil bulk density, organic carbon content, and structural stability index, were considered in conjunction with capacitive indicators estimated by the Beerkan estimation of soil transfer parameter (BEST) method. The measurements taken at the L'Alcoleja Experimental Station in Spain yielded optimal values for soil bulk density and organic carbon content in 100% and 70% of cases for organic farming. The values of structural stability index indicated that the soil was stable in 90% of cases. Differences between the soil management practices were particularly clear in terms of plant-available water capacity and saturated hydraulic conductivity. Under organic farming, the soil had the greatest ability to store and provide water to plant roots, and to quickly drain excess water and facilitate root proliferation. Management practices adopted under organic farming (such as vegetation cover between the trees, chipping after pruning, and spreading the chips on the soil surface) improved the SPQ. Conversely, the conventional management strategies unequivocally led to soil degradation owing to the loss of organic matter, soil compaction, and reduced structural stability. The results in this study show that organic farming has a clear positive impact on the SPQ, suggesting that tillage and herbicide treatments should be avoided.

Gram-positive bacterial extracellular vesicles and their impact on health and disease
Liu, Yue ; Defourny, Kyra A.Y. ; Smid, Eddy J. ; Abee, Tjakko - \ 2018
Frontiers in Microbiology 9 (2018)JUL. - ISSN 1664-302X
Actinobacteria - EV vaccination - Firmicutes - Membrane vesicles - Pathogenicity - Phage therapy - Probiotics

During recent years it has become increasingly clear that the release of extracellular vesicles (EVs) is a feature inherent to all cellular life forms. These lipid bilayer-enclosed particles are secreted by members of all domains of life: Eukarya, Bacteria and Archaea, being similar in size, general composition, and potency as a functional entity. Noticeably, the recent discovery of EVs derived from bacteria belonging to the Gram-positive phyla Actinobacteria and Firmicutes has added a new layer of complexity to our understanding of bacterial physiology, host interactions, and pathogenesis. Being nano-sized structures, Gram-positive EVs carry a large diversity of cargo compounds, including nucleic acids, viral particles, enzymes, and effector proteins. The diversity in cargo molecules may point to roles of EVs in bacterial competition, survival, material exchange, host immune evasion and modulation, as well as infection and invasion. Consequently, the impact of Gram-positive EVs on health and disease are being revealed gradually. These findings have opened up new leads for the development of medical advances, including strategies for vaccination and anti-bacterial treatment. The rapidly advancing research into Gram-positive EVs is currently in a crucial phase, therefore this review aims to give an overview of the groundwork that has been laid at present and to discuss implications and future challenges of this new research field.

Engineering de novo anthocyanin production in Saccharomyces cerevisiae
Levisson, Mark ; Patinios, Constantinos ; Hein, Sascha ; Groot, Philip A. de; Daran, Jean M. ; Hall, Robert D. ; Martens, Stefan ; Beekwilder, Jules - \ 2018
Microbial Cell Factories 17 (2018)1. - ISSN 1475-2859
Anthocyanin - Flavonoids - Metabolic engineering - Natural products - Pelargonidin - Plant secondary metabolites - Saccharomyces cerevisiae

Background: Anthocyanins are polyphenolic pigments which provide pink to blue colours in fruits and flowers. There is an increasing demand for anthocyanins, as food colorants and as health-promoting substances. Plant production of anthocyanins is often seasonal and cannot always meet demand due to low productivity and the complexity of the plant extracts. Therefore, a system of on-demand supply is useful. While a number of other (simpler) plant polyphenols have been successfully produced in the yeast Saccharomyces cerevisiae, production of anthocyanins has not yet been reported. Results: Saccharomyces cerevisiae was engineered to produce pelargonidin 3-O-glucoside starting from glucose. Specific anthocyanin biosynthetic genes from Arabidopsis thaliana and Gerbera hybrida were introduced in a S. cerevisiae strain producing naringenin, the flavonoid precursor of anthocyanins. Upon culturing, pelargonidin and its 3-O-glucoside were detected inside the yeast cells, albeit at low concentrations. A number of related intermediates and side-products were much more abundant and were secreted into the culture medium. To optimize titers of pelargonidin 3-O-glucoside further, biosynthetic genes were stably integrated into the yeast genome, and formation of a major side-product, phloretic acid, was prevented by engineering the yeast chassis. Further engineering, by removing two glucosidases which are known to degrade pelargonidin 3-O-glucoside, did not result in higher yields of glycosylated pelargonidin. In aerated, pH controlled batch reactors, intracellular pelargonidin accumulation reached 0.01 μmol/gCDW, while kaempferol and dihydrokaempferol were effectively exported to reach extracellular concentration of 20 μM [5 mg/L] and 150 μM [44 mg/L], respectively. Conclusion: The results reported in this study demonstrate the proof-of-concept that S. cerevisiae is capable of de novo production of the anthocyanin pelargonidin 3-O-glucoside. Furthermore, while current conversion efficiencies are low, a number of clear bottlenecks have already been identified which, when overcome, have huge potential to enhance anthocyanin production efficiency. These results bode very well for the development of fermentation-based production systems for specific and individual anthocyanin molecules. Such systems have both great scientific value for identifying and characterising anthocyanin decorating enzymes as well as significant commercial potential for the production of, on-demand, pure bioactive compounds to be used in the food, health and even pharma industries.

Apparent ileal digestibility of Maillard reaction products in growing pigs
Salazar-Villanea, Sergio ; Butré, Claire I. ; Wierenga, Peter A. ; Bruininx, Erik M.A.M. ; Gruppen, Harry ; Hendriks, Wouter H. ; Poel, Antonius F.B. van der - \ 2018
PLoS One 13 (2018)7. - ISSN 1932-6203

The absorption of Maillard reaction products (MRP) from dietary origin has been linked to the occurrence of chronic diseases. The aim of the present study was to determine the effects of toasting time of rapeseed meal (RSM) and the processing method of the diets (pelleting and extrusion) that included RSM on the apparent ileal digestibility (AID) of total lysine, fructosyl-lysine (FL), carboxymethyl-lysine (CML), carboxyethyl-lysine (CEL), lanthionine (LAN) and lysinoalanine (LAL) in growing pigs. The study consisted of a 2×3 factorial design with toasting time of RSM (60, 120 min) and diet processing method (mash, pelleted, extruded) as factors. Fifty growing pigs were individually fed one of the experimental diets for 4.5 consecutive days. Following euthanasia, samples of digesta were collected from the terminal 1.5 m of the small intestine. Increasing the toasting time of RSM increased the contents of FL, CML and CEL, whereas the additional effects of the diet processing methods were relatively small. Lysinoalanine and lanthionine were not detected in the diets; therefore, digestibility of these compounds could not be determined. The contents of FL, CML and CEL in the ileal chyme were positively correlated to their contents in the diets. The AID of the MRP from thermally-treated RSM were overall low and were not related to their contents in the diets. The AID of FL ranged between -8.5 and 19.1%, whilst AID of CML and CEL ranged from -0.2 to 18.3 and 3.6 to 30%, respectively. In conclusion, thermal treatments have clear effects on the contents of MRP in the diets. These compounds have relatively low digestibility in growing pigs.

Photographic comparison : a method for qualitative outdoor thermal perception surveys
Cortesão, João ; Brandão Alves, Fernando ; Raaphorst, Kevin - \ 2018
International Journal of Biometeorology (2018). - ISSN 0020-7128 - 13 p.
Field survey - Outdoor - Photographic comparison - Qualitative methods - Thermal perception - Visual semiotics

This article addresses the use of photographic comparison as a complementary visual appraisal method in an outdoor thermal perception survey. This survey was carried out during a Ph.D. research exploring how materials and vegetation influence thermal comfort in outdoor public spaces. Objective and subjective thermal perception parameters were combined and quantitative and qualitative research methods were used. The quantitative methods included microclimatic measurements, whilst the qualitative methods comprised observations and spatially localised interviews based on a questionnaire and the photographic comparison. This article explores how such visual research method allowed triangulating findings of this field survey. Three non-edited photographs of outdoor public spaces, under similar summer meteorological conditions but with contrasting spatial features, were shown to respondents to the questionnaire. The photographs depicted undisclosed locations for preventing biased emotional appreciations. Respondents were asked to select the potentially most comfortable and uncomfortable environments depicted. The choice of photographs matched the previous answers on the thermal sensation and evaluation judgement scales. Hence, we discuss the way the visual interpretations by respondents allowed the triangulation of in situ thermal perception data. The extent to which thermal comfort can be interpreted from thermal environments depicted in photographs containing clear visual signs is further discussed. The article concludes on how such a visual appraisal method can be valuable for enriching future qualitative outdoor thermal perception surveys with subjective interpretation of visual data.

Is land fragmentation facilitating or obstructing adoption of climate adaptation measures in Ethiopia?
Cholo, Tesfaye C. ; Fleskens, Luuk ; Sietz, Diana ; Peerlings, Jack - \ 2018
Sustainability 10 (2018)7. - ISSN 2071-1050
Adaptation - Gamo Highlands - Land fragmentation - Sustainable land management

Land fragmentation is high and increasing in the Gamo Highlands of southwest Ethiopia. We postulate that this substantial land fragmentation is obstructing the adoption of sustainable land management practices as climate adaptation measures. To explore this, a mixed method study was conducted with emphasis on a multivariate probit model. The results indicate that farmers adapt to climate change and variability they perceive. According to the probit model, there is no clear answer to the question whether land fragmentation facilitates or obstructs adoption of sustainable land management practices. Yet, a qualitative analysis found that farmers perceive land fragmentation as an obstacle to land improvement as adaptation strategy. Moreover, farmers invest more in land improvement on plots close to their homestead than in remote plots. However, the higher land fragmentation also promoted crop diversification, manure application and terracing. Although exogenous to farmers, we therefore suggest that land fragmentation can be deployed in climate change adaptation planning. This can be done through voluntary assembling of small neighboring plots in clusters of different microclimates to encourage investment in remote fields and to collectively optimize the benefits of fragmentation to adaptation.

Mosaic structure of the fungal community in the Kislo-Sladkoe Lake that is detaching from the White Sea
Grum-Grzhimaylo, Olga A. ; Debets, Alfons J.M. ; Bilanenko, Elena N. - \ 2018
Polar Biology (2018). - ISSN 0722-4060 - 15 p.
Brackish lake - Coastal rising - Fungal diversity - Glacioisostatic movement

The major part of the north polar region is intensely rising by postglacial crustal movement. This process gives rise to the separation of different basins from seas and oceans, which affects a combination of freshwater and marine organisms. Gradually losing contact with the seas, many near-shore lakes of the Arctic are mostly desalted and form bogs. Fungi as decomposers play an important role in all ecosystems. However, the diversity and role of fungi in Arctic aquatic ecosystems is largely unknown. It is also not clear how the taxonomic structure of the fungal community is affected by the process of gradual desalinization and waterlogging. We investigated the diversity of filamentous culturable fungi in different parts of the brackish Kislo-Sladkoe Lake (White Sea, Russia). Annually, 42 samples of the bottom and coastal soils have been collected at the lake from which fungi were recovered on standard and selective media. Based on morphological and molecular markers, a total of 127 taxa have been identified. The fungal community appeared to be influenced by its sea origin and comprised both marine (Paradendryphiella salina, Acremonium spp.) and terrestrial soil species of Penicillium, Talaromyces, Mucor, Umbelopsis, Cladosporium, Cadophora, Sistotrema, Helotiales, Pleosporales, sphagnum moss destructors (Oidiodendron spp.) and insect-associated species of Tolypocladium. The results indicate that the composition of the fungal community in the rising polar White Sea region reflects the dynamics of global changes in physical–chemical parameters and animal and plant associations because of separation from the sea.

Sex and strain dependent differences in mucosal immunology and microbiota composition in mice
Elderman, Marlies ; Hugenholtz, Floor ; Belzer, Clara ; Boekschoten, Mark ; Beek, Adriaan van; Haan, Bart de; Savelkoul, Huub ; Vos, Paul de; Faas, Marijke - \ 2018
Biology of Sex Differences 9 (2018). - ISSN 2042-6410
Background: A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a sex bias, suggesting sex differences in immune responses and in the intestinal microbiome. We hypothesized that sex differences in immune responses are associated with sex differences in microbiota composition. Methods: Fecal microbiota composition (MITchip), mRNA expression in intestinal tissue (microarray), and immune cell populations in mesenteric lymph nodes (MLNs) were studied in male and female mice of two mouse strains (C57B1/6OlaHsd and Balb/cOlaHsd). Transcriptomics and microbiota data were combined to identify bacterial species which may potentially be related to sex-specific differences in intestinal immune related genes. Results: We found clear sex differences in intestinal microbiota species, diversity, and richness in healthy mice. However, the nature of the sex effects appeared to be determined by the mouse strain as different bacterial species were enriched in males and females of the two strains. For example, Lactobacillus plantarum and Bacteroides distasonis were enriched in B6 females as compared to B6 males, while Bifidobacterium was enriched BALB/c females as compared to BALB/c males. The strain-dependent sex effects were also observed in the expression of immunological genes in the colon. We found that the abundance of various bacteria (e.g., Clostridium leptum et rel.) which were enriched in B6 females positively correlated with the expression of several genes (e.g., Il-2rb, Ccr3, and Cd80) which could be related to immunological functions, such as inflammatory responses and migration of leukocytes. The abundance of several bacteria (e.g., Faecalibacterium prausnitzii et rel. and Coprobacillus et rel.- Clostridium ramosum et rel.) which were enriched in BALB/c males positively correlated to the expression of several genes (e.g., Apoe, Il-1b, and Stat4) related to several immunological functions, such as proliferation and quantity of lymphocytes. The net result was the same, since both mouse strains showed similar sex induced differences in immune cell populations in the MLNs. Conclusions: Our data suggests a correlation between microbiota and intestinal immune populations in a sex and strain-specific way. These findings may contribute to the development of more sex and genetic specific treatments for intestinal-related disorders.
Spatial and risk factor analysis of bovine viral diarrhoea (BVD) virus after the first-year compulsory phase of BVD eradication programme in Northern Ireland
Charoenlarp, W. ; Frankena, K. ; Strain, S.A.J. ; Guelbenzu-Gonzalo, M. ; Graham, J. ; Byrne, A.W. - \ 2018
Preventive Veterinary Medicine 157 (2018). - ISSN 0167-5877 - p. 34 - 43.
Bovine viral diarrhoea virus - Northern Ireland - Risk factors - Spatial analysis - Spatial autocorrelation - Spatial risk factors

Bovine viral diarrhoea virus (BVDV) causes bovine viral diarrhoea (BVD), which is a contagious pathogen that can have a significant economic impact on cattle industries. In Northern Ireland (NI), the compulsory phase of a BVD eradication programme was implemented in 2016. The aim of this retrospective population based study was to utilize herd-level data after the first year of the compulsory phase (March 2016–March 2017) to determine the spatial distribution and variation of BVDV, to identify clusters of infection, and to quantify some risk factors associated with BVD in NI. Global spatial clustering (autocorrelation) and local spatial hot-spot analyses were used to specify the clustering areas (hot- and cold-spot). A suite of multivariable logistic analyses was performed to estimate the associations of spatial and non-spatial factors (relating to herd characteristics) with the risk of being a BVDV positive herd. Final models were compared by evaluating the model fit and the ability to account for spatial autocorrelation in the study area. There were 17,186 herds included in the analysis. The herd-level prevalence of BVDV was 11.31%. Significant spatial clustering of BVDV positive herds was presented in the central region of NI. A mixed effects logistic model, with a spatial random effect term, was considered the best model. The final model showed that a positive BVDV status during the voluntary phase prior to the compulsory phase started (OR = 2.25; CI 95% = 1.85–2.73), larger herd size (OR = 6.19; CI 95% = 5.22–7.34 for herd size > 100 animals) and a larger number of positive nearest neighbours within 4 km radius (OR = 1.24; CI 95% = 1.05–1.47 for 8–9 neighbours and OR = 1.41; CI 95% = 1.20–1.65 for 10–12 neighbours) were significantly related to the risk of a herd being tested positive for BVDV. The clear spatial pattern from the local spatial clustering analyses could be used for targeted surveillance and control measures by focusing on the central region of NI.

Calibration and validation of the AquaCrop model for repeatedly harvested leafy vegetables grown under different irrigation regimes
Nyathi, M.K. ; Halsema, G.E. van; Annandale, J.G. ; Struik, P.C. - \ 2018
Agricultural Water Management 208 (2018). - ISSN 0378-3774 - p. 107 - 119.
Biomass - Crop modelling - Evapotranspiration, indigenous leafy vegetables - Water productivity

Traditional leafy vegetables (TLVs’) are vegetables that were introduced in an area a long time ago, where they adapted to local conditions and became part of the local culture. In Sub-Saharan Africa, the use of TLVs’ as a nutrient dense alternative food source to combat micronutrient deficiency of rural resource-poor households (RRPHs), has gained attention in debates on food and nutrition security. However, TLVs’ are underutilised because of lack of information on their yield response to water and fertiliser. To better assess TLVs’ yield response to water stress, the AquaCrop model was calibrated (using 2013/14 data) and validated (using 2014/15 data) for three repeatedly harvested leafy vegetables [Amaranthus cruentus (Amaranth), Cleome gynandra (Spider flower), and Beta vulgaris (Swiss chard)] in Pretoria, South Africa. Experiments were conducted during two consecutive seasons, in which the selected leafy vegetables were subjected to two irrigation regimes; well-watered (I30) and severe water stress (I80). Measured parameters were canopy cover (CC), soil water content (SWC), aboveground biomass (AGB), actual evapotranspiration (ETa), and water productivity (WP). Statistical indicators [root mean square error (RMSE), RMSE-standard deviation ratio (RSR), R2, and relative deviation] showed good fit between measured and simulated (0.60 < R2 < 0.99, 0.94 < RMSE < 5.44, and 0.04 < RSR < 0.79) values for the well-watered treatment. However, the fit was not as good for the water-stressed treatment for CC, SWC, ETa and WP. Nevertheless, the model simulated the selected parameters satisfactorily. These results revealed that there was a clear difference between transpiration water productivity (WPTr) for C4 crops (Amaranth and Spider flower) and a C3 crop (Swiss chard); WPTr for the C4 crops ranged from 4.61 to 6.86 kg m−3, whereas for the C3 crop, WPTr ranged from 3.11 to 4.43 kg m−3. It is a challenge to simulate yield response of repeatedly harvested leafy vegetables because the model cannot run sequential harvests at one time; therefore, each harvest needs to be simulated separately, making it cumbersome. To design sustainable food production systems that are health-driven and inclusive of RRPHs, we recommend that more vegetables (including traditional vegetables) should be included in the model database, and that sequential harvesting be facilitated.

Suckling Piglets; Fructooligosaccharides
Schokker, D. ; Vastenhouw, S.A. - \ 2018
Sus scrofa - GSE101147 - PRJNA393816
Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely dependent on available nutrients and substrates required for the specific microbial community structures to expand. It is currently not known what the specificities are of intestinal microbial community structures in relation to the programming of the intestinal mucosal immune system and development of the intestinal barrier function. The objective of the present study was to investigate the effect of a nutritional intervention on intestinal development of suckling piglets by daily oral administration of fructooligosaccharides (FOS) over a period of 12 days. At the microbiota community level a clear “bifidogenic” effect of the FOS administration was observed in colon digesta at day 14. The former, however, did not translate into significant changes of local gene expression in the colonic mucosa. In the jejunum, significant changes were observed for microbiota composition at day 14, and microbiota diversity at day 25. In addition, significant differentially expressed gene sets in mucosal tissues of jejunum were identified at both days 14 and 25 of age. At the age of 14 days, lower activity of cell cycle-related processes and a higher activity of extracellular matrix processes were observed in jejunal scrapings of piglets supplemented with FOS compared to control piglets. At day 25, lower activity of immune-related processes in jejunal tissue were seen in piglets supplemented with FOS. Histological parameters, villi height and crypt depth, were significantly different at day 25 between the experimental and control group, where piglets supplemented with FOS had higher villi and deeper crypts. We conclude that oral FOS administration during the suckling period of piglets has significant bifidogenic effects on the microbiota in the colon and on gene expression in jejunal mucosa scrapings. We hypothesize that FOS supplementation of suckling piglets results in a higher butyrate production in the colon due to the increase in bifidobacteria and lactobacilli in the hindgut. We further speculate that a higher butyrate production in colonic digesta relates to changes in gene expression in the jejunum by thus far unknown mechanisms.
Supplementation of fructooligosaccharides to suckling piglets affects intestinal microbiota colonization and immune development
Schokker, Dirkjan ; Fledderus, Jan ; Jansen, Rutger ; Vastenhouw, Stephanie A. ; Bree, Freddy M. de; Smits, Mari A. ; Jansman, Alfons A.J.M. - \ 2018
Journal of Animal Science 96 (2018)6. - ISSN 0021-8812 - p. 2139 - 2153.
Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely dependent on available nutrients required for the specific microbial community structures to expand. It is currently not known what the specificities are of intestinal microbial community structures in relation to the programming of the intestinal mucosal immune system and development of the intestinal barrier function. The objective of the present study was to investigate the effects of a nutritional intervention on intestinal development of suckling piglets by daily oral administration of fructooligosaccharides (FOS) over a period of 12 d (days 2–14 of age). At the microbiota community level, a clear “bifidogenic” effect of the FOS administration was observed in the colon digesta at day 14. The former, however, did not translate into significant changes of local gene expression in the colonic mucosa. In the jejunum, significant changes were observed for microbiota composition at day 14, and microbiota diversity at day 25. In addition, significant differentially expressed gene sets in mucosal tissues of the jejunum were identified at both days 14 and 25 of age. At the age of 14 d, a lower activity of cell cycle–related processes and a higher activity of extracellular matrix processes were observed in the jejunal mucosa of piglets supplemented with FOS compared with control piglets. At day 25, the lower activity of immune-related processes in jejunal tissue was seen in piglets supplemented with FOS. Villi height and crypt depth in the jejunum were significantly different at day 25 between the experimental and control groups, where piglets supplemented with FOS had greater villi and deeper crypts. We conclude that oral FOS administration during the early suckling period of piglets had significant bifidogenic effects on the microbiota in the colon and on gene expression in the jejunal mucosa by thus far unknown mechanisms.
Effects of harness-attached tracking devices on survival, migration, and reproduction in three species of migratory waterfowl
Lameris, Thomas K. ; Müskens, Gerhard J.D.M. ; Kölzsch, Andrea ; Dokter, Adriaan M. ; Jeugd, Henk P. van der; Nolet, Bart A. - \ 2018
Animal Biotelemetry 6 (2018). - ISSN 2050-3385
Barnacle Goose - Brent Goose - Geolocators - GPS tracking - Greater White-fronted Goose - Tag effects

Background: Tracking devices have enabled researchers to study unique aspects of behavior in birds. However, it has become clear that attaching these devices to birds often affects their survival and behavior. While most studies only focus on negative effects on return rates, tracking devices can also affect the behavior under study, and it is therefore important to measure potential negative effects of tracking device attachment on the full range of behavioral aspects of birds. At the same time, we should aim to improve our current attachment methods to reduce these effects. Results: We used a modified harness to attach tracking devices to a total of 111 individuals of three goose species (Greater White-fronted Geese, Brent Geese, and Barnacle Geese) to study their migratory behavior. By creating control groups of birds marked with colored leg bands, geolocators, and/or neck collars, we were able to compare return rates, body condition, and migratory and reproductive behavior, thus allowing a much broader comparison than return rates alone. Birds with harness-attached tracking devices had lower return rates, which could partly be explained by increased rates of divorce, but is likely also the result of reduced survival induced by the harness and device. A comparison between Barnacle Geese equipped with harness-attached tracking devices and individuals fitted with geolocators attached to leg bands showed that birds equipped with tracking devices were only slightly delayed in timing of migration and reproduction and otherwise were not affected in reproductive output. Conclusions: We argue that tracking devices can be used for studies on migration timing. Nevertheless, given the effect of tracking devices on survival and divorce rate, which may differ between sexes and species, we stress that researchers should carefully consider which birds to tag in order to reduce potential negative effects.

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