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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Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds
Phiri, Sydney ; Schoustra, Sijmen E. ; Heuvel, Joost van den; Smid, Eddy J. ; Shindano, John ; Linnemann, Anita - \ 2019
PLoS ONE 14 (2019)10. - ISSN 1932-6203

Fermented cereal-based foods play a crucial role in attaining food and nutrition security for resource-poor populations in sub-Saharan Africa. These products are widely produced by spontaneous fermentation using of cereal grains as raw material. They have a unique taste and flavour, are rich sources of energy and their non-alcoholic nature makes them ideal for consumption by the entire population, including children. Lactic acid bacteria dominate the fermentation process and lead to a low pH of around 4, which suppresses the growth of pathogenic bacteria, thereby increasing the shelf-life and safety of the food. Knowledge about processing practices, consumption patterns and bacterial communities is essential to regulate processing and design appropriate mixes of micro-organisms to produce starter cultures for commercial production of standard-quality fermented foods that meet desired quality characteristics. In four regions of Zambia, we surveyed processing practices and consumption patterns of a spontaneously fermented cereal-based beverage called Munkoyo, commonly produced in Zambia and the Democratic Republic of Congo. Variations in processing practices exist in cooking time of the unfermented maize porridge and time allowed for fermentation. Consumption is mainly at household level and the product is considered as an energy drink. Characterisation of the bacterial communities of over 90 samples with 16S amplicon sequencing on DNA extracted from the entire bacterial community revealed six dominant families, namely Streptococcaceae, Leuconostocaceae, Enterobacteriaceae, Lactabacillales, Bacillaceae and Aeromonadaceae, and a Shannon index of up to 1.18 with an effective number of 3.44 bacterial species. Bacterial communities that underlie the fermentation in Munkoyo differ in their composition for the different regions using common processing steps, suggesting that different combinations of bacteria can be used to achieve successful Munkoyo fermentation. Analysis of aroma profiles in 15 different samples from two different Provinces showed that aldehydes, esters, organic acids, alkanes, alkenes and alcohols dominated.

Modelling the response of net primary productivity of the Zambezi teak forests to climate change along a rainfall gradient in Zambia
Ngoma, Justine ; Braakhekke, Maarten C. ; Kruijt, Bart ; Moors, Eddy ; Supit, Iwan ; Speer, James H. ; Vinya, Royd ; Leemans, Rik - \ 2019
Biogeosciences 16 (2019)19. - ISSN 1726-4170 - p. 3853 - 3867.

Understanding climate change effects on forests is important considering the role forests play in mitigating climate change. We studied the effects of changes in temperature, rainfall, atmospheric carbon dioxide (CO2) concentration, solar radiation, and number of wet days (as a measure of rainfall intensity) on net primary productivity (NPP) of the Zambian Zambezi teak forests along a rainfall gradient. Using 1960-1989 as a baseline, we projected changes in NPP for the end of the 21st century (2070-2099). We adapted the parameters of the dynamic vegetation model, LPJ-GUESS, to simulate the growth of Zambian forests at three sites along a moisture gradient receiving annual rainfall of between 700 and more than 1000 mm. The adjusted plant functional type was tested against measured data. We forced the model with contemporary climate data (1960-2005) and with climatic forecasts of an ensemble of five general circulation models (GCMs) following Representative Concentration Pathways (RCPs) RCP4.5 and RCP8.5. We used local soil parameter values to characterize texture and measured local tree parameter values for maximum crown area, wood density, leaf longevity, and allometry. The results simulated with the LPJGUESS model improved when we used these newly generated local parameters, indicating that using local parameter values is essential to obtaining reliable simulations at site level. The adapted model setup provided a baseline for assessing the potential effects of climate change on NPP in the studied Zambezi teak forests. Using this adapted model version, NPP was projected to increase by 1.77% and 0.69% at the wetter Kabompo and by 0.44% and 0.10% at the intermediate Namwala sites under RCP8.5 and RCP4.5 respectively, especially caused by the increased CO2 concentration by the end of the 21st century. However, at the drier Sesheke site, NPP would respectively decrease by 0.01% and 0.04% by the end of the 21st century under RCP8.5 and RCP4.5. The projected decreased NPP under RCP8.5 at the Sesheke site results from the reduced rainfall coupled with increasing temperature. We thus demonstrated that differences in the amount of rainfall received in a site per year influence the way in which climate change will affect forest resources. The projected increase in CO2 concentration would thus have more effects on NPP in high rainfall receiving areas, while in arid regions, NPP would be affected more by the changes in rainfall and temperature. CO2 concentrations would therefore be more important in forests that are generally not temperature- or precipitation-limited; however, precipitation will continue to be the limiting factor in the drier sites.

Causes and controlling factors of Valley bottom Gullies
Amare, Selamawit ; Keesstra, Saskia ; Ploeg, Martine van der; Langendoen, Eddy ; Steenhuis, Tammo ; Tilahun, Seifu - \ 2019
Land 8 (2019)9. - ISSN 2073-445X
Badlands - Erosion - Landscape restoration - Runoff - Sediment - Soil saturation - Valley bottom

Valley bottomland provides diverse agricultural and ecosystem benefits. Due to concentrated flow paths, they are more vulnerable to gully erosion than hillslope areas. The objective of this review was to show what caused valley bottoms gullies and to present deficiencies in existing rehabilitation measures. From the literature review, we found the following general trends: watershed characteristics determine location of valley bottom gullies; an increase in water transported from the watershed initiates the formation of gullies; the rate of change of the valley bottom gullies, once initiated, depends on the amount of rainfall and the soil and bedrock properties. Especially in humid climates, the presence of subsurface flow greatly enhances bank slippage and advancement of gully heads. Valley bottom gully reclamation measures are generally effective in arid and semi-arid areas with the limited subsurface flow and deep groundwater tables, whereas, for (sub) humid regions, similar remedial actions are not successful as they do not account for the effects of subsurface flows. To ensure effective implementation of rehabilitation measures, especially for humid regions, an integrated landscape approach that accounts for the combined subsurface and surface drainage is needed.

Fermentations great promise
Smid, Eddy - \ 2019
biobased economy - microorganisms - bacteria - chemicals - food - fatty acids - kerosene - fermentation
Hydrographic and Biological Survey of a Surface-Intensified Anticyclonic Eddy in the Caribbean Sea
Boog, C.G. van der; Jong, M.F. de; Scheidat, M. ; Leopold, M.F. ; Geelhoed, S.C.V. ; Schulz, K. ; Dijkstra, H.A. ; Pietrzak, J.D. ; Katsman, C.A. - \ 2019
Journal of Geophysical Research: Oceans 124 (2019)8. - ISSN 2169-9275 - p. 6235 - 6251.
anticyclone - barrier layer - Caribbean Sea - ecology - hydrographic - thermohaline staircases

In the Caribbean Sea, mesoscale anticyclonic ocean eddies impact the local ecosystem by mixing of low salinity river outflow with the nutrient-rich waters upwelling along the Venezuelan and Colombian coast. To gain insight into the physics and the ecological impact of these anticyclones, we performed a combined hydrographic and biological survey of one Caribbean anticyclone in February 2018. We found that the anticyclone had a radius of 90 km and was surface intensified with the strongest velocities (0.72 m/s) in the upper 150 m of the water column. Below, isopycnal displacements were found down to 700 dbar. The core of the anticyclone entrained waters from the Orinoco River plume and contained slightly elevated chlorophyll concentrations compared to the surroundings. At the edge of the anticyclone we observed higher densities of flying fish but not higher densities of predators like seabirds and cetaceans. Below the surface, a strong temperature inversion (0.98 °C) was present within a barrier layer. In addition, we found thermohaline staircases that originated from double diffusion processes within Tropical Atlantic Central Water.

An emulator approach to stratocumulus susceptibility
Glassmeier, Franziska ; Hoffmann, Fabian ; Johnson, Jill S. ; Yamaguchi, Takanobu ; Carslaw, Ken S. ; Feingold, Graham - \ 2019
Atmospheric Chemistry and Physics 19 (2019)15. - ISSN 1680-7316 - p. 10191 - 10203.

The climatic relevance of aerosol-cloud interactions depends on the sensitivity of the radiative effect of clouds to cloud droplet number N, and liquid water path LWP. We derive the dependence of cloud fraction CF, cloud albedo AC, and the relative cloud radiative effect rCRE D CF • AC on N and LWP from 159 large-eddy simulations of nocturnal stratocumulus. These simulations vary in their initial conditions for temperature, moisture, boundary-layer height, and aerosol concentration but share boundary conditions for surface fluxes and subsidence. Our approach is based on Gaussian-process emulation, a statistical technique related to machine learning. We succeed in building emulators that accurately predict simulated values of CF, AC, and rCRE for given values of N and LWP. Emulator-derived susceptibilities @ lnrCRE=@ lnN and @ lnrCRE=@ lnLWP cover the nondrizzling, fully overcast regime as well as the drizzling regime with broken cloud cover. Theoretical results, which are limited to the nondrizzling regime, are reproduced. The susceptibility @ lnrCRE=@ lnN captures the strong sensitivity of the cloud radiative effect to cloud fraction, while the susceptibility @ lnrCRE=@ lnLWP describes the influence of cloud amount on cloud albedo irrespective of cloud fraction. Our emulation-based approach provides a powerful tool for summarizing complex data in a simple framework that captures the sensitivities of cloud-field properties over a wide range of states.

Long-chain vitamin K2 production in Lactococcus lactis is influenced by temperature, carbon source, aeration and mode of energy metabolism
Liu, Yue ; Bennekom, Eric O. Van; Zhang, Yu ; Abee, Tjakko ; Smid, Eddy J. - \ 2019
Microbial Cell Factories 18 (2019)1. - ISSN 1475-2859
Aeration - Carbon source - Long-chain MKs - Menaquinone - Natural enrichment - Respiration - Vitamin K2

Background: Vitamin K2 (menaquinone, MK-n) is a lipid-soluble vitamin that functions as a carboxylase co-factor for maturation of proteins involved in many vital physiological processes in humans. Notably, long-chain vitamin K2 is produced by bacteria, including some species and strains belonging to the group of lactic acid bacteria (LAB) that play important roles in food fermentation processes. This study was performed to gain insights into the natural long-chain vitamin K2 production capacity of LAB and the factors influencing vitamin K2 production during cultivation, providing a basis for biotechnological production of vitamin K2 and in situ fortification of this vitamin in food products. Results: We observed that six selected Lactococcus lactis strains produced MK-5 to MK-10, with MK-8 and MK-9 as the major MK variant. Significant diversities between strains were observed in terms of specific concentrations and titres of vitamin K2. L. lactis ssp. cremoris MG1363 was selected for more detailed studies of the impact of selected carbon sources tested under different growth conditions [i.e. static fermentation (oxygen absent, heme absent); aerobic fermentation (oxygen present, heme absent) and aerobic respiration (oxygen present, heme present)] on vitamin K2 production in M17 media. Aerobic fermentation with fructose as a carbon source resulted in the highest specific concentration of vitamin K2: 3.7-fold increase compared to static fermentation with glucose, whereas aerobic respiration with trehalose resulted in the highest titre: 5.2-fold increase compared to static fermentation with glucose. When the same strain was applied to quark fermentation, we consistently observed that altered carbon source (fructose) and aerobic cultivation of the pre-culture resulted in efficient vitamin K2 fortification in the quark product. Conclusions: With this study we demonstrate that certain LAB strains can be employed for efficient production of long-chain vitamin K2. Strain selection and optimisation of growth conditions offer a viable strategy towards natural vitamin K2 enrichment of fermented foods, and to improved biotechnological vitamin K2 production processes.

Development of a low-alcoholic fermented beverage employing cashew apple juice and non-conventional yeasts
Gamero, Amparo ; Ren, Xiao ; Lamboni, Yendouban ; Jong, Catrienus de; Smid, Eddy J. ; Linnemann, Anita R. - \ 2019
Fermentation 5 (2019)3. - ISSN 2311-5637
Alcoholic beverages - Aroma profile - Cashew apple juice - Hanseniaspora guilliermondii - Non‐conventional yeasts - Saccharomyces cerevisiae - Torulaspora microellipsoides

Cashew apples are by‐products in the production of cashew nuts, which are mostly left to rot in the fields. Cashew apple juice (CAJ), a highly nutritious beverage, can be produced from them. It is rich in sugars and ascorbic acid, but its high polyphenol content makes it bitter and astringent, and therefore difficult to commercialize. The kingdom of fungi contains more than 2000 yeast species, of which only a few species have been studied in relation to their potential to produce aroma compounds. The aim of this research was to develop a new low‐alcoholic fermented beverage to valorize cashew apples. For this purpose, a screening was carried out employing non‐conventional yeast species and some species of the genus Saccharomyces for comparison, followed by a more detailed study with four selected strains cultured at different conditions. The production of volatile aroma compounds as a function of the presence of oxygen, temperature, and yeast species was investigated. The results showed that the more diverse aroma profiles appeared at 25 °C under anaerobic cultivation conditions, where Saccharomyces cerevisiae WUR 102 and Hanseniaspora guilliermondii CBS 2567 excelled in the synthesis of certain aroma compounds, such as β-phenylethanol and its acetate ester (rose aroma). Further studies are needed to test consumer acceptance of these new products.

Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota
Stolaki, Maria ; Minekus, Mans ; Venema, Koen ; Lahti, Leo ; Smid, Eddy J. ; Kleerebezem, Michiel ; Zoetendal, Erwin G. - \ 2019
FEMS microbiology ecology 95 (2019)8. - ISSN 0168-6496
in vitro model - gut health - ileum - microbial diversity - microbiota - short chain fatty acids

The important role for the human small intestinal microbiota in health and disease has been widely acknowledged. However, the difficulties encountered in accessing the small intestine in a non-invasive way in healthy subjects have limited the possibilities to study its microbiota. In this study, a dynamic in vitro model that simulates the human ileum was developed, including its microbiota. Ileostomy effluent and fecal inocula were employed to cultivate microbial communities within the in vitro model. Microbial stability was repetitively achieved after 10 days of model operation with bacterial concentrations reaching on average 107 to 108 16S rRNA copy numbers/ml. High diversities similar to those observed in in vivo ileum samples were achieved at steady state using both fecal and ileostomy effluent inocula. Functional stability based on Short Chain Fatty Acid concentrations was reached after 10 days of operation using fecal inocula, but was not reached with ileostomy effluent as inoculum. Principal Components and cluster analysis of the phylogenetic profiles revealed that in vitro samples at steady state clustered closest to two samples obtained from the terminal ileum of healthy individuals, independent of the inoculum used, demonstrating that the in vitro microbiota at steady state resembles that of the human ileum.

Large-Eddy Simulations of the Steady Wintertime Antarctic Boundary Layer
Linden, Steven J.A. van der; Edwards, John M. ; Heerwaarden, Chiel C. van; Vignon, Etienne ; Genthon, Christophe ; Petenko, Igor ; Baas, Peter ; Jonker, Harmen J.J. ; Wiel, Bas J.H. van de - \ 2019
Boundary-Layer Meteorology 173 (2019)2. - ISSN 0006-8314 - p. 165 - 192.
Antarctic boundary layer - Large-eddy simulations - Long-lived stable boundary layer - Subsidence heating

Observations of two typical contrasting weakly stable and very stable boundary layers from the winter at Dome C station, Antarctica, are used as a benchmark for two centimetre-scale-resolution large-eddy simulations. By taking the Antarctic winter, the effects of the diurnal cycle are eliminated, enabling the study of the long-lived steady stable boundary layer. With its homogeneous, flat snow surface, and extreme stabilities, the location is a natural laboratory for studies on the long-lived stable boundary layer. The two simulations differ only in the imposed geostrophic wind speed, which is identified as the main deciding factor for the resulting regime. In general, a good correspondence is found between the observed and simulated profiles of mean wind speed and temperature. Discrepancies in the temperature profiles are likely due to the exclusion of radiative transfer in the current simulations. The extreme stabilities result in a considerable contrast between the stable boundary layer at the Dome C site and that found at typical mid-latitudes. The boundary-layer height is found to range from approximately 50m to just 5m in the most extreme case. Remarkably, heating of the boundary layer by subsidence may result in thermal equilibrium of the boundary layer in which the associated heating is balanced by the turbulent cooling towards the surface. Using centimetre-scale resolutions, accurate large-eddy simulations of the extreme stabilities encountered in Antarctica appear to be possible. However, future simulations should aim to include radiative transfer and sub-surface heat transport to increase the degree of realism of these types of simulations.

Carbon-water flux coupling under progressive drought
Boese, Sven ; Jung, Martin ; Carvalhais, Nuno ; Teuling, Adriaan J. ; Reichstein, Markus - \ 2019
Biogeosciences 16 (2019)13. - ISSN 1726-4170 - p. 2557 - 2572.

Water-use efficiency (WUE), defined as the ratio of carbon assimilation over evapotranspiration (ET), is a key metric to assess ecosystem functioning in response to environmental conditions. It remains unclear which factors control this ratio during periods of extended water limitation. Here, we used dry-down events occurring at eddy-covariance flux tower sites in the FLUXNET database as natural experiments to assess if and how decreasing soil-water availability modifies WUE at ecosystem scale. WUE models were evaluated by their performance to predict ET from both the gross primary productivity (GPP), which characterizes carbon assimilation at ecosystem scale, and environmental variables. We first compared two water-use efficiency models: the first was based on the concept of a constant underlying water-use efficiency, and the second augmented the first with a previously detected direct influence of radiation on transpiration. Both models predicting ET strictly from atmospheric covariates failed to reproduce observed ET dynamics for these periods, as they did not explicitly account for the effect of soil-water limitation. We demonstrate that an ET-attenuating soil-water-availability factor in junction with the additional radiation term was necessary to accurately predict ET flux magnitudes and dry-down lengths of these water-limited periods. In an analysis of the attenuation of ET for the 31 included FLUXNET sites, up to 50 % of the observed decline in ET was due to the soil-water-availability effect we identified in this study. We conclude by noting that the rates of ET decline differ significantly between sites with different vegetation and climate types and discuss the dependency of this rate on the variability of seasonal dryness.

Shallow Cumulus Representation and Its Interaction with Radiation and Surface at the Convection Gray Zone
Pedruzo-Bagazgoitia, Xabier ; Jiménez, Pedro A. ; Dudhia, Jimy ; Vilà-Guerau De Arellano, Jordi - \ 2019
Monthly Weather Review 147 (2019)7. - ISSN 0027-0644 - p. 2467 - 2483.
This study presents a systematic analysis of convective parameterizations performance with interactive radiation, microphysics, and surface on an idealized day with shallow convection. To this end, we analyze a suite of mesoscale numerical experiments (i.e., with parameterized turbulence). In the first set, two different convection schemes represent shallow convection at a 9-km resolution. These experiments are then compared with model results omitting convective parameterizations at 9- and 3-km horizontal resolution (gray zone). Relevant in our approach is to compare the results against two simulations by different large-eddy simulation (LES) models. Results show that the mesoscale experiments, including the 3-km resolution, are unable to adequately represent the timing, intensity, height, and extension of the shallow cumulus field. The main differences with LES experiments are the following: a too late onset, too high cloud base, and a too early transport of moisture too high, overestimating the second cloud layer. Related to this, both convective parameterizations produce warm and dry biases of up to 2 K and 2 g kg−1, respectively, in the cloud layer. This misrepresentation of the cloud dynamics leads to overestimated shortwave radiation variability, both spacewise and timewise. Domain-averaged shortwave radiation at the surface, however, compares satisfactorily with LES. The shortwave direct and diffuse partition is misrepresented by the convective parameterizations with an underestimation (overestimation) of diffuse (direct) radiation both locally and, by a relative 40% (10%), of the domain average.
Dynamic modelling of brewers’ yeast and Cyberlindnera fabianii co-culture behaviour for steering fermentation performance
Rijswijck, Irma M.H. van; Mastrigt, Oscar van; Pijffers, Gerco ; Wolkers–Rooijackers, Judith C.M. ; Abee, Tjakko ; Zwietering, Marcel H. ; Smid, Eddy J. - \ 2019
Food Microbiology 83 (2019). - ISSN 0740-0020 - p. 113 - 121.

Co-cultivation of brewers' yeast (Saccharomyces cerevisiae) with Cyberlindnera fabianii makes it possible to steer aroma and alcohol levels by changing the inoculation ratio of the two yeasts. A dynamic model was developed based on mono-culture performance of brewers' yeast and C. fabianii in controlled bioreactors with aerated wort as medium, describing growth rate, carbohydrate utilization, ethanol production, maintenance, oxygen consumption and ergosterol biosynthesis/use for cell membrane synthesis (the last one only for brewers' yeast). The parameters were estimated by fitting models to experimental data of both mono-cultivations. To predict the fermentation outcome of brewers' yeast and C. fabianii in co-cultivation, the two models were combined and the same parameter settings were used. The co-cultivation model was experimentally validated for the inoculum ratios 1:10 and 1:100 brewers' yeast over C. fabianii. The use of predictive modelling supported the hypothesis that performance of brewers' yeast in co-cultivation is inhibited by oxygen depletion which is required for the biosynthesis of ergosterol. This dynamic modelling approach and the parameters involved may also be used to predict the performance of brewers’ yeast in the co-cultivation with other yeast species and to give guidance to optimize the fermentation outcome.

Integrating animal welfare into sustainable development of livestock systems
Bokkers, Eddy - \ 2019
Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal
Groenenboom, Anneloes E. ; Parker, Megan E. ; Vries, Anne De; Groot, Suzette de; Zobrist, Stephanie ; Mansen, Kimberly ; Milani, Peiman ; Kort, Remco ; Smid, Eddy J. ; Schoustra, Sijmen E. - \ 2019
PLoS ONE 14 (2019)5. - ISSN 1932-6203
Spontaneously fermented food products contain a complex, natural microbial community with potential probiotic activity. The addition of a health-promoting, probiotic bacterium to these products ensures the delivery of that probiotic activity to consumers. Here, we assess the microbial community of a traditional Senegalese milk product produced by spontaneous fermentation, called lait caillé. We produced the lait caillé in a traditional way and added a probiotic starter containing Lactobacillus rhamnosus yoba 2012 to the traditional process. We found various species that are known for their ability to ferment milk, including species from the genera Lactobacillus, Acetobacter, Lactococcus, and Streptococcus. Our results show that the addition of L. rhamnosus to the inoculum, can result in detectable levels of this strain in the final product, ranging between 0.2 and 1 percent of the total bacterial population. Subsequent rounds of fermentation using passive back-slopping without the addition of new L. rhamnosus led to a loss of this strain from the community of fermenting bacteria. Our results suggest that the addition of probiotic strains at every fermentation cycle can enrich the existing complex communities of traditionally fermented lait caillé while traditional bacterial strains remain dominant in the bacterial communities
Application of a partial cell recycling chemostat for continuous production of aroma compounds at near-zero growth rates
Mastrigt, Oscar van; Egas, Reinier A. ; Lillevang, Søren K. ; Abee, Tjakko ; Smid, Eddy J. - \ 2019
BMC Research Notes 12 (2019)1. - ISSN 1756-0500
Continuous cultivation - Fermentation - Lactic acid bacteria - Maintenance - Metabolomics - Retentostat - VOC

Objective: The partial cell recycling chemostat is a modification of the chemostat in which cells are partially recycled towards the bioreactor. This allows using dilution rates higher than the maximum growth rate resulting in higher biomass concentrations and increased process rates. In this study, we demonstrate with a single observation that this system can also be used to study microorganisms at near-zero growth rates and as production system for compounds specific for slow growth, such as those typical for ripened cheese. Results: Lactococcus lactis FM03-V2 was cultivated at growth rates between 0.0025 and 0.025 h -1 . Detailed analysis of produced aroma compounds revealed that levels of particular compounds were clearly affected by the growth rate within the studied range demonstrating that we can steer the aroma production by controlling the growth rate. With this approach, we also experimentally validated that the maintenance coefficient of this dairy strain decreased at near-zero growth rates (6.4-fold). An exponentially decreasing maintenance coefficient was included in the growth model, enabling accurate prediction of biomass accumulation in the partial cell recycling chemostat. This study demonstrates the potential of partial cell recycling chemostat both as aroma production system at near-zero growth rates and as unique research tool.

Robust sampling and preservation of DNA for microbial community profiling in field experiments
Groenenboom, Anneloes E. ; Smid, Eddy J. ; Schoustra, Sijmen E. - \ 2019
BMC Research Notes 12 (2019)1. - ISSN 1756-0500
DNA stabilisation - Fermentation - Field trial - Filter paper disks - Microbial community - Milk

Objective: Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product. Results: Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.

Source partitioning of H 2 O and CO 2 fluxes based on high-frequency eddy covariance data : A comparison between study sites
Klosterhalfen, Anne ; Graf, Alexander ; Brüggemann, Nicolas ; Drüe, Clemens ; Esser, Odilia ; González-Dugo, María P. ; Heinemann, Günther ; Jacobs, Cor M.J. ; Mauder, Matthias ; Moene, Arnold F. ; Ney, Patrizia ; Pütz, Thomas ; Rebmann, Corinna ; Rodríguez, Mario Ramos ; Scanlon, Todd M. ; Schmidt, Marius ; Steinbrecher, Rainer ; Thomas, Christoph K. ; Valler, Veronika ; Zeeman, Matthias J. ; Vereecken, Harry - \ 2019
Biogeosciences 16 (2019)6. - ISSN 1726-4170 - p. 1111 - 1132.

For an assessment of the roles of soil and vegetation in the climate system, a further understanding of the flux components of H 2 O and CO 2 (e.g., transpiration, soil respiration) and their interaction with physical conditions and physiological functioning of plants and ecosystems is necessary. To obtain magnitudes of these flux components, we applied source partitioning approaches after Scanlon and Kustas (2010; SK10) and after Thomas et al. (2008; TH08) to high-frequency eddy covariance measurements of 12 study sites covering different ecosystems (croplands, grasslands, and forests) in different climatic regions. Both partitioning methods are based on higher-order statistics of the H 2 O and CO 2 fluctuations, but proceed differently to estimate transpiration, evaporation, net primary production, and soil respiration. We compared and evaluated the partitioning results obtained with SK10 and TH08, including slight modifications of both approaches. Further, we analyzed the interrelations among the performance of the partitioning methods, turbulence characteristics, and site characteristics (such as plant cover type, canopy height, canopy density, and measurement height). We were able to identify characteristics of a data set that are prerequisites for adequate performance of the partitioning methods. SK10 had the tendency to overestimate and TH08 to underestimate soil flux components. For both methods, the partitioning of CO 2 fluxes was less robust than for H 2 O fluxes. Results derived with SK10 showed relatively large dependencies on estimated water use efficiency (WUE) at the leaf level, which is a required input. Measurements of outgoing longwave radiation used for the estimation of foliage temperature (used in WUE) could slightly increase the quality of the partitioning results. A modification of the TH08 approach, by applying a cluster analysis for the conditional sampling of respiration-evaporation events, performed satisfactorily, but did not result in significant advantages compared to the original method versions developed by Thomas et al. (2008). The performance of each partitioning approach was dependent on meteorological conditions, plant development, canopy height, canopy density, and measurement height. Foremost, the performance of SK10 correlated page1112 negatively with the ratio between measurement height and canopy height. The performance of TH08 was more dependent on canopy height and leaf area index. In general, all site characteristics that increase dissimilarities between scalars appeared to enhance partitioning performance for SK10 and TH08.

The art of mabisi production : A traditional fermented milk
Moonga, Himoonga Bernard ; Schoustra, Sijmen E. ; Linnemann, Anita R. ; Kuntashula, Elias ; Shindano, John ; Smid, Eddy J. - \ 2019
PLoS ONE 14 (2019)3. - ISSN 1932-6203

Fermented dairy products can be rich in beneficial microbes and one such product with potential is mabisi. Mabisi is a traditional fermented milk product from Zambia made through spontaneous fermentation of raw milk at ambient temperature using a calabash (gourd), clay pot, plastic or metal container. The fermentation takes about 48 hours after which the product is stirred and ready for consumption. This study was aimed at determining the types of production methods of mabisi and identifying the critical production process parameters. A survey was conducted using interviews and observations to determine the existing production practices/technologies and to capture indigenous knowledge on mabisi production in nine provinces of Zambia. We found seven different production methods which we coined; Tonga, thick-Tonga, illa, barotse, backslopping, cooked and creamy types. Interestingly, the Tonga-type mabisi was produced throughout the country by different ethnic groups. The main process parameters were found to be fermentation time and temperature, type of containers, presence/absence of backslopping, agitation, heating and cooling, removal of whey and addition of raw milk. And further found that mabisi is a versatile product consumed with a wide variety of foods. This basic information is crucial for production process optimisation and microbial communities dynamics studies.

State-of-the-art global models underestimate impacts from climate extremes
Schewe, Jacob ; Gosling, Simon N. ; Reyer, Christopher ; Zhao, Fang ; Ciais, Philippe ; Elliott, Joshua ; Francois, Louis ; Huber, Veronika ; Lotze, Heike K. ; Seneviratne, Sonia I. ; Vliet, Michelle T.H. Van; Vautard, Robert ; Wada, Yoshihide ; Breuer, Lutz ; Büchner, Matthias ; Carozza, David A. ; Chang, Jinfeng ; Coll, Marta ; Deryng, Delphine ; Wit, Allard De; Eddy, Tyler D. ; Folberth, Christian ; Frieler, Katja ; Friend, Andrew D. ; Gerten, Dieter ; Gudmundsson, Lukas ; Hanasaki, Naota ; Ito, Akihiko ; Khabarov, Nikolay ; Kim, Hyungjun ; Lawrence, Peter ; Morfopoulos, Catherine ; Müller, Christoph ; Müller Schmied, Hannes ; Orth, René ; Ostberg, Sebastian ; Pokhrel, Yadu ; Pugh, Thomas A.M. ; Sakurai, Gen ; Satoh, Yusuke ; Schmid, Erwin ; Stacke, Tobias ; Steenbeek, Jeroen ; Steinkamp, Jörg ; Tang, Qiuhong ; Tian, Hanqin ; Tittensor, Derek P. ; Volkholz, Jan ; Wang, Xuhui ; Warszawski, Lila - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
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