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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    Lateral root formation and the multiple roles of auxin
    Du, Yujuan ; Scheres, Ben - \ 2018
    Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 155 - 167.
    Arabidopsis - auxin - emergence - founder cell specification - initiation - lateral root - oscillation - outgrowth - primordium
    Root systems can display variable architectures that contribute to survival strategies of plants. The model plant Arabidopsis thaliana possesses a tap root system, in which the primary root and lateral roots (LRs) are major architectural determinants. The phytohormone auxin fulfils multiple roles throughout LR development. In this review, we summarize recent advances in our understanding of four aspects of LR formation: (i) LR positioning, which determines the spatial distribution of lateral root primordia (LRP) and LRs along primary roots; (ii) LR initiation, encompassing the activation of nuclear migration in specified lateral root founder cells (LRFCs) up to the first asymmetric cell division; (iii) LR outgrowth, the 'primordium-intrinsic' patterning of de novo organ tissues and a meristem; and (iv) LR emergence, an interaction between LRP and overlaying tissues to allow passage through cell layers. We discuss how auxin signaling, embedded in a changing developmental context, plays important roles in all four phases. In addition, we discuss how rapid progress in gene network identification and analysis, modeling, and four-dimensional imaging techniques have led to an increasingly detailed understanding of the dynamic regulatory networks that control LR development.
    Contribution of Dynamic Vegetation Phenology to Decadal Climate Predictability
    Weiss, M. ; Miller, P.A. ; Hurk, B.J.J.M. van den; Noije, T. van; Stefanescu, S. ; Haarsma, R. ; Ulft, L.H. van; Hazeleger, W. ; Sager, P. Le; Smith, B. ; Schurgers, G. - \ 2014
    Journal of Climate 27 (2014)22. - ISSN 0894-8755 - p. 8563 - 8577.
    leaf-area index - ensemble forecasts - data assimilation - soil-moisture - model - prediction - system - impact - skill - oscillation
    In this study, the impact of coupling and initializing the leaf area index from the dynamic vegetation model Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) is analyzed on skill of decadal predictions in the fully coupled atmosphere-land-ocean-sea ice model, the European Consortium Earth System Model (EC-Earth). Similar to the impact of initializing the model with the observed oceanic state, initializing the leaf area index (LAI) fields obtained from an offline LPJ-GUESS simulation forced by the observed atmospheric state leads to a systematic drift. A different treatment of the water and soil moisture budget in LPJ-GUESS is a likely cause of this drift. The coupled system reduces the cold bias of the reference model over land by reducing LAI (and the associated evaporative cooling), particularly outside the growing season. The coupling with the interactive vegetation module implies more degrees of freedom in the coupled model, which generates more noise that can mask a portion of the extra signal that is generated. The forecast reliability improves marginally, particularly early in the forecast. Ranked probability skill scores are also improved slightly in most areas analyzed, but the signal is not fully coherent over the forecast interval because of the relatively low number of ensemble members. Methods to remove the LAI drift and allow coupling of other variables probably need to be implemented before significant forecast skill can be expected.
    Recent trends in sea surface temperature off Mexico
    Lluch-Cota, S.E. ; Tripp-Valdéz, M. ; Lluch-Cota, D.B. ; Lluch-Belda, D. ; Verbesselt, J. ; Herrera-Cervantes, H. ; Bautista-Romero, J. - \ 2013
    Atmósfera 26 (2013)4. - ISSN 0187-6236 - p. 537 - 546.
    california current system - variability - atlantic - climate - oscillation - pacific - hypoxia - shelf
    Changes in global mean sea surface temperature may have potential negative implications for natural and socioeconomic systems; however, measurements to predict trends in different regions have been limited and sometimes contradictory. In this study, an assessment of sea surface temperature change signals in the seas off Mexico is presented and compared to other regions and the world ocean, and to selected basin scale climatic indices of the North Pacific, the Atlantic and the tropical Pacific variability. We identified eight regions with different exposure to climate variability: In the Pacific, the west coast of the Baja California peninsula with mostly no trend, the Gulf of California with a modest cooling trend during the last 20 to 25 years, the oceanic area with the most intense recent cooling trend, the southern part showing an intense warming trend, and a band of no trend setting the boundary between North-Pacific and tropical-Pacific variability patterns; in the Atlantic, the northeast Gulf of Mexico shows cooling, while the western Gulf of Mexico and the Caribbean have been warming for more than three decades. Potential interactions with fisheries and coastal sensitive ecosystems are discussed
    Spatial patterns and trends in abundance of larval saneels in the North Sea: 1950 - 2005
    Lynam, C.P. ; Halliday, N.C. ; Hoffle, H. ; Wright, P.J. ; Damme, C.J.G. van; Pitois, S.G. - \ 2013
    ICES Journal of Marine Science 70 (2013)3. - ISSN 1054-3139 - p. 540 - 553.
    continuous plankton recorder - ammodytes-marinus - lesser sandeel - multimodel approach - european shelf - trophic levels - zooplankton - atlantic - fish - oscillation
    Early recruitment indices based on larval fish data from the Continuous Plankton Recorder (CPR) have the potential to inform stock assessments of Ammodytes marinus in the North Sea. We evaluate whether the CPR data are reliable for sandeel larvae. Spatially, CPR larval data were comparable with catches by dedicated larval samplers (Gulf and bongo nets) during ICES coordinated surveys in 2004 and 2009. ICES data are also used to explore environmental influences on sandeel distributions. Temporally, CPR data correlate with larval data from plankton surveys off Stonehaven (1999–2005), with sandeel 0-group trawl data at the east Fair Isle ground (since 1984), and with recruitment data (since 1983) for the Dogger Banks stock assessment area. Therefore, CPR data may provide an early recruit index of relative abundance for the Dogger Banks assessment area, where the majority of the commercial catch of A. marinus is taken, and the Wee Bankie area that is particularly important for seabird foraging. While warm conditions may stimulate the production of sandeel larvae, their natural mortality is typically greater, in the Dogger Banks and Wadden Sea areas, when the larvae are hatched in warm years and/or with abundant 1-year-old sandeel that are likely to be cannibalistic.
    Onderzoek naar de affecten van de aanleg van damwanden en grondverdichting op tandwalvissen in het Dolfinarium Harderwijk
    Haan, D. de - \ 2013
    IJmuiden : IMARES (Report / IMARES Wageningen UR C020/13) - 62
    dammen - uitrusting - zeezoogdieren - dierentuindieren - simulatie - diergedrag - dierenwelzijn - geluiden - veluwe - walvissen - oscillatie - dams - equipment - marine mammals - zoo animals - simulation - animal behaviour - animal welfare - sounds - veluwe - whales - oscillation
    Voor het vaststellen van de effecten van de aanleg van damwandinstallaties en grondverdichting als onderdelen van het grootschalig bouwplan Waterfront Harderwijk van de gemeente Harderwijk werden op vijf verschillende locaties van het bouwplan installaties gesimuleerd en de geluidseffecten daarvan in vier verschillende bassins op het terrein van het dolfinarium simultaan gemeten. Het onderzoek naar de effecten van het trilgeluid was beperkt tot de bassins waar bruinvissen en tuimelaars werden gehouden. Omdat er tijdens de proeven sterke reacties van haaien en roggen in het roggenbasin werden waargenomen, zijn in dit rapport enkele mitigerende maatregelen voor deze diersoorten opgenomen.
    Climate Variability and Trends in Bolivia
    Seiler, C. ; Hutjes, R.W.A. ; Kabat, P. - \ 2013
    Journal of Applied Meteorology and Climatology 52 (2013)1. - ISSN 1558-8424 - p. 130 - 146.
    amazon basin - interdecadal variability - tropical pacific - rainfall - circulation - oscillation - altiplano - andes - enso - ocean
    Climate-related disasters in Bolivia are frequent, severe, and manifold and affect large parts of the population, economy, and ecosystems. Potentially amplified through climate change, natural hazards are of growing concern. To better understand these events, homogenized daily observations of temperature (29 stations) and precipitation (68 stations) from 1960 to 2009 were analyzed in this study. The impact of the positive (+) and negative (-) phases of the three climate modes (i) Pacific decadal oscillation (PDO), (ii) El Niño–Southern Oscillation (ENSO) with El Niño (EN) and La Niña (LN) events, and (iii) Antarctic Oscillation (AAO) were assessed. Temperatures were found to be higher during PDO(+), EN, and AAO(+) in the Andes. Total amounts of rainfall, as well as the number of extreme events, were higher during PDO(+), EN, and LN in the lowlands. During austral summer [December–February (DJF)], EN led to drier conditions in the Andes with more variable precipitation. Temperatures increased at a rate of 0.1°C per decade, with stronger increases in the Andes and in the dry season. Rainfall totals increased from 1965 to 1984 [12% in DJF and 18% in June–August (JJA)] and decreased afterward (-4% in DJF and -10% in JJA), following roughly the pattern of PDO. Trends of climate extremes generally corresponded to trends of climate means. Findings suggest that Bolivia’s climate will be warmer and drier than average in the near-term future. Having entered PDO(-) in 2007, droughts and LN-related floods can be expected in the lowlands, while increasing temperatures suggest higher risks of drought in the Andes.
    Projecting climate change, drought conditions and crop productivity in Turkey
    Sen, B. ; Topcu, S. ; Türkes, M. ; Warner, J.F. - \ 2012
    Climate Research 52 (2012). - ISSN 0936-577X - p. 175 - 191.
    standardized precipitation index - mediterranean region - change impacts - variability - simulations - oscillation - temperature - environment - streamflow - yield
    This paper focuses on the evaluation of regional climate model simulation for Turkey for the 21st century. A regional climate model, ICTP-RegCM3, with 20 km horizontal resolution, is used to downscale the reference and future climate scenario (IPCC-A2) simulations. Characteristics of droughts as well as the crop growth and yields of first- and second-crop corn are then calculated and simulated based on the data produced. The model projects an increase in air temperature of 5 to 7°C during the summer season over the west and an increase of 3.5°C for the winter season for the eastern part of the country. Precipitation is predicted to be 40% less in the southwest, although it may increase by 25% in the eastern part of the Black Sea region and northeastern Turkey. Trends in drought intensity and crop growth are related to climate changes. The results suggest more frequent, intense and long-lasting droughts in the country particularly along the western and southern coasts under future climate conditions. A shift of climate classes towards drier conditions is also projected for the western, southern and central regions during the 21st century. Evaluating the role of the climate change trends in crop production reveals significant decreases in yield and shortened growth seasons for first- and second-crop corn, a likely result of high temperatures and water stresses. In addition to rising temperatures and declining precipitation, increasing frequency, severity and duration of drought events may significantly affect food production and socio-economic conditions in Turkey. Our results may help policy makers and relevant sectors to implement appropriate and timely measures to cope with climate-change-induced droughts and their effects in the future.
    Interdecadal North-Atlantic meridional overturning circulation variability in EC-EARTH
    Wouters, B. ; Drijfhout, D. ; Hazeleger, W. - \ 2012
    Climate Dynamics 39 (2012)11. - ISSN 0930-7575 - p. 2695 - 2712.
    multidecadal climate variability - sea-surface temperature - ocean-atmosphere gcm - thermohaline circulation - gulf-stream - decadal variability - oscillation - model - mechanism - transport
    The Atlantic meridional overturning circulation (AMOC) in a 600 years pre-industrial run of the newly developed EC-EARTH model features marked interdecadal variability with a dominant time-scale of 50–60 years. An oscillation of approximately 2 Sverdrup (1 Sv = 106 m3 s-1) is identified, which manifests itself as a monopole causing the overturning to simultaneously strengthen (/weaken) and deepen (/shallow) as a whole. Eight years before the AMOC peaks, density in the Labrador-Irminger Sea region reaches a maximum, triggering deep water formation. This density change is caused by a counterclockwise advection of temperature and salinity anomalies at lower latitudes, which we relate to the north-south excursions of the subpolar-subtropical gyre boundary and variations in strength and position of the subpolar gyre and the North Atlantic Current. The AMOC fluctuations are not directly forced by the atmosphere, but occur in a delayed response of the ocean to forcing by the North Atlantic Oscillation, which initiates “intergyre”-gyre fluctuations. Associated with the AMOC is a 60-year sea surface temperature variability in the Atlantic, with a pattern and timescale showing similarities with the real-world Atlantic Multidecadal Variability. This good agreement with observations lends a certain degree of credibility that the mechanism that is described in this article could be seen as representative of the real climate system.
    Nine decades of North Sea sole and plaice distribution
    Engelhard, G.H. ; Pinnegar, J.K. ; Kell, L.T. ; Rijnsdorp, A.D. - \ 2011
    ICES Journal of Marine Science 68 (2011)6. - ISSN 1054-3139 - p. 1090 - 1104.
    atlantic shelf seas - climate-change - pleuronectes-platessa - community structure - fish assemblage - bristol channel - marine fishes - trends - oscillation - recruitment
    Recent studies based mainly on research survey data suggest that within the North Sea, sole Solea solea and plaice Pleuronectes platessa have exhibited distribution shifts in recent decades—on average southward for sole and northward to deeper waters for plaice. Various hypotheses may account for such shifts, including climate change effects and more intensive fishing in southern and shallower waters; but the relatively short time-span of datasets analysed so far (~3 decades) has complicated the separation of these two effects. We have made use of a unique dataset of catch and effort data for British North Sea trawlers; these cover nine decades (spanning the period 1913–2007) and are spatially detailed by ICES rectangle (0.5° latitude by 1° longitude). We quantify, for the first time, long-term distribution changes of North Sea sole and plaice over a period approaching a century, and demonstrate that the distribution shift in plaice was attributable to climate change rather than to fishing, but that both climate and fishing played a role in the distribution shift of sole. The discussion also highlights the potential impact of additional factors, including eutrophication, prey availability, and habitat modification
    A conceptual view on inertial oscillations and nocturnal low-level jets
    Wiel, B.J.H. van de; Moene, A.F. ; Steeneveld, G.J. ; Baas, P. ; Bosveld, F.C. ; Holtslag, A.A.M. - \ 2010
    Journal of the Atmospheric Sciences 67 (2010)8. - ISSN 0022-4928 - p. 2679 - 2689.
    oscillatie - wind - frictie - meteorologische waarnemingen - oscillation - wind - friction - meteorological observations - stable-boundary-layer - tropospheric wind maxima - intermittent turbulence - resistance laws - cabauw - model - cases-99 - energy - land - climatology
    In the present work Blackadar's concept on nocturnal inertial oscillations is extended. Blackadar's concept describes frictionless inertial oscillations above the nocturnal inversion layer. The current work includes frictional effects within the nocturnal boundary layer. As a result it is shown that the nocturnal wind speed profile describes an oscillation around the nocturnal equilibrium wind vector, rather than around the geostrophic wind vector (as in the Blackadar case). By using this perspective continuous time-dependent wind profiles are predicted. As such, information on both the height and the magnitude of the nocturnal low-level jet is available as a function of time. Preliminary analysis shows that the proposed extension performs well in comparison with observations, when a simple Ekman model is used to represent the equilibrium state in combination with a realistic initial velocity profile. In addition to jet dynamics, backward inertial oscillations are predicted at lower levels close to the surface, which also appear to be present in observations. The backward oscillation forms an important mechanism behind weakening low-level winds during the afternoon transition. Both observational and theoretical modeling studies are needed to explore this phenomenon further
    Effects of climate variability on water storage in the Colorado river basin
    Hurkmans, R.T.W.L. ; Troch, P.A.A. ; Uijlenhoet, R. ; Torfs, P.J.J.F. ; Durcik, M. - \ 2009
    Journal of Hydrometeorology 10 (2009)5. - ISSN 1525-755X - p. 1257 - 1270.
    watervoorraden - hydrologie van stroomgebieden - klimaatverandering - monitoring - colorado (rivier) - vs - water resources - catchment hydrology - climatic change - monitoring - colorado river - usa - western united-states - sea-surface temperatures - enso - pacific - precipitation - oscillation - streamflow - frequency - drought - pdo
    Understanding the long-term (interannual–decadal) variability of water availability in river basins is paramount for water resources management. Here, the authors analyze time series of simulated terrestrial water storage components, observed precipitation, and discharge spanning 74 yr in the Colorado River basin and relate them to climate indices that describe variability of sea surface temperature and sea level pressure in the tropical and extratropical Pacific. El Niño–Southern Oscillation (ENSO) indices in winter [January–March (JFM)] are related to winter precipitation as well as to soil moisture and discharge in the lower Colorado River basin. The low-frequency mode of the Pacific decadal oscillation (PDO) appears to be strongly correlated with deep soil moisture. During the negative PDO phase, saturated storage anomalies tend to be negative and the “amplitudes” (mean absolute anomalies) of shallow soil moisture, snow, and discharge are slightly lower compared to periods of positive PDO phases. Predicting interannual variability, therefore, strongly depends on the capability of predicting PDO regime shifts. If indeed a shift to a cool PDO phase occurred in the mid-1990s, as data suggest, the current dry conditions in the Colorado River basin may persist
    De fysiologie van bewegen : door beweging en aanraking blijven planten korter
    Kierkels, T. ; Heuvelink, E. - \ 2008
    Onder Glas 5 (2008)5. - p. 38 - 39.
    kassen - teelt onder bescherming - sierplanten - beweging - oscillatie - celwanden - verwringing - cultivars - remming - glastuinbouw - groenten - potplanten - greenhouses - protected cultivation - ornamental plants - movement - oscillation - cell walls - distortion - cultivars - inhibition - greenhouse horticulture - vegetables - pot plants
    Door het bewegen of aanraken van planten vervormt de celwand. Dat zet een aantal reacties in werking waardoor uiteindelijk nieuwe cellen korter blijven met dikkere celwanden. Al met al kan trillen, aanraken en borstelen wel perspectief hebben als alternatief voor chemische remming, maar het vergt heel veel uitproberen omdat met de huidige kennis niet te voorspellen valt welk soort of cultivar effectief te remmen valt
    Estimating annual rainfall threshold for establishment of tree species in water-limited ecosystems using tree-ring data
    Lopez, B.C. ; Holmgren, M. ; Sabate, S. ; Gracia, C.A. - \ 2008
    Journal of Arid Environments 72 (2008)5. - ISSN 0140-1963 - p. 602 - 611.
    el-nino - semiarid ecosystems - atacama desert - south-america - enso events - climate - vegetation - demography - australia - oscillation
    In arid and semi-arid ecosystems, water availability is discontinuous, highly variable, and characterized by discrete pulse events separated by long periods of limited resource availability. Plant recruitment in these ecosystems is also episodic and dependent on the water available during and after these discrete rainfall events. Precipitation thresholds for plant establishment have been estimated mainly for herbaceous plants and tree seedlings, but extrapolation of short-term results based on seedlings to natural tree populations is difficult. Nevertheless, estimations of water availability thresholds for tree recruitment are essential for successful policies on forest conservation and restoration. We propose a methodology to estimate precipitation thresholds for adult tree populations using tree-ring series and precipitation data. We used this methodology with two Prosopis species from South America: Prosopis pallida and Prosopis chilensis. Results indicate a precipitation threshold of around 85 mm for the establishment of P. pallida trees, whereas the threshold for P. chilensis is likely to be much higher.
    Climate modulates the effects of Sardinella aurita fisheries off Northwest Africa
    Zeeberg, J.J. ; Corten, A.A.H.M. ; Tjoe-Awie, P.J. ; Coca, J. ; Hamady, H. - \ 2008
    Fisheries Research 89 (2008)1. - ISSN 0165-7836 - p. 65 - 75.
    interannual variability - upwelling systems - sea-surface - atlantic - guinea - larvae - coast - oscillation - temperature - recruitment
    The fluctuating abundance of round sardinella (Sardinella aurita) in Mauritanian waters over the past ca. 20 years can be related to environmental dynamics off Northwest Africa. Trends in the fishery are evaluated using FAO data, acoustic surveys, and catch statistics from the EU fleet (1996¿2006). Remote sensing data demonstrate rising annual sea surface temperatures, up to 3 °C higher than the long-term average in 2002¿2003, following a shift in ocean climate in 1995. Fish abundance and repeated expansion of the sardinella population in the past 10 years are attributed to favorable oceanographic conditions and increased recruitment success. Sardinella thrives with intense upwelling and high primary production during spring, and retention of waters over the shelf during summer and autumn. The stock of S. aurita over the Northwest African shelf oscillates with the cold¿warm states of the habitat. Favorable hydrographic conditions and extended habitat has resulted in unprecedented rise of sardinella abundance in the late 1990s, which was counterbalanced by the impact of fisheries. A backshift to a cold-state ecosystem, with extensive regional upwelling and decreased sardinella habitat, would topple that balance.
    Tree establishment along an ENSO experimental gradient in the Atacama desert
    Squeo, F.A. ; Holmgren, M. ; Jimenez, L. ; Alban, L. ; Reyes, J. ; Gutierrez, J.R. - \ 2007
    Journal of Vegetation Science 18 (2007)2. - ISSN 1100-9233 - p. 195 - 202.
    el-nino - prosopis-chilensis - water relations - arid ecosystem - climate-change - south-america - soil texture - growth - oscillation - variability
    Questions: (1) What are the roles of regional climate and plant growth rate for seedling establishment during ENSO rainy pulses along the western coast of South America? (2) What is the water threshold for tree seedling establishment in these arid ecosystems? Location: Atacama Desert, western South America: Piura (5°10' S, 80°37' W), Mejia (17°00' S, 71°59' W), Fray Jorge (30°41' S, 71°37' W). Methods: We experimentally simulated a gradient of ENSO rainfall in three locations encompassing the total extent of the Atacama Desert to test the relative importance of regional climate for seedling establishment during rainy pulses. We also carried out a common garden experiment to test the role of potential interspecific differences in growth rate among two Prosopis tree species. Results: Water threshold for seedling survival increased towards the south with less than 27 mm required in Piura, 100 mm in Mejia and 450 mm in Fray Jorge. We found that seedling survival and growth rate (shoots and roots) were much higher in Piura than in the other two sites for both Prosopis species. Conclusions: Our results indicate that tree establishment during rainy pulses is more likely to be successful in regions where rain falls during warm months and stimulates fast plant growth, and where loose soil texture facilitates deep root growth and therefore access to more stable water sources.
    Spatial and temporal fluctuations in bacteria, microfauna and mineral nitrogen in response to a nutrient impulse in soil
    Zelenev, V.V. - \ 2004
    Wageningen University. Promotor(en): Ariena van Bruggen, co-promotor(en): A.M. Semenov. - Wageningen : s.n. - ISBN 9789058089885 - 190
    bodembiologie - bodemfauna - micro-organismen - bacteriën - biologische bodemactiviteit - rizosfeer - variatie - oscillatie - populatiedynamica - bevolkingsspreiding - organisch bodemmateriaal - organisch afval - voedingsstoffen - wiskundige modellen - simulatiemodellen - soil biology - soil fauna - microorganisms - bacteria - biological activity in soil - rhizosphere - variation - oscillation - population dynamics - population distribution - soil organic matter - organic wastes - nutrients - mathematical models - simulation models
    Fluctuations of bacterial populations can be observed when frequent and sufficiently long series of samples are obtained for direct microscopic or plate counts of bacteria. Such fluctuations in time and space have been observed for both bacteria and other soil inhabitants. These fluctuations of bacterial numbers are especially noticeable after some disturbance of soil such as tillage, drying and rewetting, and substrate addition, for example in the form of fresh plant material. However, very seldom were bacterial fluctuations subjected to proper statistical analysis to detect significant periodical components in the analyzed data (Chapter 1). The phenomenon of wave-like bacterial oscillations was investigated in short-term (1 month) controlled experiments for rhizosphere and bulk soil after substrate input from plant roots and fresh plant debris, respectively. Short-term oscillating dynamics of bacterial populations were simulated in a mechanistic model, which may contribute significantly to our understanding of the reasons and consequences of bacterial oscillations after addition of substrate to soil.



    To determine the spatial variation in density of different trophic bacterial groups (copiotrophic and oligotrophic) and carbon sources in the rhizosphere, colony-forming units (CFUs) and soluble total organic carbon (TOC) were quantified along the root from rhizosphere and corresponding bulk soil samples at 2 cm intervals along wheat roots two, three, and four weeks after planting (Chapter 2). There was a moderate rhizosphere effect in one experiment with soil rich in fresh plant debris (1% C in soil), and a very pronounced rhizosphere effect in the second experiment with soil low in organic matter (0.7% C). Wave-like patterns of both trophic groups of bacteria as well as TOC could be discerned along the whole root length (60 or 90 cm). Harmonical analysis revealed significant oscillations in bacterial populations and TOC. TOC concentrations were maximal at the root tip and base and minimal in the middle part of the roots. Populations of copiotrophic and oligotrophic bacteria had two maxima close to the root tip and at the root base, or three maxima close to the tip, in the middle section, and at the root base. Phases and periods of the two trophic groups differed slightly. The location and pattern of the waves in bacterial populations changed progressively from week to week, and was not consistently correlated with TOC concentrations or the location of lateral root formation. Thus, the traditional view that patterns in bacterial numbers along the root directly reflect patterns in exudation and rhizodeposition from several fixed sources along the root may not be true. We attributed the observed wave-like patterns in bacterial populations to bacterial growth and death cycles (due to autolysis or grazing by predators). Considering the root tip as a moving nutrient source, temporal oscillations in bacterial populations at any location where the root tip passed would result in moving waves along the root. This change in concept about bacterial populations in the rhizosphere could have significant implications for plant growth promotion and soil health.



    To check the hypothesis that the principal mechanism underlying the wave-like distribution of bacteria along the root is a cycle of growth, death, autolysis, and regrowth of copiotrophic bacteria in response to a moving substrate source (root tip) a simulation model was created (Chapter 3). After transformation of observed spatial data to presumed temporal data based on root growth rates, a simulation model was constructed with the Runge-Kutta integration method to simulate the dynamics of colony-forming bacterial biomass, with relative growth and death rates depending on substrate content so that the rate curves crossed over at a substrate concentration within the range of substrate availability. The original source of substrate was the root tip, supplemented with a background flux (BGF) of substrate from soil organic matter and dead root cells. Dead necromass from bacteria was partially recycled into substrate. This model was named "BACWAVE", standing for 'bacterial waves'. The model generated cyclic dynamics of bacteria, which were translated into traveling spatial waves along a moving nutrient source. Parameter values were estimated from calculated initial substrate concentrations and observed microbial distributions along wheat roots by an iterative optimization method. The kinetic parameter estimates fell in the range of values reported in the literature. The model was validated with an independent data set of bacteria along wheat roots in relatively C-rich soil. Calculated microbial biomass values produced spatial fluctuations similar to those obtained for experimental biomass data derived from colony forming units. Concentrations of readily utilizable substrate (RUS) calculated from biomass dynamics did not mimic measured concentrations of TOC, which consists not only of substrate but also various polymers and humic acids. Thus, a moving impulse of nutrients into soil resulting in cycles of growth and death of bacteria can explain the observed phenomenon of moving bacterial waves along roots. This was the first report of wave-like dynamics of micro-organisms in soil along a root resulting from the interaction of a single organism group with its substrate.



    The model "BACWAVE" for wave-like dynamics of copiotrophic bacteria (CB) was extended to include dynamics of oligotrophic bacteria (OB) (Chapter 4). CFUs ofOBand CB along wheat roots (24 samples) in a low C soil were transformed to temporal biomass taking root growth rate and cell sizes into account. Growth rates of both groups of bacteria increased with readily utilizable substrate (RUS) according to Monod equations, but each with their own characteristic parameter values. The death rate of CB decreased monotonically with substrate concentration, while the death rate ofOBfirst decreased and then increased with substrate concentration. Model parameters were estimated from literature and with an iterative optimization method. Initial biomass and kinetic parameters were lower forOBthan for CB, and fell in the range of values in the literature. The model was validated with an independent data set of bacteria along wheat roots in relatively C-rich soil, so that BGF and initial microbial populations were higher, but other model parameters were the same for both data sets. A satisfactory fit was obtained between experimental and modeled data. This is the first rhizosphere model in which oligotrophic bacteria are taken into account.



    Several microcosm experiments were carried out to investigate the hypothesis that an impulse of fresh substrate into soil would invoke oscillations in bacterial populations (Chapter 5). Soil bacterial populations, mineral nitrogen content, pH, and redox potential (ROP) were monitored daily for one month after incorporation of clover-grass (CG) plant material in soil. Colony-forming units (CFUs) and direct microscopic counts of FDA-stained and FITC-stained bacteria increased immediately after incorporation of the plant material, dropped within 2 days, and fluctuated thereafter. Harmonics analysis demonstrated that there were significant wave-like fluctuations with three or four significant peaks within one month after incorporation of clover-grass material. Ammonium (NH 4+ )concentrations increased from the start of the experiments until nitrification commenced. Nitrate (NO 3−) concentrations dropped immediately after plant incorporation, and then rose monotonically until the end of the experiments. There were no wave-like fluctuations in NH 4+and NO 3−concentrations, so that bacterial fluctuations could not be attributed to alternating mineral N shortage and sufficiency. pH levels rose and declined with NH 4+levels. ROP dropped shortly before NH 4+concentrations rose, and increased before NH 4+concentrations decreased; there were no regular fluctuations in ROP, so that temporary oxygen shortages may not have been responsible for the observed fluctuations in bacterial populations. Thus, for the first time, regular wave-like dynamics were demonstrated for bacterial populations after perturbation by addition of fresh organic matter to soil, and several potential reasons for the death phase of the fluctuations could be excluded from further consideration.



    To elucidate possible reasons for the oscillations in bacterial populations, potential interactions with populations of bacterial predators, in particular bacterial-feeding nematodes (BFN), were investigated (Chapter 6). In two microcosm experiments, soil bacteria (CFU's and microscopic counts of stained bacteria) and nematode populations in 22 families were monitored daily for 25 or 30 days after incorporation of clover+grass (CG) plant material into soil. Soil bacterial populations fluctuated significantly after incorporation of the plant material with 2 peaks within the first week and 3 or 4 smaller peaks thereafter. Total nematodes and BFN populations started to increase in the course of the second week after CG incorporation, but the proportion of BFN increased within one week. Inactive juvenile BFN (dauerlarvae) seemed to be activated after two days (as the percentage of Rhabditidae increased and dauerlarvae decreased), followed by step-wise increases in dauerlarvae every four days, indicating that there was a new generation every four days. There were significant wave-like fluctuations in daily population changes of BFN, but not in total nematode communities, over the duration of these experiments. These fluctuations had similar periods (5 days) as those of bacterial populations, but were shifted about 3 days relatively to the bacterial fluctuations.



    In another microcosm experiment, dynamics of bacterial populations were monitored in response to gamma-irradiated plant material added to gamma-irradiated soil mixed with filtered bacterial suspensions and to non-irradiated soil. Gamma-irradiation of soil significantly increased the periods and amplitudes of bacterial oscillations compared to untreated field soil. Nematode populations were decimated in gamma-irradiated soils, but a small number of protozoa were accidentally introduced in the irradiated soil, and may have been partially responsible for the delayed regulation of bacterial growth. We conclude that fluctuations in bacterial populations were not directly related to similar fluctuations in populations of BFN, as expected from classical Lotka-Volterra equations for predator-prey relationships, but were related to changes in growth rates of BFN. An alternation in active and inactive stages in a synchronized predator community after a disturbance could allow periods of bacterial growth alternated with periods of death. Fluctuations in bacterial populations were dampened after a much longer period when the soil fauna was largely eliminated.



    Findings of regular oscillations in bacterial populations and in the rate of change in numbers of bacterial predators after addition of fresh organic matter to soil stimulated the development of a simulation model to investigate potential mechanisms of those oscillations, and whether they were initiated by bacteria- substrate interactions or predatory regulation of bacteria (Chapter 7). The model could also be used to investigate mineral nitrogen release during short-term organic matter decomposition. A substrate-based food web model was constructed with 3 plant residue and 5 soil organic matter compartments, 3 trophic groups of bacteria (copiotrophic, oligotrophic and hydrolytic), and two predatory groups (BFN and protozoa). Both carbon and nitrogen flows were modeled. Fluctuations in microbial populations in soil after plant residue incorporation could be reproduced with and without participation of predators. The first two peaks in bacterial numbers were mainly related to bacteria-substrate interactions, while predators (particularly protozoa) influenced bacterial dynamics during later stages of bacterial community development. Oligotrophic bacteria had a stabilizing effect on fluctuations of other trophic groups, and were the main source of nutrients for predators. A peak in soil ammonium occurred within one week after residue incorporation. Nitrate increased sigmoidally after a short lag phase. The final nitrate concentration was primarily determined by bacterial dynamics and to a lesser extent by protozoa and nematodes. This model emphasized the importance of substrate-consumer relations for regulation of populations at different trophic levels and nutrient release from fresh organic matter added to soil.



    This research has given insight in potential mechanisms underlying oscillations in populations of soil bacteria and their predators after a disturbance. Despite the advances achieved in this thesis, there are still some problems to be solved. Precise regulation of substrate-consumer interactions and mechanisms that initiate growth and death cycles of soil bacteria have to be investigated in detail. Nevertheless, the "BACWAVE-WEB" model has good potential to predict responses of microbial communities to a disturbance, which could be used to characterize soil health. The model could be expanded to include denitrification and nitrate leaching, so that the extent of N losses after soil disturbance could be predicted.
    Lichtbelasting; overzicht van de effecten op mens en dier
    Molenaar, J.G. de - \ 2003
    Wageningen : Alterra (Alterra-rapport 778) - 72
    wegen - licht - verlichting - dieren - mens - dierecologie - sociale ecologie - biologische ritmen - levenscyclus - effecten - oscillatie - kunstlicht - habitats - milieu - biota - gedrag - roads - light - lighting - animals - man - animal ecology - human ecology - biological rhythms - life cycle - effects - oscillation - artificial light - habitats - environment - biota - behaviour
    Kunstmatige verlichting van de nachtelijke omgeving was tot voor minder dan driekwart eeuw geleden van een dusdanig beperkte omvang en intensiteit dat die tegenwoordig voor velen nauwelijks meer voorstelbaar is. In het reilen en zeilen van onze moderne maatschappij heeft openbare verlichting inmiddels een dusdanig belangrijke plaats verworven dat die nu niet meer weg te denken is. Die verlichting dringt vanuit de steden en dorpen steeds verder in het buitengebied door. Duisternis wordt een schaars goed. Deze ontwikkeling gaat niet onopgemerkt voorbij. Er voltrekt zich een bewustwordingsproces dat zich uit in een groeiende zorg over mogelijk risico voor mens en dier. Recente studies laten inderdaad zien dat kunstmatige verlichting een veelzijdige negatieve invloed kan hebben. In dit rapport wordt een toepassingsgericht overzicht gegeven van de kennis van de effecten van lichtbelasting op mens en dier, alsmede suggesties voor preventie, mitigatie en kwalificatie van relatief kwetsbare gebiedstypen, ten behoeve van het generieke en gebiedsgerichte beleid.
    Quantitative modelling of the biomechanics of the avian syrinx
    Elemans, C.P.H. ; Larsen, O.N. ; Hoffmann, M.R. ; Leeuwen, J.L. van - \ 2003
    Animal Biology 53 (2003)2. - ISSN 1570-7555 - p. 183 - 193.
    sound generation - songbirds - vocalizations - oscillation - mechanisms - behavior - birds - song
    We review current quantitative models of the biomechanics of bird sound production. A quantitative model of the vocal apparatus was proposed by Fletcher (1988). He represented the syrinx (i.e. the portions of the trachea and bronchi with labia and membranes) as a single membrane. This membrane acts as a valve that rapidly closes and opens during phonation. This model can be used as a basis to address comparative morphological and physiological questions. More recently, the syrinx was modelled as a simple modified oscillator. Many features of the sound were captured remarkably well. The parameter values, however, did not represent the distribution of the actual material properties of the syrinx. These models demonstrated the minimum number of parameters required to describe the essential dynamics of the sound signal. Furthermore, we address possible interesting future directions for modelling.
    Intermittent turbulence and oscillations in the stable boundary layer: a system dynamics approach
    Wiel, B.J.H. van de; Moene, A.F. ; Hartogensis, O.K. ; Ronda, R.J. ; DeBruin, H.A.R. ; Holtslag, A.A.M. - \ 2002
    In: 15th Symposium on Boundary Layers and Turbulence, 15-19 July 2002, Wageningen, the Netherlands Boston, U.S.A. : American Meteorological Society - p. 477 - 480.
    meteorologie - turbulentie - oscillatie - meteorology - turbulence - oscillation
    The stable boundary layer (SBL) is often characterised by turbulence which is not continuous in space and time. This socalled intermittent turbulence may affect the whole depth of the SBL. In this study intermittent turbulence is studied from both theoretical and experimental point of view. The study is restricted to the type of intermittency which is caused by the so-called Businger-Blackader mechanism. According to this mechanism the following picture emerges: During clear and stable nights often stability develops faster than shear due to the strong surface radiation. This causes the Richardson number to increase, leading to cessation of turbulence. As a consequence air becomes decoupled from the surface. Soon however air will be accelerated by the omnipresent pressure force until shear is strong enough to break down the stability causing a turbulence burst. Because of strong mixing shear is rapidly reduced and stability takes over. Now the situation has returned to its begin and the mechanism starts over again, causing intermittent bursts of turbulence. In this study we seek for a theoretical foundation and an experimental validation of this mechanism. In the theoretical part of the study, the mechanism described above is simplified to its physical essence. For a certain parameter range the outcome from the numerical runs shows intermittent behaviour. Furthermore this model is studied analytically from a system-dynamics point of view. By doing so a dimensionless parameter is found which determines the equilibrium behaviour of the model (e.g. intermittent or non-intermittent behaviour). This critical parameter is merely a function of external ‘forcings’ such as pressure gradient, cloud cover and soil roughness. The experimental part of our study on intermittent turbulence was tackled during an extensive cooperative nocturnal boundary layer experiment( CASES99) in Kansas, USA. Apart from conventional eddy correlation systems, two types of scintillometers were used; a large aperture and a split-beam laser scintillometer. These instruments provide directly an areally averaged flux which has the main advantage of interchanging of space over time averaging. This allows shorter averaging times of fluxes, which is a major advantage in the non-stationary conditions encountered of the SBL. Our results indicate that the intermittency mechanism described above is indeed a likely candidate to explain intermittent turbulence in the stable boundary layer over land
    Photoperiodiciteit bij Sorghum vulgare Pers.
    Keulemans, N.C. - \ 1959
    Wageningen University. Promotor(en): C. Coolhaas. - Wageningen : [s.n.] - 107
    sorghum bicolor - plantenfysiologie - licht - fotoperiodiciteit - fotoreceptoren - plantkunde - fotoperiode - schaduw - oscillatie - biologische ritmen - levenscyclus - sorghum bicolor - plant physiology - light - photoperiodism - photoreceptors - botany - photoperiod - shade - oscillation - biological rhythms - life cycle
    Great millet of 35 varieties from several tropical and subtropical countries were tested for response to photoperiod. Some were analysed and measured extensively with photoperiods ranging from 5 to 24 h in a 24-h day. The development of the growing point was observed in relation to duration of growth from sowing until flower initiation and anthesis. Leaf number, elongation and length of leaves, stem and panicle, dry weight of plant and panicle were noted. The influence of solar radiation, intensity of supplementary light and temperature were, where possible, recorded.

    Great millet was a short-day plant highly variable between varieties and types. A range of variations was found 'from quantitative to entirely qualitative responding plants'. In general photoperiodic sensitivity of types decreases with increasing distance from the equator. The optimum photoperiod was about 10 to 11 h in a 24-h day for 10-14 days (dependent on age). Flower initiation starts 4 to 5 weeks after sowing, anthesis 4 to 6 weeks later. A minimum age must be reached before flowering could be induced.

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