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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De effecten van gereduceerde grondbewerking : groenbemesters beschermen bodem in winter en verminderen onkruiddruk in groeiseizoen
Balen, D.J.M. van; Leeuwen-Haagsma, W.K. van - \ 2017
Ekoland 37 (2017)5. - ISSN 0926-9142 - p. 12 - 13.
groenbemesters - biologische landbouw - bodemkwaliteit - bodem - bodembiologie - organische stof - gereduceerde grondbewerking - green manures - organic farming - soil quality - soil - soil biology - organic matter - reduced tillage
Binnen de biologische landbouw was er altijd extra aandacht voor bodemkwaliteit. De bodem voedt de plant tenslotte. Intussen beginnen wat meer te leren over welke processen er zich in de bodem afspelen. En over de rol die planten spelen. Naast gewas- en rassenkeuze kunnen groenbemesters en mengsels van gewassen en groenbemesters een belangrijke rol spelen. Zo kan ook de plant de bodem voeden.
Biotic interactions and trait-based ecosystem functioning in soil
Sechi, Valentina - \ 2017
University. Promotor(en): Lijbert Brussaard, co-promotor(en): Ron de Goede; C. Mulder; M. Rutgers. - Wageningen : Wageningen University - ISBN 9789463431316 - 176
soil - ecosystems - plant-animal interactions - interactions - soil biology - soil quality - grasslands - collembola - diversity - bodem - ecosystemen - plant-dier interacties - interacties - bodembiologie - bodemkwaliteit - graslanden - diversiteit

Recent emphasis on ecosystem services as a framework to evaluate ecosystems and to promote their sustainable use has drawn attention to how organisms contribute to the delivery of services. Soil attributes and biotic interactions play important roles in ecological processes (e.g. soil formation, nutrient turnover, carbon sequestration and transformation) and, consequently, in the related delivery of ecosystem services.

Therefore, understanding how soil organisms interact and how they respond to environmental conditions is fundamental to preserve soil functioning and provide a meaningful assessment of ecosystem services. Functional traits determine individual responses to pressures and their effects on ecosystem functioning hence, investigating soil ecosystems from a trait-based perspective offers an interesting opportunity to link the functional responses of the organisms to environmental pressures and to give insight into how the entire community influences ecological processes.

The main objective of this thesis is to develop and to test concepts for a trait-driven quantification of ecosystem services through the assessment of the effects of land management on soil processes. In particular, it focuses on exploring the potential of a trait-based approach in identifying and better understanding the response of the soil biota to environmental pressures and analyses the responses of soil organisms in terms of changes in functional trait distribution and trophic interactions.

This work shows that approaches taking the whole soil community into consideration are more suitable to give insight into the effect of anthropogenic pressure on ecosystem functioning than approaches based on single taxonomic groups. Moreover, performing combined analysis (e.g. analysing body-mass distribution and trophic grouping) helps to better identify community response to environmental pressure.

A clear methodology for the next step, i.e. quantification of ecosystem services, is still lacking due to the current difficulties to link and quantify the effect of anthropogenic pressure to ecosystem functioning in soil. For this reason, it is essential that methods analysed in this thesis will be further explored under different environmental pressures to enable the development of tools to be used at the interface of science and society for sustainable development.

Impact of trophic ecologies on the whereabouts of nematodes in soil
Quist, Casper W. - \ 2017
University. Promotor(en): Jaap Bakker, co-promotor(en): Hans Helder. - Wageningen : Wageningen University - ISBN 9789463430814 - 129
nematoda - spatial distribution - soil fauna - biota - trophic levels - food webs - soil ecology - soil biology - farming systems - soil types (ecological) - geostatistics - ruimtelijke verdeling - bodemfauna - trofische graden - voedselwebben - bodemecologie - bodembiologie - bedrijfssystemen - bodemtypen (ecologisch) - geostatistiek

Soil life is highly diverse, and ecologically intricate due to myriad of biotic interactions that take place. Terrestrial nematodes have a high potential to serve as an effective and policy-relevant indicator group for ecosystem functioning and soil biodiversity. The work described in this thesis contributed to the robust mapping of nematode communities at scales relevant in both agronomic and environmental contexts. The overarching aim of the work described in this thesis was to contribute to a sound exploration of the potential of nematode communities as an indicator group for the biological condition of soils. Therefore, the distributions of a wide range of nematode taxa were studied, within and between trophic groups and in soils conditioned by various plant species and/or farming systems.

In Chapter 2 nematode taxon-specific qPCR assays were used to pinpoint responses of nematode communities to invasive plant species Solidago gigantea in two invaded ecosystems: semi-natural grasslands and riparian floodplains. Nematode communities and fungal biomass were examined in adjacent invaded and uninvaded patches. The dominant presence of the invasive plant causes a decrease of plant species-richness and diversity, and an about twofold increase of fungal biomass. Only the density of a single group of fungivorous nematodes (Aphelenchoididea) increased, whereas the densities of two other, phylogenetically distinct lineages of fungivorous nematodes, Aphelenchidae and Diphtherophoridae, were unaffected by the local increase in fungal biomass. Apparently S. gigantea induces a local asymmetric boost of the fungal community, and only Aphelenchoididae were able to benefit from this change induced by the invasive plant.

In Chapter 3 the outcome is shown of a test whether farming system effects are mirrored in compositional changes in nematode communities. The long-term impact of three farming systems (conventional, integrated and organic) on nematode communities was investigated at the Vredepeel, an experimental farm in the southeastern part of The Netherlands. The results showed that organic farming causes specific shifts in nematode community composition, exceeding the usually large crop-related assemblage shifts. Strongest effects were observed for the (putative) bacterivore Prismatolaimus, which was relatively common in organic fields and nearly absent in conventional and integrated farming. A reverse effect was observed for Pristionchus; this necromenic bacterivore and facultative predator made up about 7 – 21% of the total nematode community in integrated and conventional farming, whereas it was nearly absent from organic fields. The observed farming system effects suggest that specific nematode taxa might be indicative for the impact of farming practices on soil biota. Knowledge of spatial distribution patterns of soil organisms with distinct trophic preferences will contribute to our understanding of factors that maintain and regulate soil biodiversity, and is essential information to design soil sampling strategies with predictable accuracies.

Chapter 4 deals with microscale patchiness of 45 nematode taxa (at family, genus or species-level) in arable fields and semi-natural grasslands, on marine clay, river clay or sandy soils. Contrary to our expectations, an increase of the number of cores per composite sample above 3, did not result in more accurate detection for any of the taxa under investigation (range of number of cores per composite sample: 3, 6, 12 or 24). Neither system nor soil type did influence microscale distribution. The insights in the spatial distribution of nematodes at microscale presented here, sheds light on the impact of trophic preferences on the spatial distribution of individual nematode taxa, and will allow for the design of statistically sound soil sampling strategies.

Chapter 5 shows belowground distribution patterns of 48 nematode taxa in 12 visually homogeneous fields (each 100 x 100 m) on three soil types (marine clay, river clay and sand) and two land-use types (arable and natural grasslands) across the Netherlands. Over 35,000 nematode-taxon specific qPCR assays allowed us to quantitative analyse nematode taxa at family, genus or species level in over 1,200 soil samples. A sampling scheme was optimized for Bayesian geostatistical analysis (Integrated nested Laplace approximations; INLA). Multivariate analysis show soil type and land-use related differences in the nematode community composition, which underline the effects of environmental filtering and niche partitioning of nematodes. All individual nematode taxa together show a wide range of degrees of spatial variabilities were found (expressed by the range-parameter and the spatial variance parameter (s2spatial). No general effects were detected of soil characteristics or nematode traits (cp-value, trophic group, weight) on the spatial distribution parameters. The relatively high percentages of unexplained spatial variability – 92.5% of the variation for the range-parameter and 74% for spatial variance (s2spatial) – point at a major role of stochasticity for variability of nematode densities within fields. This study adds empirical evidence that distribution patterns of terrestrial nematodes, in areas without noticeable gradients, are driven by neutral / stochastic processes, within the boundaries set by the environment.

In the final Chapter 6, I discuss the opportunities and challenges of the use of molecular tools in soil ecological research, the impact of trophic preferences on the whereabouts of nematodes, the use of nematode communities as indicator for soil condition and how this might be developed and applied to facilitate more sustainable ecosystem management.

De bodem onder ons Bestaan
Brussaard, Lijbert - \ 2016
Wageningen : Wageningen University & Research - ISBN 9789463430081 - 24
bodem - bodembiologie - bodemkwaliteit - soil - soil biology - soil quality
Leve(n) de bodem! : de basis onder ons bestaan
Brussaard, L. ; Govers, F.P.M. ; Buiter, R.M. - \ 2016
Den Haag : Stichting Bio-Wetenschappen en Maatschappij (Cahier / Biowetenschappen en Maatschappij 35e jaargang (2016) kwartaal 3) - ISBN 9789073196834 - 88
bodemkunde - bodembiologie - bodemkwaliteit - landbouwgronden - bodemvruchtbaarheid - bodembeheer - bodemweerbaarheid - bodemmicrobiologie - duurzaam bodemgebruik - lesmaterialen - soil science - soil biology - soil quality - agricultural soils - soil fertility - soil management - soil suppressiveness - soil microbiology - sustainable land use - teaching materials
De bodem is niet alleen letterlijk de grond onder ons bestaan, ze is dat ook figuurlijk. Vruchtbare bodems leveren ons bijvoorbeeld voedsel, water en grondstoffen, maar ook een heel scala aan andere ecosysteemdiensten. In één theelepel zwarte grond leven meer organismen dan er mensen zijn op de hele aarde. Ze zorgen ervoor dat planten gebruik kunnen maken van de voedingsstoffen in de bodem en in een gezonde bodem krijgen ziekteverwekkers ook minder kans. Nu we steeds beter begrijpen hóe ze dat doen, kunnen wij zelfs nieuwe antibiotica vinden in de bodem! In dit cahier laten wetenschappers van naam op het gebied van het bodemonderzoek niet alleen zien welke diensten een gezonde bodem al vele eeuwen levert. Ze vertellen ook hoe de figuurlijke bodem onder ons bestaan tegelijk grond voor inspiratie is voor voedsel en technologie voor de toekomst.
Bodemverbeteraars met focus op biochar
Reuler, H. van; Baltissen, A.H.M.C. - \ 2016
- 15 p.
bodemverbeteraars - biochar - bodemkwaliteit - bodemvruchtbaarheid - bodembiologie - soil conditioners - soil quality - soil fertility - soil biology
Biochar is een stabiele organische verbinding die hoofdzakelijk uit koolstof bestaat. Het ontstaat bij verhitting van biomassa onder zuurstofloze omstandigheden, z.g. pyrolyse. Biochar wordt geproduceerd als bodemverbeteraar. De discussie gaat om het effect van Biochar toediening op een aantal bodemfuncties, zoals b.v. het vermogen om vocht en voedingsstoffen vast te houden, biologische activiteit.
De relatie tussen bodemdieren en hydro- en morfodynamiek in het sublitoraal en litoraal van de Westerschelde
Ysebaert, T. ; Craeymeersch, J.A.M. ; Wal, Daphne van der - \ 2016
IMARES (Rapport / IMARES C066/16) - 84 p.
bodemfauna - bodembiologie - hydrodynamica - westerschelde - soil fauna - soil biology - hydrodynamics - western scheldt
Deze studie, in opdracht van Rijkswaterstaat, heeft als doel de relatie tussen bodemdiergemeenschappen en abiotische omgevingsvariabelen nader te onderzoeken en daarmee een betere onderbouwing te verkrijgen van de grens tussen hoog- en laagdynamische gebieden in de sublitorale en litorale gebieden van de Westerschelde.
Arriving at the right time : a temporal perspective on above-belowground herbivore interactions
Wang, Minggang - \ 2016
University. Promotor(en): Wim van der Putten, co-promotor(en): T.M. Bezemer; A. Biere. - Wageningen : Wageningen University - ISBN 9789462578142 - 174 p.
herbivores - aboveground belowground interactions - herbivory - defence mechanisms - roots - leaves - mycorrhizas - population dynamics - soil biology - herbivoren - boven- en ondergrondse interacties - herbivorie - verdedigingsmechanismen - wortels - bladeren - mycorrhizae - populatiedynamica - bodembiologie
Natuurherstel door grondtransplantatie
Wubs, E.R.J. ; Putten, W.H. van der; Bosch, M. - \ 2016
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 33 (2016)1. - ISSN 0169-6300 - p. 11 - 14.
ecologisch herstel - natuurbeheer - grondverzet - landverbetering - landbouwgronden - zandgronden - heidegronden - graslanden - veldproeven - natuurgebieden - bodembiologie - ecological restoration - nature management - earth moving - land improvement - agricultural soils - sandy soils - heathland soils - grasslands - field tests - natural areas - soil biology
Natuurherstel op voormalige landbouwpercelen, vooral op zandgronden, wordt uitgevoerd om bestaande natuurgebieden te vergroten en ecologische verbindingszones te versterken. Belangrijke beperkende factoren zijn bodemgerelateerd: hoge nutriëntengehaltes, ongeschikte zaadbanken en tekort aan geschikt bodemleven. Een combinatie van ontgronden en transplantatie van grond uit verder ontwikkelde natuurgebieden kan het natuurherstel op akkers sterk versnellen.
Organische mestkwaliteit beïnvloedt bodemmicroben en bodemfuncties
Heijboer, A. ; Berge, H.F.M. ten; Ruiter, P.C. de; Kowalchuk, G.A. ; Jorgensen, H.B. ; Bloem, J. - \ 2016
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 27-29 (2016). - ISSN 0169-6300 - p. 27 - 29.
agro-ecosystemen - bemesting - bodembiologie - micro-organismen - bodemmicrobiologie - stikstofkringloop - fosfolipiden - veldproeven - brassica oleracea var. gemmifera - agroecosystems - fertilizer application - soil biology - microorganisms - soil microbiology - nitrogen cycle - phospholipids - field tests
Micro-organismen spelen een sleutelrol in bodemfuncties zoals de kringlopen van koolstof en stikstof. Voor een duurzame landbouw is het van belang dat deze kringlopen optimaal functioneren om verliezen van nutriënten zoveel mogelijk te voorkomen. Dit onderzoek geeft inzicht in de rol van bodemmicroben bij optimalisatie van de stikstofkringloop door toevoeging van zowel minerale kunstmest als verschillende kwaliteiten organisch materiaal.
Effecten bodem- en structuurverbeteraars : Onderzoek op klei- en zandgrond 2010-2015 eindrapportage
Balen, D.J.M. van; Topper, C.G. ; Geel, W.C.A. van; Berg, W. van den; Haas, M.J.G. de; Bussink, Wim ; Schoutsen, M.A. - \ 2016
Lelystad : Praktijkonderzoek Plant & Omgeving, onderdeel van Wageningen UR, Business Unit Akkerbouw, Groene Ruimte en Vollegrondsgroenten - 121 p.
bodemkwaliteit - bodemstructuur - fysische bodemeigenschappen - chemische bodemeigenschappen - bodembiologie - bodemvruchtbaarheid - bodemvruchtbaarheidsbeheer - zware kleigronden - zandgronden - calciummeststoffen - biochar - soil quality - soil structure - soil physical properties - soil chemical properties - soil biology - soil fertility - soil fertility management - clay soils - sandy soils - calcium fertilizers
In de praktijk lopen telers vaak tegen problemen aan van een slechte bodemkwaliteit. Intensieve bouwplannen, steeds zwaardere mechanisatie, uitloging (Ca-uitspoeling), piekneerslagen en de schaalvergroting in de landbouw leiden tot vermindering van de fysische bodemvruchtbaarheid en de structuur van de bodem. Dit veroorzaakt:  toenemende problemen bij de bewerkbaarheid van de bodem;  minder efficiënt gebruik van meststoffen;  verhoogd risico van uit- en afspoeling van nutriënten;  wateroverlast;  verlaging van de opbrengst. Om de bodemstructuur te verbeteren, worden door industrie en handel zogeheten bodemverbeteraars en kalkmeststoffen aangeboden. Er is een grote variatie in type producten, de wijze waarop ze werken en de mate waarin ze een directe dan wel indirecte invloed op de bodemvruchtbaarheid kunnen hebben. Objectieve informatie over het effect van deze producten op de gewasopbrengsten en de fysische, chemische en biologische bodemvruchtbaarheid ontbreekt. Uit eerdere proeven is bekend dat effecten van bodem verbeterende maatregelen vaak pas na enkele jaren zichtbaar worden. Om het effect van verschillende bodemverbeteraars op opbrengst en bodemeigenschappen op de langere termijn te toetsen, zijn proefvelden aangelegd op drie kleilocaties (Kollumerwaard, Lelystad en Westmaas) en twee zandlocaties (Vredepeel, Valthermond). Op deze proefvelden zijn bouwplannen toegepast die gangbaar zijn voor de betreffende regio. Eventuele positieve effecten worden sterker met het verstrijken der jaren. Bovendien zijn deze het duidelijkst te onderscheiden wanneer op alle locaties hetzelfde gewas wordt geteeld. Daarom stonden er in het laatste jaar op alle proefvelden aardappels. In de proef zijn de ontwikkeling van de gewasopbrengst, de gewaskwaliteit en de bodemeigenschappen gevolgd over een periode van zes jaar (2010-2015).
Genetic variation in plant chemistry : consequences for plant-insect interactions
Geem, Moniek van - \ 2016
University. Promotor(en): Wim van der Putten; J.A. Harvey, co-promotor(en): Rieta Gols. - Wageningen : Wageningen University - ISBN 9789462576681 - 141 p.
phytochemistry - plant composition - genetic variation - insect plant relations - interactions - defence mechanisms - soil biology - fytochemie - plantensamenstelling - genetische variatie - insect-plant relaties - interacties - verdedigingsmechanismen - bodembiologie

Plants form the basis of many food webs and are consumed by a wide variety of organisms, including herbivorous insects. Over the course of evolution, plants have evolved mechanisms to defend themselves against herbivory, whereas herbivorous insects have evolved counter-mechanisms to overcome these defences (a.k.a. co-evolutionary arms races). Plant-insect interactions are not restricted to plants and their herbivores (bi-trophic interactions), but also involve natural enemies of the herbivores such as parasitoids and predators (tri-trophic interactions). Plant quality can affect the quality of the host or prey for parasitoids and predators, respectively. In addition, other plant traits are important in providing shelter, alternative food sources, or chemical cues that can be used for host/prey location. Moreover, as plants reside in both soil and air, they mediate interactions between organisms above- and belowground through changes in plant quality. Plant quality is determined by secondary metabolites and morphological traits that may negatively affect the performance of insects, as well as by primary metabolites that plants produce in order to grow, develop and reproduce, which also provide essential nutrients for insects.

Natural plant populations often exhibit genetic variation in various plant traits that include, amongst others, primary and secondary chemistry. Genetic variation in plant defence traits, such as the production of secondary metabolites, can be under selection pressure from a suite of biotic and abiotic factors that vary in space and time. Herbivorous insects may encounter a wide range of plant metabolites because the total concentrations of primary and secondary metabolites and the concentrations of individual compounds vary between genetically different plants. Also as a consequence of genetic variation, plants can respond differently to herbivory in terms of induced defence chemistry and re-allocation of metabolites.

The main aim of this thesis was to study how genetic variation in plant chemistry affects (multi)trophic interactions between wild cabbage plants and associated insects, both above- and belowground. As a model system I used five naturally occurring populations of wild cabbage (Brassica oleracea) located in the Dorset area in the UK. These populations have been shown to genetically differ in their defence chemistry profiles even though they are located in relatively close proximity to each other. Wild cabbages belong to the Brassicaceae, a plant family that is characterized by the production of glucosinolates, a group of secondary metabolites. Together with the enzyme myrosinase they form the chemical defence system of Brassicaceous plants including wild cabbage. Glucosinolates and myrosinases are stored separately in plant tissues but upon tissue damage they come into contact with each other upon which the glucosinolates are hydrolysed into potentially toxic break down products. The wild cabbage populations used in this thesis differ in their total glucosinolate concentrations as well as in the expression of individual glucosinolates.

In chapter 1 I describe plant-insect interactions in a multi-trophic framework, including both the above- and belowground compartments. Genetic variation in plant traits is introduced as the main topic of this thesis, and I present the main aim and outline of my work.

In chapter 2 I discuss how aboveground-belowground interactions influence the evolution and maintenance of genetic variation in plant defence chemistry. I review literature on AG-BG interactions as selection pressures for genetic variation, discuss hypotheses about plant mediation of AG-BG interactions, identify gaps in our knowledge such as the influence of spatial-temporal variation in AG-BG interactions, and in the end present new data on genetic variation in secondary chemistry of wild cabbage and related species.

The co-evolutionary arms race between plants and insects has resulted in adaptations in herbivores to cope with plant defence traits. Some insect herbivore species concentrate or sequester secondary metabolites from their food plant and use them in defence against their own enemies. In chapter 3 I studied whether sequestration of glucosinolates by a specialist herbivore is an effective defence mechanism against a generalist predatory bug. I used the sequestering herbivore Athalia rosae as one prey species, and the non-sequestering herbivore Pieris rapae as the control prey species. I compared the performance of the predatory stink bug Podisus maculiventris on these two prey species. As an extra factor, the two prey species were each reared on three different wild cabbage populations to test if plant population would have an effect on the predator through the sequestering herbivore. I found no consistent effect of plant population on the performance of the predator, and prey species only marginally affected its performance. Based on the results I suggest that in some trophic interactions sequestration is not an effective defence mechanism but merely an alternative way of harmlessly dealing with plant secondary metabolites.

In addition to aboveground plant-insect interactions, belowground interactions were considered as well. To test whether the performance of the belowground specialist herbivore Delia radicum, of which the larvae feed on root tissues, was influenced by population-related variation in defence chemistry, I reared this species on the five wild cabbage populations (chapter 4). Chemical analyses of root tissues revealed that there were differences amongst the populations in plant primary (amino acids and sugars) and secondary (glucosinolates) chemistry, but this did not affect the performance of the root herbivore, suggesting that D. radicum is well adapted to a wide range of total concentrations and concentrations of individual metabolites.

Whereas in chapters 3 and 4 I only focused on one compartment (aboveground and belowground respectively), in chapter 5 I included both compartments in one experiment. I studied the effect of belowground herbivory by larvae of the root fly D. radicum on the performance of an aboveground multi-trophic food chain, and whether this effect differed among three wild cabbage populations. I found that belowground herbivory differentially affected the performances of a specialist aboveground herbivore, the diamondback moth Plutella xylostella, and its parasitoid, Cotesia vestalis, with the parasitoid being more affected than the herbivore. Their performance also differed between the wild cabbage populations, often in interaction with the presence/absence of the belowground herbivore. For both the above- and belowground herbivore I found correlations between performance and plant chemistry, which differed between the insect species and also between males and females.

In chapter 6 I discuss the results of my experiments in relation to other studies. I finish with a general conclusion about my work and provide some ideas for future studies that could contribute to our knowledge in the field of (multi)trophic above-belowground interactions with regard to genetic variation in plant chemistry.

In my thesis I show that genetic variation in plant chemistry can affect the outcome of above-belowground plant-insect interactions. Herbivores and higher trophic levels were differently affected by the wild cabbage populations, and this difference was also influenced by the location of herbivory (i.e. aboveground or belowground). In both chapter 4 and chapter 5 I found no strong, unidirectional links between plant chemistry and insect performance, suggesting that other metabolites may have played a role in the observed differential effects of the wild cabbage populations. I also show that sequestration of plant allelochemicals in some herbivores is an alternative way of harmlessly dealing with plant secondary metabolites instead of an effective defence mechanism against predators (chapter 3).

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

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

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

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

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

Biophysical soil quality of tillage systems in conventional and organic farming
Crittenden, S. - \ 2015
University. Promotor(en): Lijbert Brussaard, co-promotor(en): Mirjam Pulleman; Marius Heinen. - Wageningen : Wageningen University - ISBN 9789462575981 - 135
bodemkwaliteit - bodemfysica - grondbewerking - biologische landbouw - bedrijfssystemen - bodembiologie - bodemecologie - soil quality - soil physics - tillage - organic farming - farming systems - soil biology - soil ecology
Barsten in het ammoniakbastion
Ploeg, J.D. van der - \ 2015
Huib Schoonhoven produkties
landbouw - ammoniakemissie - landbouw en milieu - bodembiologie - mestbeleid - emissiereductie - wetenschappelijk onderzoek - kennis van boeren - agriculture - ammonia emission - agriculture and environment - soil biology - manure policy - emission reduction - scientific research - farmers' knowledge
In deze korte film spreken Jan Douwe van der Ploeg en Jaap Hanekamp over het ammoniakbeleid. Jan Douwe van der Ploeg (WUR): "Het is echt een bastion geworden wat zich afkeert van de wereld, maar het wordt steeds duidelijker dat er enorme gaten en barsten zitten in hun redenering en bewijsvoering." Jaap Hanekamp: "Tot op heden hebben we nog geen gegevens gezien die ons inzicht kunnen geven in hoe nou de verhouding is tussen de emissiefactoren die voor de wetgever gelden en de fundamentele data die daaraan ten grondslag liggen."
On the biology and evolution of fungi from soda soils
Grum-Grzhimaylo, A. - \ 2015
University. Promotor(en): Bas Zwaan, co-promotor(en): Fons Debets. - Wageningen : Wageningen University - ISBN 9789462574281 - 232
bodemschimmels - zoute gronden - diversiteit - bodembiologie - evolutie - soil fungi - saline soils - diversity - soil biology - evolution

Summary to the thesis “On the biology and evolution of fungi from soda soils”

Alexey Grum-Grzhimaylo

The presented thesis addresses aspects of biology and evolution of fungi that were recovered from saline soda soils. The work highlights the fact that saline soda soils are populated by a large diversity of fungi capable of withstanding high salts content and high pH. Some of these fungi have been shown to require exceptionally high pH and salts to grow optimally and therefore are called alkaliphiles.

Introductory CHAPTER 1 provides examples of seemingly inhabitable environments and some of its most prominent tenants, with the emphasis on soda lakes ecosystem and alkaliphilic organisms. Aspects of physiology and major adaptive strategies to high pH and salts found in bacteria are portrayed. To our knowledge, there are no studies devoted to the fungi inhabiting saline soda lakes making this work a starting point towards further explorations in the field.

In CHAPTER 2, I show that fungi are actually present in saline soils and focus closely on the fungus that dominated across all our soda soils samples. This fungus displayed a rare obligate alkaliphilic phenotype – it was capable of growing at pH 11.4 on agar plates, with the optimum of around 9–10 and no ability to grow at pH 5.2. Using a combination of morphological and phylogenetic approaches, I describe it as a new name Sodiomyces alkalinus (previously known as Heleococcum alkalinum). We looked at the morphological details of its life cycle and tested for the capacity of utilizing various carbon sources. Given its unique extreme physiology, dominance across the soil samples, and partly for historical reasons, S. alkalinus has become our model organism that found considerable attention across this thesis.

Inspired by the fact that saline soda soils harbour new fungi, I moved on to the investigation of another set of isolates we obtained from soda soils, which belong to the Emericellopsis group (Hypocreales). CHAPTER 3 presents an investigation of the Emericellopsis isolates that showed a much broader pH preference tagging them as facultative alkaliphiles. Here again, combined morphological, phylogenetic, and physiological data allowed us to set this group apart from the rest and described it as a new species – Emericellopsis alkalina. This species is genetically unrelated to S. alkalinus, which provides evidence for the alkaliphilic trait to be polyphyletic, i.e. arisen several times throughout evolutionary history. I showed E. alkalina to be genetically closer to marine-bourne isolates than typical terrestrial species. Such a result provides evidence for the origin of alkaliphilic trait in this group from the marine-bourne fungi, as sea and soda soils environmental factors coincide.

CHAPTER 4 is devoted to a systematic study of our whole collection of fungi recovered from saline soda soils across the world. I investigate over a hundred isolates morphologically, phylogenetically, and test them for growth pH preference. These data confirms the notion that alkaliphily is polyphyletic and has emerged in several lineages of the fungal phylogenetic tree. Detailed morphological descriptions and phylogenetic reconstructions gave me confidence in describing several more new species. A prominent finding is the discovery of two additional Sodiomyces species that also show the obligate alkaliphilic adaptation. Systematic approaches let me to link certain morphological characters of the species to the alkaliphilic phenotype they possess. Although a substantial part of fungi from soda soils indeed displayed alkaliphilic capabilities, we detected typical neutrophilic species that presumably are transient or reside in a dormant state as spores or survival structures.

The next chapters of the thesis are focused on S. alkalinus, chosen as a model organism for studying alkaliphily that we sequenced in collaboration with Joint Genome Institute (Walnut Creek, USA). CHAPTER 5 looks into the aspects of the hydrolytic capabilities of S. alkalinus. The genome and transcriptome provide immense body of data that gave insight on the enzyme sets encoded in the genome involved in the degradation of carbohydrate compounds (so-called CAZymes). Such in silico analysis was backed-up by the enzyme bioassays carried out at various pH and substrates. In S. alkalinus, I found cellulolytic and hemicellulolytic enzymes that act at high pH, as opposed to neutrophilic A. oryzae enzymes that were active mostly at pH 6. Another prominent finding was the detection of strong proteolytic enzymes acting optimally at pH 8. Based on the genome data and bioassays patterns, I speculate on the ecological role of S. alkalinus in soda soils.

CHAPTER 6 addresses the aspects of the PacC transcription factor, a key player in mediating the gene expression under different ambient pH. I sought to find differences in the primary structure of PacC or detecting the multicopiness of the pacC gene, given its function under extreme alkaline conditions. It turned out that the primary structure of the PacC was the same as in other fungi and the pacC gene is presented in a single copy in S. alkalinus genome. However, I noted a shifted expression and proteolytic activation pattern of PacC if compared to neutrophilic fungi. This results provides evidence for the re-tuned pH-sensors on the plasma membrane, however we could not convincingly detect signs of positive selection affecting the PalH sensors that would change its threshold to trigger the downstream molecular cascade.

CHAPTER 7 gives insights into a quite unexpected finding – the presence of viruses in several of the S. alkalinus isolates. I show their effective vertical but not horizontal transmission. Possession of dsRNA as genetic material, icosahedral shapes, and symptomless phenotypes are common characters for a mycovirus. The virus I studied in S. alkalinus exhibits these exact same features. Curiously, no other alkaliphiles from our collection nor known sister species harboured mycoviruses, making this the first instance of mycoviruses detected in an alkaliphilic filamentous fungus.

CHAPTER 8 focuses on another peculiar finding – a bacterial gene in the genome of S. alkalinus. Presumably introduced by a horizontal gene transfer event, this gene encodes for a DD-peptidase homologue commonly found in bacteria, but only in very few eukaryotes. I found only three fungi that possess this gene; two are alkaliphilic – S. alkalinus and its sister species Acremonium alcalophilum. This suggests the importance of this gene for alkaliphily in those species. The DD-peptidase gene appears to be functional and its peak expression was observed at pH 8. Comparative analysis showed this fungal DD-peptidase to be closely related to the homologues derived from halophilic and alkaliphilic bacteria, rather than from neutrophilic ones. I speculate on the putative function of this unusual gene, including the role in the build-up of exo-cellular matrix or defense against dense communities of prokaryotes in soda soils.

The discussion in CHAPTER 9 contemplates on the results obtained throughout the thesis and provides future perspectives on the topic.

Ecological functions of earthworms in soil
Andriuzzi, W.S. - \ 2015
University. Promotor(en): Lijbert Brussaard; T. Bolger, co-promotor(en): O. Schmidt. - Wageningen : Wageningen University - ISBN 9789462574175 - 154
aardwormen - oligochaeta - bodemfauna - bodembiologie - bodemecologie - ecosystemen - bodemstructuur - earthworms - soil fauna - soil biology - soil ecology - ecosystems - soil structure

Ecological functions of earthworms in soil

Walter S. Andriuzzi

Abstract

Earthworms are known to play an important role in soil structure and fertility, but there are still big knowledge gaps on the functional ecology of distinct earthworm species, on their own and in interaction with other species. This thesis investigated how earthworms affect soil biochemical and biophysical functioning, and other organisms such as plants and smaller soil organisms.

Two field experiments with stable isotope tracers were performed to investigate how anecic earthworms (which feed on organic matter at the soil surface and dig deep burrows) transfer carbon and nitrogen from fresh plant litter into soil, and how this in turn affects soil organic matter composition, protists and nematodes. Another field experiment tested whether the anecic earthworm Lumbricus terrestris can counteract negative effects of intense rainfall on soil and plants (ryegrass). A greenhouse experiment was carried out to study how co-occurring earthworm species – two anecic and one endogeic (smaller, soil-feeding) – affect transfer of nitrogen from dung to soil and plants, nitrogen retention in soil, and plant growth. For the latter experiment, a method to produce herbivore (rabbit) dung triple-labelled with carbon, nitrogen and sulphur stable isotopes was developed.

Overall, the findings highlight important functions of earthworms in carbon and nitrogen cycling, soil biophysical structure maintenance due to burrow formation, and resulting biotic interactions. A novel finding was that the sphere of influence of anecic earthworms in soil (the ‘drilosphere’) is a much larger biochemical and biological hotspot than hitherto assumed. Rapid movement of carbon and nitrogen from surface to soil thanks to anecic earthworm activity resulted in spatial heterogeneity in soil carbon content, organic matter composition, and density of smaller eukaryotes (e.g. bacterial-feeding protists). Evidence was found that distinct earthworm anecic species may have dissimilar effects on soil biochemistry and plant growth, and that both anecic and endogeic earthworms may feed on surface organic matter (dung). This shows that the validity of earthworm ecological groups depends on the function under study, and suggests that, for some research questions, species identity should not be neglected; other approaches to quantify ecological differences between species (e.g. functional traits) are appraised. Finally, L. terrestris was found to ameliorate the disturbance of intense rain on plants, giving evidence to the idea that some components of soil biodiversity may contribute to ecosystem stability in the face of disturbance.

Omgaan met bodemverontreiniging in het landelijk gebied
Waarde, J.J. van der; Boels, D. ; Hopman, M. - \ 2015
De Levende Natuur 105 (2015)3. - ISSN 0024-1520 - p. 110 - 114.
bodemverontreiniging - bodembiologie - herstel - natuurbescherming - ecologie - risicoschatting - bodemkwaliteit - soil pollution - soil biology - rehabilitation - nature conservation - ecology - risk assessment - soil quality
Bodemverontreiniging kan leiden tot ecologische effecten en risico's voor plant en dier. Soms moeten er daarom maatregelen worden getroffen. In de praktijk van natuurbeheer en natuurontwikkeling is er nog veel onduidelijkheid over hoe deze effecten bepaald moeten worden. Daartoe is door VROM, LNV, RIZA, RIVM en Bioclear (mede gefinancierd door SKB) PERISCOOP opgezet (Platform Ecologische Risicobeoordeling)
Tot de bodem uitzoeken : micro-organismen beïnvloeden plantengroei
Beintema, N. ; Groenigen, J.W. van - \ 2015
WageningenWorld (2015)2. - ISSN 2210-7908 - p. 10 - 15.
bodembiologie - bodembeheer - organische stof - aardwormen - bodemkwaliteit - organisch bodemmateriaal - koolstof - micro-organismen - bodemvruchtbaarheid - gewasbescherming - plantenontwikkeling - soil biology - soil management - organic matter - earthworms - soil quality - soil organic matter - carbon - microorganisms - soil fertility - plant protection - plant development
Per vierkante meter bodem leven honderden wormen en insecten samen met kilometers aan schimmeldraden, vele miljoenen aaltjes en miljarden bacteriën. Onderzoek maakt steeds meer duidelijk van het precaire evenwicht ondergronds, en de grote invloed daarvan op het leven bovengronds. Het levert nieuwe strategieën op voor gewasbescherming.
Predictability of plant-soil feedback
Cortois, R. - \ 2015
University. Promotor(en): Wim van der Putten, co-promotor(en): Gerlinde de Deyn. - Wageningen : Wageningen University - ISBN 9789462573406 - 152
bodem-plant relaties - bodem - planten - biodiversiteit - graslanden - bodembiologie - bodemfauna - soil plant relationships - soil - plants - biodiversity - grasslands - soil biology - soil fauna

ABSTRACT

In my thesis project I studied the role of soil biota as possible drivers of linkages between plant community diversity and plant productivity. My study was carried out in the framework of a large grassland biodiversity experiment in Jena, the so-called Jena Experiment.
In chapter 1 I explain how soil biota may exert control over plant community productivity by recycling organic material and by intimately interacting with plant roots, either acting as antagonists to plants or as plant growth-promoting symbionts. Reciprocal interactions between plant and soil communities are an important component of so-called ‘plant-soil feedbacks’ (PSFs). In the PSF loop, plant community composition drives changes in belowground communities and abiotic conditions, which can subsequently alter plant community composition and productivity. Such PSF interactions have been proposed to play a major role in plant community composition and functioning.
In the second chapter I review studies that use an experimental approach of inoculating live soils into sterilized background soils to study the effects of root symbionts on plant growth. I demonstrate that we make many assumptions when translating results of controlled studies to natural systems. I propose that we should continuously and carefully consider these assumptions and aim for rigid hypothesis testing by cross-talking between different levels of ecological realism.
In chapter 3 I test how plant traits relate to PSF using a 49 grassland plant species of the Jena Experiment. First, I grew individuals of all species for two months in sterilized soil inoculated with field soil. In the subsequent feedback phase, I grew all plant species for 6 weeks in sterilized soil inoculated with (I) species-specific inoculum (conspecific conditioned soil), (II) sterilized species-specific inoculum, or (III) a mixture of all 49 species-specific inoculums (mixed conditioned soil). Subsequently I compared biomass production in conspecific conditioned soil to biomass production in sterilized soil (PSFsterilized) and in mixed conditioned soil (PSFmixed). Species with increasing specific root length (SRL) were increasingly susceptible to antagonistic interactions in conspecific conditioned soil (i.e. they had strong negative PSFsterilized), while thick-rooted plants had both positive PSFsterilized and high colonization rates of arbuscular mycorrhizal fungi (AMF). Finally, I showed that species ranking of PSFmixed was similar to species ranking of PSFsterilized, indicating that plants with increasingly negative net interactions in conspecific conditioned soil increasingly

benefit from growing in mixed conditioned soil. With these findings, I made a first important

step in placing PSFs in plant ecological strategy frameworks: high SRL is typical for plants

that adopt a ‘fast’ growth strategy, characterized by fast resource acquisition but poor defense

against antagonists and little reliance on AMF.
In chapter 4, I test the relation between phylogenetic relatedness and the feedback effect of one (soil conditioning) plant species to another (responding) plant species. This is named indirect PSF. I grew eleven focal plant species, chosen to represent plants that had negative, neutral and positive PSFsterilized, in soils that were conditioned by conspecifics and soils conditioned by three to four other species with a varying degree of phylogenetic relatedness to the focal plant species. I found that plant species with negative PSF had no different or slightly better growth when growing in soil conditioned by plant species with larger phylogenetic distance to the focal plant. In contrast, plant species with neutral PSF grew less well, and species with positive PSF even worse, in soil conditioned by plant species with increasing phylogenetic distance to the focal plant. I conclude that the effect of phylogenetic relatedness on PSF interactions between plant species may depend on the tendency of the focal plant species to develop detrimental or beneficial interactions with soil microbes.
In chapter 5, I use the PSFmixed values of chapter 3 in a correlational analysis to test how short-term PSFs relate to longer-term species’ performances in the field, using established monocultures and species-rich (60 species) plant communities of the Jena Experiment. Based on some recently published studies I expected that plants with more negative PSFmixed would benefit most from growing in mixtures; these plant species were expected to overyield most in mixed plant communities. However, opposite to the expectation, plant species with the most negative PSF produced least biomass in the 60-species plant communities, whereas plant performance in monoculture was not related to its short-term PSF. I conclude that species-specific overyielding was positively related to species-specific PSF, and that community overyielding was mostly driven by plant species with a neutral to positive PSF. Finally, in chapter 6 I examine the role of quality and quantity of plant biomass in driving nematode feeding group abundance and diversity. I found strong positive effects of both plant species- and plant functional group-richness on abundances of plant feeding, bacterial feeding and fungal feeding nematodes, as well as omnivores, but not for predators. Structural equation modeling (SEM) analysis showed that the positive effect of plant diversity on the abundance of microbial feeding nematodes (fungal plus bacterial feeders) could not be explained by increased microbial biomass. Similarly, the abundance of plant feeding nematodes was not driven by the higher plant biomass in species rich plant communities. Instead, increased plant biomass explained the positive relation between plant species richness and the abundance of microbial feeding nematodes, while for plant feeding nematodes, increased C to N ratio of aboveground plant biomass appeared to explain the positive relation between the abundance of plant feeding nematodes and plant species and functional group richness. Importantly, the density of plant feeding nematodes per unit root biomass decreased with increasing plant diversity, indicating a root feeder dilution effect. I conclude that plant diversity does not explain nematode community composition primarily by simple bottom-up relations, but that other aspects, such as quality of resource and microhabitats quality, may play a role as well.

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