Antibiotic resistance reservoirs : the cases of sponge and human gut microbiota
Versluis, Dennis - \ 2016
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): Mark van Passel; Detmer Sipkema. - Wageningen : Wageningen University - ISBN 9789462579057 - 197
antibiotic resistance - reservoirs - intestinal microorganisms - luffa - forest soils - sediment - escherichia coli - penicillium - faecal examination - antibioticaresistentie - reservoirs - darmmicro-organismen - luffa - bosgronden - sediment - escherichia coli - penicillium - fecesonderzoek
One of the major threats to human health in the 21st century is the emergence of pathogenic bacteria that are resistant to multiple antibiotics, thereby limiting treatment options. An important route through which pathogens become resistant is via acquisition of resistance genes from environmental and human-associated bacteria. Yet, it is poorly understood to what extent and by what mechanisms these so-called reservoirs contribute to emerging resistance. Therefore, the work described in this thesis focussed on generating novel insights into different niches as sources of resistance, with a particular focus on the human gut microbiota as well as on microbial communities associated with marine sponges, especially because the latter have been described as one of the richest sources of bioactive secondary metabolites, including a broad range of antimicrobials. Cultivation-based methods were complemented with culture-independent approaches in order to study bacterial taxa that are not readily cultivated.
Using metatranscriptomics it was found that clinically relevant antibiotic resistance genes are expressed in a broad range of environmental niches including human, mouse and pig gut microbiota, sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment. The diversity of resistance gene transcripts differed greatly per niche indicating that the environment contains a rich reservoir of functional resistance that could be accessible by pathogens. Even though resistance gene expression might be linked to the presence of natural antibiotics, we did not detect expression of the corresponding secondary metabolite biosynthesis clusters.
Thirty-one antibiotic-resistant bacteria, amongst which three belonging to potentially novel Flavobacteriaceae spp., were isolated from the Mediterranean sponges Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis. Isolates were identified in a high throughput manner by double-barcoded 16S rRNA gene amplicon sequencing. Furthermore, analysis of sponge tissue-derived bacterial biomass growing on agar media showed that many novel bacterial taxa can still be isolated by conventional cultivation methods. Genomic DNA from the 31 antibiotic resistant bacteria was interrogated with respect to the presence of active resistance genes by functional metagenomics. In addition, we also screened metagenomic libraries prepared from DNA directly isolated from sponge tissue in order to circumvent the need for cultivation. In total, 37 unique resistance genes were identified, and the predicted gene products of 15 of these shared <90% amino acid identity with known gene products. One resistance gene (blaPSV-1), which was classified into a new β-lactamase family, was found to be exclusive to the marine specific genus Pseudovibrio. These findings raised questions as to the functional roles of these genes in sponges, but more importantly, the functionality of these genes in E. coli shows that they can potentially be harnessed by phylogenetically distinct bacteria in other environments, including human pathogens. As such, it is a wake-up call as to the significance of marine resistance reservoirs.
Pseudovibrio, a genus of α-Proteobacteria, was studied in more detail by comparative genomics as it comprises bacteria that potentially play a role as sponge symbionts and marine hubs of antibiotics resistance. Based on gene content, members of the genus Pseudovibrio were found to cluster by sponge sampling location indicating geographic speciation. Furthermore, Pseudovibrio spp. isolated from sponges near the Spanish coast clustered by sponge, suggesting host-specific colonization or adaptation. Strong support for Pseudovibrio spp. forming symbiotic relations with sponges came from the presence of a plethora of (predicted) conserved symbiosis-related functions in their genomes.
A final study aimed to isolate novel antibiotic resistant reservoir species from the human gut microbiota using a targeted approach. Faecal samples from hospitalized patients that received Selective Digestive Decontamination (SDD), a prophylactic treatment with a cocktail of different antibiotics (tobramycin, polymyxin E, amphotericin B and cefotaxime), were inoculated anaerobically on agar media, after which bacterial biomass was analysed by 16S rRNA gene amplicon sequencing. Six novel taxa were identified that, based on their growth on media supplemented with the SDD antibiotics, could serve as clinically relevant reservoirs of antibiotic resistance. For one of these six taxa a member was obtained in pure culture by targeted isolation. The abundance of antibiotic resistant uncultivated taxa in the human gut microbiota warrants further research as to their potential roles in resistance dissemination.
In conclusion, this thesis provides deeper insights into different environmental niches as reservoirs of antibiotic resistance. The results can serve to prime and inspire future research.
Terug naar de basis
Willems, Arno ; Schreppers, Harrie ; Jans, Rino ; Klingen, Simon ; Ouden, J. den; Schoonderwoerd, Henny ; Wijdeven, Sander ; Staak, Erik van der - \ 2016
Vakblad Natuur Bos Landschap 13 (2016)127. - ISSN 1572-7610 - p. 40 - 41.
bosbeheer - houtachtige planten - duurzaamheid (sustainability) - bosgronden - bodemuitputting - bosecologie - voedingsstoffenbalans - verzuring - bodemverdichting - mechanisatie - forest administration - woody plants - sustainability - forest soils - soil exhaustion - forest ecology - nutrient balance - acidification - soil compaction - mechanization
Als bosbeheerders gaan we er prat op dat we het begrip duurzaamheid hebben uitgevonden. Dat is inderdaad iets om trots op te zijn en bewijst dat we als sector gewend zijn ver vooruit te kijken en te denken. Het is echter de vraag of we onze bossen nog wel volgens de principes van duurzaamheid beheren. Met name over de mogelijke uitputting van de bodem en de invloed van de exploitatie op de bodem bestaan veel vragen waarvan de antwoorden niet voor het oprapen liggen. Op 17 mei 2016 ging de Studiekring van de KNBV terug naar de basis: de bosbodem.
Legacies of Amazonian dark earths on forest composition, structure and dynamics
Quintero Vallejo, E.M. - \ 2015
Wageningen University. Promotor(en): Frans Bongers; Lourens Poorter, co-promotor(en): Marielos Pena Claros; T. Toledo. - Wageningen : Wageningen University - ISBN 9789462574267 - 168
bossen - bosgronden - bosdynamiek - bodemvruchtbaarheid - botanische samenstelling - soortensamenstelling - plantengemeenschappen - amazonia - bolivia - forests - forest soils - forest dynamics - soil fertility - botanical composition - species composition - plant communities - amazonia - bolivia
Amazonian forest is seen as the archetype of pristine forests, untouched by humans, but this romantic view is far from reality. In recent years, there is increasing evidence of long and extensive landscape modification by humans. Processes of permanent inhabitation, expansion and retreat of human populations have not always been obvious in those ecosystems, leaving sometimes weak and overlooked imprints in the landscape. An example of one of these inconspicuous alterations are the modifications in the soil known as Amazonian Dark Earths (ADE) or ‘terra preta’ (black earth in Portuguese), which are the product of the accumulation of residuals from permanent or semi-permanent human inhabitation. They are named after the black color of the soils, which is a consequence of the accumulation of charcoal pieces and organic matter in the soil. These soils also contain higher levels of phosphorous, calcium (mainly originated from bone residuals), and nitrogen that increase fertility of the naturally poor soils, thus favouring agricultural practices. Amazonian Dark Earths are distributed in Brazil, Bolivia, Colombia, and Peru, and it is estimated that they could occupy 3% of the area of the Amazon basin.
With the decrease in human population in the Americas after the encounter with European colonists, sites where ADE had been formed were abandoned and the vegetation recovered. So far, the effects of ADE on old growth forest had not been widely examined and we are just starting to understand the consequences of past human inhabitation on forest composition and structure. In my thesis, I evaluated the effects of ADE on the forest that has re-grown after abandonment by indigenous people in the La Chonta forest, situated at the southern edge of the Amazon basin, in Bolivia. First, I assessed the magnitude of the changes in the soil as a consequence of human occupation. Then, I studied how soil changes affected plant species composition in the forest understory, forest structure and forest dynamics, and finally I determined how seedlings of tree species respond to anthropogenic changes in soil properties.
Detailed information on soil characteristics and its heterogeneity in the landscape is needed to evaluate the effects of soil on the vegetation. Soil heterogeneity in some sites in the Amazon basin can be increased by the presence of ADE. Therefore, I did detailed soil surveys that allowed me to understand the relationship between past human occupation and alteration in the concentration of soil nutrients. I found that natural soils in the southern Amazonian forest are more fertile than their Central and Eastern Amazon counterparts. Past human presence in the area resulted in soil enrichment, due to increases in the concentration of phosphorus, calcium, potassium, and increases in soil pH. Thus, with this information I could test specific hypothesis about the effects of soil fertility on the vegetation that occurs in these sites.
In the Amazonian forest in general, soil characteristics influences the composition of understory angiosperm herbs, ferns and palm species. Thus, increases in soil fertility in ADE could affect the distribution of understory angiosperm herbs, ferns and palm species. I evaluated the effect of ADE on composition, richness and abundance of understory species (ferns, angiosperm herbs, and palms). I correlated soil variables associated with ADE, such as Ca, P, and soil pH, with species composition, richness and abundance. I found that the presence of ADE created a gradient in soil nutrients and pH, which changed the composition of understory species, especially of ferns and palms. Additionally, the higher nutrient concentration and the more neutral pH on ADE soils were associated with a decrease in the richness of fern species. I therefore conclude that the current composition of the understory community in La Chonta is a reflection of past human modification of the soil.
Soil heterogeneity drives forest structure and forest dynamics across the Amazon region, but at a local scale the role of soils on forest dynamics is not well understood. The study of Amazonian Dark Earths (ADE) opens an opportunity to test how increases in soil fertility could affect forest structure and dynamics at local scales. I evaluated the effect of ADE on forest attributes, such standing basal area, tree liana infestation and successional composition, defined by the relative presence of pioneers, to shade tolerant species in the forest. I also evaluated the effect of ADE on individual components of forest dynamics: basal area growth, recruitment, and mortality. Surprisingly, I found that these fertile ADE affected only few forest attributes and components of forest dynamics. Soil pH was one of the edaphic variables that significantly explained forest structure and dynamics. A higher soil pH increased recruitment of intermediate-sized trees (with stem diameter between 20 and 40 cm) and decreased mortality of large trees (stem diameter > 40 cm). The most important effect of pH, however, was on initial basal area and successional composition, which directly affected growth in basal area of intermediate-sized trees.
Increases in soil nutrients can drive plant responses promoting higher growth rates and lower mortality. Plants respond to soil nutrient availability through a suite of traits, by adjusting their biomass allocation patterns, morphology, tissue chemistry and physiology, which allow them successful establishment and regeneration. The higher amount of nutrients found on ADE compared to natural soils could improve the growth of tropical tree species. I studied the effect of ADE on seedling growth, morphology and physiology in a greenhouse experiment with seedlings of 17 tree species from La Chonta. I found that seedlings did not invest more in roots in non-ADE (to take up scarce soil resources) but they invested in leaves and leaf area in ADE (to enhance light capture), although this did not lead to faster growth rate. Tree species responded differently to an increase in soil Ca concentration, which was 2.4 times higher in ADE than in non-ADE soils. Some species seemed to suffer from Ca toxicity as indicated by higher seedling mortality on ADE; others suffered from nutrient imbalance; whereas other species increased their leaf Ca, P and N concentrations in ADE. Only for this latter group of nutrient accumulators, there was a positive relationship between leaf Ca concentration and the growth rates of seedlings. Contrary to expectations, ADE did not lead to increased seedling growth. The ability of plants to colonize patches of ADE might depend on plant responses to increased soil Ca and their capacity to regulate internal tissue calcium to balance nutrition.
In summary, in this southern Amazon forest the increased soil nutrient concentrations are a legacy of the humans that inhabited the area. This nutrient addition caused changes in understory species composition and decreased fern species richness and had modest effects on forest structure and dynamics. Increases in nutrients, specifically Ca, can cause positive and negative responses of tree species, resulting in potentially long term effects on the tree species composition of the forest.
Methane, Carbon Dioxide and Nitrous Oxide Fluxes in Soil Profile under a Winter Wheat-Summer Maize Rotation in the North China Plain
Wang, Y.Y. ; Hu, C.S. ; Ming, H. ; Oenema, O. ; Schaefer, D.A. ; Dong, W.X. ; Zhang, Y.M. ; Li, X.X. - \ 2014
PLoS ONE 9 (2014)6. - ISSN 1932-6203
forest soils - co2 efflux - gas emissions - n2o fluxes - ch4 - respiration - temperature - mitigation - diffusion - slurry
The production and consumption of the greenhouse gases (GHGs) methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) in soil profile are poorly understood. This work sought to quantify the GHG production and consumption at seven depths (0-30, 30-60, 60-90, 90-150, 150-200, 200-250 and 250-300 cm) in a long-term field experiment with a winter wheat-summer maize rotation system, and four N application rates (0; 200; 400 and 600 kg N ha(-1) year(-1)) in the North China Plain. The gas samples were taken twice a week and analyzed by gas chromatography. GHG production and consumption in soil layers were inferred using Fick's law. Results showed nitrogen application significantly increased N2O fluxes in soil down to 90 cm but did not affect CH4 and CO2 fluxes. Soil moisture played an important role in soil profile GHG fluxes; both CH4 consumption and CO2 fluxes in and from soil tended to decrease with increasing soil water filled pore space (WFPS). The top 0-60 cm of soil was a sink of atmospheric CH4, and a source of both CO2 and N2O, more than 90% of the annual cumulative GHG fluxes originated at depths shallower than 90 cm; the subsoil (>90 cm) was not a major source or sink of GHG, rather it acted as a 'reservoir'. This study provides quantitative evidence for the production and consumption of CH4, CO2 and N2O in the soil profile.
Production-ecological modelling explains the difference between potential soil N mineralisation and actual herbage N uptake
Rashid, M.I. ; Goede, R.G.M. de; Brussaard, L. ; Bloem, J. ; Lantinga, E.A. - \ 2014
Applied Soil Ecology 84 (2014). - ISSN 0929-1393 - p. 83 - 92.
winter-wheat fields - nitrogen mineralization - organic-matter - food webs - grassland soils - forest soils - community - manure - earthworms - management
We studied two different grassland fertiliser management regimes on sand and peat soils: above-ground application of a combination of organic N-rich slurry manure and solid cattle manure (SCM) vs. slit-injected, mineral N-rich slurry manure, whether or not supplemented with chemical fertiliser (non-SCM). Measurements of field N mineralisation as estimated from herbage N uptake in unfertilised plots were compared with (i) potential N mineralisation as determined from a standard laboratory soil incubation, (ii) the contribution of groups of soil organisms to N mineralisation based on production-ecological model calculations, and (iii) N mineralisation calculated according to the Dutch fertilisation recommendation for grasslands. Density and biomass of soil biota (bacteria, fungi, enchytraeids, microarthropods and earthworms) as well as net plant N-uptake were higher in the SCM input grasslands compared to the non-SCM input grasslands. The currently used method in Dutch fertilisation recommendations underestimated actual soil N supply capacity by, on average, 102 kg N ha-1 (202 vs. 304 kg ha-1 = 34%). The summed production-ecological model estimate for N mineralisation by bacteria, fungi, protozoa, and enchytraeids was 87–120% of the measured potential soil N mineralisation. Adding the modelled N mineralisation by earthworms to potential soil N mineralisation explained 98–107% of the measured herbage N uptake from soil. For all grasslands and soil biota groups together, the model estimated 105% of the measured net herbage N uptake from soil. Soil biota production-ecological modelling is a powerful tool to understand and predict N uptake in grassland, reflecting the effects of previous manure management and soil type. The results show that combining production ecological modelling to predict N supply with existing soil N tests using aerobic incubation methods, can add to a scientifically based improvement of the N fertilisation recommendations for production grasslands.
The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia
Nunes da Rocha, U. ; Plugge, C.M. ; George, I. ; Elsas, J.D. van; Overbeek, L.S. van - \ 2013
PLoS ONE 8 (2013)12. - ISSN 1932-6203
16s ribosomal-rna - bacterial community structure - hitherto-uncultured bacteria - allium-porrum rhizosphere - soil microbial community - phylum acidobacteria - gen. nov. - subdivision 1 - forest soils - diversity
There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence
Improving national-scale carbon stock inventories using knowledge on land use history
Schulp, C.J.E. ; Verburg, P.H. ; Kuikman, P.J. ; Nabuurs, G.J. ; Olivier, J.G.J. ; Vries, W. de; Veldkamp, T. - \ 2013
Environmental Management 51 (2013)3. - ISSN 0364-152X - p. 709 - 723.
soil organic-carbon - landscape units - regional-scale - forest soils - belgium - dynamics - database - france - europe
National-scale inventories of soil organic carbon (SOC) and forest floor carbon (FFC) stocks have a high uncertainty. Inventories are often based on the interpolation of sampled information, often using a number of covariables to help such interpolation. The rationale for the choice of these covariables is not always documented, despite the fact that many local-scale studies have identified the factors explaining spatial variability of SOC and FFC stocks. These studies indicate, among others the importance of long-term land use history. Despite this, information on the effects of land use history has never been used to explain variability of carbon stocks in national-scale inventories. We designed an alternative method to improve national-scale inventories of SOC and FCC for the Dutch sand area that takes stock of the findings of detailed case studies. Determinants for SOC and FFC stocks derived from landscape-scale case studies were used to map national-scale spatial variability and to calculate national totals. The resulting national-scale spatial distribution was compared with the SOC stock map from the current Dutch greenhouse gas inventory. Using land use history to explain SOC variability decreased the error of the SOC stock estimate in 60 % of the area. The error in FFC stocks decreased in half of the forest area after including soil fertility, tree species, and forest age as explanatory factors. Estimates with reduced uncertainty will make land use and land management a more attractive and acceptable mitigation option to reduce emissions of greenhouse gases for the LULUCF sector.
Variation in soil carbon stocks and their determinants across a precipitation gradient in West Africa
Saiz, G. ; Bird, M.I. ; Domingues, T.F. ; Schrodt, F. ; Schwartz, M. ; Veenendaal, E.M. - \ 2012
Global Change Biology 18 (2012)5. - ISSN 1354-1013 - p. 1670 - 1683.
land-use change - organic-matter - biotic controls - cycle feedback - savanna soils - forest soils - sequestration - texture - senegal - stabilization
We examine the influence of climate, soil properties and vegetation characteristics on soil organic carbon (SOC) along a transect of West African ecosystems sampled across a precipitation gradient on contrasting soil types stretching from Ghana (15°N) to Mali (7°N). Our findings derive from a total of 1108 soil cores sampled over 14 permanent plots. The observed pattern in SOC stocks reflects the very different climatic conditions and contrasting soil properties existing along the latitudinal transect. The combined effects of these factors strongly influence vegetation structure. SOC stocks in the first 2 m of soil ranged from 20 Mg C ha-1 for a Sahelian savanna in Mali to over 120 Mg C ha-1 for a transitional forest in Ghana. The degree of interdependence between soil bulk density (SBD) and soil properties is highlighted by the strong negative relationships observed between SBD and SOC (r2 > 0.84). A simple predictive function capable of encompassing the effect of climate, soil properties and vegetation type on SOC stocks showed that available water and sand content taken together could explain 0.84 and 0.86 of the total variability in SOC stocks observed to 0.3 and 1.0 m depth respectively. Used in combination with a suitable climatic parameter, sand content is a good predictor of SOC stored in highly weathered dry tropical ecosystems with arguably less confounding effects than provided by clay content. There was an increased contribution of resistant SOC to the total SOC pool for lower rainfall soils, this likely being the result of more frequent fire events in the grassier savannas of the more arid regions. This work provides new insights into the mechanisms determining the distribution of carbon storage in tropical soils and should contribute significantly to the development of robust predictive models of biogeochemical cycling and vegetation dynamics in tropical regions.
Estimating nitrogen fluxes at the European scale by upscaling INTEGRATOR model outputs from selected sites
Reinds, G.J. ; Heuvelink, G.B.M. ; Hoogland, T. ; Kros, J. ; Vries, W. de - \ 2012
Biogeosciences 9 (2012)11. - ISSN 1726-4170 - p. 4527 - 4536.
no emissions - forest soils - n2o
A comparison was made between upscaled model results of nitrogen (N) fluxes to air and water from 450 sites within the EU27 and results derived for the entire EU27 area using the model INTEGRATOR. The 450 sites were selected using stratified random sampling, dividing the EU27 into 150 strata and selecting three sites at random within each stratum. The strata were based on important environmental factors influencing N fluxes. Hierarchical divisive cluster analysis was used to reduce the numerous combinations of environmental factors to the required total of 150, such that the heterogeneity of environmental factors within strata was as small as possible. Modelled NH3, N2O and NOx emissions and N leaching/runoff obtained were scaled up from the 450 sites to the entire EU27 and were within 10% of results obtained by running the model for the whole of the EU27. This implies that a reliable estimate of N fluxes for EU27can be made by upscaling results of the 450 selected sites suggesting that dramatic reductions in computation time can be achieved without substantial deterioration of results.
Scientific arguments for net carbon increase in soil organic matter in Dutch forests
Mol, J.P. ; Wyngaert, I.J.J. van den; Vries, W. de - \ 2012
Wageningen : Alterra (Alterra-report 2324) - 32
organisch bodemmateriaal - bosgronden - bossen - koolstofvastlegging - nederland - soil organic matter - forest soils - forests - carbon sequestration - netherlands
If reporting of emissions associated with Forest Management becomes obligatory in the next commitment period, the Netherlands will try to apply the 'not-a-source' principle to carbon emissions from litter and soil in land under Forest Management. To give a scientific basis for the principle of carbon stock change being 'not-a-source', a review is first made of the methods and arguments of other countries and the acceptance or disapproval by UNFCCC experts. Second, we investigated whether available Dutch datasets and literature information confirm the claim that Dutch forest soils are not a carbon source. This review indeed showed convincing arguments for soil being a carbon sink in the Netherlands under forest management, based on a combination of (i) measurements in Loobos, (ii) literature on soil carbon increases based on repeated measurement in comparable areas, (iii) N retention assessments, assuming that the soil C/N ratio stays constant, (iv) European scale modelling approaches on soil carbon changes including the Netherlands and (v) argumentation from expected changes in climate and N deposition in the Netherlands, combined with the results from meta-analysis and modelling.
Specific features of the ecological functioning of urban soils in Moscow and Moscow oblast
Vasenev, V.I. ; Ananyeva, N.D. ; Makarov, O.A. - \ 2012
Eurasian Soil Science 45 (2012)2. - ISSN 1064-2293 - p. 194 - 205.
microbial biomass carbon - land-use change - organic-carbon - metabolic quotient - forest soils - arable soils - ecosystems - ratios - qco2
Urban soils (constructozems) were studied in Moscow and several cities (Dubna, Pushchino, and Serebryanye Prudy) of Moscow oblast. The soil sampling from the upper 10-cm-thick layer was performed in the industrial, residential, and recreational functional zones of these cities. The biological (the carbon of the microbial biomass carbon, Cmic and the microbial (basal) respiration, BR) and chemical (pHwater and the contents of Corg, heavy metals, and NPK) indices were determined in the samples. The ratios of BR to Cmic (the microbial respiration quotient, qCO2) and of Cmic to Corg were calculated. The Cmic varied from 120 to 738 µg C/g soil; the BR, from 0.39 to 1.94 µg CO2-C/g soil per hour; the Corg, from 2.52 to 5.67%; the qCO2, from 1.24 to 5.28 µg CO2-C/mg Cmic/g soil per h; and the Cmic/Corg, from 0.40 to 1.55%. Reliable positive correlations were found between the Cmic and BR, the Cmic and Cmic/Corg, and the Cmic and Corg values (r = 0.75, 0.95, and 0.61, respectively), as well as between the BR and Cmic/Corg values (r = 0.68). The correlation between the Cmic/Corg and qCO2 values was negative (r = -0.70). The values of Cmic, BR, Corg, and Cmic/Corg were found to correlate with the ammonium nitrogen content. No correlative relationships were revealed between the determined indices and the climatic characteristics. The principal component analysis described 86% of the variances for all the experimental data and clearly subdivided the locations of the studied soil objects. The ANOVA showed that the variances of Cmic, Corg, and BR are controlled by the site location factor by 66, 63, and 35%, respectively. The specificity of the functioning of the anthropogenic soils as compared with their natural analogues was clearly demonstrated. As shown in this study, measurable biological indices might be applied to characterize the ecological, environmental-regulating, and productive functions of soils, including urban soils
Natural and fire-induced soil water repellency in a Portugese Shrubland
Stoof, C.R. ; Moore, D. ; Ritsema, C.J. ; Dekker, L.W. - \ 2011
Soil Science Society of America Journal 75 (2011)6. - ISSN 0361-5995 - p. 2283 - 2295.
coarse-textured soils - forest soils - pine forests - hydrological behavior - eucalyptus-globulus - spatial variability - prescribed fire - sandy soil - hydrophobicity - moisture
Post-fire land degradation is often attributed to fire-induced soil water repellency, despite the fact that soil water repellency is a natural phenomenon in many soils and is therefore not necessarily caused by fire. To improve our understanding of the role of soil water repellency in causing fire-induced land degradation, a long-term monitoring study was performed in which the temporal variation of topsoil water repellency (0–2.5-cm depth) was captured in a Portuguese shrubland before and after fire between November 2007 and March 2010. In addition, similarities and dissimilarities between changes following burning and clipping were assessed in a plot experiment. Soil water repellency appeared to be the rule rather than the exception, both before and after fire, and was strongly related to soil moisture and organic matter content. Surprisingly, despite the low soil temperatures during the fire (60°C) and the lack of direct soil moisture changes, fire significantly increased the persistence of soil water repellency (the water drop penetration time). Vegetation removal by burning and clipping played a key role in determining post-fire water repellency in litter and at the soil surface and considerably reduced the time needed to both develop and eliminate water repellency of the litter and surface soil. Where pre-fire (or “natural”) soil water repellency is abundant, an increase in erosion after fire cannot be solely caused by soil water repellency. Nevertheless, fire-induced removal of the protective canopy cover may increase the hydrologic significance of soil water repellency in burned landscapes
Effects of soil oven-drying on concentrations and speciation of trace metals and dissolved organic matter in soil solution extracts of sandy soils
Koopmans, G.F. ; Groenenberg, J.E. - \ 2011
Geoderma 161 (2011)3-4. - ISSN 0016-7061 - p. 147 - 158.
m calcium-chloride - phosphorus solubility - ion activity - agricultural soils - heavy-metals - forest soils - water - binding - carbon - copper
Weak salt extracts can be used to assess the availability of trace metals for leaching and uptake by soil organisms and plants in soil. Before extraction, the International Organization for Standardization recommends to dry soils in an oven at a temperature of 40 °C. Effects of soil oven-drying on different fractions of dissolved organic matter (DOM) and the effect thereof on total concentrations and speciation of trace metals in weak salt extracts have, however, not been quantified yet. In this study, free metal concentrations and DOM speciation were determined in 2 mM Ca(NO3)2 extracts obtained from twelve field-contaminated soils in their field-moist state and after drying at 40 °C. Free metal concentrations were measured with the Donnan Membrane Technique. DOM was fractioned into humic acid (HA), fulvic acid (FA), and hydrophilic (Hy) compounds. Soil oven-drying led to significant increases in the concentrations of total DOM and total dissolved Cu and Ni. For the measurement of total dissolved Cu and Ni concentrations, it is, therefore, better to use field-moist soils. The release of Hy compounds was mainly responsible for the increase in DOM, which accounted for 64 to 77% of the increase in total dissolved organic carbon. Soil oven-drying left the free Cd2+, Cr3+, Cu2+, Ni2+, and Zn2+ concentrations unchanged. Both field-moist and oven-dried soils can, therefore, be used for the measurement of free metal concentrations. Free Cd2+, Cu2+, Ni2+, and Zn2+ concentrations were predicted very well for both field-moist and oven-dried soils using ORCHESTRA, which includes the NICA-Donnan model. However, poor predictions were obtained for Cr3+, for which better NICA parameters need to be derived. --------------------------------------------------------------------------------
Quantifying impacts of nitrogen use in European agriculture on global warming potential.
Vries, W. de; Kros, J. ; Reinds, G.J. ; Butterbach-Bahl, K. - \ 2011
Current Opinion in Environmental Sustainability 3 (2011)5. - ISSN 1877-3435 - p. 291 - 302.
greenhouse-gas inventory - c-n-p - forest soils - carbon sequestration - oxide emissions - climate-change - n2o budget - deposition - methane - management
This paper summarizes current knowledge on the impacts of changes of nitrogen (Nr) use in agriculture on the global warming potential (GWP) by its impact on carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) emissions from agricultural and terrestrial nonagricultural systems and from aquatic and marine ecosystems. Ranges in ‘N induced exchange factors’, giving responses of CO2–C, N2O–N and CH4–C exchange per kg N input, are presented for all ecosystems. Using these factors, a quantification is made of CO2, N2O and CH4 exchange (emissions or uptake) induced by the use of Nr in agriculture at European scale for the year 2000. This includes: (i) direct impacts in the agricultural systems due to Nr inputs by fertilizer and manure and NH3 deposition and (ii) indirect impacts due to Nr leaching and NH3 deposition caused by agriculture on terrestrial, aquatic and marine ecosystems. Results show that the increase in GWP caused by elevated N2O emission due to Nr use in agriculture is completely counteracted by elevated carbon sequestration in nonagricultural systems. Nr effects on biodiversity, eutrophication and human health, however, need to be considered when considering the overall impacts of Nr use in agriculture.
Predicting soil N mineralization: Relevance of organic matter fractions and soil properties.
Ros, G.H. ; Hanegraaf, M.C. ; Hoffland, E. ; Riemsdijk, W.H. van - \ 2011
Soil Biology and Biochemistry 43 (2011)8. - ISSN 0038-0717 - p. 1714 - 1722.
nitrogen mineralization - microbial biomass - chemical methods - grassland soils - forest soils - indexes - availability - carbon - respiration - temperature
Distinct extractable organic matter (EOM) fractions have been used to assess the capacity of soils to supply nitrogen (N). However, substantial uncertainty exists on their role in the N cycle and their functional dependency on soil properties. We therefore examined the variation in mineralizable N and its relationship with EOM fractions, soil physical and chemical properties across 98 agricultural soils with contrasting inherent properties and management histories. Mineralizable N was determined by aerobic incubation at 20 °C and optimum moisture content for 20 weeks. We used multivariate statistical modelling to account for multi-collinearity, an issue generally overlooked in studies evaluating the predictive value of EOM fractions. Mineralization of N was primarily related to the size of OM pools and fractions present; they explained 78% of the variation in mineralizable N whereas other soil variables could explain maximally 8%. Both total and extractable OM expressed the same soil characteristic from a mineralization perspective; they were positively related to mineralizable N and explained a similar percentage of the variation in mineralizable N. Inclusion of mineralizable N in fertilizer recommendation systems should be based on at least one OM variable. The most appropriate EOM fraction can only be identified when the underlying mechanisms are known; regression techniques are not suitable for this purpose. Combination of single EOM fractions is not likely to improve the prediction of mineralizable N due to high multi-collinearity. Inclusion of texture-related soil variables or variables reflecting soil organic matter quality may be neglected due to their limited power to improve the prediction of mineralizable N.
Comparison of land nitrogen budgets for European agriculture by various modeling approaches
Vries, W. de; Leip, A. ; Reinds, G.J. ; Lesschen, J.P. ; Bouwman, A.F. - \ 2011
Environmental Pollution 159 (2011)11. - ISSN 0269-7491 - p. 3254 - 3268.
no emissions - forest soils - n2o - inventory - ecosystems - balances - losses - fields - carbon - water
A comparison of nitrogen (N) budgets for the year 2000 of agro-ecosystems is made for the EU 27 countries by four models with different complexity and data requirements, i.e. INTEGRATOR, IDEAg, MITERRA and IMAGE. The models estimate a comparable total N input in European agriculture, i.e. 23.3–25.7 Mton N yr-1, but N uptake varies more, i.e. from 11.3 to 15.4 Mton N yr-1 leading to total N surpluses varying from 10.4 to 13.2 Mton N yr-1. The estimated overall variation at EU 27 is small for the emissions of ammonia (2.8–3.1 Mton N yr-1) and nitrous oxide (0.33–0.43 Mton N yr-1), but large for the sum of N leaching and runoff (2.7–6.3 Mton N yr-1). Unlike the overall EU estimates, the difference in N output fluxes between models is large at regional scale. This is mainly determined by N inputs, differences being highest in areas with high livestock density.
Effecten van verzuring op bodemleven en stikstofstromen in bossen : verkenning van mogelijkheden voor herstelmaatregelen
Kemmers, R.H. - \ 2011
Wageningen : Alterra (Alterra-rapport 2204) - 42
verzuring - bodemchemie - bodembiodiversiteit - bosgronden - stikstofbalans - stikstofkringloop - ecologisch herstel - acidification - soil chemistry - soil biodiversity - forest soils - nitrogen balance - nitrogen cycle - ecological restoration
Dit rapport geeft een samenvatting van de resultaten van de analyses van het bodemleven, de stikstofstromen en bodemcondities over een brede range van bosgronden. In dit rapport staat de vraag centraal of door verzuring de relatie tussen ondergrondse en bovengrondse biodiversiteit via de N-kringloop is beinvloed. De conclusie is dat door verzuring de activiteit van bacterien (protozoa) en regenwormen is afgenomen en die van schimmels, nematoden en potwormen is toegenomen. Hierdoor is een verschuiving opgetreden in de stikstofbalans van N-immobilisatie naar netto N-mineralisatie. Hiervan profiteren opportunistische soorten in de ondergroei door het extra N-aanbod om te zetten in biomassa waardoor kritischer soorten worden benadeeld. Herstelmaatregelen moeten gericht zijn op herstel van de N-balans tussen bovengronds en ondergronds leven in de richting van een grotere N-retentie door het bodemleven. Hierin kan via het beheer worden gestuurd.
SOMPROF: A vertically explicit soil organic matter model
Braakhekke, M.C. ; Beer, M. ; Hoosbeek, M.R. ; Kruijt, B. ; Kabat, P. - \ 2011
Ecological Modelling 222 (2011)10. - ISSN 0304-3800 - p. 1712 - 1730.
temperature sensitivity - carbon dynamics - atmospheric co2 - climate-change - forest soils - elevated co2 - turnover - respiration - transport - decomposition
Most current soil organic matter (SOM) models represent the soil as a bulk without specification of the vertical distribution of SOM in the soil profile. However, the vertical SOM profile may be of great importance for soil carbon cycling, both on short (hours to years) time scale, due to interactions with the soil temperature and moisture profile, as well as on long (years to centuries) time scale because of depth-specific stabilization mechanisms of organic matter. It is likely that a representation of the SOM profile and surface organic layers in SOM models can improve predictions of the response of land surface fluxes to climate and environmental variability. Although models capable of simulating the vertical SOM profile exist, these were generally not developed for large scale predictive simulations and do not adequately represent surface organic horizons. We present SOMPROF, a vertically explicit SOM model, designed for implementation into large scale ecosystem and land surface models. The model dynamically simulates the vertical SOM profile and organic layer stocks based on mechanistic representations of bioturbation, liquid phase transport of organic matter, and vertical distribution of root litter input. We tested the model based on data from an old growth deciduous forest (Hainich) in Germany, and performed a sensitivity analysis of the transport parameters, and the effects of the vertical SOM distribution on temporal variation of heterotrophic respiration. Model results compare well with measured organic carbon profiles and stocks. SOMPROF is able to simulate a wide range of SOM profiles, using parameter values that are realistic compared to those found in previous studies. Results of the sensitivity analysis show that the vertical SOM distribution strongly affects temporal variation of heterotrophic respiration due to interactions with the soil temperature and moisture profile.
Simulation of daily Nitrous Oxide emissions from managed peat soils
Stolk, P.C. ; Hendriks, R.F.A. ; Jacobs, C.M.J. ; Duyzer, J. ; Moors, E.J. ; Groenigen, J.W. van; Kroon, P.S. ; Schrier-Uijl, A.P. ; Veenendaal, E.M. ; Kabat, P. - \ 2011
Vadose Zone Journal 10 (2011)1. - ISSN 1539-1663 - p. 156 - 168.
covariance flux measurements - n2o emissions - water-flow - grazed grasslands - model development - rainfall events - co2 exchange - forest soils - new-zealand - denitrification
Simulation of emissions of the greenhouse gas N2O from agricultural land is still a challenge. This is mainly due to its high temporal variability, with low background emissions and a few transient peaks. In this study, a first attempt was made to simulate observations of N2O fluxes with a daily time step from managed peat soils. We used a new N2O module added to the extensively tested hydrological–biogeochemical model combination SWAP-ANIMO, hypothesizing that accurate simulation of the controlling factors would imply accurate simulation of the dynamics of the N2O emissions as well. We used daily N2O emission data from three sites in the Netherlands, with complementary data on soil moisture, mineral N content, and soil N2O concentration. Simulation of soil moisture, mineral N, and N2O concentration was reasonable to good. Still, simulation of the daily N2O emissions was poor, with model efficiencies
Assessing denitrification and N leaching in a field with organic amendments
Radersma, S. ; Smit, A.L. - \ 2011
NJAS Wageningen Journal of Life Sciences 58 (2011)1-2. - ISSN 1573-5214 - p. 21 - 29.
nitrate vulnerable zone - paper-mill sludge - crop yields - nitrogen mineralization - plant residues - barley straw - forest soils - decomposition - management - release
Denitrification and leaching of nitrogen (N) from agriculture are a loss of nutrients to farmers and sources of pollution to water and air, and should therefore be minimized. In a field experiment on loamy soil, denitrification and N leaching were measured after late summer incorporation of fodder radish residues with or without paper pulp as N-immobilizing organic material. A set of relatively simple methods were used to measure and calculate denitrification and N leaching during the first two weeks after application and during the rest of the winter period. The methods were acetylene inhibition of nitrification, anion-exchange resin, the mineralization model MINIP, and inorganic-N balance calculations. Paper pulp increased N immobilization after the first day of application throughout the winter. This led to a 63–70% reduction in N losses compared with the sole fodder radish field and with the control. Denitrification was highest in the sole fodder radish treatment, at 65% of its total N losses. N leaching during the winter period was highest in the control, at 70% of its total N losses. This N was mainly liberated by mineralization of soil organic matter after ploughing in late summer. The application of paper pulp plus fodder radish did not affect sugar beet yields in the next year. The methodology for determining leaching and denitrification enabled the assessment of differences among treatments. It showed clearly that paper pulp strongly reduced N losses on this type of soil. The anion resin method that was used to measure leaching during the winter period showed clear and consistent differences between treatments, but may need additional calibration before fully relying on the absolute amounts of N leached