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  • Koegel-Knabner, Ingrid  (82)
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  • 1
    Language: English
    In: Applied and environmental microbiology, July 2010, Vol.76(14), pp.4765-71
    Description: A novel PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD(alpha)) genes of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The specificities and target ranges of the primers predicted in silico were confirmed experimentally by cloning and sequencing of PAH-RHD(alpha) gene amplicons from soil DNA. Cloning and sequencing showed the dominance of phnAc genes in the contaminated Luvisol. In contrast, high diversity of PAH-RHD(alpha) genes of Gram-positive and Gram-negative bacteria was observed in the phenanthrene-spiked Cambisol. Quantitative real-time PCR based on the same primers revealed that 63 days after phenanthrene spiking, PAH-RHD(alpha) genes were 1 order of magnitude more abundant in the Luvisol than in the Cambisol, while they were not detected in both control soils. In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD(alpha) gene-carrying soil bacteria to phenanthrene spiking.
    Keywords: Biodiversity ; Metagenome ; Soil Microbiology ; Bacteria -- Classification ; Bacterial Proteins -- Genetics ; Dioxygenases -- Genetics ; Phenanthrenes -- Metabolism
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 2
    Language: English
    In: Geochimica et Cosmochimica Acta, 01 May 2016, Vol.180, pp.284-302
    Description: We evaluated the impact of nano-structural characteristics of allophanic compounds and Fe oxide speciation on the efficiency of organo-mineral interactions in an allophanic derived from volcanic ash (Eifel mountains, Germany). The samples selected for our work represented a gradient from: (i) a pure synthetic allophane and (ii) model organo-mineral mixtures to (iii) particle size fractions of the natural Andosol. We thus aimed to link the processes operating at the individual molecular scale to the phenomena active at the aggregate scale. For a non-destructive characterization of the samples, we applied Xe NMR spectroscopy of adsorbed Xe atoms (to identify the mineral nano-structure and surface acid centres), ESEM (verifying the nano-spherical structure of allophane), C CPMAS NMR (for the nature of the soil organic matter (SOM)), Fe Mössbauer spectroscopy (Fe oxide speciation), and N adsorption (contribution of micro- and mesoporosity). By using the atomic probe Xe, we obtained evidence for a mechanism of adsorption onto allophane requiring both the narrow pores (voids formed by the primary nano-spherules) and the acid centres located at the defect surfaces of the primary spherules. The validity of this coupled mechanism for the sorption of organic matter was confirmed by the concomitant blocking of acid centres ( Xe NMR data) and the decrease of the N -available pore volumes ( and ) in the model samples DOM/- and NOM/allophane (DOM = dissolved OM, NOM = natural OM). In the Andosol, the high resistance of SOM against oxidation (OC = 15–50%) was combined with preferential accumulation of certain organic compounds, e.g. potentially labile substrates such as carbohydrates, and the low molecular weight species such as amino acids. This feature was attributed to the peculiar microporous tortuous structure of allophane aggregates that likely impose certain criteria for the chemical nature and size of mineral-bound SOM. On the other hand, the revealed dominance of nanoparticulate Fe oxyhydroxides (57% ferrihydrite) and Fe-substituted allophane (supposedly formed due to co-precipitation of the Al, Si and Fe in the course of volcanic soil formation) may substantially contribute to the formation of highly resistant organo-mineral associations through the enhanced extent of reactive surface groups in nanoparticles, increased surface charge density and electron accepting properties of substituting Fe species that supposedly enhance the proportion of oxidised organic components.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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  • 3
    Language: English
    In: Geochimica et Cosmochimica Acta, 15 May 2012, Vol.85, pp.1-18
    Description: Interactions between organic and mineral constituents prolong the residence time of organic matter in soils. However, the structural organization and mechanisms of organic coverage on mineral surfaces as well as their development with time are still unclear. We used clay fractions from a soil chronosequence (15, 75 and 120 years) in the foreland of the retreating Damma glacier (Switzerland) and from mature soils outside the proglacial area (〉700 and 〈3000 years) to elucidate the evolution of organo–mineral associations during initial soil formation. The chemical composition of the clay-bound organic matter (OM) was assessed by solid-state C NMR spectroscopy while the quantities of amino acids and neutral sugar monomers were determined after acid hydrolysis. The mineral phase was characterized by X-ray diffraction, oxalate extraction, specific surface area by N adsorption (BET approach), and cation exchange capacity at pH 7 (CEC ). The last two methods were applied before and after H O treatment. We found pronounced shifts in quantity and quality of OM during aging of the clay fractions, especially within the first one hundred years of soil formation. The strongly increasing organic carbon (OC) loading of clay-sized particles resulted in decreasing specific surface areas (SSA) of the mineral phases and increasing CEC . Thus, OC accumulation was faster than the supply of mineral surfaces and cation exchange capacity was mainly determined by the OC content. Clay-bound OC of the 15-year-old soils showed high proportions of carboxyl C and aromatic C. This may point to remnants of ancient OC which were inherited from the recently exposed glacial till. With increasing age (75 and 120 years), the relative proportions of carboxyl and aromatic C decreased. This was associated with increasing O-alkyl C proportions, whereas accumulation of alkyl C was mainly detected in clay fractions from the mature soils. These findings from solid-state C NMR spectroscopy are in line with the increasing amounts of microbial-derived carbohydrates with soil age. The large accumulation of proteins, which was comparable to those of carbohydrates, and the very low C/N ratios of H O -resistant OM indicated strong and preferential associations between proteinaceous compounds and mineral surfaces. In the acid soils, poorly crystalline Fe oxides were the main providers of mineral surface area and important for the stabilization of OM during aging of the clay fractions. This was indicated by (I) the strong correlations between oxalate soluble Fe and both, SSA of H O -treated clay fractions and OC content, and (II) the low formation of expandable clays due to small extents of mineral weathering. Our chronosequence approach provided new insights into the evolution of organo–mineral interactions in acid soils. The formation of organo–mineral associations started with the sorption of proteinaceous compounds and microbial-derived carbohydrates on mineral surfaces which were mainly provided by ferrihydrite. The sequential accumulation of different organic compounds and the large OC loadings point to multiple accretion of OM in distinct zones or layers during the initial evolution of clay fractions.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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  • 4
    In: Nature, 2011, Vol.478(7367), p.49
    Description: Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming. Journal Article.
    Keywords: Environmental Sciences Geosciences;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 5
    Language: English
    In: Plant and Soil, 2011, Vol.338(1), pp.63-81
    Description: Grazed steppe ecosystems are discussed as one of the big global carbon sinks that may have the potential to sequester large amounts of atmospheric CO 2 and mitigate the effects of global change if grazing is abandoned or management improved. But until today, little is known about sequestration potentials and stabilisation mechanisms in complete soil profiles of semiarid grasslands and how these systems react to grazing cessation. We applied a combined aggregate size, density and particle size fractionation procedure to sandy steppe soils under different grazing intensities (continuously grazed = Cg, winter grazing = Wg, ungrazed since 1999 = Ug99, ungrazed since 1979 = Ug79). Higher inputs of organic matter in ungrazed treatments led to higher amounts of OC in coarse aggregate size classes (ASC) and especially in particulate organic matter (POM) fractions across all depth. These processes started in the topsoil and took more than 5 years to reach deeper soil horizons (〉10 cm). After 25 years of grazing cessation, subsoils showed clearly higher POM amounts. We found no grazing-induced changes of soil organic matter (SOM) quantity in fine ASC and particle size fractions. Current C-loading of fine particle size fractions was similar between differently grazed plots and decreased with depth, pointing towards free sequestration capacities in deeper horizons. Despite these free capacities, we found no increase in current C-loading on fine mineral soil fractions after 25 years of grazing exclusion. Silt and clay fractions appeared to be saturated. We suppose empirical estimations to overestimate sequestration potentials of particle size fractions or climatic conditions to delay the decomposition and incorporation of OM into these particle size fractions. POM quality was analysed using solid-state 13 C NMR spectroscopy to clarify if grazing cessation changed chemical composition of POM in different ASC and soil depths via changing litter quality or changing decomposition dynamics. We found comparable POM compositions between different grazing intensities. POM is decomposed hierarchically from coarse to fine particles in all soil depths and grazing cessation has not affected the OM decomposition processes. The surplus of OM due to grazing cessation was predominately sequestered in readily decomposable POM fractions across all affected horizons. We question the long-term stabilisation of OM in these steppe soils during the first 25 years after grazing cessation and request more studies in the field of long-term OM stabilisation processes and assessment of carbon sequestration capacities to consider deeper soil horizons.
    Keywords: Solid-state C NMR spectroscopy ; SOM composition ; Carbon loading ; SOM sequestration ; Grazing ; Physical fractionation
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 6
    Language: English
    In: Plant and Soil, 1 January 2011, Vol.338(1/2), pp.143-158
    Description: Despite their low carbon (C) content, most subsoil horizons contribute to more than half of the total soil C stocks, and therefore need to be considered in the global C cycle. Until recently, the properties and dynamics of C in deep soils was largely ignored. The aim of this review is to synthesize literature concerning the sources, composition, mechanisms of stabilisation and destabilization of soil organic matter (SOM) stored in subsoil horizons. Organic C input into subsoils occurs in dissolved form (DOC) following preferential flow pathways, as aboveground or root litter and exudates along root channels and/or through bioturbation. The relative importance of these inputs for subsoil C distribution and dynamics still needs to be evaluated. Generally, C in deep soil horizons is characterized by high mean residence times of up to several thousand years. With few exceptions, the carbon-to-nitrogen (C/N) ratio is decreasing with soil depth, while the stable C and N isotope ratios of SOM are increasing, indicating that organic matter (OM) in deep soil horizons is highly processed. Several studies suggest that SOM in subsoils is enriched in microbial-derived C compounds and depleted in energy-rich plant material compared to topsoil SOM. However, the chemical composition of SOM in subsoils is soil-type specific and greatly influenced by pedological processes. Interaction with the mineral phase, in particular amorphous iron (Fe) and aluminum (Al) oxides was reported to be the main stabilization mechanism in acid and near neutral soils. In addition, occlusion within soil aggregates has been identified to account for a great proportion of SOM preserved in subsoils. Laboratory studies have shown that the decomposition of subsoil C with high residence times could be stimulated by addition of labile C. Other mechanisms leading to destabilisation of SOM in subsoils include disruption of the physical structure and nutrient supply to soil microorganisms. One of the most important factors leading to protection of SOM in subsoils may be the spatial separation of SOM, microorganisms and extracellular enzyme activity possibly related to the heterogeneity of C input. As a result of the different processes, stabilized SOM in subsoils is horizontally stratified. In order to better understand deep SOM dynamics and to include them into soil C models, quantitative information about C fluxes resulting from C input, stabilization and destabilization processes at the field scale are necessary.
    Keywords: Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Agriculture -- Agricultural sciences
    ISSN: 0032079X
    E-ISSN: 15735036
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  • 7
    Language: English
    In: PLoS ONE, 01 January 2014, Vol.9(9), p.e106865
    Description: The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Applied and environmental microbiology, March 2010, Vol.76(6), pp.1831-41
    Description: The relationships between plant carbon resources, soil carbon and nitrogen content, and ectomycorrhizal fungal (EMF) diversity in a monospecific, old-growth beech (Fagus sylvatica) forest were investigated by manipulating carbon flux by girdling. We hypothesized that disruption of the carbon supply would not affect diversity and EMF species numbers if EM fungi can be supplied by plant internal carbohydrate resources or would result in selective disappearance of EMF taxa because of differences in carbon demand of different fungi. Tree carbohydrate status, root demography, EMF colonization, and EMF taxon abundance were measured repeatedly during 1 year after girdling. Girdling did not affect root colonization but decreased EMF species richness of an estimated 79 to 90 taxa to about 40 taxa. Cenococcum geophilum, Lactarius blennius, and Tomentella lapida were dominant, colonizing about 70% of the root tips, and remained unaffected by girdling. Mainly cryptic EMF species disappeared. Therefore, the Shannon-Wiener index (H') decreased but evenness was unaffected. H' was positively correlated with glucose, fructose, and starch concentrations of fine roots and also with the ratio of dissolved organic carbon to dissolved organic nitrogen (DOC/DON), suggesting that both H' and DOC/DON were governed by changes in belowground carbon allocation. Our results suggest that beech maintains numerous rare EMF species by recent photosynthate. These EM fungi may constitute biological insurance for adaptation to changing environmental conditions. The preservation of taxa previously not known to colonize beech may, thus, form an important reservoir for future forest development.
    Keywords: Biodiversity ; Fagus -- Microbiology ; Fungi -- Classification ; Mycorrhizae -- Classification
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 9
    Language: English
    In: Plant and Soil, 2011, Vol.340(1), pp.35-58
    Description: Semiarid steppe ecosystems account for large terrestrial areas and are considered as large carbon (C) sinks. However, fundamental information on topsoil sensitivity to grazing is lacking across different spatial scales including the effects of topography. Our interdisciplinary approach considering soil chemical, physical, and vegetation properties included investigations on pit scale (square-metre scale), plot scale (hectare scale), and the scale of a landscape section (several hectares). Five different sites, representing a grazing intensity gradient, ranging from a long-term grazing exclosure to a heavily grazed site were used. On the pit scale, data about aggregate size distribution, quantity of different soil organic carbon (SOC) pools, SOC mineralisation, hydraulic conductivity and shear strength was available for topsoil samples from representative soil profiles. Spatial variability of topographical parameters, topsoil texture, bulk density, SOC, water repellency, and vegetation cover was analysed on the basis of regular, orthogonal grids in differently grazed treatments by using two different grid sizes on the plot scale and landscape section. On the pit scale, intensive grazing clearly decreased soil aggregation and the amount of fresh, litter-like particulate organic matter (POM). The weak aggregation in combination with animal trampling led to an enhanced mineralisation of SOC, higher topsoil bulk densities, lower infiltration rates, and subsequently to a higher risk of soil erosion. On the plot scale, the effects of soil structure disruption due to grazing are enhanced by the degradation of vegetation patches and resulted in a texture-controlled wettability of the soil surface. In contrast, topsoils of grazing exclosures were characterised by advantageous mechanical topsoil characteristics and SOC-controlled wettability due to higher POM contents. A combined geostatistical and General Linear Model approach identified topography as the fundamental factor creating the spatial distribution of texture fractions and related soil parameters on the scale of a landscape section. Grazing strongly interfered with the topography-controlled particle relocation processes in the landscape and showed strongest effects on the aboveground biomass production and biomass-related soil properties like SOC stocks. We conclude that interdisciplinary multi-scale analyses are essential (i) to differentiate between topography- and grazing-controlled spatial patterns of topsoil and vegetation properties, and (ii) to identify the main grazing-sensitive processes on small scales that are interacting with the spatial distribution and relocation processes on larger scales.
    Keywords: Steppe soils ; Soil organic matter fractions ; Organic carbon mineralisation ; Wind erosion ; Texture ; Vegetation cover ; Shear strength ; Hydraulic conductivity ; Water repellency ; Anisotropy
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 10
    Language: English
    In: Soil Science Society of America Journal, 2011, Vol.75(6), p.2158
    Description: To characterize biogeochemical interface properties in soil with respect to oxide surfaces, the contribution of weakly crystalline and crystalline oxides to soil specific surface area (SSA) of particle size fractions was determined. Three arable topsoils with intermediate to high clay content were subjected to ultrasonic dispersion and particle size fractionation. The obtained silt and clay fractions were treated with hydrogen peroxide, extracted with oxalate and dithionite and the SSA of all fractions was determined using BET-[N.sub.2]. Results show that stable microaggregates were present in the coarse and medium silt fractions of all soils that could not be dispersed physically even at the highest ultrasonic dispersion energy and were probably stabilized by organic matter and iron oxides. Iron oxides were a major contributor to the SSA of all particle size fractions and the losses of carbon after oxalate and dithionite extraction showed that a major part of the organic matter in all particle size fractions was stabilized by iron oxides, even in these clay-rich soils. Weakly crystalline oxide surface area did not increase with decreasing partide size and calculated negative surface areas for some of the fine fractions indicated that weakly crystalline oxides were present as coatings on other minerals. The results demonstrate the importance of (iron) oxides for microaggregation and stabilization of organic matter in soil. However, the actual interface provided by these oxides depends on particle size and crystallinity due to the possible occlusion of mineral surfaces by organic matter and weakly crystalline oxides. Abbreviations: OC, organic carbon; OM, organic matter; SSA, specific surface area; XRD, X-ray diffraction. doi: 10.2136/sssaj2010.0455
    Keywords: Iron Oxides -- Chemical Properties ; Iron Oxides -- Environmental Aspects ; Loams -- Chemical Properties ; Loams -- Composition ; Soil Chemistry -- Research ; Geochemistry -- Research;
    ISSN: Soil Science Society of America Journal
    E-ISSN: 0361-5995
    E-ISSN: 14350661
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