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  • 1
    Language: English
    In: Soil Biology and Biochemistry, Dec, 2013, Vol.67, p.235(10)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2013.09.006 Byline: Geertje Johanna Pronk, Katja Heister, Ingrid Kogel-Knabner Abstract: Interactions between organic matter (OM), minerals and charcoal may play an important role in the development and stabilization of OM in soils. However, these interactions are difficult to characterize in natural soils, which are usually very complex systems with unknown initial conditions. We developed so-called 'artificial soils' with a texture and OM content similar to natural arable soils that were incubated up to 18 months. The aim was to determine the turnover and development of OM with incubation time, and to establish the effect of mineral composition and charcoal presence on organic carbon (OC) and N distribution and properties. Artificial soils were composed of quartz, manure as OM source and a microbial community extracted from a natural arable soil, with 8 different mixtures of montmorillonite, illite, ferrihydrite, boehmite and charcoal. We determined C and N particle size distribution with time and used solid-state.sup.13C nuclear magnetic resonance (NMR) spectroscopy and acid hydrolysis to determine the development of OM composition. The CO.sub.2 respiration rate and distribution of OC and N with particle size was similar for all artificial soil compositions. OC and N accumulated in the 〈20 [mu]m fraction over time and approximately 50% of coarse (〉200 [mu]m) particulate OM was lost after 18 months of incubation..sup.13C NMR spectroscopy indicated accumulation of protein-rich OC in the 〈20 [mu]m fraction, likely in the form of microbially produced substances. Acid hydrolysis showed a higher content of non-hydrolysable N in the mixtures containing clay minerals, indicating that some of the nitrogen present was strongly bound to phylosilicate surfaces. Ferrihydrite did not have any effect on non-hydrolysable N. From this, it can be concluded that in the artificial soils, clay minerals were more important than metal-oxides for the binding of nitrogen and OC. Overall, the artificial soils developed similarly to incubation experiments with natural soils, and were therefore a valuable model system where the effect of specific components on the development and turnover of soil OM could be determined under simplified conditions. Author Affiliation: (a) Lehrstuhl fur Bodenkunde, Technische Universitat Munchen, 85350 Freising-Weihenstephan, Germany (b) Institute of Advanced Study, Technische Universitat Munchen, Lichtenbergstrasse 2a, D-85748 Garching, Germany Article History: Received 10 May 2013; Revised 1 September 2013; Accepted 8 September 2013
    Keywords: Clay -- Analysis ; Montmorillonite -- Analysis ; Iron Oxides -- Analysis ; Hydrolysis -- Analysis ; Nuclear Magnetic Resonance Spectroscopy -- Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, December 2013, Vol.67, pp.235-244
    Description: Interactions between organic matter (OM), minerals and charcoal may play an important role in the development and stabilization of OM in soils. However, these interactions are difficult to characterize in natural soils, which are usually very complex systems with unknown initial conditions. We developed so-called ‘artificial soils’ with a texture and OM content similar to natural arable soils that were incubated up to 18 months. The aim was to determine the turnover and development of OM with incubation time, and to establish the effect of mineral composition and charcoal presence on organic carbon (OC) and N distribution and properties. Artificial soils were composed of quartz, manure as OM source and a microbial community extracted from a natural arable soil, with 8 different mixtures of montmorillonite, illite, ferrihydrite, boehmite and charcoal. We determined C and N particle size distribution with time and used solid-state C nuclear magnetic resonance (NMR) spectroscopy and acid hydrolysis to determine the development of OM composition. The CO respiration rate and distribution of OC and N with particle size was similar for all artificial soil compositions. OC and N accumulated in the 〈20 μm fraction over time and approximately 50% of coarse (〉200 μm) particulate OM was lost after 18 months of incubation. C NMR spectroscopy indicated accumulation of protein-rich OC in the 〈20 μm fraction, likely in the form of microbially produced substances. Acid hydrolysis showed a higher content of non-hydrolysable N in the mixtures containing clay minerals, indicating that some of the nitrogen present was strongly bound to phylosilicate surfaces. Ferrihydrite did not have any effect on non-hydrolysable N. From this, it can be concluded that in the artificial soils, clay minerals were more important than metal-oxides for the binding of nitrogen and OC. Overall, the artificial soils developed similarly to incubation experiments with natural soils, and were therefore a valuable model system where the effect of specific components on the development and turnover of soil OM could be determined under simplified conditions.
    Keywords: Clay Mineral ; Ferrihydrite ; Charcoal ; Acid Hydrolysis ; Organic Nitrogen ; Artificial Soil ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Soil biology & biochemistry, 2013, Vol.67, pp.235-244
    Description: Interactions between organic matter (OM), minerals and charcoal may play an important role in the development and stabilization of OM in soils. However, these interactions are difficult to characterize in natural soils, which are usually very complex systems with unknown initial conditions. We developed so-called ‘artificial soils’ with a texture and OM content similar to natural arable soils that were incubated up to 18 months. The aim was to determine the turnover and development of OM with incubation time, and to establish the effect of mineral composition and charcoal presence on organic carbon (OC) and N distribution and properties. Artificial soils were composed of quartz, manure as OM source and a microbial community extracted from a natural arable soil, with 8 different mixtures of montmorillonite, illite, ferrihydrite, boehmite and charcoal. We determined C and N particle size distribution with time and used solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy and acid hydrolysis to determine the development of OM composition. The CO₂ respiration rate and distribution of OC and N with particle size was similar for all artificial soil compositions. OC and N accumulated in the 200 μm) particulate OM was lost after 18 months of incubation. ¹³C NMR spectroscopy indicated accumulation of protein-rich OC in the 〈20 μm fraction, likely in the form of microbially produced substances. Acid hydrolysis showed a higher content of non-hydrolysable N in the mixtures containing clay minerals, indicating that some of the nitrogen present was strongly bound to phylosilicate surfaces. Ferrihydrite did not have any effect on non-hydrolysable N. From this, it can be concluded that in the artificial soils, clay minerals were more important than metal-oxides for the binding of nitrogen and OC. Overall, the artificial soils developed similarly to incubation experiments with natural soils, and were therefore a valuable model system where the effect of specific components on the development and turnover of soil OM could be determined under simplified conditions. ; p. 235-244.
    Keywords: Particle Size ; Charcoal ; Texture ; Illite ; Organic Matter ; Ferrihydrite ; Carbon Dioxide ; Mineral Content ; Nitrogen ; Acid Hydrolysis ; Microbial Communities ; Carbon ; Quartz ; Respiratory Rate ; Arable Soils ; Particle Size Distribution ; Nuclear Magnetic Resonance Spectroscopy ; Montmorillonite
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 4
    Language: English
    In: Soil Science Society of America journal, 2011, Vol.75(6), pp.2158-2168
    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-N2. 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 particle 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. ; p. 2158-2168.
    Keywords: Clay ; Particle Size ; Iron Oxides ; Soil Organic Matter ; Crystal Structure ; Silt ; Organic Matter ; Iron ; Soil Properties ; Carbon ; Hydrogen Peroxide ; Coatings ; Microaggregates ; Fractionation ; Energy ; Surface Area
    ISSN: 0361-5995
    E-ISSN: 14350661
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  • 5
    Language: English
    In: Soil Biology and Biochemistry, December 2014, Vol.79, pp.57-67
    Description: The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (〉2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO respiration were determined. The second manure input resulted in higher CO respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.
    Keywords: Dgge ; Illite ; Montmorillonite ; Decomposition ; Respiration ; Soil Formation ; 16s Rrna Gene ; Its Fragment ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 6
    In: Applied and Environmental Microbiology, 2010, Vol. 76(14), p.4765
    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: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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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
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.15-25
    Description: To study the influence of the clay minerals montmorillonite (M) and illite (I), the metal oxides ferrihydrite (F) and aluminum hydroxide (A), and charcoal (C) on soil bacterial communities, seven artificial soils with identical texture provided by quartz (Q) were mixed with sterilized manure as organic carbon source before adding a microbial inoculant derived from a Cambisol. Bacterial communities established in artificial soils after 90 days of incubation were compared by DGGE analysis of bacterial and taxon-specific 16S rRNA gene amplicons. The bacterial community structure of charcoal-containing soils highly differed from the other soils at all taxonomic levels studied. Effects of montmorillonite and illite were observed for Bacteria and Betaproteobacteria , but not for Actinobacteria or Alphaproteobacteria . A weak influence of metal oxides on Betaproteobacteria was found. Barcoded pyrosequencing of 16S rRNA gene amplicons done for QM, QI, QIF, and QMC revealed a high bacterial diversity in the artificial soils. The composition of the artificial soils was different from the inoculant, and the structure of the bacterial communities established in QMC soil was most different from the other soils, suggesting that charcoal provided distinct microenvironments and biogeochemical interfaces formed. Several populations with discriminative relative abundance between artificial soils were identified.
    Keywords: Clay Minerals ; Charcoal ; Bacterial Communities ; 16s Rrna Gene ; Dgge ; Pyrosequencing
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 9
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.3-14
    Description: Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike.
    Keywords: Artificial Soils ; Rhdα Genes ; 16s Rrna Genes ; Its ; Dgge
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 10
    Language: English
    In: Applied Clay Science, 2011, Vol.53(1), pp.20-26
    Description: The specific surface area of natural particles is an important parameter to quantify processes such as mineral dissolution and sorptive interactions in soils and sediments. In this study, the external specific surface area (SSA), specific edge surface area (ESA) and specific basal surface area (BSA) of an illite (Inter-ILI) and a montmorillonite (Ceratosil) were determined by atomic force microscopy (AFM) and compared with the SSA obtained by N gas adsorption (BET) and by liquid adsorption using ethylene glycol monomethyl ether (EGME). For the illite we found an SSA of 41 ± 3 m g by BET and of 83 ± 5 m g by analysing 54 particles by AFM. For the montmorillonite BET we estimated a SSA of 61 ± 2 m g , whereas the analysis of 62 particles by AFM images gave a much larger mean SSA of 346 ± 37 m g . We assume that the sample treatment prior to AFM imaging (involving dispersion by NaOH in a dilute dispersion and sonication for 2 min) resulted in delamination of the clay mineral particles. The ESA was 5.6 ± 0.4 m g for the illite, and 15 ± 2 m g for the montmorillonite. This leads to an ESA/BSA ratio of 0.07 for the illite and 0.05 for the montmorillonite for the delaminated particles. For the untreated, non-delaminated particles we calculated an ESA/BSA ratio of 0.16 for the illite and of 0.27 for the montmorillonite. The specific surface area as estimated by EGME was 112 m g for the illite and 475 m g for the montmorillonite, i.e. about 30–40% larger than the respective AFM values. However, this difference in specific surface area was not in agreement with the expected interlayer surface area of both minerals. ► Specific surface area and edge surface area of an illite and a montmorillonite were determined by atomic force microscopy (AFM). ► The AFM specific surface area was found to be much larger than the respective gas adsorption (N -BET) specific surface area. ► Delamination of the particles during dispersion in 10-6 M NaOH during AFM sample preparation may explain this discrepancy.
    Keywords: Montmorillonite ; Illite ; Specific Basal Surface Area ; Specific Lateral Surface Area ; Specific Edge Surface Area ; Afm ; Engineering ; Environmental Sciences ; Geology ; Visual Arts
    ISSN: 0169-1317
    E-ISSN: 1872-9053
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