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  • 1
    Language: English
    In: Applied and environmental microbiology, 01 May 2018, Vol.84(9)
    Description: The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing, Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of catalyzed amplification reporter deposition fluorescence hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities, and interactions among the two most abundant microbial community members (i.e., sp. and spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II) oxidizer sp. under autotrophic conditions as well as of spp. under heterotrophic conditions. We used NanoSIMS to monitor the fate of C-labeled bicarbonate and acetate as well as N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions, only the sp. was actively incorporating C-labeled bicarbonate and N-labeled ammonium. Interestingly, both spp. and sp. became enriched in [C]acetate and [N]ammonium under heterotrophic conditions. Our experiments demonstrated that sp. was capable of assimilating [C]acetate while spp. were not able to fix CO, although a metagenomics survey of culture KS recently revealed that sp. lacks genes for acetate uptake and that the sp. carries the genetic potential to fix CO The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment. Microbial mechanisms by which Fe(II) is oxidized with nitrate as the terminal electron acceptor are generally referred to as "nitrate-dependent Fe(II) oxidation" (NDFO). NDFO has been demonstrated in laboratory cultures (such as the one studied in this work) and in a variety of marine and freshwater sediments. Recently, the importance of NDFO for the transport of sediment-derived Fe in aquatic ecosystems has been emphasized in a series of studies discussing the impact of NDFO for sedimentary nutrient cycling and redox dynamics in marine and freshwater environments. In this article, we report results from an isotope labeling study performed with the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS, which was first described by Straub et al. (1) about 20 years ago. Our current study builds on the recently published metagenome of culture KS (2).
    Keywords: Bradyrhizobium ; Gallionellaceae ; Chemolithoautotrophic Ferrous Iron [Fe(II)] Oxidation ; Fluorescence in Situ Hybridization (FISH) ; Nanoscale Secondary-Ion Mass Spectrometry (Nanosims) ; Neutrophilic ; Nitrate-Dependent Fe(II) Oxidation (Ndfo) ; Bradyrhizobium -- Metabolism ; Carbon -- Metabolism ; Ferrous Compounds -- Metabolism ; Gallionellaceae -- Metabolism ; Nitrates -- Metabolism
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 2
    Language: English
    In: Science of the Total Environment, 01 December 2017, Vol.601-602, pp.987-997
    Description: The Circumpolar Active Layer Monitoring – South (CALM-S) site was established in February 2014 on James Ross Island as the first CALM-S site in the eastern Antarctic Peninsula region. The site, located near Johann Gregor Mendel Station, is labelled CALM-S JGM. The grid area is gently sloped (〈 3°) and has an elevation of between 8 and 11 m a.s.l. The lithology of the site consists of the muddy sediments of Holocene marine terrace and clayey-sandy Cretaceous sedimentary rocks, which significantly affect the texture, moisture content, and physical parameters of the ground within the grid. Our objective was to study seasonal and interannual variability of the active layer depth and thermal regime at the CALM-S site, and at two ground temperature measurement profiles, AWS-JGM and AWS-CALM, located in the grid. The mean air temperature in the period March 2013 to February 2016 reached − 7.2 °C. The mean ground temperature decreased with depth from − 5.3 °C to − 5.4 °C at 5 cm, to − 5.5 °C to − 5.9 °C at 200 cm. Active layer thickness was significantly higher at AWS-CALM and ranged between 86 cm (2014/15) and 87 cm (2015/16), while at AWS-JGM it reached only 51 cm (2013/14) to 65 cm (2015/16). The mean probed active layer depth increased from 66.4 cm in 2013/14 to 78.0 cm in 2014/15. Large differences were observed when comparing the minimum (51 cm to 59 cm) and maximum (100 cm to 113 cm) probed depths. The distribution of the active layer depth and differences in the thermal regime of the uppermost layer of permafrost at CALM-S JGM clearly show the effect of different lithological properties on the two lithologically distinct parts of the grid.
    Keywords: Active Layer Thickness ; Ground Thermal Regime ; Permafrost ; CALM-S ; Antarctic Peninsula ; Climate ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 3
    In: Global Change Biology, July 2015, Vol.21(7), pp.2804-2817
    Description: Permafrost‐affected soils of the northern circumpolar region represent 50% of the terrestrial soil organic carbon () reservoir and are most strongly affected by climatic change. There is growing concern that this vast pool could transition from a net sink to a source. But so far little is known on how the organic matter () in permafrost soils will respond in a warming future, which is governed by composition and possible stabilization mechanisms. To investigate if and how in the active layer and adjacent permafrost is protected against degradation, we employed density fractionation to separate differently stabilized fractions. We studied the quantity and quality of in different compartments using elemental analysis, solid‐phase nuclear magnetic resonance (‐) spectroscopy, and analyses. The soil samples were derived from 16 cores from drained thaw lake basins, ranging from 0 to 5500 years of age, representing a unique series of developing Arctic soils over time. The normalized stocks ranged between 35.5 and 86.2 kg  m, with the major amount of located in the active layers. The stock is dominated by large amounts of particulate organic matter (), whereas mineral‐associated especially in older soils is of minor importance on a mass basis. We show that tremendous amounts of over 25 kg  per square meter are stored as presumably easily degradable rich in carbohydrates. Only about 10 kg  per square meter is present as presumably more stable, mineral‐associated . Significant amounts of the easily degradable, carbohydrate‐rich are preserved in the yet permanently frozen soil below the permafrost table. Forced by global warming, this vast labile pool could soon become available for microbial degradation due to the continuous deepening of the annually thawing active layer.
    Keywords: 13 C ‐ Cpmas Nmr Spectroscopy ; 14 C ; Density Fractionation ; Drained Thaw Lake Basin ; Free Particulate Organic Matter ; Mineral‐Associated Organic Matter ; Occluded Organic Matter
    ISSN: 1354-1013
    E-ISSN: 1365-2486
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  • 4
    In: Global Change Biology, April 2018, Vol.24(4), pp.1637-1650
    Description: Global change contributes to the retreat of glaciers at unprecedented rates. The deglaciation facilitates biogeochemical processes on glacial deposits with initiating soil formation as an important driver of evolving ecosystems. The underlying mechanisms of soil formation and the association of soil organic matter () with mineral particles remain unclear, although further insights are critical to understand carbon sequestration in soils. We investigated the microspatial arrangement of coatings at intact soil microaggregate structures during various stages of ecosystem development from 15 to 〉700 years after deglaciation in the proglacial environment of the Damma glacier (Switzerland). The functionally important clay‐sized fraction (2.2 g/cm). To quantify how extends across the surface of mineral particles (coverage) and whether coatings are distributed in fragmented or connected patterns (connectivity), we developed an image analysis protocol based on nanoscale secondary ion mass spectrometry (Nano). We classified and mineral areas depending on the O, C, and CN distributions. With increasing time after glacial retreat, the microspatial coverage and connectivity of increased rapidly. The rapid soil formation led to a succession of patchy distributed to more connected coatings on soil microaggregates. The maximum coverage of 55% at 〉700 years suggests direct evidence for sequestration being decoupled from the mineral surface, as it was not completely masked by and retained its functionality as an ion exchange site. The chemical composition of coatings showed a rapid change toward a higher :C ratio already at 75 years after glacial retreat, which was associated with microbial succession patterns reflecting high N assimilation. Our results demonstrate that rapid sequestration drives the microspatial succession of coatings in soils, a process that can stabilize for the long term. The pronounced retreat of glaciers due to climate change leads to the exposure of glacial deposits where initial soil formation starts along with the accrual of soil carbon. Soil organic matter (SOM) coatings at soil microaggregates were investigated in a chronosequence of soils 15 to 〉700 years after glacial retreat at the Damma glacier (Switzerland). Our results show a rapidly increasing coverage of mineral surfaces by SOM up to a maximum of 55% and a development from patchy distributed to more connected SOM coatings. The microspatial patterns of SOM coatings shaped the sequestration of SOM and partially decoupled it from the mineral particle surfaces, which retain their functionality as an ion exchange sites.
    Keywords: Biogeochemical Soil Interfaces ; Glacier Forefield ; Mineral‐Associated Organic Matter ; Nanoscale Secondary Ion Mass Spectrometry ; Organic Coating ; Organo‐Mineral Associations ; Soil Carbon Sequestration ; Spatial Complexity
    ISSN: 1354-1013
    E-ISSN: 1365-2486
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  • 5
    Language: English
    In: Analytical and Bioanalytical Chemistry, 2018, Vol.410(3), pp.923-931
    Description: We examined the potential of stable-isotope Raman microspectroscopy (SIRM) for the evaluation of differently enriched 13 C-labeled humic acids as model substances for soil organic matter (SOM). The SOM itself can be linked to the soil water holding capacity. Therefore, artificial humic acids (HA) with known isotopic compositions were synthesized and analyzed by means of SIRM. By performing a pregraphitization, a suitable analysis method was developed to cope with the high fluorescence background. Results were verified against isotope ratio mass spectrometry (IRMS). The limit of quantification was 2.1 × 10 −1 13 C/ C tot for the total region and 3.2 × 10 −2 13 C/ C tot for a linear correlation up to 0.25 13 C/ C tot . Complementary nanoscale secondary ion mass spectrometry (NanoSIMS) analysis indicated small-scale heterogeneity within the dry sample material, even though—owing to sample topography and occurring matrix effects—obtained values deviated in magnitude from those of IRMS and SIRM. Our study shows that SIRM is well-suited for the analysis of stable isotope-labeled HA. This method requires no specific sample preparation and can provide information with a spatial resolution in the micrometer range. Graphical abstract Analysis of the isotopic composition of humic acids by Raman microspectroscopy in combination with isotope ratio mass spectrometry and nanoscale secondary ion mass spectrometry.
    Keywords: Raman microspectroscopy ; Stable isotopes ; Humic acids ; Soil organic matter
    ISSN: 1618-2642
    E-ISSN: 1618-2650
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  • 6
    Language: English
    In: Applied Microbiology and Biotechnology, 2015, Vol.99(2), pp.957-968
    Description: Natural attenuation maybe a cost-efficient option for bioremediation of contaminated sites but requires knowledge about the activity of degrading microbes under in situ conditions. In order to link microbial activity to the spatial distribution of contaminant degraders, we combined the recently improved in situ microcosm approach, so-called ‘direct-push bacterial trap’ (DP-BACTRAP), with nano-scale secondary ion mass spectrometry (NanoSIMS) analysis on samples from contaminated constructed wetlands. This approach is based on initially sterile microcosms amended with 13 C-labelled benzene as a source of carbon and energy for microorganisms. The microcosms were introduced directly in the constructed wetland, where they were colonised by indigenous microorganisms from the sediment. After incubation in the field, the samples were analysed by NanoSIMS, scanning electron microscopy (SEM) and fluorescence microscopy in order to visualise 13 C-labelled microbial biomass on undisturbed samples from the microcosms. With the approach developed, we successfully visualised benzene-degrading microbes on solid materials with high surface area by means of NanoSIMS. Moreover, we could demonstrate the feasibility of NanoSIMS analysis of unembedded porous media with a highly complex topography, which was frequently reasoned to not lead to sufficient results.
    Keywords: NanoSIMS ; C ; Microbial activity ; In situ microcosms ; DP-BACTRAPs ; Benzene
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 7
    Language: English
    In: Journal of Environmental Management, 01 March 2018, Vol.209, pp.216-226
    Description: Reclamation of post-mining sites commonly results in rapid accrual of carbon (C) and nitrogen (N) contents due to increasing plant inputs over time. However, little information is available on the distribution of C and N contents with respect to differently stabilized soil organic matter (SOM) fractions during succession or as a result of different reclamation practice. Hence, it remains widely unknown how stable or labile these newly formed C and N pools are. Gaining a deeper understanding of the state of these pools may provide important implications for reclamation practices with respect to C sequestration. We thus investigated C, N, and plant-derived compounds in bulk soil and SOM fractions during succession in post-mining chronosequences (reclaimed with overburden or salvaged topsoil) located along a northwest to southeast transect across the USA. Our results indicate that current reclamation practices perform well with respect to rapid recovery of soil aggregates and the partitioning of C and N to different SOM fractions, these measures being similar to those of natural climax vegetation sites already 2–5 years after reclamation. A general applicability of our results to other post-mining sites with similar reclamation practices may be inferred from the fact that the observed patterns were consistent along the investigated transect, covering different climates and vegetation across the USA. However, regarding SOM stability, the use of salvaged topsoil may be beneficial as compared to that of overburden material because C and N in the fraction regarded as most stable was by 26 and 35% lower at sites restored with overburden as compared to those restored with salvaged topsoil. Plant-derived compounds appeared to be mainly related to bio-available particulate organic matter and particulate organic matter partly stabilized within aggregates, challenging the long-term persistence of plant input C in post-mining soils.
    Keywords: Carbon Sequestration ; Plant-Derived Lipids ; Succession ; Chronosequence ; Stockpiled Topsoil ; Overburden ; Environmental Sciences ; Economics
    ISSN: 0301-4797
    E-ISSN: 1095-8630
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, April 2017, Vol.107, pp.188-197
    Description: Forest subsoils may represent an important C sink in a warming world, but rhizodeposition as the key biogeochemical process determining the C sink strength of mature forests has not yet been quantified in subsoils. According to studies conducted in topsoil or laboratory experiments, soil C inputs by root exudation are increasing with increasing temperature and decreasing nutrient availability. We examined whether these relationships apply to forest subsoil by analyzing the response of root exudation to increasing soil depth up to 130 cm in a mature European beech ( L.) forest. In two subsequent growing seasons differing in temperature and precipitation, we investigated root exudation with a cuvette-based method and analyzed root morphology, microbial biomass, and soil nutrient availability. We proved that root exudation greatly decreases with soil depth as a consequence of a significant decrease in root-mass specific exudation activity to nearly a fifth of topsoil activity. The decrease in specific metabolic activity from 312 mg C g yr in the topsoil to 80 mg C g yr at 130 cm depth was amplified by an exponential decrease in root biomass per soil volume, leading to a relative decrease in root exudation per volume in the deep subsoil to 2% of topsoil root exudation (1 g C 10 cm  m yr at 130 cm depth). Specific root area decreased and mean fine root diameter and root tissue density increased with soil depth, indicating a shift in primary root functionality from fibrous roots in the topsoil to pioneer roots in the subsoil. The decrease in root exudation was accompanied by decreases in soil microbial biomass, extractable organic C (EOC), and N and P availability and increases in the aromatic C portion in SOM, but it did not relate to seasonal differences in climatic conditions. More specifically, it responded positively to an increase in EOC and ETN in the topsoil, but remained at its minimum rate in the SOC-poor subsoil, probably due to a lower organic N and higher mineral N content. The vertical pattern of beech root exudation is in accordance with a strategy to maximize whole-tree carbon-use efficiency, as it reduces C loss by exudation in soil spots where positive priming effects are unlikely, but enhances C exudation where microbes can mine less bioavailable SOM. The exudation patterns further suggest that increased C allocation to root systems as a likely tree response to elevated atmospheric [CO ] may not lead to enhanced soil C input by root exudation to subsoils poor in SOM.
    Keywords: Fagus Sylvatica ; Nitrogen ; Pioneer Roots ; Rhizodeposition ; Soc ; Subsoil ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 9
    Language: English
    In: Soil Biology and Biochemistry, February 2014, Vol.69, pp.168-178
    Description: The stabilization of soil organic matter (SOM) is triggered by three main mechanisms: (i) low bioavailability due to aggregation, (ii) recalcitrance due to the chemical structure, and (iii) association of the SOM with mineral surfaces. In the present study we used particle size SOM fractions (sand, silt and clay), derived from the Ah soil horizon from a Norway spruce forest in Southern Germany, to study the effects of different stabilization mechanisms on the bioavailability of soil organic carbon (SOC) in a one year incubation experiment. The respired CO was hourly recorded, additionally CO was analysed 20 times and CO three times during the incubation experiment. To better differentiate between particulate OM (POM) and mineral associated OM (MIN), the incubated fractions and bulk soil were separated according to density (1.8 g cm ) after the incubation experiment. C-CPMAS NMR spectroscopy was used to study the chemical composition of the incubated samples. We demonstrate a clear increase in SOM bioavailability due to aggregate disruption, as the calculated theoretical CO evolution of the SOM fractions recombined by calculation was 43.8% higher in relation to the intact bulk soil. The incubated sand fraction, dominated by POM rich in O/N-alkyl C, showed a prolonged bioavailability of SOC moieties with mean residence times (MRT) of 78 years. Interestingly, the silt fraction, dominated by highly aliphatic, more recalcitrant POM, showed low mineralization rates and slow MRT's (192 years) close to values for the clay fraction (171 years), which contained a large amount of mineral-associated SOM. The recorded CO signatures showed a high depletion in C during the initial stage of the incubation, but an enrichment of the respired CO of up to 3.4‰ relative to the incubated SOM was observed over longer time periods (after 3 and 4 days for bulk soil and sand, respectively, and after 14 days for silt and clay). Therefore, we found no evidence for a C enrichment of SOM as driven by metabolic isotopic fractionation during microbial SOM mineralization, but an indication of a change in the isotopic composition of the C-source over time.
    Keywords: 13co2 ; 14co2 ; Laboratory Incubation ; Heterotrophic Respiration ; 13c-Cpmas NMR Spectroscopy ; Particle Size Fractionation ; Density Fractionation ; Mean Residence Time ; Microbial Biomass ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 10
    Language: English
    In: Agriculture, Ecosystems and Environment, 01 May 2016, Vol.223, pp.211-222
    Description: Organic matter (OM) amendments, originating from waste materials, could be used to enhance soil organic carbon (SOC) storage and fertility of cropland soils. However, there is a limited understanding about the long-term effect of different urban waste compost amendments on soil organic matter (SOM) formation processes and their impact on SOC storage. Accordingly, the long-term effects of different OM amendments on the amount and composition of particulate and mineral associated SOM were investigated. Surface soils were sampled from a Luvisol under cropping rotation, which received biannually 0.4 kg organic carbon m in form of three different urban composts or cattle manure for a period of 15 years. Despite similar C input, different urban waste compost amendments resulted in contrasting C storage. While there were no C stock changes for municipal solid waste compost amended soils, composts from organic waste and green waste and sewage sludge increased SOC stocks in a similar range as conventional farmyard manure. In bulk soils, SOC stocks were increased by approximately 30%, in occluded particulate OM 〈20 μm by 155% (organic waste compost) and 71% (green waste and sewage sludge compost). Carbon storage in clay fractions showed approximately 20% higher values in all treatments. Organic matter amendments result in C–N coupling as for N proportional stock increases were recorded. The high variability of the composition of different amendment types was reflected in the particulate OM fractions but not in the highly uniform composition of the mineral-associated OM. Bulk soil wettability was not affected by the amendments, as only POM fractions showed increased hydrophobicity, but not clay fractions. Clay fractions showed high alkyl/O-alkyl and low C/N ratios, characteristic for microbial material. The OM composition in the clay fraction is determined by the microbial residues that are independent in their composition from the input material. The increased C storage in the clay fractions of the soil amended with organic wastes and green waste and sewage sludge compost and farmyard manure might be promoted by a better microbial use efficiency leading to C sequestration as microbial compounds.
    Keywords: Soil Organic Matter: Som ; 13c Solid-State NMR Spectroscopy ; Density Fractionation ; Carbon Sequestration ; Agriculture ; Environmental Sciences
    ISSN: 0167-8809
    E-ISSN: 1873-2305
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