Hotspots of soil organic carbon storage revealed by laboratory hyperspectral imaging

Subsoil organic carbon (OC) is generally lower in content and more heterogeneous than topsoil OC, rendering it difficult to detect significant differences in subsoil OC storage. We tested the application of laboratory hyperspectral imaging with a variety of machine learning approaches to predict OC distribution in undisturbed soil cores. Using a bias-corrected random forest we were able to reproduce the OC distribution in the soil cores with very good to excellent model goodness-of-fit, enabling us to map the spatial distribution of OC in the soil cores at very high resolution (~53 × 53 µm). Despite a large increase in variance and reduction in OC content with increasing depth, the high resolution of the images enabled statistically powerful analysis in spatial distribution of OC in the soil cores. In contrast to the relatively homogeneous distribution of OC in the plough horizon, the subsoil was characterized by distinct regions of OC enrichment and depletion, including biopores which contained ~2–10 times higher SOC contents than the soil matrix in close proximity. Laboratory hyperspectral imaging enables powerful, fine-scale investigations of the vertical distribution of soil OC as well as hotspots of OC storage in undisturbed samples, overcoming limitations of traditional soil sampling campaigns

Complementary effects of sorption and biochemical processing of dissolved organic matter for emerging structure formation controlled by soil texture

Background: Percolating dissolved organic matter (DOM) from the topsoil is considered the main source of subsoil organic carbon (OC) in temperate soils, but knowledge about its influence on OC storage and structure-forming processes is limited. Aims: We conducted a 30-day incubation experiment with artificial soils to study the effects of percolating DOM and soil texture on OC turnover and initial structure formation. Methods: Artificial soils with contrasting texture, but identical mineral composition, were used to mimic subsoil conditions, where mineral surfaces free of OM come into contact with percolating DOM. After the incubation, we assessed the solution exchange, OM covers on minerals, microbial community and OC turnover, and aggregate formation and stability. Results: A higher sand content caused a lower porosity, accompanied by a lower moisture content. In contrast, the OC retention (21% of the OC input), microbial activity, and community size were unaffected by soil texture. The OM covered 10% of the mineral surfaces within an otherwise OC-free mineral matrix. The formation of large, water-stable aggregates occurred in all soils, but was pronounced in the clay-rich soils (58% mass contribution), which also supported a higher mechanical stability of the aggregates. Conclusions: The initial retention and microbial mineralization of DOM are decoupled from pore sizes and soil solution exchange but are driven by the mineral composition and OC input. The biochemical processing of the percolating DOM can induce large aggregates. Here, the presence of fine mineral particles enhances the formation and mechanical stability of the aggregates, irrespective of their surface charge or sorptive properties

Contrasting soil organic matter properties of a Hawaiian Andosol revealed by fractionations procedures

Volcanic Andosols are recognized by their strong capacity to accumulate soil organic carbon (SOC), and for presenting a singular aggregation pattern. However, the factors that govern their SOC storage and aggregation hierarchy are still poorly understood. In this way, the objective of this study was to evaluate the soil organic matter (SOM) properties of an Andosol through CN analysis, NMR spectroscopy, and scanning electron microscopy (SEM) with subsequent nano scale secondary ion mass spectrometry (NanoSIMS) analysis in the soil mineral fraction testing different fractionation methods. We tested three Andosol samples from two sites of the Kohala region – Hawaii with contrasting precipitation levels. The samples tested were as follow: 1784-60, 1784-80 and 2286-50 (precipitation - average depth in cm). We performed the SOM fractionation using ultrasonic dispersion at 1500 J ml-1, wet sieving and sedimentation. The procedure was carried out in three sets: in deionized water, in 1M NaCL solution, and in polytungstate solution (SPT) 1.8 g cm-3. Six fractions were obtained as follow: free particulate organic matter (fPOM), occluded particulate organic matter (oPOM), 4000-63, 63-20, 20-2 and < 2µm, respectively. Overall, the pre-dispersion treatment with NaCL saturation did not influence the C content and its distribution, as well as the SOM composition observed by NMR and NanoSIMS analysis. The oPOM fraction revealed great differences between the contrasting samples 1784-60 and 2286-50 in C content and SOM composition. More than 90% of the soil mass was concentrated in the fractions below 20 µm. The <2µm fraction was the most representative for the evaluated Andosol, accounting with 83% of the C content and 74% of the soil mass for the three samples evaluated overall. The 2286-50 presented a higher C content than the other samples especially for fPOM and the < 2 µm fraction. The 2286-50 sample presented overall a dominance of alkyl-C, while 1784-60 showed higher amounts of carboxyl-C and O/N alkyl groups, which can be explained by differences in the mineral composition of each sample. In addition, the NanoSIMS analysis demonstrated distinct spatial differences in the distribution of 12C- and 12C14N- in organo-mineral associations at the micro scale between the two sites. The results of this study suggest that mineral interactions in the smaller size-fractions (<2µm) can be the key to explain the mechanisms of C storage in Andosols

Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1

SummaryCcr4-Not is a conserved protein complex that shortens the 3′ poly(A) tails of eukaryotic mRNAs to regulate transcript stability and translation into proteins. RNA-binding proteins are thought to facilitate recruitment of Ccr4-Not to certain mRNAs, but lack of an in-vitro-reconstituted system has slowed progress in understanding the mechanistic details of this specificity. Here, we generate a fully recombinant Ccr4-Not complex that removes poly(A) tails from RNA substrates. The intact complex is more active than the exonucleases alone and has an intrinsic preference for certain RNAs. The RNA-binding protein Mmi1 is highly abundant in preparations of native Ccr4-Not. We demonstrate a high-affinity interaction between recombinant Ccr4-Not and Mmi1. Using in vitro assays, we show that Mmi1 accelerates deadenylation of target RNAs. Together, our results support a model whereby both RNA-binding proteins and the sequence context of mRNAs influence deadenylation rate to regulate gene expression

Correction to: Role of root hair elongation in rhizosheath aggregation and in the carbon flow into the soil

The above article’s initial published version contained an error regarding the co-author Vincent J. M. N. L. Felde’s affiliation. Instead of “Institute of Soil Science and Soil Conservation, Justus Liebig University Giessen, Giessen, Germany”, the right affiliation should have been “Institute of Soil Science, Leibniz University of Hannover, Germany”. The original article has been corrected

Organische Bodensubstanz in sulfatsauren Böden

Sulfatsaure Böden sind Böden und Sedimente, die Eisensulfide enthalten und verbreitet in Küstenregionen und Binnenländern vorkommen. Unter wassergesättigten Bedingungen sind sie produktive Böden der Feuchtgebiete. Eine Austrocknung dieser Böden (durch Entwässerung oder Dürreperioden) führt zur Oxidation der Eisensulfide und damit zu einer starken Versauerung aufgrund der Freisetzung von Schwefelsäure. Nach Wiedervernässung und Wiedereinsetzen reduzierender Bedingungen führt die Aktivität sulfatreduzierender Bakterien zur Bildung von Pyrit und damit zur pH-Erhöhung. Sulfatreduzierende Bakterien sind heterotroph und benötigen ausreichend verfügbares organisches Material. In vielen Regionen kommt es jedoch nach Wiedervernässung solcher Standorte nicht zum erwarteten pH-Anstieg. Dies weist auf eine geringe Aktivität sulfatreduzierender Bakterien hin, obwohl die Gesamtmenge an organischer Bodensubstanz (OBS) in diesen Böden oft hoch ist. Wir vermuten daher, dass eine geringe Verfügbarkeit von OBS die Aktivität der Sulfatreduzierer in wiedervernässten sulfatsauren Böden limitiert. In unserer Studie wurden Menge und Zusammensetzung der OBS in Bodenprofilen zweier wiedervernässter sulfatsaurer Böden in Südaustralien untersucht. Hierbei wurde das Augenmerk besonders auf die verfügbare, nicht-mineralassoziierte OBS gelegt. Bei beiden Standorten handelte es sich um Flußsedimente, die während einer extremen Dürreperiode zwischen 2008 und 2010 tiefgründig austrockneten und stark versauerten (pH <4). Seit dem Ende der Dürreperiode sind beide Standorte wieder vollständig vernässt. In einem Standort erholte sich der pH-Wert vollständig und zeigte 2015 neutrale pH-Werte, während der andere Standort im Unterboden noch immer deutlich versauert war. In den Bodenproben wurde die Menge der OBS bestimmt und mittels Dichtefraktionierung der Anteil der nicht-mineralassoziierten OBS analysiert. Die chemische Zusammensetzung der OBS wurde mittels Festkörper 13C NMR Spektroskopie und Neutralzuckeranalytik untersucht. Es zeigte sich, dass die sulfatsauren Böden zwar hohe OBS-Mengen, jedoch niedrige Anteile an leicht abbaubaren Kohlenhydraten und Proteinen und hohe Anteile an schwer abbaubaren Lipiden und Lignin enthalten. Die geringsten Gehalte an Kohlenhydraten und Proteinen fanden sich im immer noch stark versauerten Boden. Schwer abbaubare OBS ist kaum als Substrat für Sulfatreduzierer geeignet und erschwert somit die pH-Erhöhung in wiedervernässten sulfatsauren Böden

Dissipation of potassium and proton gradients inhibits mitochondrial hyperpolarization and cytochrome c release during neural apoptosis.

Exposure of rat hippocampal neurons or human D283 medulloblastoma cells to the apoptosis-inducing kinase inhibitor staurosporine induced rapid cytochrome c release from mitochondria and activation of the executioner caspase-3. Measurements of cellular tetramethylrhodamine ethyl ester fluorescence and subsequent simulation of fluorescence changes based on Nernst calculations of fluorescence in the extracellular, cytoplasmic, and mitochondrial compartments revealed that the release of cytochrome c was preceded by mitochondrial hyperpolarization. Overexpression of the anti-apoptotic protein Bcl-xL, but not pharmacological blockade of outward potassium currents, inhibited staurosporine-induced hyperpolarization and apoptosis. Dissipation of mitochondrial potassium and proton gradients by valinomycin or carbonyl cyanide p-trifluoromethoxy-phenylhydrazone also potently inhibited staurosporine-induced hyperpolarization, cytochrome c release, and caspase activation. This effect was not attributable to changes in cellular ATP levels. Prolonged exposure to valinomycin induced significant matrix swelling, and per se also caused release of cytochrome c from mitochondria. In contrast to staurosporine, however, valinomycin-induced cytochrome c release and cell death were not associated with caspase-3 activation and insensitive to Bcl-xL overexpression. Our data suggest two distinct mechanisms for mitochondrial cytochrome c release: (1) active cytochrome c release associated with early mitochondrial hyperpolarization, leading to neuronal apoptosis, and (2) passive cytochrome c release secondary to mitochondrial depolarization and matrix swelling

Root Exudates Induce Soil Macroaggregation Facilitated by Fungi in Subsoil

Subsoils are known to harbor large amounts of soil organic carbon (SOC) and may represent key global carbon (C) sinks given appropriate management. Although rhizodeposition is a major input pathway of organic matter to subsoils, little knowledge exists on C dynamics, particularly stabilization mechanisms, such as soil aggregation, in the rhizosphere of different soil depths. The aim of this study was to investigate the influence of natural and elevated root exudation on C allocation and aggregation in the topsoil and subsoil of a mature European beech (Fagus sylvatica L.) forest. We experimentally added model root exudates to soil at two different concentrations using artificial roots and analyzed how these affect SOC, nitrogen, microbial community composition, and size distribution of water-stable aggregates. Based on the experimental data, a mathematical model was developed to describe the spatial distribution of the formation of soil aggregates and their binding strength. Our results demonstrate that greater exudate additions affect the microbial community composition in favor of fungi which promote the formation of macroaggregates. This effect was most pronounced in the C-poor subsoil, where macroaggregation increased by 86% and SOC content by 10%. Our modeling exercise reproduced the observed increase in subsoil SOC at high exudate additions. We conclude that elevated root exudation has the potential to increase biotic macroaggregation and thus the C sink strength in the rhizosphere of forest subsoils

On the defect pattern evolution in sapphire irradiated by swift ions in a broad fluence range

Sapphire samples, irradiated with swift Kr (245 MeV) ions at room temperature in a broad fluence range, were investigated using a continuous and a pulsed positron beam to study the defect structure created by the passage of the ions in depths of a few micrometers. At small doses, monovacancies were identified as dominant defects and positron trapping centres. These monovacancies are assumed to be highly concentrated inside a cylindrical volume around the ion path with an estimated radius of ~1.5 nm. For higher doses a second type of trapping centre emerges. This second class of structural imperfection was associated with the overlap of the individual ion tracks leading to the formation of larger vacancy clusters or voids.http://www.sciencedirect.com/science/article/B6THY-4SHF49N-1S/1/3eb43650299e0466e76cbbbfdaca9fa

Biotic and abiotic controls on carbon storage in aggregates in calcareous alpine and prealpine grassland soils

Alpine and prealpine grasslands provide various ecosystem services and are hotspots for the storage of soil organic C (SOC) in Central Europe. Yet, information about aggregate-related SOC storage and its controlling factors in alpine and prealpine grassland soils is limited. In this study, the SOC distribution according to the aggregate size classes large macroaggregates (> 2000 μm), small macroaggregates (250–2000 μm), microaggregates (63–250 μm), and silt-/clay-sized particles (< 63 μm) was studied in grassland soils along an elevation gradient in the Northern Limestone Alps of Germany. This was accompanied by an analysis of earthworm abundance and biomass according to different ecological niches. The SOC and N stocks increased with elevation and were associated with relatively high proportions of water-stable macroaggregates due to high contents of exchangeable Ca$^{2+}$ and Mg$^{2+}$. At lower elevations, earthworms appeared to act as catalyzers for a higher microaggregate formation. Thus, SOC stabilization by aggregate formation in the studied soils is a result of a joined interaction of organic matter and Ca$^{2+}$ as binding agents for soil aggregates (higher elevations), and the earthworms that act as promoters of aggregate formation through the secretion of biogenic carbonates (low elevation). Our study highlights the importance of aggregate-related factors as potential indices to evaluate the SOC storage potential in other mountainous grassland soils