Degradability of organic matter (OM) in soil depends on its spatial location in the soil matrix. A recent breakthrough in 3D-localization of OM combined dual-energy X-ray CT-scanning with OsO 4 staining of OM. The necessity for synchrotron-based µCT and the use of highly toxic OsO 4 severely limit applications in soil biological experiments. Here, we evaluated the potential of alternative staining agents (silver nitrate, phosphomolybdenic acid (PMA), lead nitrate, lead acetate) to selectively enhance X-ray attenuation and contrast of OM in CT volumes of soils containing specific mineral soil particle fractions, obtained via lab-based X-ray µCT. In comparison with OsO 4 , administration of Ag + and Pb 2+ resulted in insufficient contrast enhancement of OM versus fine silt (< 20 µm) or clay (< 2 µm) mineral particles. The perfusion procedure used in this work induced changes in soil structure. In contrast, PMA staining resulted in a selective increase of OM’s attenuation contrast, which was comparable to OsO 4 . However, OM discrimination from other soil phases remained a challenge. Further development of segmentation algorithms accounting for grey value patterns and shape of stained particulate OM may enable its automated identification. If successful in undisturbed soils, PMA staining may form an alternative to OsO 4 in non-synchrotron based POM detection.

Knowledge about the response of root biomass and root system architecture (RSA) to soil conditions would increase efficiency in selecting high performance crop varieties and predicting the impact of rotations on long-term soil organic matter (SOM) stock. We evaluated the effect of variety and site on maize (Zea mays L.) root growth. Two-dimensional (2D) and 3D techniques were used to quantify changes of RSA. Commercial maize varieties were grown in three sites with typical soil types for maize cultivation in Belgium. We observed that at Merelbeke, above- and belowground biomass and root-to-shoot ratios (R/S) were larger compared to those at Ravels. Both factors interactively influenced an index of biological stability (ISB) based on biochemical quality of the roots. There were also more fine roots at Merelbeke than at Bassevelde and Ravels. Together with a lower ISB value, this suggests that site had an inherent effect on root biochemical quality. We conclude that a strong impact of site exists on both above- and belowground biomass; however, they are not necessarily correlated. With a fixed R/S, predictions of root biomass were misestimated in one half of the cases. This complex response of root phenotyping to varying soil conditions should not be overlooked.

Increasing interest in plant-root phenotyping has stimulated the development of X-ray mu CT-based root/soil segmentation protocols. However, most scanning and CT volume processing protocols were only applied for detection of simple and small juvenile roots. We tested a new methodology for its ability to extract large mature maize roots from X-ray mu CT volumes of undisturbed soil monoliths (10 x 20 x 15 cm) and compared its performance with two existing (semi-)automated segmentation algorithms. The X-ray mu CT based root assessments were validated by means of the measured root biomass. Segmentation of maize root systems proved to be particularly challenging because regardless of soil type, within-sample vertical gradients in X-ray attenuation caused an overlap in CT-reconstructed grey values of roots, water and mineral phases. However, in contrast to the two existing algorithms, a new alternative methodology did allow for relatively fast and accurate segmentation of the mature roots. This was evidenced by a highly significant correlation between the CT-derived root volume and its measured root biomass. Despite the large size of the investigated soil monoliths, roots could be resolved down to a diameter of 200 mu m. This methodology opens up new possibilities for investigating large and complex root systems, and may become an invaluable new tool in plant breeding research.

Mineral nitrogen (N) availability to heterotrophic micro-organisms is known to impact organic matter (OM) decomposition. Different pathways determining the N accessibility depend to a large extent on soil structure. Contact between soil mineral and OM substrate particles can facilitate N transport toward decomposition hot spots. However, the impact of soil structure on N availability to microbes and thus heterotrophic microbial activity and community structure is not yet fully understood. We hypothesized that carbon mineralization (Cmin) from low-N substrate would be stimulated by increased N availability caused by closer contact with soil particles or by a higher moisture level, enhancing potential for N-diffusion. Under opposite conditions retarded heterotrophic activity and a dominance of fungi were expected. A 128-days incubation experiment with CO2 emission monitoring from artificially reconstructed miniature soil cores with contrasting soil structures, viz. high or low degree of contact between soil particles, was conducted to study impacts on heterotrophic activity. The soil cores were subjected to different water filled pore space percentages (25 or 50% WFPS) and amended with either easily degradable OM high in N (grass) or more resistant OM low in N (sawdust). X-ray μCT image processing allowed to quantify the pore space in 350 μm around OM substrates, i.e., the microbial habitat of involved decomposers. A lower local porosity surrounding sawdust particles in soils with stonger contact was confirmed, at least at 25% WFPS. Mineral N addition to sawdust amended soils with small particle contact at 25% WFPS resulted in a stimulated respiration. Cmin in the latter soils was lower than in case of high particle contact. This was not observed for grass substrate particles or at 50% WFPS. The interactive effect of substrate type and soil structure suggests that the latter controls Cmin through mediation of N diffusion and in turn N availability. Phospholipid fatty acid did not reveal promotion of fungal over bacterial biomarkers in treatments with N-limited substrate decomposition. Combining X-ray μCT with tailoring soil structure allows for more reliable investigation of effects on the soil microbial community, because as also found here, the established soil pore network structure can strongly deviate from the intended one.

Biochar addition to soils is heralded to reduce N2O emissions, but still, the explanatory mechanisms have not been resolved. Moreover, it is uncertain whether N2O emission reductions would persist after prolonged biochar incorporation in the field. In this study, we incorporated four biochar types in a loam textured cropland field and intact soil cores were sampled to investigate the physical control of biochar on denitrification after 7 months. During a first incubation experiment, we measured N2O emissions from undisturbed and disturbed (i.e. sieved (2 mm) and grounded) soil cores. Both in the disturbed and undisturbed soil cores biochar at water filled pore space (WFPS) of 80% reduced the N2O emissions by 50–90%, refuting the hypothesis that biochar exerts an indirect physical control over soil denitrification several months after incorporation. Secondly, we hypothesized that biochar creates denitrification ‘hotspots’ in soil, where complete reduction of N2O to N2 is promoted compared to non-amended soil. In these hotspots biochar particles could act as microlocations with local anaerobic conditions and local higher pH, stimulating in this way complete denitrification. Via the acetylene inhibition method we did not observe a reduction in the N2O/(N2O + N2) ratio, which could suggest that biochar did not promote the reduction of N2O to N2. Manipulations likely to promote labile C bioavailability, here either by glucose addition or by soil particulate OM disclosure after disruption of soil aggregates, resulted in the most prominent biochar-induced N2O emission reductions.

There is growing interest in the application of the natural fallout radionuclide Be-7 as a soil erosion and sediment tracer. Development of robust datasets is, however, hampered by unquantified variability in its vertical distribution within surface soil. Models that convert Be-7 inventory measurements to soil erosion estimates are all based on the observed depth distribution of Be-7, described by the relaxation mass depth (110) parameter. Previous work, however, has not considered potential spatial variation in 110 linked to natural variability in soil physical properties, which could have major implications for the reliability of soil erosion estimates.Two complementary experiments were designed to study the variability in depth distribution within and between potential reference sites. First, a field sampling programme was carried out whereby two reference sites with variable degree of compaction were sampled using two different sectioning techniques, i.e. by use of a fine increment soil collector (FISC) and the scraping methodology. During a laboratory rainfall simulation experiment, water spiked with stable Be-9 was used to study the variability in 9Be soil depth distribution within and between the two reference sites. In the field experiment, variations in the Be-7 depth distribution, and thus in 110, were limited between both reference sites (13 to 16%). In contrast, the impact of the sectioning technique was remarkable, with scraping resulting in a higher 110 (up to 60%) compared to the estimates based on the use of a FISC. The rainfall simulation experiment offered the opportunity to study the variation in 9Be depth distribution in more detail. With an average 110 of 4.66 kg m(-2), Be-9 penetrated deeper in the non-compacted (NC) reference site cores, while the compacted (C) cores showed an average 110 of 2.42 kg m(-2). The reported 110 values at the former site were also characterized by a larger coefficient of variation (24%) than those at the latter site (11%). Lower bulk density, higher infiltration rates and a pore network characterized by a higher macroporosity and connectivity, as revealed by the X-ray Computed Tomography (a) scans, explained the deeper penetration of Be into the topsoil of reference site NC.The results indicate the importance of selecting appropriate reference sites and for ensuring an adequate sampling strategy to encompass local variability in soil physical properties. Hydraulic conductivity assessment could be a useful tool to properly assess suitable reference sites and the number of samples needed to assess the reference inventory. (C) 2016 Elsevier B.V. All rights reserved.

To understand the roles of nematodes in organic matter (OM) decomposition, experimental setups should include the entire nematode community, the native soil microflora, and their food sources. Yet, published studies are often based on either simplified experimental setups, using only a few selected species of nematode and their respective prey, despite the multitude of species present in natural soil, or on indirect estimation of the mineralization process using O2 consumption and the fresh weight of nematodes. We set up a six-month incubation experiment to quantify the contribution of the entire free living nematode community to carbon (C) mineralization under realistic conditions. The following treatments were compared with and without grass-clover amendment: defaunated soil reinoculated with the entire free living nematode communities (+Nem) and defaunated soil that was not reinoculated (-Nem). We also included untreated fresh soil as a control (CTR). Nematode abundances and diversity in +Nem was comparable to the CTR showing the success of the reinoculation. No significant differences in C mineralization were found between +Nem and -Nem treatments of the amended and unamended samples at the end of incubation. Other related parameters such as microbial biomass C and enzymatic activities did not show significant differences between +Nem and -Nem treatments in both amended and unamended samples. These findings show that the collective contribution of the entire nematode community to C mineralization is small. Previous reports in literature based on simplified experimental setups and indirect estimations are contrasting with the findings of the current study and further investigations are needed to elucidate the extent and the mechanisms of nematode involvement in C mineralization.

Incorporation of biochar into soils has frequently been found to reduce soil emission of the greenhouse gas N2O, formed as an intermediate during microbial denitrification. The exact mechanism that regulates N2O emission reduction after biochar incorporation is still unknown and diverse hypotheses on either chemical, physical or biological controls over soil denitrification exist. The porous structure of biochar may directly and indirectly influence the soil pore structure upon its incorporation. Firstly biochar may increase soil aeration and thereby reduce denitrification which requires an anaerobic atmosphere to continue. In order to investigate this hypothesis we incorporated 4 biochar types in a sandy loam soil and collected undisturbed soil cores after 8 months of field incorporation. We then crushed half of the soil cores and replaced them. We followed N2O emissions from undisturbed and disturbed biochar amended soil cores by GC headspace analysis. From the disturbed soil cores no emission reduction was expected because soil pore structure was severely disrupted. However, both disturbed and undisturbed soil cores showed emission reductions when compared to the soil cores without biochar amendment. This allowed us to reject the hypothesis that biochar would affect soil denitrification through increased soil aeration.

Soil pore network structure can have a significant impact on microbial utilization of soil organic matter and hence its stability. This stabilization is essentially the result of suboptimal conditions for substrate and metabolite diffusion connected to moisture distribution and aeration. All these factors depend on the spatial organization of the pore network. Because of the small dimensions of the soil pores, X-ray Computed Tomography (CT) is commonly used to study the soil pore network. This non-destructive technique allows to visualize the 3D architecture of soils at scales relevant for microbial activity.