Designing sustainable soils in Earth’s critical zone

The demographic drivers of increasing human population and wealth are creating tremendous environmental pressures from growing intensity of land use, resulting in soil and land degradation worldwide. Environmental services are provided through multiple soil functions that include biomass production, water storage and transmission, nutrient transformations, contaminant attenuation, carbon and nitrogen storage, providing habitat and maintaining the genetic diversity of the land environment. One of the greatest challenges of the 21st century is to identify key risks to soil, and to design mitigation strategies to manage these risks and to enhance soil functions that can last into the future. The scientific study of Earth’s Critical Zone (CZ), the thin surface layer that extends vertically from the top of the tree canopy to the bottom of aquifers, provides an essential integrating scientific framework to study, protect and enhance soil functions. The research hypothesis is that soil structure, the geometric architecture of solids, pores and biomass, is a critical indicator and essential factor of productive soil functions. The experimental design selects a network of Critical Zone Observatories (CZOs) as advanced field research sites along a gradient of land use intensity in order to quantify soil structure and soil processes that dictate the flows and transformations of material and energy as soil functions. The CZOs focus multidisciplinary expertise on soil processes, field observation and data interpretation, management science and ecological economics. Computational simulation of biophysical processes provides a quantitative method of integration for the range of theory and observations that are required to quantify the linkages between changes in soil structure and soil functions. Key results demonstrate that changes in soil structure can be quantified through the inputs of organic carbon and nitrogen from plant productivity and microbial activity, coupled with particle aggregation dynamics and organic matter mineralization. Simulation results show that soil structure is highly dynamic and is sensitive to organic matter production and mineralisation rates as influenced by vegetation, tillage and organic carbon amendments. These results point to a step-change in the capability to design soil management and land use through computational simulation. This approach of “sustainability by design” describes the mechanistic process linkages that exist between the above-ground inputs to the CZ and the internal processes that produce soil functions. This approach provides a rational, scientific approach to selecting points of intervention with the CZ in order to design methods to mitigate soil threats and to enhance and sustain vital soil functions. Furthermore, this approach provides a successful pilot study to the use of international networks of CZOs as a planetary-scale laboratory to test the response of CZ process rates along gradients of global environmental change – and to test adaptation strategies to manage the risks arising from the CZ impacts.JRC.H.8-Sustainability Assessmen

The abundance of nitrogen cycle genes and potential greenhouse gas fluxes depends on land use type and little on soil aggregate size

Soil structure is known to influence microbial communities in soil and soil aggregates are the fundamental ecological unit of organisation that support soil functions. However, still little is known about the distribution of microbial communities and functions between soil aggregate size fractions in relation to land use. Thus, the objective of this study was to determine the gene abundance of microbial communities related to the nitrogen cycle and potential greenhouse gas (GHG) fluxes in six soil aggregate sizes (0–0.25, 0.25–0.5, 0.5–1.0, 1–2, 2–5, 5–10 mm) in four land uses (i.e. grassland, cropland, forest, young forest). Quantitative-PCR (Q-PCR) was used to investigate the abundance of bacteria, archaea and fungi, and functional guilds involved in N-fixation (nifH gene), nitrification (bacterial and archaeal amoA genes) and denitrification (narG, nirS, and nosZ genes). Land use leads to significantly different abundances for all genes analysed, with the cropland site showing the lowest abundance for all genes except amoA bacteria and archaea. In contrast, not a single land use consistently showed the highest gene abundance for all the genes investigated. Variation in gene abundance between aggregate size classes was also found, but the patterns were gene specific and without common trends across land uses. However, aggregates within the size class of 0.5–1.0 mm showed high bacterial 16S, nifH, amoA bacteria, narG, nirS and nosZ gene abundance for the two forest sites but not for fungal ITS and archaeal 16S. The potential GHG fluxes were affected by land use but the effects were far less pronounced than for microbial gene abundance, inconsistent across land use and soil aggregates. However, few differences in GHG fluxes were found between soil aggregate sizes. From this study, land use emerges as the dominant factor that explains the distribution of N functional communities and potential GHG fluxes in soils, with less pronounced and less generalized effects of aggregate size

DataSheet_1_Development of a standardized and validated flow cytometry approach for monitoring of innate myeloid immune cells in human blood.zip

Innate myeloid cell (IMC) populations form an essential part of innate immunity. Flow cytometric (FCM) monitoring of IMCs in peripheral blood (PB) has great clinical potential for disease monitoring due to their role in maintenance of tissue homeostasis and ability to sense micro-environmental changes, such as inflammatory processes and tissue damage. However, the lack of standardized and validated approaches has hampered broad clinical implementation. For accurate identification and separation of IMC populations, 62 antibodies against 44 different proteins were evaluated. In multiple rounds of EuroFlow-based design-testing-evaluation-redesign, finally 16 antibodies were selected for their non-redundancy and separation power. Accordingly, two antibody combinations were designed for fast, sensitive, and reproducible FCM monitoring of IMC populations in PB in clinical settings (11-color; 13 antibodies) and translational research (14-color; 16 antibodies). Performance of pre-analytical and analytical variables among different instruments, together with optimized post-analytical data analysis and reference values were assessed. Overall, 265 blood samples were used for design and validation of the antibody combinations and in vitro functional assays, as well as for assessing the impact of sample preparation procedures and conditions. The two (11- and 14-color) antibody combinations allowed for robust and sensitive detection of 19 and 23 IMC populations, respectively. Highly reproducible identification and enumeration of IMC populations was achieved, independently of anticoagulant, type of FCM instrument and center, particularly when database/software-guided automated (vs. manual “expert-based”) gating was used. Whereas no significant changes were observed in identification of IMC populations for up to 24h delayed sample processing, a significant impact was observed in their absolute counts after >12h delay. Therefore, accurate identification and quantitation of IMC populations requires sample processing on the same day. Significantly different counts were observed in PB for multiple IMC populations according to age and sex. Consequently, PB samples from 116 healthy donors (8-69 years) were used for collecting age and sex related reference values for all IMC populations. In summary, the two antibody combinations and FCM approach allow for rapid, standardized, automated and reproducible identification of 19 and 23 IMC populations in PB, suited for monitoring of innate immune responses in clinical and translational research settings.Peer reviewe

Reaction capacity characterization of shallow sedimentary deposits in geologically different regions of the Netherlands

Quantitative insight into the reaction capacity of porous media is necessary to assess the buffering capacity of the subsurface against contaminant input via groundwater recharge. Here, reaction capacity is to be considered as a series of geochemical characteristics that control acid/base conditions, redox conditions and sorption intensity. Using existing geochemical analyses, a statistical regional assessment of the reaction capacity was performed for two geologically different areas in the Netherlands. The first area is dominated by Pleistocene aquifer sediments only, in the second area a heterogeneous Holocene confining layer is found on top of the Pleistocene aquifer sediments. Within both areas, two or more regions can be distinguished that have a distinctly different geological build-up of the shallow subsurface. The reactive compounds considered were pyrite, reactive Fe other than pyrite, sedimentary organic matter, carbonate and clay content. This characterization was complemented by the analysis of a dataset of samples newly collected, from two regions within the Pleistocene area, where the sedimentary facies of samples was additionally distinguished. The statistical assessment per area was executed at the levels of region, geological formation and lithology class. For both areas, significant differences in reaction capacities were observed between: 1. different lithology classes within a geological formation in a single region, 2. identical geological formations in different regions and 3. various geological formations within a single region. Here, the reaction capacity is not only controlled by lithostratigraphy, but also by post-depositional diagenesis and paleohydrology. Correlation coefficients among the reactive compounds were generally higher for sand than for clay, but insufficiently high to allow good estimation of reactive compounds from each other. For the sandy Pleistocene aquifer sediments, the content of reactive compounds was frequently observed to be below detection limits. From this, future characterization of sediment reaction capacity is best performed at the sublevel of lithology class, being the geochemically near-uniform unit identifiable for individual geological formations within geographic regions. Additional subdivision on facies provides particular insight in the spatial entity where relatively high reaction capacities may be encountered. To obtain quantitative insight into the reaction capacity of aquifer sediments, non-sandy minor subunits should be well characterised on their reaction capacity as well as their spatial occurrence in the geological formations. A straightforward approach is presented in which the regional statistics on geochemical reactivity become combined with a 3-dimensional geological voxel model. This results into 3-dimensional data fields on reactivity, which are suitable for, for example, groundwater transport modelling. The sedimentological architecture of the deposits becomes well maintained in the geochemical data field, which is an advantage in itself. © 2011 Elsevier B.V. All rights reserved

Reaction capacity characterization of shallow sedimentary deposits in geologically different regions of the Netherlands

Quantitative insight into the reaction capacity of porous media is necessary to assess the buffering capacity of the subsurface against contaminant input via groundwater recharge. Here, reaction capacity is to be considered as a series of geochemical characteristics that control acid/base conditions, redox conditions and sorption intensity. Using existing geochemical analyses, a statistical regional assessment of the reaction capacity was performed for two geologically different areas in the Netherlands. The first area is dominated by Pleistocene aquifer sediments only, in the second area a heterogeneous Holocene confining layer is found on top of the Pleistocene aquifer sediments. Within both areas, two or more regions can be distinguished that have a distinctly different geological build-up of the shallow subsurface. The reactive compounds considered were pyrite, reactive Fe other than pyrite, sedimentary organic matter, carbonate and clay content. This characterization was complemented by the analysis of a dataset of samples newly collected, from two regions within the Pleistocene area, where the sedimentary facies of samples was additionally distinguished. The statistical assessment per area was executed at the levels of region, geological formation and lithology class. For both areas, significant differences in reaction capacities were observed between: 1. different lithology classes within a geological formation in a single region, 2. identical geological formations in different regions and 3. various geological formations within a single region. Here, the reaction capacity is not only controlled by lithostratigraphy, but also by post-depositional diagenesis and paleohydrology. Correlation coefficients among the reactive compounds were generally higher for sand than for clay, but insufficiently high to allow good estimation of reactive compounds from each other. For the sandy Pleistocene aquifer sediments, the content of reactive compounds was frequently observed to be below detection limits. From this, future characterization of sediment reaction capacity is best performed at the sublevel of lithology class, being the geochemically near-uniform unit identifiable for individual geological formations within geographic regions. Additional subdivision on facies provides particular insight in the spatial entity where relatively high reaction capacities may be encountered. To obtain quantitative insight into the reaction capacity of aquifer sediments, non-sandy minor subunits should be well characterised on their reaction capacity as well as their spatial occurrence in the geological formations. A straightforward approach is presented in which the regional statistics on geochemical reactivity become combined with a 3-dimensional geological voxel model. This results into 3-dimensional data fields on reactivity, which are suitable for, for example, groundwater transport modelling. The sedimentological architecture of the deposits becomes well maintained in the geochemical data field, which is an advantage in itself. © 2011 Elsevier B.V. All rights reserved

Combination of aquifer thermal energy storage and enhanced bioremediation : Biological and chemical clogging

Interest in the combination concept of aquifer thermal energy storage (ATES) and enhanced bioremediation has recently risen due to the demand for both renewable energy technology and sustainable groundwater management in urban areas. However, the impact of enhanced bioremediation on ATES is not yet clear. Of main concern is the potential for biological clogging which might be enhanced and hamper the proper functioning of ATES. On the other hand, more reduced conditions in the subsurface by enhanced bioremediation might lower the chance of chemical clogging, which is normally caused by Fe(III) precipitate. To investigate the possible effects of enhanced bioremediation on clogging with ATES, we conducted two recirculating column experiments with differing flow rates (10 and 50 mL/min), where enhanced biological activity and chemically promoted Fe(III) precipitation were studied by addition of lactate and nitrate respectively. The pressure drop between the influent and effluent side of the column was used as a measure of the (change in) hydraulic conductivity, as indication of clogging in these model ATES systems. The results showed no increase in upstream pressure during the period of enhanced biological activity (after lactate addition) under both flow rates, while the addition of nitrate lead to significant buildup of the pressure drop. However, at the flow rate of 10 mL/min, high pressure buildup caused by nitrate addition could be alleviated by lactate addition. This indicates that the risk of biological clogging is relatively small in the investigated areas of the mimicked ATES system that combines enhanced bioremediation with lactate as substrate, and furthermore that lactate may counter chemical clogging.</p

Combination of aquifer thermal energy storage and enhanced bioremediation : resilience of reductive dechlorination to redox changes

To meet the demand for sustainable energy, aquifer thermal energy storage (ATES) is widely used in the subsurface in urban areas. However, contamination of groundwater, especially with chlorinated volatile organic compounds (CVOCs), is often being encountered. This is commonly seen as an impediment to ATES implementation, although more recently, combining ATES and enhanced bioremediation of CVOCs has been proposed. Issues to be addressed are the high water flow velocities and potential periodic redox fluctuation that accompany ATES. A column study was performed, at a high water flow velocity of 2 m/h, simulating possible changes in subsurface redox conditions due to ATES operation by serial additions of lactate and nitrate. The impacts of redox changes on reductive dechlorination as well as the microbial response of Dehalococcoides (DHC) were evaluated. The results showed that, upon lactate addition, reductive dechlorination proceeded well and complete dechlorination from cis-DCE to ethene was achieved. Upon subsequent nitrate addition, reductive dechlorination immediately ceased. Disruption of microorganisms’ retention was also immediate and possibly detached DHC which preferred attaching to the soil matrix under biostimulation conditions. Initially, recovery of dechlorination was possible but required bioaugmentation and nutrient amendment in addition to lactate dosing. Repeated interruption of dechlorination and DHC activity by nitrate dosing appeared to be less easily reversible requiring more efforts for regenerating dechlorination. Overall, our results indicate that the microbial resilience of DHC in biosimulated ATES conditions is sensitive to redox fluctuations. Hence, combining ATES with bioremediation requires dedicated operation and monitoring on the aquifer geochemical conditions.</p