DenNit – Experimental analysis and modelling of soil N2O efflux in response on changes of soil water content, soil temperature, soil pH, nutrient availability and the time after rain event

To quantify the effects of soil temperature (T_soil), and relative soil water content (RSWC) on soil N₂O emission we measured N₂O soil efflux with a closed dynamic chamber in situ in the field and from soil cores in a controlled climate chamber experiment. Additionally we analysed the effect of soil acidity, ammonium, and nitrate concentration in the field. The analysis was performed on three meadows, two bare soils and in one forest. We identified soil water content, soil temperature, soil nitrogen content, and pH as the main parameters influencing soil N₂O emission. The response of N₂O emission to soil temperature and relative soil water content was analysed for the field and climate chamber measurements. A non-linear regression model (DenNit) was developed for the field data to describe soil N₂O efflux as a function of soil temperature, soil moisture, pH value, and ammonium and nitrate concentration. The model could explain 81% of the variability in soil N₂O emission of all individual field measurements, except for data with short-term soil water changes, namely during and up to 2 h after rain stopped. We validated the model with an independent dataset. For this additional meadow site 73% of the flux variation could be explained with the model.     

Bioremediation of a petroleum‐contaminated cryic soil: Effects of phosphorus,nitrogen, and temperature

Bioremediation has been shown to be an effective means of treating petroleum‐contaminated soils in cold areas, although the conditions required to maximize bioremediation in cold region (cryic) soils are not well documented. A laboratory study was conducted to investigate the effects of nitrogen and phosphorus levels and temperature on petroleum bioremediation. A cryic entisol contaminated with diesel fuel was treated with nitrogen (0, 400, 800, or 1200 mg/kg of soil) and phosphorus (0, 60, 120, or 180 mg/kg of soil) and incubated at two temperatures (10 and 20°C). At 10°C, bioremediation rates were not affected by fertility treatments. At 20°C, reaction rates were increased by the addition of P, but unaffected by N. Regardless of fertility regime, the rate of diesel loss was much greater in soil incubated at 20°C than in soil incubated at 10°C.     

Fate of [carbonyl-14C]methabenzthiazuron in an arid region soil — effect of organic amendment,soil disturbance and fumigation

[Carbonyl-¹⁴C] methabenzthiazuron (MBT) was applied to an arid region soil at a rate of 5mg kg⁻¹ soil to give a¹⁴C content of 2400 KB kg⁻¹ soil. After 15 weeks of incubation at 22°C and 50% of the maximum water holding capacity of the soil, 7.2% of the applied¹⁴C was mineralized to¹⁴CO₂. Where the soil was amended with wheat straw, total mineralization increased to 17.3%. Soil disturbance caused a significant increase while chloroform fumigation caused a significant decrease in the rate of¹⁴CO₂ production, both from amended and unamended soils. These results suggest that MBT is degraded mainly through microbial co-metabolism. Wheat straw amendment resulted in increased transformation of MBT into soil humus. In unamended soil, a major portion of¹⁴C was recovered in fulvic acid and in fractions extracted with organic solvents. Recovery of¹⁴C in non-extractable bound residues (humins) increased as incubation progressed and seemed to be derived from the fulvic acid fraction, which showed a concomitant decrease. More than 99% of the residual¹⁴C in unamended soil consisted of unaltered MBT; the remainder occurred as 1-methyl-1 (benzthiazolyl) urea. In amended soil, a relatively higher percentage of the extractable¹⁴C was found in the metabolite. Small amounts of three unidentified¹⁴C-labelled compounds were also observed. In amended soil, disturbance caused a decrease in extractable-¹⁴C whereas fumigation caused a significant increase, as compared to the untreated control. The effects were more pronounced when the soils were reated at an early stage of incubation. In general, soil disturbance increased the availability of MBT for further transformations while chloroform fumigation decreased the process.     

Isolation of facultatively anaerobic soil bacteria from Ny-Ålesund, Svalbard

Anaerobic conditions in soil commonly occur even in upland environments. Physiological and biogeochemical properties of individual anaerobic bacteria, however, have been poorly understood due to difficulties in culture. This study aimed to isolate anaerobic bacteria in the Arctic tundra soil and to identify their physiological characteristics. Anaerobic culture and 16S rRNA gene sequence-based phylogenetic analysis showed that total 33 bacterial strains were affiliated with 15 species from the following 8 genera: Bacillus, Carnobacterium, Clostridium, Paenibacillus, and Trichococcus (Firmicutes), Pseudomonas and Rahnella (Gamma-proteobacteria), and Cellulomonas (Actinobacteria). All isolates were identified as facultatively anaerobic bacteria; this finding might be partially attributed to the characteristics of sampling sites, which temporarily developed anaerobic conditions because of the presence of stagnant melting snow. Six of the 33 bacterial strains were revived subsequently from glycerol stocks held ?80 °C, and these were used for the physiological study: four isolates from Firmicutes, one isolate from Gamma-proteobacteria, and one isolate from Actinobacteria. Five isolates except KOPRI 80146 (Bacillus sp.) could grow at either 4 or 10 °C within a week. All six isolates showed cellulase or protease activities at 10 or 15 °C. Endospores were observed from four isolates belonging to Firmicutes. These physiological characteristics may contribute to the survival of these organisms at low temperatures and to their involvement in biogeochemical cycles in the tundra soil. These isolates may be used for further detailed studies for identifying their cold adaptation mechanisms and ecological roles in the Arctic.     

Is soil carbon disappearing? The dynamics of soil organic carbon in Java

Research in the soil of the tropics mostly has demonstrated the decline of soil organic carbon (SOC) after conversion of primary forest to plantation and cultivated lands. This paper illustrates the dynamics of SOC on the island of Java, Indonesia, from 1930 to 2010. We used 2002 soil profile observations containing organic carbon (C) analysis in the topsoil, which were collected by the Indonesian Center for Agricultural Land Resources Research & Development from 1923 to 2007. Results show the obvious decline of SOC values from around 2% in 1930–1940 to 0.8% in 1960–1970. However, there has been an increase of SOC content since 1970, with a median level of 1.1% in the year 2000. Our analysis suggests that the human influence and agricultural practices on SOC in Java have been a stronger influence than the environmental factors. SOC for the top 10 cm has shown a net accumulation rate of 0.2–0.3 Mg C ha^?1 yr^?1 during the period 1990–2000. These findings give rise to optimism for increased soil C sequestration in the tropics.     

Components of forest soil CO2 efflux estimated from Δ14C values of soil organic matter

Aims

The partitioning of the total soil CO₂ efflux into its two main components: respiration from roots (and root-associated organisms) and microbial respiration (by means of soil organic matter (SOM) and litter decomposition), is a major need in soil carbon dynamics studies in order to understand if a soil is a net sink or source of carbon.

Methods

The heterotrophic component of the CO₂ efflux was estimated for 11 forest sites as the ratio between the carbon stocks of different SOM pools and previously published (Δ¹⁴C derived) turnover times. The autotrophic component, including root and root-associated respiration, was calculated by subtracting the heterotrophic component from total soil chamber measured CO₂ efflux.

Results

Results suggested that, on average, 50.4 % of total soil CO₂ efflux was derived from the respiration of the living roots, 42.4 % from decomposition of the litter layers and less than 10 % from decomposition of belowground SOM.

Conclusions

The Δ¹⁴C method proved to be an efficient tool by which to partition soil CO₂ efflux and quantify the contribution of the different components of soil respiration. However the average calculated heterotrophic respiration was statistically lower compared with two previous studies dealing with soil CO₂ efflux partitioning (one performed in the same study area; the other a meta-analysis of soil respiration partitioning). These differences were probably due to the heterogeneity of the SOM fraction and to a sub-optimal choice of the litter sampling period.     

The diversity of soil communities, the ‘poor man's tropical rainforest’

This paper reviews the various factors that facilitate the high biodiversity of soil communities, concentrating on soil animals. It considers the problems facing soil ecologists in the study of soil communities and identifies the important role such communities play in terrestrial ecosystems. The review also considers diversity and abundance patterns. A range of factors are identified that may contribute to the biodiversity of soil and their role is reviewed. These include diversity of food resources and trophic specialization, habitat favourableness, habitat heterogeneity in space and time, scale and spatial extent of the habitat, niche dynamics and resource partitioning, productivity, disturbance and aggregation.Biodiversity of soil organisms appears high, largely attributable to the nested set of ecological worlds in the soil — the relationship between the range of size groupings of soil organisms relative to the spatial heterogeneity perceived by these various groups — that provide a large area for life for the micro- and mesofauna. The role of aggregation and how it relates to the spatial scale under consideration and to species interactions amongst soil animals is largely unknown at present. The role of disturbance is equivocal and man's activities more often than not seem to lead to a reduced biodiversity of soil communities. This paper also identifies areas where further work is desirable to improve our understanding of the structure and functioning of soil communities.     

Wetting properties of fungi mycelium alter soil infiltration and soil water repellency in a γ-sterilized wettable and repellent soil

Soil water repellency (SWR) has a drastic impact on soil quality resulting in reduced infiltration, increased runoff, increased leaching, reduced plant growth, and increased soil erosion. One of the causes of SWR is hydrophobic fungal structures and exudates that change the soil–water relationship. The objective of this study was to determine whether SWR and infiltration could be manipulated through inoculation with fungi. The effect of fungi on SWR was investigated through inoculation of three fungal strains (hydrophilic – Fusarium proliferatum, chrono-amphiphilic – Trichoderma harzianum, and hydrophobic – Alternaria sp.) on a water repellent soil (WR-soil) and a wettable soil (W-soil). The change in SWR and infiltration was assessed by the water repellency index and cumulative infiltration respectively. F. proliferatum decreased the SWR on WR-soil and slightly increased SWR in W-soil, while Alternaria sp. increased SWR in both the W-soil and the WR-soil. Conversely T. harzianum increased the SWR in the W-soil and decreased the SWR in the WR-soil. All strains showed a decrease in infiltration in W-soil, while only the F. proliferatum and T. harzianum strain showed improvement in infiltration in the WR-soil. The ability of fungi to alter the SWR and enmesh soil particles results in changes to the infiltration dynamics in soil.     

Changes in soil organic carbon and total nitrogen after 28 years grassland afforestation: effects of tree species, slope position, and soil order

The effect of conversion of grassland to woodland on organic carbon (OC) and total nitrogen (TN) has significance for global change, land resource use and ecosystem management. However, these effects are always variable. Here, we show results of a study in an arid area in China on profile distribution of OC and TN in soils covered by two different woody tree canopies and outer canopy space (grassland between woody plant canopies). The soils were at various slope positions (upper, middle and lower slopes) for Chinese pine (Pinus tabulaeformis) and Korshrinsk peashrub (Caragana korshinskii) lands, and of different soil orders (Castanozems, Skeletal, Loessial and Aeolian soils). The objectives were to relate the effects of land use change on OC and TN to slope position and soil order. Soil OC and TN were significantly larger at Korshrinsk peashrub slope locations than at Chinese pine slope locations. Soil OC and TN were small at the lower slope position for Korshrinsk peashrub, however, they were largest at the middle slope for Chinese pine. Korshrinsk peashrub always increased soil OC and TN under brush canopy at the three slope positions, while Chinese pine increased them at lower slopes and decreased them at upper slopes. For the soil types, OC and TN in Korshrinsk peashrub land were in the order of Castanozems > Skeletal > Loessial > Aeolian soils. Korshrinsk peashrub also increased OC and TN under brush canopy in the four soils. Our results indicated that soil OC and TN in canopy soils differed greatly from associated values in the outer canopy soils, and the effects of grassland afforestation varied significantly with tree species, slope position, and soil type. Therefore, we suggest that differentiating such factors can be an effective approach for explaining variances in OC and N changes caused by land use conversion.     

Screening,identification, and characterization of a novel saccharide-stimulated β-glycosidase from a soil metagenomic library

Applied Microbiology and Biotechnology - MeBglD2, a β-glycosidase that is highly activated in the presence of various monosaccharides and disaccharides, was isolated from a soil metagenomic...     

Contribution of lead in soil to children’s lead burden,an update

Abstract

Blood lead levels in children in the USA have dropped dramatically since lead in food, air and drinking water was reduced. In inner cities and older residential areas, increased lead exposure may still be a problem because of dilapidated housing with high lead paint levels. In these areas, at mining sites and around smelters lead levels in soil may be very high. A review of many studies indicates that lead in soil or mine tailings does not make a meaningful contribution to lead absorption by children. The contribution of lead in soil to overall exposure, if any, lies within the variation of the analytical method for blood lead measurements. The results of exposure studies in the pediatric population reviewed in this article do not support exposure predictions for children under 6 years of age based on the US EPA Integrated Exposure Uptake Biokinetic Model (using default parameters or using results obtained with in vitro digestion models). They also do not support predictions based on the percent of solubility of lead in soil (accessibility studies).     

Can composition and physical protection of soil organic matter explain soil respiration temperature sensitivity?

The importance of soil organic matter (SOM) in the global carbon (C) cycle has been highlighted by many studies, but the way in which SOM stabilization processes and chemical composition affect decomposition rates under natural climatic conditions is not yet well understood. To relate the temperature sensitivity of heterotrophic soil respiration to the decomposition potential of SOM, we compared temperature sensitivities of respiration rates from a 2-year long soil translocation experiment from four elevations along a ~3000 m tropical forest gradient. We determined SOM stabilization mechanisms and the molecular structure of soil C from different horizons collected before and after the translocation. Soil samples were analysed by physical fractionation procedures, ¹³C nuclear magnetic resonance (NMR) spectroscopy, and differential scanning calorimetry (DSC). The temperature sensitivity (Q ₁₀) of heterotrophic soil respiration at the four sites along the elevation transect did not correlate with either the available amount of SOM or its chemical structure. Only the relative distribution of C into physical soil fractions correlated with Q ₁₀ values. We therefore conclude that physical fractionation of soil samples is the most appropriate way to assess the temperature sensitivity of SOM.     

Is vegetation composition or soil chemistry the best predictor of the soil microbial community?

With the species composition and/or functioning of many ecosystems currently changing due to anthropogenic drivers it is important to understand and, ideally, predict how changes in one part of the ecosystem will affect another. Here we assess if vegetation composition or soil chemistry best predicts the soil microbial community. The above and below-ground communities and soil chemical properties along a successional gradient from dwarf shrubland (moorland) to deciduous woodland (Betula dominated) were studied. The vegetation and soil chemistry were recorded and the soil microbial community (SMC) assessed using Phospholipid Fatty Acid Extraction (PLFA) and Multiplex Terminal Restriction Fragment Length Polymorphism (M-TRFLP). Vegetation composition and soil chemistry were used to predict the SMC using Co-Correspondence analysis and Canonical Correspondence Analysis and the predictive power of the two analyses compared. The vegetation composition predicted the soil microbial community at least as well as the soil chemical data. Removing rare plant species from the data set did not improve the predictive power of the vegetation data. The predictive power of the soil chemistry improved when only selected soil variables were used, but which soil variables gave the best prediction varied between the different soil microbial communities being studied (PLFA or bacterial/fungal/archaeal TRFLP). Vegetation composition may represent a more stable ‘summary’ of the effects of multiple drivers over time and may thus be a better predictor of the soil microbial community than one-off measurements of soil properties.     

Chemical, microbiological and plant analysis of soil fertilized with alkaline hydrolysate of sheep’s wool waste

Summary The effect of adding alkaline hydrolysate of sheep’s wool waste on the chemical and microbiological properties of a park soil (Sofia, Bulgaria) has been assessed in a 9 month laboratory experiment. The waste product contained 75–80% water-soluble materials: peptides, amino acids, salts, dyes, lipids, some carbohydrates, potassium ions, and it seemed likely that the hydrolysate obtained could be used as a harmless and valuable fertilizer in agriculture. It was demonstrated that the organic material positively influenced microbial soil populations and ryegrass growth. As the remaining partially degraded keratin is highly dispersed it should act as a slow release fertilizer thus feeding plants additionally. The results suggest that the wool hydrolysate is beneficial for improving soil characteristics and could successfully be used as alternative biofertilizer. The authors hope that by utilization of the keratin wastes, the environment around leather and fur plants could be influenced positively and that the expense of removing the wastes to controlled landfill sites and part of the expenses for sustaining the latter will be saved.     

Distribution features and internal relations of heavy metals in soil–maize system of mining area,Anhui Province,Eastern China

A total of 59 topsoil and corresponding maize plants were collected from this study area. The spatial distribution, correlation analysis, and multiple linear regression of heavy metals were researched detailedly in this article. The results showed that distribution characteristics of heavy metals (Pb, Cd, and Ni) in different parts of maize plants (immature stage) accumulated mostly in stems, with Pb mainly accumulated in roots (mature period), and Cd and Ni mostly in leaves. Except for the southeastern local region of this mining area, Mn and Cu possessed roughly similar spatial distribution characteristics. The results of partial correlation analysis indicated that Cu, Cd in the roots of the tested maize plants and Ni in soil may have antagonistic effects, Cu (soil)–Cu (stem) and Ni (soil)–Pb (stem) had a certain promoting effect. Besides, Cu, Pb, and Ni in soil promoted the absorption of Cu, Pb, and Ni in the leaves, whereas Cr and Pb in soil can promote the enrichment of Mn in maize grains. Our findings suggested that the concentrations of heavy metals in maize organs could be predicted accurately using the established models.     

Resource, biological community and soil functional stability dynamics at the soil–litter interface

The interface between decaying plant residues and soil is a focus for soil ecological processes because of resources from the residues diffusing into the soil, and microfauna that proliferate in the adjacent soil. Given that the recovery of soil function following disturbance depends on immigration, colonization and establishment of exotic organisms from adjacent un-disturbed habitats, and the availability of bio-available resources, we hypothesized that the soil–litter interface could contribute to soil functional stability. In laboratory pot trials, soil was separated into two parts by a mesh bag with the inner section amended, or not amended, with rice straw; an outer layer of unamended soil, adjacent to the litter (1.5 cm thick, either heated or not), provided a soil–litter interface. This enabled us to examine the dynamics of dissolved organic carbon (DOC), mineral nitrogen, microbial biomass carbon (MBC), nematode assemblages and functional stability during 35 days incubation. Either 1 mm or 5 μm meshes were used, which allowed nematodes to migrate (SR1) or not (SR5) through the mesh to the soil–litter interface; thus also enabling us to evaluate the role of nematodes in soil functional stability. Higher DOC and MBC but lower mineral nitrogen concentrations were found at the soil–litter interface. Heating increased the availability of soil resources such as mineral nitrogen and DOC, but decreased the MBC and total nematode abundance in the soil. The soil–litter interface was characterized by a higher abundance of nematodes, particularly microbivores, regardless of mesh aperture or disturbance. The difference in nematode abundance between SR1 and SR5 indicated that nematode propagation, due to resource diffusion and nematode migration through the mesh, contributed to the changing numbers of microbivorous nematodes depending on incubation time. The soil functional stability was calculated as a relative change in the functioning of short-term barley decomposition. Soil functional resistance, defined as the instantaneous effect of disturbance on decomposition measured on the first day, was highest in the SR5 treatment. However, soil functional resilience, defined as the recovery of soil function over the whole incubation period (35d), was highest in the SR1 treatment, which is most probably attributed to the functioning of microbivorous nematodes. Our results suggest that small-scale spatial heterogeneity, due to organic residue decomposition, can help maintain soil functions following disturbance.     

Density‐dependent parasitism in biological control of soil‐borne insects,nematodes, fungi and bacteria

Temporal density‐dependent parasitism appears to explain the development of some pest‐ and pathogen‐suppressive soils. In many examples, an enrichment of hosts (soil‐borne pests or pathogens) precedes and supports a build up of beneficial parasites in perennial crops or in monocultures, and the population dynamics of hosts and parasites may be described in epidemiological terms. Although the examples support the concept of a balance of nature based on density‐dependent regulation, we lack detailed understanding of the processes that drive these beneficial epidemics. In addition, the epidemics develop slowly and often do not provide the control expected by farmers. Current research, therefore, emphasizes inundative release of beneficial agents. Nevertheless, we should study epidemics in soil in order to learn how they might be enhanced; to learn how better to utilize inoculum that is inundatively added to soil; and to contribute to the general discussion of population biology and regulation.     

Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil

The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOGGN system analysis method as well as two conventional methods(DHA and SIR). All results of DGGE banding fingerprint pat-terns(amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition, the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the b     

urce, biological community and soil functional stability dynamics at the soil–litter interface

The interface between decaying plant residues and soil is a focus for soil ecological processes because of resources from the residues diffusing into the soil, and microfauna that proliferate in the adjacent soil. Given that the recovery of soil function following disturbance depends on immigration, colonization and establishment of exotic organisms from adjacent un-disturbed habitats, and the availability of bio-available resources, we hypothesized that the soil–litter interface could contribute to soil functional stability. In laboratory pot trials, soil was separated into two parts by a mesh bag with the inner section amended, or not amended, with rice straw; an outer layer of unamended soil, adjacent to the litter (1.5 cm thick, either heated or not), provided a soil–litter interface. This enabled us to examine the dynamics of dissolved organic carbon (DOC), mineral nitrogen, microbial biomass carbon (MBC), nematode assemblages and functional stability during 35 days incubation. Either 1 mm or 5 μm meshes were used, which allowed nematodes to migrate (SR1) or not (SR5) through the mesh to the soil–litter interface; thus also enabling us to evaluate the role of nematodes in soil functional stability. Higher DOC and MBC but lower mineral nitrogen concentrations were found at the soil–litter interface. Heating increased the availability of soil resources such as mineral nitrogen and DOC, but decreased the MBC and total nematode abundance in the soil. The soil–litter interface was characterized by a higher abundance of nematodes, particularly microbivores, regardless of mesh aperture or disturbance. The difference in nematode abundance between SR1 and SR5 indicated that nematode propagation, due to resource diffusion and nematode migration through the mesh, contributed to the changing numbers of microbivorous nematodes depending on incubation time. The soil functional stability was calculated as a relative change in the functioning of short-term barley decomposition. Soil functional resistance, defined as the instantaneous effect of disturbance on decomposition measured on the first day, was highest in the SR5 treatment. However, soil functional resilience, defined as the recovery of soil function over the whole incubation period (35d), was highest in the SR1 treatment, which is most probably attributed to the functioning of microbivorous nematodes. Our results suggest that small-scale spatial heterogeneity, due to organic residue decomposition, can help maintain soil functions following disturbance.