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.     

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.     

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.     

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.     

Potential soil P mobilisation capacity–method development and comparison of rhizosphere soil from different crops

Background

Phosphorus (P) deficiency is wide-spread in agricultural soils. In light of increasing P fertilizer costs, it is of interest to assess the capacity of soil microbes to mobilise native soil P and added P. There is currently no method to assess P mobilisation in situ.

Methods

The soil P mobilisation potential was assessed by incubating low P soil for up to 30?days with poorly available P sources; C and N were added to increase microbial activity and ensure that only P was limiting microbial growth.

Results

The increase in microbial P from day 0 to day 15 showed that microbes were able to mobilise P from FePO₄ and phytate. The P mobilisation potential (sum of microbial and resin P) of the rhizosphere soil decreased in the following order: faba bean > chickpea and white lupin > wheat. After 10?days, up to 80% of the mobilised P was microbial P, whereas after 30?days, almost all P mobilised was resin P.

Conclusions

The method developed in this study is useful assessing not only potential of a soil to mobilise P but also, by using different poorly available P sources, the mechanisms of P mobilisation.     

Antimicrobial susceptibilities of strains of Nocardia brasiliensis isolated from soil of Tucumán

The activity of antimicrobial agents against soil isolates of N. brasiliensis was studied by determination of the minimum inhibitory concentrations (MICs) and disk diffusion technique, according to the National Committee for Clinical Laboratory Standards (NCCLS). The objectives were: (a) to study the patterns of sensitivity among regional strains of N. brasiliensis isolated from natural sources (soil) of different zones of Tucumán province; (b) to correlate these results with those previously obtained with regional strains of N. brasiliensis isolated from human mycetomas, as a contribution in the evaluation of the importance of the natural reservoir area of the potentially pathogen strains. The results obtained by both methods identified strains of N. brasiliensis from soils with similar patterns of susceptibility to the strains N. brasiliensis isolated from human mycetomas. This showed strains sensitive and resistant to antibiotics. The majority of the isolates of N. brasiliensis from soils showed higher susceptibilities to antibiotics than the strains isolated from human mycetomas. Among the antibiotics studied, cefotaxime, ceftriaxone and gentamicin were the most effective against all the regional strains tested, and these results are correlated with those obtained with regional strains that cause human mycetomas. This revised version was published online in June 2006 with corrections to the Cover Date.     

Measurement of the apparent diffusion coefficient of N‐butane in soil

Measurements of in‐soil diffusion coefficients and the application of an appropriate diffusional model can allow for a more accurate prediction of soil gas concentrations and movement to locate subterranean contamination of volatile materials. The present study was undertaken to measure and evaluate the “apparent in‐soil diffusion coefficient”; for n‐butane through soil columns under non‐steady‐state conditions. The term “apparent in‐soil diffusion coefficient”; refers to a numerical coefficient that primarily describes the movement of the material by diffusion but also contains effects due to other mechanisms (e.g., adsorption and solubility).

Six test columns were evaluated at three soil porosity levels ranging from 0.30 to 0.43 and at two column temperature conditions, nominally 18°C and 7°C. Soil columns measured 25.4 cm in diameter by 84 cm in height and contained a moist sand/silt/clay mixture. The numerical range for the apparent in‐soil diffusion coefficients for n‐butane was 0.447 × 10^‐3cm²/s to 0.561 × 10^‐3cm²/s. The lower coefficient values were associated with lower soil porosity levels and cooler column conditions.     

Does an earthworm species acclimatize and/or adapt to soil calcium conditions? The consequences of soil nitrogen mineralization in forest soil

Calcium (Ca)-rich food can increase feeding of Lumbricidae. Earthworms can be genetically differentiated at a small spatial scale and acclimatize to the local environment during growth. Soil feeding and subsequent cast production by earthworms affects soil N mineralization. Here, we hypothesized that soil feeding and subsequent cast production by Lumbricidae species increases with high soil Ca content and that this increase is stronger in worms from high-Ca soil. We also hypothesized that changes in the soil feeding of Lumbricidae species along with the Ca content affects the soil N mineralization via changes in the cast production. Using a geophageous earthworm species (Eisenia japonica) originated from two different Ca environments (calcareous soil and sedimentary soil), we investigated cast production and soil N mineralization in three soils (sedimentary soil, sedimentary soil with Ca addition, and calcareous soil). The soil feeding of E. japonica from both origins did not always increase despite the high soil Ca content. We suggest that both the Ca content and other soil conditions (e.g., soil C:N) might be major factors in increasing soil feeding by E. japonica. Furthermore, the influence of Ca addition on cast production varied according to the earthworm origin. As expected, these differences in cast production are linked to soil N mineralization (especially nitrification). In summary, our study suggests that the acclimatization and/or adaptation of Lumbricidae species to local environmental factors not only soil Ca content explains spatially heterogeneous soil N mineralization in forest soil.     

Intrinsic capacities of soil microfloræ for gasoline degradation

A methodology to determine the intrinsic capacities of a microflora to degrade gasoline was developed, in particular for assessing the potential of autochtonous populations of polluted and non polluted soils for natural attenuation and engineered bioremediation. A model mixture (GM23) constituted of the 23 most representative hydrocarbons of a commercial gasoline was used. The capacities of the microfloræ (kinetics and extent of biodegradation) were assessed by chromatographic analysis of hydrocarbon consumption and of CO2 production. The degradation of the components of GM23 was assayed in separate incubations of each component and in the complete mixture. For the microflora of an unpolluted spruce forest soil, all hydrocarbons of GM23 except cyclohexane, 2,2,4- and 2,3,4-trimethylpentane isomers were degraded to below detection limit in 28 days. This microflora was reinforced with two mixed microbial communities selected from gasoline-polluted sites and shown to degrade cyclohexane and 2,2,4- trimethylpentane. With the reinforced microflora, complete degradation of GM23 was observed. The degradation patterns of individual components of GM23 were similar when the compounds were present individually or in the GM23 mixture, as long as the concentrations of 2-ethyltoluene and trimethylbenzene isomers were kept sufficiently low ( 35 mg.l-1) to remain below their inhibitory level.     

Bioavailability of Cd in a soil–rice system in China: soil type versus genotype effects

Human exposure to toxic heavy metals via dietary intake is of increasing concern. In this regard, the bioavailability of heavy metals in the soil–crop system is considered to be a key factor controlling plant uptake and, therefore, public health risk through food chain transfer [J. Environ. Sci. Health B 34(4) (1999) 681]. In 2002, a pot experiment was conducted to elucidate the relative significance of soil types and rice genotype on the bioavailability, uptake and partitioning of Cd by two rice cultivars with distinct affinity for Cd. The results indicated that the total uptake of Cd and accumulation in grain was dependent on both soil type and genotype effects. Cd spiking enhanced high Cd uptake and partitioning in grain. Inherent differences in soil type effecting Cd bioavailability were less significant under the Cd spiking regime as compared to non-Cd spiking. In the case of Soil-P, with low Cd bioavailability as indicated by the comparatively lower MgCl₂ extractableCd, differences in metal affinity between genotypes dominated uptake. Conversely, inherent differences in soil type affecting Cd bioavailability dominated uptake in the low metal affinity cultivar treatments. Under the experimental conditions evaluated, the positive interaction between soil type and genotype results in elevated levels of Cd in rice grain with the Cd values exceeding the Chinese food guideline limit of 0.2 mg kg^–1. The results indicated that Cd bioavailability and plant uptake is dependent on soil chemical and physical properties affecting Cd mobility, rice genotype and soil pollution status. The results further suggested that caution should be paid to rice production with the new high metal affinity genotypes on soils with inherent Cd bioavailability as with acidic Red Soils of Jiangxi Provinces, China.     

Does the temperature sensitivity of decomposition of soil organic matter depend upon water content,soil horizon,or incubation time?

Several studies have shown multiple confounding factors influencing soil respiration in the field, which often hampers a correct separation and interpretation of the different environmental effects on respiration. Here, we present a controlled laboratory experiment on undisturbed organic and mineral soil cores separating the effects of temperature, drying–rewetting and decomposition dynamics on soil respiration. Specifically, we address the following questions:

• 1 Is the temperature sensitivity of soil respiration (Q₁₀) dependent on soil moisture or soil organic matter age (incubation time) and does it differ for organic and mineral soil as suggested by recent field studies.
• 2 How much do organic and mineral soil layers contribute to total soil respiration?
• 3 Is there potential to improve soil flux models of soil introducing a multilayer source model for soil respiration?

Eight organic soil and eight mineral soil cores were taken from a Norway spruce (Picea abies) stand in southern Germany, and incubated for 90 days in a climate chamber with a diurnal temperature regime between 7 and 23°C. Half of the samples were rewetted daily, while the other half were left to dry and rewetted thereafter. Soil respiration was measured with a continuously operating open dynamic soil respiration chamber system. The Q₁₀ was stable at around 2.7, independent of soil horizon and incubation time, decreasing only slightly when the soil dried. We suggest that recent findings of the Q₁₀ dependency on several factors are emergent properties at the ecosystem level, that should be analysed further e.g. with regard to rhizosphere effects. Most of the soil CO₂ efflux was released from the organic samples. Initially, it averaged 4.0 μmol m^?2 s^?1 and declined to 1.8 μmol m^?2 s^?1 at the end of the experiment. In terms of the third question, we show that models using only one temperature as predictor of soil respiration fail to explain more than 80% of the diurnal variability, are biased with a hysteresis effect, and slightly underestimate the temperature sensitivity of respiration. In contrast, consistently more than 95% of the diurnal variability is explained by a dual‐source model, with one CO₂ source related to the surface temperature and another CO₂ source related to the central temperature, highlighting the role of soil surface processes for ecosystem carbon balances.     

Natural occurrence of Nocardia in soil of Tucumán: Physiological characteristics

This is the first study initiated in Argentina to establish the presence of species of Nocardia from soil samples. These samples were gathered in different areas of Tucumán.Thirty three pathogenic strains of Nocardia were isolated by the paraffin bait method. Out of them, 28 were N. brasiliensis, 3 N. asteroides and 2 N. caviae. N. brasiliensis was widely distributed in the soil of the areas tested.It is proved that N. caviae, so rarely found in other regions of the world, occurs in Tucumán.A detailed study of the morphological and physiological characteristics for identification is discussed.     

Is diversification history of maize influencing selection of soil bacteria by roots?

A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21-day-old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning/sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings.     

Influence of Bt-plants on soil biota and pleiotropic effect of δ-endotoxin-encoding genes

The critical review of experimental conclusions stating environmental safety of transgenic plants reveals that the methods and test materials employed in some studies were inadequate to the goals pursued. A large-scale application of transgenic Bt-plants may result in long-lasting negative impact on the environment. First, the cultivation of these plants leads to accumulation of Bt-toxins in soil. Second, the decomposition of transgenic plants takes significantly longer time compared to that of isogenic lines. Third, the biological activity of soils under transgenic crops is lower than in the control plots. The transfer of δ-endotoxin-encoding genes to the genome of agricultural crops affects simultaneously several entirely different traits of genetically modified plants, thus exerting pleiotropic effects. This gives rise to a paradoxical situation: the genetically engineered crops selected on the trait of resistance to herbivorous insects of the order Lepidoptera become more attractive for herbivores from the other order, Homoptera.     

Oxidation of arsenite by two β-proteobacteria isolated from soil

Two heterotrophic As(III)-oxidizing bacteria, SPB-24 and SPB-31 were isolated from garden soil. Based on 16S rRNA gene sequence analysis, strain SPB-24 was closely related to genus Bordetella, and strain SPB-31 was most closely related to genus Achromobacter. Both strains exhibited high As(III) (15 mM for SPB-24 and 40 mM for SPB-31) and As(V) (>300 mM for both strains) resistance. Both strains oxidized 5 mM As(III) in minimal medium with oxidation rate of 554 and 558 μM h⁻¹ for SPB-24 and SPB-31, respectively. Washed cells of both strains oxidized As(III) over broad pH and temperature range with optimum pH 6 and temperature 42°C for both strains. The As(III) oxidation kinetic by washed cells showed K _m and V _max values of 41.7 μM and 1,166 μM h⁻¹ for SPB-24, 52 μM and 1,186 μM h⁻¹ for SPB-31. In the presence of minimal amount of carbon source, the strains showed high As(III) oxidation rate and high specific arsenite oxidase activity. The ability of strains to resist high concentration of arsenic and oxidize As(III) with highest rates reported so far makes them potential candidates for bioremediation of arsenic-contaminated environment.     

Bioremediation of oil‐contaminated soil in Kuwait. I. landfarming to remediate oil‐contaminated soil

During the Gulf Crisis, the State of Kuwait was subjected to hazards caused by the oil well fires. The discharged oil formed over 300 oil lakes, covering land areas in excess of 49 km². In addition, deposits from aerial fallout covered massive areas of Kuwait's desert soil. It has been widely recognized that the heavily oil‐contaminated soil must be remediated in order to avoid total damage to the land, water ecosystems, and/or the eventual release of hazardous particulate compositions to the atmosphere. A large number of diverse technological options were being considered for the remediation of contaminated soil. Bioremediation techniques involving enhanced landfarming was selected and evaluated at pilot scale

The experiments were initiated in November 1992 at the Burgan oil field in which 16 landfarming plots of 120 m² each were constructed. The study continued for 18 months, during which time petroleum hydrocarbon concentration, polycyclic aromatic hydrocarbon (PAH), and heavy metals were monitored regularly. The result obtained showed that landfarming treatment resulted in more than 80% reduction of oil contamination within 15 months. The treatment also resulted in a substantial reduction of the PAHs concentrations.     

Glyphosate translocation from plants to soil – does this constitute a significant proportion of residues in soil?

Thallium is an extremely toxic metal which, due to its similarities to K, is readily taken up by plants grown in Tl-contaminated soils. Thallium is also a precious metal nearly as economically valuable as gold. Thallium is efficiently hyperaccumulated in Iberis intermedia as aqueous Tl(I) with highest concentrations within the vascular network of leaves. In this study we examine the utility of synchrotron X-ray differential absorption-edge computed microtomography (CMT) in determining the distribution and compartmentalization of thallium (Tl) in Iberis intermedia. We found Tl to be distributed in solution throughout the vascular system of I. intermedia. Current laboratory experiments are examining the characteristics and potential recovery of Tl by I. intermedia with the objectives to remediate its toxic risks and to facilitate its reclamation for reuse. However, the recovery and reuse of Tl from I. intermedia by way of phytomining requires knowledge on the speciation, distribution and compartmentalization of thallium. CMT shows great promise for application in a wide variety of metal-related structural issues due to its high 3D resolution and being a non-destructive analysis tool. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users. An erratum to this article can be found at