Co-Composting of Soil Heavily Contaminated with Creosote with Cattle Manure and Vegetable Waste for the Bioremediation of Creosote–Contaminated Soil

Mispah form (FAO: Lithosol) soil contaminated with >380 000 mg kg^?1 creosote was co-composted with cattle manure and mixed vegetable waste for 19 months. The soil was mixed with wood chips to improve aeration and then mixed with cattle manure or mixed vegetable waste in a ratio of 4:1. Moisture, temperature, pH, ash content, C:N ratios, and the concentrations of creosote in the compost systems were monitored monthly. The concentrations of selected hydrocarbons in the compost systems were determined at the end of composting. Temperature rose to about 45°C in the cattle manure compost within two months of incubation while temperature in the control and vegetable waste remained below 30°C until the fourth month. Creosote concentration was reduced by 17% in the control and by more than 99% in the cattle manure and vegetable waste compost after composting. The rate of reduction in concentration in the mixed vegetable waste compost was initially lower than in the cattle manure compost. The reduction rate became similar in later months with only small differences towards the end of the composting. The concentrations of selected creosote components were reduced by between 96% and 100% after composting. There was no significant difference in reduction in concentration in both compost systems at p 0.05. Microbial activity correlated with reduction in creosote concentration.     

Evaluation of Iodide and Iodate for Adsorption–Desorption Characteristics and Bioavailability in Three Types of Soil

Adsorption–desorption of iodine in two forms, viz., iodide (I⁻) and iodate (IO₃⁻), in three types of soil were investigated. The soils were: red soil developed on Quaternary red earths (REQ)— clayey, kaolintic thermic plinthite Aquult, Inceptisol soil (IS) and alluvial soil (AS)—Fluvio-marine yellow loamy soil. The isothermal curves of iodine adsorption on soils were described by Langmuir and Freundlich equation, and the maximum adsorption values (y _m) were obtained from the simple Langmuir model. As compared with the iodide, the iodate was adsorbed in higher amounts by the soils tested. Among three soils, the REQ soil adsorbed more iodine (I⁻ and IO₃⁻) than the IS and AS. The distribution coefficient (K _d) of iodine in the soils decreased exponentially with increasing iodine loading concentration. Desorption of iodine in soil was increased correspondingly with increasing adsorption values. The REQ soil had a greater affinity for iodine than the IS and AS at the same iodine loadings. In the pot experiment cultivated with pakchoi (Brassica chinensis L.) and added with two exogenous iodine sources, the iodide form was quickly taken up by pakchoi and caused more toxicity to the vegetable. The rate of iodine loss from soil was higher for iodide form as compared with the iodate. The iodine bioavailability was the highest but the persistence was the weakest in AS among the three soils tested, and the REQ soil showed just the opposite trend to that of the AS soil. This study is of theoretical importance to understand the relationship between iodine adsorption–desorption characteristics and their bioavailability in different soils and it also has practical implications for seeking effective alternatives of iodine biofortification to prevent iodine deficiency disorders.     

Dynamics of Inorganic Nitrogen in Nitrate and Glucose-amended Alkaline–saline Soil

Induction of assimilatory NO ₃ ⁻ reduction through the application of an easily decomposable substrate in alkaline–saline soils of the former lake Texcoco (Mexico) resulted in a fast immobilization of NO ₃ ⁻ in excess of N required for metabolic activity and the release of large concentrations of NO ₂ ⁻ and smaller amounts of NH ₄ ⁺ . We postulated that this was regulated by the amounts of NO ₃ ⁻ and glucose added, and affected by the specific characteristics of soil from the former lake Texcoco. This was investigated by spiking soils of different electrolytic conductivity (EC) 56.0 dS m⁻¹ (soil A of Texcoco) and 11.6 dS m⁻¹ (soil B of Texcoco) with different concentrations of NO ₃ ⁻ and glucose while dynamics of CO₂, NH ₄ ⁺ , NO ₂ ⁻ and NO ₃ ⁻ were monitored in an aerobic incubation for 7 days. For comparison reasons (control) an agricultural soil with low EC (0.3 dS m⁻¹) was included as well. In the agricultural soil, 67% of the added glucose mineralized within 7 days, but only 15% in soil A of Texcoco and 20% in soil B of Texcoco. The application of NO ₃ ⁻ to the agricultural soil added with glucose increased cumulative production of CO₂ 1.2 times, 1.5 times in soil A of Texcoco and 1.8 times in soil B of Texcoco. Concentration of NO ₂ ⁻ increased to > 100 mg NO ₂ ⁻ -N kg⁻¹ when 1000 mg glucose-C kg⁻¹ and 500 mg NO ₃ ⁻ -N kg⁻¹ were added to soil A and B of Texcoco, but remained < 3 mg NO ₂ ⁻ -N kg⁻¹ in the agricultural soil. The ratio between the cumulative production of CO₂ and the decrease in concentration of NO ₃ ⁻ was approximately one in soil A and B of Texcoco, but 10 in the agricultural soil after 3 days. It was found that micro-organisms in the alkaline–saline soil of the former lake Texcoco were capable of immobilizing large quantities of NO ₃ ⁻ when an easy decomposable substrate was available in excess of what might be required for metabolic activity while producing large concentrations of NO ₂ ⁻ , but these phenomena were absent in an agricultural soil. In soil of Texcoco, concentrations of NO ₂ ⁻ and NH ₄ ⁺ increased with increased salinity and availability of NO ₃ ⁻ . This ability to remove large quantities of NO ₃ ⁻ under these conditions and then utilize it at a later time might benefit micro-organisms of the N limited alkaline–saline soils of Texcoco.     

Differential Nutrient Limitation of Soil Microbial Biomass and Metabolic Quotients (qCO2): Is There a Biological Stoichiometry of Soil Microbes?

Background

Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils.

Methodology/Principal Findings

To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO₂ (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO₂) were most strongly associated with inorganic P availability.

Conclusions/Significance

Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.     

Isolation and Characterization of Polycyclic Aromatic Hydrocarbon–Degrading Mycobacterium Isolates from Soil

Bioremediation of soils contaminated with wood preservatives containing polycyclic aromatic hydrocarbons (PAHs) is desired because of their toxic, mutagenic, and carcinogenic properties. Creosote wood preservative–contaminated soils at the Champion International Superfund Site in Libby, Montana currently undergo bioremediation in a prepared-bed land treatment unit (LTU) process. Microbes isolated from these LTU soils rapidly mineralized the ¹⁴C-labeled PAH pyrene in the LTU soil. Gram staining, electron microscopy, and 16S rDNA-sequencing revealed that three of these bacteria, JLS, KMS, and MCS, were Mycobacterium strains. The phylogeny of the 16S rDNA showed that they were distinct from other Mycobacterium isolates with PAH-degrading activities. Catalase and superoxide dismutase (SOD) isozyme profiles confirmed that each isolate was distinct from each other and from the PAH-degrading mycobacterium, Mycobacterium vanbaalenii sp. nov, isolated from a petroleum-contaminated soil. We find that dioxygenase genes nidA and nidB are present in each of the Libby Mycobacterium isolates and are adjacent to each other in the sequence nidB-nidA, an order that is unique to the PAH-degrading mycobacteria.This revised version was published online in November 2004 with corrections to Volume 48.     

Hybridization Analysis of Microbial DNA from Fuel Oil–Contaminated and Noncontaminated Soil

Abstract The enrichment of several genes (xylE, nahAcd, todC1C2BA, tmoABCDE, alkB) that encode enzymes responsible for key steps in the degradation of hydrocarbons, and one gene specific to rRNA group I of the genus Pseudomonas, was studied in DNA extracted from a fuel oil–contaminated field site, and in laboratory microcosms (with the exception of alkB). Toluene, ethylbenzene, xylene, and naphthalene concentrations were related to the extent of hybridization of the genes in the field studies. Significant differences were observed in the extent of hybridization of some of the genes between contaminated and noncontaminated samples. In the microcosm studies, gasoline at rates ranging from 0.5 mg to 125 mg gasoline/g of soil as applied to soils, and the changes in hybridization intensity of these genes monitored with time. The lower threshold of gene enrichment of these genes in response to gasoline addition was below 0.5 mg/g soil. Small increases were observed at the 0.5-mg exposure level, but hybridization intensity quickly decreased to levels below detection 6–8 days after addition of the gasoline. A dose-response effect was observed from treatments with gasoline concentrations ranging from 0.5 to 35 mg/g soil. Inhibition by toxic components in gasoline was observed at 75 and 125 mg/g soil levels. Hybridization of the Pseudomonas group 1 probe to field DNA was not significantly enriched in the contaminated field site, although these sequences were enriched in the microcosm studies. Among the genes tested, xylE was the most sensitive indicator of low levels of fuel oil contamination. Received: 23 July 1996; Accepted 9 October 1996     

Soil volume and carbon storage shifts in drained and afforested wetlands of the Paraná River Delta

Wetland ecosystems have a high carbon storage potential as a result of high primary productivity and low decomposition rates dictated by water saturation. In the herbaceous wetlands of the Paraná River Delta, drainage and afforestation with poplars represents one of the dominant land uses. We explored the effects of these interventions on the volume and carbon storage of the young sedimentary soils of the region. At three sites we identified paired stands occupying similar landscape positions and soil types but subject to natural flooding and covered by natural herbaceous communities or drainage and flood control by dikes and covered by poplar plantations established 12, 17 and 19 years ago. Soil sampling at these sites revealed a reduction of the litter compartment (?86 %) and decreasing volume and porosity of its underlying mineral layer (0–10 cm in the wetland reduced to 0–4 cm in the plantation). Our comparisons of carbon storage accounted for these volumetric shifts by using accumulated mineral mass rather than depth as a reference, showing that tree plantations gained in the mineral soil (22 Mg C ha^?1) almost as much as what they lost in the litter. These gains were particularly large at intermediate depths (4–43 cm in the plantations) were soil porosity remained unaffected and C was raised by 64 % explained by (1) the pulse of inputs from overlaying litter and organic layers subject to rapid decomposition and mobilization after drainage and (2) root colonization, since tree plantations had 75 % of their fine root biomass at these intermediate soil depths, whereas roots in the wetlands did not explore the mineral soil profile and were completely confined to the organic layer. A neutral C balance following wetland drainage and afforestation resulted from the opposing effects of aeration, favoring decomposition in the organic layer, root colonization and organic matter stabilization, favoring its accumulation in the mineral soil.     

Dynamics of Aboveground and Soil Carbon and Nitrogen Stocks and Cycling of Available Nitrogen along a Land-use Gradient in Rondônia,Brazil

High rates of deforestation in the Brazilian Amazon have the potential to alter the storage and cycling of carbon (C) and nitrogen (N) across this region. To investigate the impacts of deforestation, we quantified total aboveground biomass (TAGB), aboveground and soil pools of C and N, and soil N availability along a land-use gradient in Rondônia, Brazil, that included standing primary forest, slashed primary and secondary forest, shifting cultivation, and pasture sites. TAGB decreased substantially with increasing land use, ranging from 311 and 399 Mg ha^–1 (primary forests) to 63 Mg ha^–1 (pasture). Aboveground C and N pools declined in patterns and magnitudes similar to those of TAGB. Unlike aboveground pools, soil C and N concentrations and pools did not show consistent declines in response to land use. Instead, C and N concentrations were strongly related to percent clay content of soils. Concentrations of NO₃-N and NH₄-N generally increased in soils following slash-and-burn events along the land-use gradient and decreased with increasing land use. Increasing land use resulted in marked declines in NO₃-N pools relative to NH₄-N pools. Rates of net nitrification and N-mineralization were also generally higher in postfire treatments relative to prefire treatments along the land-use gradient and declined with increasing land use. Results demonstrate the linked responses of aboveground C and N pools and soil N availability to land use in the Brazilian Amazon; steady reductions in aboveground pools along the land-use gradient were accompanied by declines in inorganic soil N pools and transformation rates.     

Soil carbon dynamics and aquatic metabolism of a wet–dry tropics wetland system

Freshwater wetlands are a key component of the global carbon cycle. Wet–dry tropics wetlands function as wet-season carbon sinks and dry-season carbon sources with low aquatic metabolism controlled by predictably seasonal, yet magnitude-variable flow regimes and inundation patterns. However, these dynamics have not been adequately quantified in Australia’s relatively unmodified wet–dry tropics freshwater wetlands. A baseline understanding is required before analysis of land-use or climate change impacts on these aquatic ecosystems can occur. This study characterises geomorphology and sedimentology within a seasonally connected wet–dry tropics freshwater wetland system at Kings Plains, Queensland, Australia, and quantifies soil carbon stocks and wet- and dry-season aquatic metabolism. Soil carbon stocks derived from loss-on-ignition on samples to 1 m depth were 51.5?±?7.8 kg C m^?2, higher than other wet–dry tropics wetlands globally, with potential for long-term retention at greater depths. Gross primary productivity of phytoplankton (GPP) and planktonic respiration (PR) measured through biological oxygen demand bottle experiments in the water column of sediment inundated under laboratory conditions show overall low GPP and PR in both wet- and dry-season samples (all wetland samples were heterotrophic with GPP/PR?<?1). Despite the short-term dominance of aquatic respiration processes leading to net release of carbon in the water column under these conditions, there is appreciable long-term storage of carbon in sediment in the Kings Plains wetlands. This demonstrates the importance of wet–dry-tropics wetland systems as hotspots of carbon sequestration, locally, regionally and globally, and consideration should be given to their conservation and management in this context.

     

Acclimation to Soil Flooding–sensing and signal-transduction

Flooding results in major changes in the soil environment. The slow diffusion rate of gases in water limits the oxygen supply, which affects aerobic root respiration as well as many (bio)geochemical processes in the soil. Plants from habitats subject to flooding have developed several ways to acclimate to these growth-inhibiting conditions, ranging from pathways that enable anaerobic metabolism to specific morphological and anatomical structures that prevent oxygen shortage. In order to acclimate in a timely manner, it is crucial that a flooding event is accurately sensed by the plant. Sensing may largely occur in two ways: by the decrease of oxygen concentration, and by an increase in ethylene. Although ethylene sensing is now well understood, progress in unraveling the sensing of oxygen has been made only recently. With respect to the signal-transduction pathways, two types of acclimation have received most attention. Aerenchyma formation, to promote gas diffusion through the roots, seems largely under control of ethylene, whereas adventitious root development appears to be induced by an interaction between ethylene and auxin. Parts of these pathways have been described for a range of species, but a complete overview is not yet available. The use of molecular-genetic approaches may fill the gaps in our knowledge, but a lack of suitable model species may hamper further progress.     

Biogenic Catalysis of Soil Formation on Mars?

The high iron abundance and the weak ferric iron spectral features of martian surface material are consistent with nanophase (nm-sized) iron oxide minerals as a major source of iron in the bright region soil on Mars. Nanophase iron oxide minerals, such as ferrihydrite and schwertmannite, and nanophase forms of hematite and goethite are formed by both biotic and abiotic processes on Earth. The presence of these minerals on Mars does not indicate biological activity on Mars, but it does raise the possibility. This work includes speculation regarding the possibility of biogenic soils on Mars based on previous observations and analyses. A remote sensing goal of upcoming missions should be to determine if nanophase iron oxide minerals, clay silicates and carbonates are present in the martian surface material. These minerals are important indicators for exobiology and their presence on Mars would invoke a need for further investigation and sample return from these sites.     

Water-Saving and High-Yielding Irrigation for Lowland Rice by Controlling Limiting Values of Soil Water Potential

The present study investigated whether an irrigation system could be established to save water and increase grain yield to enhance water productivity by proper water management at the field level in irrigated lowland rice （Oryza sativa L.）. Using two field-grown rice cultivars, two irrigation systems; conventional irrigation and water-saving irrigation, were conducted. In the water-saving irrigation system, limiting values of soil water potential related to specific growth stages were proposed as irrigation indices. Compared with conventional irrigation where drainage was in mid-season and flooded at other times, the water-saving irrigation increased grain yield by 7.4% to 11.3%, reduced irrigation water by 24.5% to 29.2%, and increased water productivity （grain yield per cubic meter of irrigation water） by 43.1% to 50.3%. The water-saving irrigation significantly increased harvest index, improved milling and appearance qualities, elevated zeatin-I-zeaUn riboside concentrations in root bleedings and enhanced activities of sucrose synthase, adenosine diphosphate glucose pyrophosphorylase, starch synthase and starch branching enzyme in grains. Our results indicate that water-saving irrigation by controlling limiting values of soil water potential related to specific growth stages can enhance physiological activities of roots and grains, reduce water input, and increase grain yield.     

Feeding Habits in Soil Nematode Families and Genera—An Outline for Soil Ecologists

Because research on nematode involvement in trophic interactions, foodweb structure, and biodiversity is constrained by lack of an overview of nematode feeding habits, this outline presents a consensus of current thought on nematode feeding habits. The source of food is fundamental to trophic interactions and provides the basis for our definitions of the essential feeding types: 1) plant feeder, 2) hyphal feeder, 3) bacterial feeder, 4) substrate ingester, 5) predator of animals, 6) unicellular eucaryote feeder, 7) dispersal or infective stage of parasites, and 8) omnivore. Lists of families and genera with their presumed feeding types are given. Major gaps in knowledge of feeding in the smaller tylenchids and many dorylaims are noted.     

Soil N mineralization, nitrification and dynamic changes in abundance of ammonia-oxidizing bacteria and archaea along a 2000 year chronosequence of rice cultivation

Background and Aims

Soil mineralization, nitrification, and dynamic changes in abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were studied to validate our hypothesis that soil mineralization and nitrification decreased along the chronosequence of rice cultivation.

Methods

Paddy soils with a 300, 700 and 2000-year cultivation history (P300, P700 and P2000) were selected to study net mineralization and nitrification processes. Dynamic abundance of AOB and AOA was estimated by quantifying their respective amoA gene copies.

Results

The net mineralization rate was higher for P300 than P700 and P2000. Potential nitrification (N _p ) and average nitrification rates (V _a ) were similar for P300 and P700 soils, but the simulated potential nitrification rate (V _p ) and nitrification rate (k₁) was 72 % and 88 % higher for P300 than P700, respectively. V _a was about 70 % lower than for P2000 than P300 and P700. AOB amoA gene copies were higher for P300 than P700 and P2000, whereas AOA abundance did not show significant differences. AOB abundance showed a positive response to NH₄ supply but AOA did not.

Conclusions

Both N mineralization and nitrification were depressed with increased cultivation time. Archaea responded to mineralization positively rather than nitrification, which suggested that readily mineralized organic matter may play an important role in AOA.     

Soil carbon storage and nitrogen and phosphorous availability in loblolly pine plantations over 4 to16 years of herbicide and fertilizer treatments

The impact of extended herbicide (H) and annual fertilizer (F) treatments on the mineral soil carbon (C) pool and nitrogen (N) and phosphorous (P) availability were analyzed in managed loblolly pine (Pinus taeda L.) plantations in the Piedmont of Georgia in stands ranging from 4 to 16 years old. Mineral soil C, N, P, and extractable P were measured in 66 plots in three locations comparing H, F, and their combination HF to the Control plots. Soils were sampled in January 2000 near Eatonton (n = 40), in August 2001 near Athens (n = 12), and in March 2003 near Dawsonville (n = 14). In addition, twelve plots (two H and two HF at each location) were measured on 17 dates using a mixed bead resin core technique to estimate mineral soil N availability. At all three study locations the H treatment tended to deplete the mineral soil C pool while, overall, the F treatments did not determine any significant mineral soil C increase. The soil C pool (0- to 50-cm depth) was depleted by about 5 Mg C ha⁻¹ under the H-treated plots near Eatonton. The HF plots had much higher resin-extractable N than the corresponding H plots in all months of the year. At a plot level, HF values ranged from about 9 to 3,195 μg N g⁻¹ resin while H values ranged from about 4 to 858 μg N g⁻¹ resin. The corresponding annual cumulative resin-extractable N ranged from about 13 kg N ha⁻¹ in the H to about 372 kg N ha⁻¹ in the HF. Extractable P values were also elevated in all F-treated plots. Fertilization and herbicide treatments favored C sequestration only in the aboveground biomass. No significant change was observed in the mineral soil C pool, despite the generally observed increases in soil available N and P.     

Does a General Temperature-Dependent Q10 Model of Soil Respiration Exist at Biome and Global Scale?

Soil respiration (SR) is commonly modeled by a Q10 (an indicator of temperature sensitivity)function in ecosystem models. Q10is usually treated as a constant of 2 in these models, although Q10 value of SR often decreases with increasing temperatures. It remains unclear whether a general temperaturedependent Q10 model of SR exists at biome and global scale. In this paper, we have compiled the long-term Q10 data of 38 SR studies ranging from the Boreal, Temperate, to Tropical/Subtropical biome on four continents.Our analysis indicated that the general temperature-dependent biome Q10 models of SR existed, especially in the Boreal and Temperate biomes. A single-exponential model was better than a simple linear model in fitting the average Q10 values at the biome scale. Average soil temperature is a better predictor of Q10 value than average air temperature in these models, especially in the Boreal biome. Soil temperature alone could explain about 50% of the Q10 variations in both the Boreal and Temperate biome single-exponential Q10 model. Q10 value of SR decreased with increasing soil temperature but at quite different rates among the three biome Q10 models. The k values (Q10 decay rate constants) were 0.09, 0.07, and 0.02/℃ in the Boreal, Temperate, and Tropical/Subtropical biome, respectively, suggesting that Q10 value is the most sensitive to soil temperature change in the Boreal biome, the second in the Temperate biome, and the least sensitive in the Tropical/Subtropical biome. This also indirectly confirms that acclimation of SR in many soil warming experiments probably occurs. The k value in the "global" single-exponential Q10 model which combined both the Boreal and Temperate biome data set was 0.08/℃. However, the global general temperature-dependent Q10model developed using the data sets of the three biomes is not adequate for predicting Q10 values of SR globally.The existence of the general temperature-dependent Q10 models of SR in the Boreal and Temperate biome has important implications for modeling SR, especially in the Boreal biome. More detail model runs are needed to exactly evaluate the impact of using a fixed Q10 vs a temperature-dependent Q10 on SR estimate in ecosystem models (e.g., TEM, Biome-BGC, and PnET).     

Do Current Standards of Practice in Canada Measure What is Relevant to Human Exposure at Contaminated Sites? I: A Discussion of Soil Particle Size and Contaminant Partitioning in Soil

Human health risk estimates for sites with contaminated soils are often based on the assumption that the bulk concentration of substances in outdoor soil samples is a reasonable predictor of exposures via incidental soil ingestion, soil particle inhalation, and dermal absorption. Most underlying conceptual models are grossly simplistic, however, when considered in light of (i) biases in the distribution of contaminants across soil particle sizes, (ii) the size range of particles in soils and dusts that is environmentally available, and (iii) factors that influence desorption from particles and uptake into humans. The available studies indicate that contaminant distribution across soil particle size fractions varies widely between different soil types and contaminant delivery mechanisms, and it cannot be assumed that higher masses of contaminants per unit mass of soil are correlated with smaller particles sizes. Soil data gathered in support of detailed human health risk assessments, therefore, should allow for the examination of distribution across particle sizes of contaminants of concern, and consider those size fractions most critical to human exposure. Soil evaluations for health risk assessments of metals/metalloids should also consider mineralogical characterization.