Biodegradation of pyrene and catabolic genes in contaminated soils cultivated with Lolium multiflorum L

Background, aim, and scope  

In the soil environment, polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are of great environmental and human health concerns due to their widespread occurrence, persistence, and carcinogenic properties. Bioremediation of contaminated soil is a cost-effective, environmentally friendly, and publicly acceptable approach to address the removal of environmental contaminants. However, bioremediation of contaminants depends on plant–microbe interactions in the rhizosphere. The microorganisms that can mineralize various PAHs have PAH dioxygenase genes like nahAc, phnAc, and pdo1. To understand the fate of pyrene in rhizospheric and non-rhizospheric soils in the presence or absence of Pb, pyrene biodegradation, bacterial community structure, and dioxygenase genes were investigated in a pot experiment.     

Time-dependent sorption of imidacloprid in two different soils

Time-dependent sorption of imidacloprid [1-[(6-chloro-3-pyridinyl)-methyl]-N-nitro-2-imidazolidinimine] was investigated with two German soils (sandy loam and silt loam). Soil batches containing the active ingredient (0.33 mg/kg) were incubated for 100 days. After selected aging periods, imidacloprid desorbed by 0.01 M CaCl(2) (soluble phase) and by organic solvents (methanol and acetonitrile) and reflux extraction with acidified methanol (sorbed phase) was determined. Calculated sorption coefficients K(d) and K(oc) increased by a factor of 3.2-3.8 during 100 days of aging. Additionally, the time-dependent sorption was verified by a column leaching experiment with the aged soil. The amount of imidacloprid in column eluates (0.01 M CaCl(2)) decreased compared to total recovered by a factor of approximately 2. Sorption of imidacloprid thus increased with residence time in soil, making it more resistant to leaching. These results are further information to explain the low leaching potential of imidacloprid in the field, despite its high water solubility.     

Temporal denitrification patterns in different horizons of two riparian soils

The dynamics of biological denitrification in riparian soil is still poorly understood. We studied the spring‐time pattern of denitrifying enzyme activity (DEA) and the rate of denitrification (DNT) in two hydromorphic riparian soils, one a mollic Gleysol and the other a terric Histosol. The average DEA ranged from 73 to 1232 ng N g^?1 hour^?1, and DNT ranged from 4 to 36 ng N g^?1 hour^?1. Both DEA and DNT diminished with increasing depth in both soil types. This decrease corresponded to a decrease in total and K₂SO₄‐extractable organic carbon and K₂SO₄‐extractable mineral nitrogen. The DEA and DNT differed in their dynamics. The former had no evident pattern in subsurface horizons but increased with temperature at the end of spring in surface and structural horizons. The DNT diminished as the soil dried in the mollic Gleysol when the water table fell. In the terric Histosol, the water table was still too high at the end of spring to affect the DNT. The results suggest that the vertical pattern of denitrification is related to that of organic carbon content. This organic carbon content determines biological activity and the supply of carbon and nitrous oxides. In biologically active horizons temperature drives the dynamics of DEA, whereas soil moisture drives the dynamics of DNT. Our results show the importance of the dynamic soil–water relationship in controlling denitrification within the riparian zone.     

Environmental fate of trifloxystrobin in soils of different geographical origins and photolytic degradation in water

In vitro biodegradation of trifloxystrobin (TFS) under darkness could best be explained by two-compartment first + first-order rate kinetics with half-lives ranging between 1.8 and 2.3 days. Hydrolysis was found to be the major pathway of degradation resulting in the formation of the acid metabolite, TFS-acid, with an EE conformation. The adsorption rate kinetics of both TFS and TFS-acid followed linear and Freundlich isotherms. The extent of adsorption was directly correlated with organic matter and clay contents, whereas desorption had a negative correlation. The high partition coefficients (KD) indicate strong adsorption of TFS on all of the test soils without any appreciable risk of groundwater contamination. In case of the TFS-acid, however, the adsorption was weaker; hence, if its further degradation is slow, it may contaminate lower soil horizons under worst case conditions. TFS did not cause any adverse effect on the soil microbial population. TFS was susceptible to aquatic photolysis in summer with an environmental half-life of 0.7-1.3 days irrespective of the latitudes.     

Nitrification in two coniferous forest soils after different fertilization treatments

The effects of seven different fertilization treatments on nitrification in the organic horizons of a Myrtillus-type (MT) and a Calluna-type pine forest in southern Finland were studied. No (NO^?₃ + NO^?₂)-N accumulated in unfertilized soils during 6 weeks at 14 or 20°C in the laboratory. Net nitrification was stimulated by urea in both soils (but more in the MT pine forest soil) and to a lesser degree by wood ash but not by ammonium nitrate or nitroform (ureaformaldehyde). Nitrification was not detected in nitroform fertilized soils although ammonium accumulation was high during incubation. In the MT pine forest soil, net nitrification appeared to be stimulated by apatite, biotite and micronutrients. Nitrapyrin inhibited nitrification indicating that it was carried out by autotrophic nitrifiers. In the urea-fertilized MT pine forest soil, nitrification took place at an incubation temperature of 0°C. Accumulation of (N0^?₃ + NO^?₂)-N was highest in soil sampled at < 10°C.     

Selective enrichment of a pyrene degrader population and enhanced pyrene degradation in Bermuda grass rhizosphere

Rhizosphere soil has a more diverse and active microbial community compared to nonvegetated soil. Consequently, the rhizosphere pyrene degrader population (PDP) and pyrene degradation may be enhanced compared to nonvegetated bulk soil (NVB). The objectives of this growth chamber study were to compare (1) Bermuda grass (Cynodon dactylon cv. Guymon) growth in pyrene-contaminated and noncontaminated soils and (2) pyrene degradation and PDP among NVB, Bermuda grass bulk (BB), and Bermuda grass rhizosphere soil (BR). Soils were amended with pyrene at 0 and 500 mg kg^–1, seeded with Bermuda grass, and thinned to two plants per pot 14 days after planting (DAP). Pyrene degradation was evaluated over 63 days. The PDP was enumerated via a most probable number (MPN) procedure at 63 DAP. Bermuda grass root growth was more sensitive to pyrene contamination than shoot growth. Pyrene degradation followed first-order kinetics. Pyrene degradation was significantly greater in BR compared to BB and NVB with rate constants of 0.082, 0.050, and 0.052 day^–1, respectively. The PDPs were 8.01, 7.30, and 6.83 log₁₀ MPN g^–1 dry soil for BR, BB, and NVB, respectively. The largest PDP was in soil with the most rapid pyrene degradation. These results indicate that Bermuda grass can grow in pyrene-contaminated soil and enhance pyrene degradation through a rhizosphere effect.     

Microbial degradation of hydrolysable and condensed tannin polyphenol-protein complexes in soils from different land-use histories

Polyphenols are capable of binding to proteins and form polyphenol-protein complexes thus reducing the release of N from decomposing plant materials. The objective of this work was to test if under polyphenol-rich vegetations adapted microbial communities had developed capable of breaking down recalcitrant polyphenol-protein complexes. Soils used for this investigation were from different 10-year-old tropical agricultural systems (maize, sugarcane plots and Gliricidia sepium or Peltophorum dasyrrachis woodlots) and natural systems (secondary forest and Imperata cylindrica grassland). TA (tannic acid, hydrolysable tannin), QUE (quebracho, condensed tannin), BSA (bovine serum albumin, protein) or TA/BSA and QUE/BSA polyphenol-protein complexes were incubated at 28 °C in these soils. CO₂-C and ¹³C evolution were periodically monitored and mineral N release, microbial biomass N and phospholipid fatty acid (PLFA) profiles measured at the end.QUE was able to bind about 25% more protein than TA. In all systems the individual uncomplexed substrates were more easily degraded than the complexes. On average, net cumulative CO₂-C evolution from TA/BSA complexes was more than 5 times higher than from QUE/BSA complexes, indicating higher C availability and/or lower protection capability of TA compared to QUE. However, net N release was higher from QUE/BSA than from TA/BSA probably due to their higher protein-binding capacity and associated larger degradation of partly unprotected protein as suggested by ¹³C-CO₂ signatures. Microbial respiration patterns indicated that polyphenol complexes were initially degraded more quickly in the maize cropping system than in soils from under polyphenol-rich communities (Peltophorum and natural forest) but this pattern reversed with time. Long-term incubation of QUE/BSA complexes even caused a negative effect on microbial respiration in agricultural soils with low polyphenol contents (e.g. maize and sugarcane).Incubation of polyphenol complexes in soil depressed microbial biomass N in maize, sugarcane, Imperata and forest systems and led to reduced soil pH. However, microbial biomass was increased under the polyphenol-rich vegetation of Peltophorum. The PLFA group 18:2w6,9 was highly enhanced by condensed tannin-protein complexes additions as compared to control and hydrolysable polyphenol-protein complexes in soils with high polyphenol contents. Polyphenol complexes increased the fungi:bacteria ratio in systems with a high polyphenol content, particularly with condensed tannin complexes. The results indicated that systems with a high polyphenol content favoured development of fungal communities that are highly adaptable to phenol-rich soil conditions and high acidity, particularly with regards to the more recalcitrant condensed tannin-protein complexes.     

Comparison of two different methods to measure nitric oxide turnover in soils

 The NO turnover in soils was measured in two different experimental set-ups, a flow-through system, which is very time-consuming and needs rather sophisticated equipment, and a closed system using serum bottles. We compared the NO turnover parameters (NO consumption rate constant, NO production rate, NO compensation concentration) that were measured with both systems in different soils, under different conditions and in the presence of 10 Pa acetylene to inhibit nitrification. The values of the NO turnover parameters that were measured with the two systems under oxic conditions were usually comparable. The addition of acetylene did not affect the NO consumption rate constants of the soils with the exception of soil G1. However, the NO production rates and the NO compensation concentrations decreased significantly in the presence of acetylene, indicating that nitrification was the main source of NO in these soils. Only one soil (Bol) showed no nitrifying activity. Increasing soil moisture content resulted in decreasing NO consumption rate constants and NO production rates. Even at a high soil moisture content of 80% water holding capacity, nitrification was the main source of NO. The values of the NO turnover parameters that were measured with the two systems were not comparable under anoxic conditions. The NO consumption rate constants and the NO production rates were much lower in the closed than in the flow-through system, indicating that the NO consumption activity became saturated by the high NO concentrations accumulating in the closed system. Under oxic conditions, however, closed serum bottles were a cheap, easy and reliable tool with which to determine NO turnover parameters and to distinguish between nitrification and denitrification as sources of NO. Received: 21 April 1998     

Nitrogen losses from two grassland soils with different fungal biomass

Nitrogen losses from agricultural grasslands cause eutrophication of ground- and surface water and contribute to global warming and atmospheric pollution. It is widely assumed that soils with a higher fungal biomass have lower N losses, but this relationship has never been experimentally confirmed. With the increased interest in soil-based ecosystem services and sustainable management of soils, such a relationship would be relevant for agricultural management. Here we present a first attempt to test this relationship experimentally. We used intact soil columns from two plots from a field experiment that had consistent differences in fungal biomass (68 ± 8 vs. 111 ± 9 μg C g⁻¹) as a result of different fertilizer history (80 vs. 40 kg N ha⁻¹ y⁻¹ as farm yard manure), while other soil properties were very similar. We performed two greenhouse experiments: in the main experiment the columns received either mineral fertilizer N or no N (control). We measured N leaching, N₂O emission and denitrification from the columns during 4 weeks, after which we analyzed fungal and bacterial biomass and soil N pools. In the additional ¹⁵N experiment we traced added N in leachates, soil, plants and microbial biomass. We found that in the main experiment, N₂O emission and denitrification were lower in the high fungal biomass soil, irrespective of the addition of fertilizer N. Higher ¹⁵N recovery in the high fungal biomass soil also indicated lower N losses through dentrification. In the main experiment, N leaching after fertilizer addition showed a 3-fold increase compared to the control in low fungal biomass soil (11.9 ± 1.0 and 3.9 ± 1.0 kg N ha⁻¹, respectively), but did not increase in high fungal biomass soil (6.4 ± 0.9 after N addition vs. 4.5 ± 0.8 kg N ha⁻¹ in the control). Thus, in the high fungal biomass soil more N was immobilized. However, the ¹⁵N experiment did not confirm these results; N leaching was higher in high fungal biomass soil, even though this soil showed higher immobilization of ¹⁵N into microbial biomass. However, only 3% of total ¹⁵N was found in the microbial biomass 2 weeks after the mineral fertilization. Most of the recovered ¹⁵N was found in plants (approximately 25%) and soil organic matter (approximately 15%), and these amounts did not differ between the high and the low fungal biomass soil. Our main experiment confirmed the assumption of lower N losses in a soil with higher fungal biomass. The additional ¹⁵N experiment showed that higher fungal biomass is probably not the direct cause of higher N retention, but rather the result of low nitrogen availability. Both experiments confirmed that higher fungal biomass can be considered as an indicator of higher nitrogen retention in soils.     

Factors affecting triadimefon degradation in soils

The degradation of triadimefon [1-(4-chlorophenoxy)-3,3-dimethyl-1-(1H-1,2,4-triazol-1-yl)butan-2-one] was studied in two soils, mollisol and inseptisol, under varying conditions of moisture and temperature, and the role of cow manure amendment and soil sterilization on fungicide degradation was ascertained. The soil moisture content affected the pathway followed for triadimefon degradation. In nonflooded soils (60% water-holding capacity), triadimefon was reduced to triadimenol, and in flooded soils, it was metabolized to the diol derivative [1-(1H-1,2,4-triazol-1-yl)-3,3-dimethylbutan-2-one-1,4-diol]. In nonflooded soils, triadimefon was more persistent in soil having more organic carbon content (mollisol), and the amendment of cow manure (5%) further enhanced its persistence. On the contrary, in flooded soil systems, the higher the soil organic carbon content was, the less persistent was the fungicide, and amendment of cow manure further enhanced its degradation. Triadimefon degradation was faster at 35 degrees C than at 27 degrees C. Triadimefon degradation in soils was mediated by the microorganisms, and no triadimefon degradation was observed in sterile soils. Triadimefon (1 mg/kg) did not affect soil phosphatase activity in either of the soils; however, soil dehydrogenase activity was significantly reduced, especially in mollisol soil.     

Application of microbes to the soils of Siberian tree nurseries

The introduction of Trichoderma viride spores (10⁸ CFU per 1 cm²) essentially changed the structure of micromycetes in the soils of tree nurseries in Krasnoyarsk region. During the first 20 days, in the variants with dark gray forest soils and podzolized chernozems, the total number of fungi decreased by 3–4 and 1.5 times, respectively, as compared to that in the control plots. During the intense development of the introduced microbes, the species composition of the soil fungi changed considerably. The treatment of Scots pine seeds with metabolites of Trichoderma fungi, as well as Pseudomonas and Bacillus bacteria, in the form of water suspensions, biopreparations, and dry spores promoted an increase in the yield of seedlings and improve their morphometric parameters. At the end of the growing period, the treatment with Trichoderma and the biopreparation on its basis increased these parameters, on average, by 18–70%, and the treatment with bacteria increased the same parameters by 13–15%. The application of microbial preparations improved the phytosanitary state of the soils in the studied tree nurseries. The use of the strains of indigenous microorganisms might be feasible for solving bioremediation problems more successfully in particular regions.     

Formation and degradation of ethylene in submerged rice soils

Ethylene formation in submerged soils and ethylene degradation by rice roots and soils were investigated. Ethylene was formed in rice soils in amounts which may deleteriously affect the growth of rice seedlings. Ethylene formation was markedly enhanced when organic materials such as glucose or rice straw were added to the soil. The rice roots, especially those taken from lowland and rice fields, showed notable ethylene-degradation activity; the rhizosphere microorganisms of the lowland rice appeared to be responsible for the ethylene-degradation activity. Lowland soils which have been continually submerged for a long time also showed ethylene-degradation activity. Upland soil and soil recently submerged, however, showed little degradation activity.     

Methane emission from two Indian soils planted with different rice cultivars

In a greenhouse study, methane emissions were measured from two diverse Indian rice-growing soils planted to five rice cultivars under similar water regimes, fertilizer applications and environmental conditions. Significant variations were observed in methane emitted from soils growing different cultivars. Total methane emission varied between 8.04 and 20.92gm^–2 from IARI soil (Inceptisol) and between 1.47 and 10.91gm^–2 from Raipur soil (Vertisol) planted to rice. In all the cultivars, emissions from IARI soil were higher than from Raipur soil. The first methane flux peak was noticed during the reproductive phase and the second peak coincided with the grain-ripening stage of the rice cultivars. Received: July 7, 1996     

Ammonium fixation by clay minerals in different layers of two paddy soils after flooding

 The influence of flooding and cellulose addition on the fixation of NH₄ ⁺ in different soil layers of two paddy soils from China (an entisol and an ultisol) was investigated. In both soils the content of total reducing substances (TRS) sharply increased during the first days after flooding and was highest in the anoxic layers. This increase, which was more pronounced in the entisol with the higher total C content, was accompanied by an increase in the concentration of non-exchangeable NH₄ ⁺ in both soils. The increase in mineralization after flooding, resulting in higher concentrations of exchangeable NH₄ ⁺, favoured the fixation of NH₄ ⁺. Although the application of cellulose resulted in higher TRS contents, the fixation of NH₄ ⁺ ions decreased, which may have been the result of microbiological N immobilization. Received: 29 April 1998     

Community level functional diversity and enzyme activities in paddy soils under different long-term fertilizer management practices

Soil microbial community structure and function are commonly used as indicators for soil quality and fertility. The present study deals with the effect of different long-term fertilizer management practices on community-level physiological profiles (CLPP) and soil enzyme activities of paddy soils. Since 1954, chemical fertilizers have been applied in the fields as N–P₂O₅–K₂O, and compost has been added as rice straw at 0, 7.5, 22.5, and 30.0 Mg ha⁻¹ in NPK, NPKC750, NPKC2250, and NPKC3000 treatments, respectively. Community-level functional diversity was significantly enhanced in the plots treated with both chemical fertilizer and compost as compared to only chemical fertilizer and untreated control plots. Average well color development (AWCD) obtained by the Biolog Eco plate indicates that there were few differences among soil samples. Shannon diversity and evenness indices were the highest in NPKC750-treated soil and the lowest in chemically fertilized soil. Dehydrogenase, cellulose, β-glucosidase, and acid and alkaline phosphomonoesterase activities were significantly increased depending on the amount of added compost with inorganic fertilizers; the alkaline phosphomonoesterase activity was the most sensitive to treatments. Our results demonstrated that enzyme activities can be used as sensitive and liable indicators in long-term managed rice-paddy ecosystems.     

Phosphorus sorption capacities and saturation of soils in two regions with different livestock densities in northwest Germany

Abstract. Soils in areas with high livestock density contribute to the eutrophication of aquatic ecosystems through loss of nutrients, especially phosphorus (P). In order to identify the potential for P loss from such soils we determined phosphorus extracted by water (H₂O-P), by double lactate (DL-P), and P sorption capacity (PSC) and degree of P saturation (DPS) in soil samples from two counties, one with low (Harle-catchment) and the other with very high livestock density (Vechta). Both catchments are hydrologically connected with the tidal areas of the North Sea.
The mean concentrations of H₂O-P (0.4mmol/kg) and DL-P (3.9 mmol/kg) were lower in the Harle-catchment than in the Vechta area (1.2 mmol/kg, 6.8mmol/kg). Although oxalate-extractable Al (Al_ox) and Fe (Fe_ox) and the derived PSCs varied according to soil type and to land use, the livestock density and the resulting high concentrations of oxalate-extractable P (P_ox) were shown to be the main reason for the very high DPS of up to 179% in the county of Vechta. These values exceeded DPS reported from other intensive pig feeding areas in western Europe and indicate the potential for significant P loss. Less than 40% of the variation in P_ox could be explained by the routinely determined H₂O-Por DL-P. Geostatistical analyses indicated that the spatial variability of P_ox depended on manurial history of fields and Al_ox, showed still smaller-scale variability. These were the major constraints for regional assessments of P losses and eutrophication risk from agricultural soils using available soil P-test values, digital maps and geostatistical methods.     

Enrichment of N2 and Ar in the atmosphere of CO2-consuming soils

The phenomenon of unexplained N₂Ar-enrichment in soil air is quite frequently to be encountered in soil air studies on anthropogenically influenced sites. In the present study two anthropogenic deposits and a calcareous fluvisol were investigated for their soil air composition. While in the alkaline deposits extreme enrichments of N₂ and Ar (N₂ + Ar: up to 99%, v/v) were found as persistent site characteristics, the fluvisol showed only slight (about 1%, v/v) transient N₂/Ar-enrichments in summer. All sites, which did not show substantial vertical seepage percolation, exhibited enhanced CO₂-solubility-either due to strong calcite precipitation or dissolution. So, it was concluded that intensive continuous depletion of CO₂ was responsible for the subsequent convective influx of atmospheric air. From the results obtained it was concluded that an encasement of the concerned soil volume rather impermeable to gas transport as well as intense dissolution of CO₂ in the pore water are prerequisites for substantial N₂/Ar-enrichments in soil air.     

Effects of acetylene on nitrification and denitrification in two soils during incubation with ammonium nitrate

A loam from the Frilsham and one from the Wickham Series were incubated at 50 and 90 per cent of their water contents at saturation with 100 μg NH₄NO₃-N_g^?1 soil in the presence and absence of C₂H₂ (0.5 per cent, v/v). Acetylene inhibited nitrification in both soils, but had no effect on mineralization of N. No denitrification (measured as the production of N₂O in the presence of C₂H₂) occurred during incubation at 50 per cent saturation. At 90 per cent saturation, denitrification resulted in a loss of 28.4 and 36.7 μg N_g^?1 after 48 h from the Frilsham and Wickham soils, respectively. The concurrent inhibition of nitrification had no effect on the extent of denitrification at this time. In the Wickham soil, NO₃^? was exhausted after 168 h incubation in the presence of C₂H₂ and denitrification was underestimated by 13 μg N_g^?. The data suggested that concurrent inhibition of nitrification during measurement of denitrification using the C₂H₂ inhibition technique is most likely to affect the estimate of denitrification loss when NO₃^?supply is limited by the inhibition of nitrification.     

Revision of two colorimetric methods to quantify glomalin-related compounds in soils subjected to different managements

The aim of this study was to analyze two colorimetric methods used to determine easily extracted glomalin-related soil proteins (EE-GRSP). The historically and most commonly used method for measurement of EE-GRSP as total protein has been the Bradford assay. After some troubles/inconsistencies with this method, we carefully analyzed the Bradford assay, measuring a dilution series of the EE-GRSP fraction and analyzing the time stability of the product. In addition, we did similar analysis of another colorimetric method that quantifies total protein, the bicinchoninic acid (BCA) assay. Unexpectedly, we found that the EE-GRSP concentration values determined by Bradford assay were dependent and variable with the dilution level of the soil extract; moreover, the Bradford assay shows a great instability with the time when soil samples were analyzed but not when protein solution as bovine serum albumin (BSA) was used as control. On the contrary, the BCA assay was independent of the dilution levels of the soil extract and showed stability in the time either for soil samples or BSA protein quantification. These results were consistent and independent on the different type of soils corresponding to different locations and with different textures.