Molecular tools to investigate Rhizoctonia solani distribution in soil

Real-time PCR protocols were developed to detect and discriminate 11 anastomosis groups (AGs) of Rhizoctonia solani using ribosomal internal transcribed spacer (ITS) regions (AG-1-IA, AG-1-IC, AG-2-1, AG-2-2, AG-4HGI+II, AG-4HGIII, AG-8) or beta-tubulin (AG-3, AG-4HGII, AG-5 and AG-9) sequences. All real-time assays were target group specific, except AG-2-2, which showed a weak cross-reaction with AG-2tabac. In addition, methods were developed for the high throughput extraction of DNA from soil and compost samples. The DNA extraction method was used with the AG-2-1 assay and shown to be quantitative with a detection threshold of 10-7 g of R. solani per g of soil. A similar DNA extraction efficiency was observed for samples from three contrasting soil types. The developed methods were then used to investigate the spatial distribution of R. solani AG-2-1 in field soils. Soil from shallow depths of a field planted with Brassica oleracea tested positive for R. solani AG-2-1 more frequently than soil collected from greater depths. Quantification of R. solani inoculum in field samples proved challenging due to low levels of inoculum in naturally occurring soils. The potential uses of real-time PCR and DNA extraction protocols to investigate the epidemiology of R. solani are discussed.

Developing a fluorimetric sequential injection methodology to study adsorption/desorption of glyphosate on soil and sediment samples

This paper describes the development of a sequential injection method to automate the fluorimetric determination of glyphosate based on a first step of oxidation to glycine by hypochlorite at 48 degrees C, followed by reaction with the fluorogenic reagent o-phthaldialdehyde in presence of 2-mercaptoethanol in borate buffer (pH > 9) to produce a fluorescent 1-(2`-hydroxyethylthio)-2-N-alkylisoindole. The proposed method has a linear response for glyphosate concentrations between 0.25 and 25.0 mu mol L(-1), with limits of detection and quantification of 0.08 and 0.25 mu mol L(-1), respectively. The sampling rate of the method is 18 samples per hour, consuming only a fraction of reagents consumed by the chromatographic method based on the same chemistry. The method was applied to study adsorption/desorption properties in a soil and in a sediment sample. Adsorption and desorption isotherms were properly fitted by Freundlich and Langmuir equations, leading to adsorption capacities of 1384 +/- 26 and 295 +/- 30 mg kg(-1) for the soil and sediment samples, respectively. These values are consistent with the literature, with the larger adsorption capacity of the soil being explained by its larger content of clay minerals, while the sediment was predominantly sandy. (C) 2011 Elsevier B.V. All rights reserved.

Modelling the fate of chromated copper arsenate in a sandy soil

A pulse of chromated copper arsenate (CCA, a timber preservative) was applied in irrigation water to an undisturbed field soil in a laboratory column. Concentrations of various elements in the leachate from the column were measured during the experiment. Also, the remnants within the soil were measured at the end of the experiment. The geochemical modelling package, PHREEQC-2, was used to simulate the experimental data. Processes included in the CCA transport modelling were advection, dispersion, non-specific adsorption (cation exchange) and specific adsorption by clay minerals and organic matter, as well as other possible chemical reactions such as precipitation/dissolution. The modelling effort highlighted the possible complexities in CCA transport and reaction experiments. For example, the uneven dosing of CCA as well as incomplete knowledge of the soil properties resulted in simulations that gave only partial, although reasonable, agreement with the experimental data. Both the experimental data and simulations show that As and Cu are strongly adsorbed and therefore, will mostly remain at the top of the soil profile, with a small proportion appearing in leachate. On the other hand, Cr is more mobile and thus it is present in the soil column leachate. Further simulations show that both the quantity of CCA added to the soil and the pH of the irrigation water will influence CCA transport. Simulations suggest that application of larger doses of CCA to the soil will result in higher leachate concentrations, especially for Cu and As. Irrigation water with a lower pH will dramatically increase leaching of Cu. These results indicate that acidic rainfall or significant accidental spillage of CCA will increase the risk of groundwater pollution.

Biodegradation of benzo[a]pyrene in soil by Mucor sp. SF06 and Bacillus sp. SB02 co-immobilized on vermiculite

Two indigenous microorganisms, Bacillus sp. SB02 and Mucor sp. SF06, capable of degrading polycyclic aromatic hydrocarbons (PAHs) were co-immobilized on vermiculite by physical adsorption and used to degrade benzo[a] pyrene (BaP). The characteristics of BaP degradation by both free and co-immobilized microorganism were then investigated and compared. The removal rate using the immobilized bacterial-fungal mixed consortium was higher than that of the freely mobile mixed consortium. 95.3% of BaP was degraded using the co-immobilized system within 42 d, which was remarkably higher than the removal rate of that by the free strains. The optimal amount of inoculated co-immobilized system for BaP degradation was 2%. The immobilized bacterial-fungal mixed consortium also showed better water stability than the free strains. Kinetics of BaP biodegradation by co-immobilized SF06 and SB02 were also studied. The results demonstrated that BaP degradation could be well described by a zero-order reaction rate equation when the initial BaP concentration was in the range of 10—200 mg/kg. The scanning electronic microscope (SEM) analysis showed that the co-immobilized microstructure was suitable for the growth of SF06 and SB02. The mass transmission process of co-immobilized system in soil is discussed. The results demonstrate the potential for employing the bacterial-fungal mixed consortium, co-immobilized on vermiculite, for in situ bioremediation of BaP.

Short-term temporal changes of soil carbon losses after tillage described by a first-order decay model

Tillage stimulates soil carbon (C) losses by increasing aeration, changing temperature and moisture conditions, and thus favoring microbial decomposition. In addition, soil aggregate disruption by tillage exposes once protected organic matter to decomposition. We propose a model to explain carbon dioxide (CO2) emission after tillage as a function of the no-till emission plus a correction due to the tillage disturbance. The model assumes that C in the readily decomposable organic matter follows a first-order reaction kinetics equation as: dC(sail)(t)/dt = -kC(soil)(t) and that soil C-CO2 emission is proportional to the C decay rate in soil, where C-soil(t) is the available labile soil C (g m(-2)) at any time (t). Emissions are modeled in terms soil C available to decomposition in the tilled and non-tilled plots, and a relationship is derived between no-till (F-NT) and tilled (F-Gamma) fluxes, which is: F-T = a1F(NT)e(-a2t), where t is time after tillage. Predicted and observed fluxes showed good agreement based on determination coefficient (R-2), index of agreement and model efficiency, with R-2 as high as 0.97. The two parameters included in the model are related to the difference between the decay constant (k factor) of tilled and no-till plots (a(2)) and also to the amount of labile carbon added to the readily decomposable soil organic matter due to tillage (a,). These two parameters were estimated in the model ranging from 1.27 and 2.60 (a(1)) and - 1.52 x 10(-2) and 2.2 x 10(-2) day(-1) (a(2)). The advantage is that temporal variability of tillage-induced emissions can be described by only one analytical function that includes the no-till emission plus an exponential term modulated by tillage and environmentally dependent parameters. (C) 2008 Elsevier B.V. All rights reserved.

Short-term temporal changes of bare soil CO2 fluxes after tillage described by first-order decay models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Reaction of sugarcane genotypes to Pratylenchus brachyurus and P. zeae

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Prediction of Soil Properties from the Concepts of Energy Transfer in Dynamic Penetration Tests

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Cyclodextrin glycosyltransferase production by new Bacillus sp. strains isolated from brazilian soil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diesel Degradation in Soil by Fenton Process

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

First-order decay models to describe soil C-CO2 Loss after rotary tillage

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Environmental implications of soil remediation using the Fenton process

This work evaluates some collateral effects caused by the application of the Fenton process to 1,1-bis(4-chlorophenyl)-2,2,2-trichloroethane (DDT) and diesel degradation in soil. While about 80% of the diesel and 75% of the DDT present in the soil were degraded in a slurry system, the dissolved organic carbon (DOC) in the slurry filtrate increased from 80 to 880 mg l(-1) after 64 h of reaction and the DDT concentration increased from 12 to 50 mu g l(-1). Experiments of diesel degradation conducted on silica evidenced that soluble compounds were also formed during diesel oxidation. Furthermore, significant increase in metal concentrations was also observed in the slurry filtrate after the Fenton treatment when compared to the control experiment leading to excessive concentrations of Cr, Ni, Cu and Mn according to the limits imposed for water. Moreover, 80% of the organic matter naturally present in the soil was degraded and a drastic volatilization of DDT and 2,2-bis(4-chlorophenyl)-1,1-dichloroethylene was observed. Despite the high percentages of diesel and DDT degradation in soil, the potential overall benefits of its application must be evaluated beforehand taking into account the metal and target compounds dissolution and the volatilization of contaminants when the process is applied. (c) 2007 Elsevier Ltd. All rights reserved.

Soil-lime reactions: the behaviour of a Brazilian red soil.

A red tropical soil was selected, with the main purpose of investigating how it reacted with calcitic and dolomitic limes, and which products are formed. Under normal (23-28oC) or slightly accelerated (40o and 60oC) conditions there is a rapid and substantial interaction between lime (calcitic or dolomitic) and the soil. The reactions take place in two steps, one before 7 g lime/100 g soil, and the other after 8 g lime/100 g of soil, either for calcitic or dolomitic lime. A morphologically discrete reaction product (tri-calcium aluminate hexahydrate) was found in the study, and in spite of the difference in morphology the product is shown to be the same by XRD for all compositions and T.-J.M.H.

Development and Biotechnological Application of a Novel Endoxylanase Family GH10 Identified from Sugarcane Soil Metagenome

Metagenomics has been widely employed for discovery of new enzymes and pathways to conversion of lignocellulosic biomass to fuels and chemicals. In this context, the present study reports the isolation, recombinant expression, biochemical and structural characterization of a novel endoxylanase family GH10 (SCXyl) identified from sugarcane soil metagenome. The recombinant SCXyl was highly active against xylan from beechwood and showed optimal enzyme activity at pH 6,0 and 45°C. The crystal structure was solved at 2.75 Å resolution, revealing the classical (β/α)8-barrel fold with a conserved active-site pocket and an inherent flexibility of the Trp281-Arg291 loop that can adopt distinct conformational states depending on substrate binding. The capillary electrophoresis analysis of degradation products evidenced that the enzyme displays unusual capacity to degrade small xylooligosaccharides, such as xylotriose, which is consistent to the hydrophobic contacts at the +1 subsite and low-binding energies of subsites that are distant from the site of hydrolysis. The main reaction products from xylan polymers and phosphoric acid-pretreated sugarcane bagasse (PASB) were xylooligosaccharides, but, after a longer incubation time, xylobiose and xylose were also formed. Moreover, the use of SCXyl as pre-treatment step of PASB, prior to the addition of commercial cellulolytic cocktail, significantly enhanced the saccharification process. All these characteristics demonstrate the advantageous application of this enzyme in several biotechnological processes in food and feed industry and also in the enzymatic pretreatment of biomass for feedstock and ethanol production. © 2013 Alvarez et al.

Spectrophotometric determination of arsenic in soil samples using 2-(5-bromo-2-pyridylazo)-5-di-ethylaminophenol (Br-PADAP)

Um novo método, simples e sensível para a determinação de arsênio em solo é proposto neste trabalho. Este método é baseado na redução de prata (I) e ferro (III) pela arsina seguida da reação de complexação do ferro (II) com o reagente espectrofotométrico 2-(5-bromo-2-piridilazo)-5-di-etilaminofenol (Br-PADAP). A determinação de arsênio apresentou uma sensitividade de Sandell de 3.1x10^-4 cm^-2, foi linear na faixa de 0.1 µg ml^-1 to 2.0 µg ml^-1 (r₅₆₀ = 0.9995), apresentou uma absortividade molar de 2.45x10⁵ l mol^-1 cm^-1 e um limite de detecção de 1.4 ng ml^-1 (3s) estes dados foram obtidos para 10 ml de amostra. A seletividade foi melhorada com o uso de EDTA com agente mascarante. O método proposto foi aplicado na determinação do arsênio na presença de outros íons e em amostras de solo. Os resultados revelaram que antimônio (III), mercúrio (II), germânio (IV), platina (IV) interferem na análise em todas as proporções analisadas. As interferências podem ser facilmente removidas pelo uso do EDTA. A precisão e a exatidão deram resultados satisfatórios, com desvio padrão relativo abaixo de 5%. As recuperações de arsênio em solo variaram de 95,55 a 102,70% com uma média de 99,63%. Estes resultados demonstraram que o método proposto é aplicável para a análise do arsênio em diferentes amostras de solo.