Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area

Purpose

The purpose of this study was to determine the first-order rate constants and half-lives of aerobic and anaerobic biomineralization of atrazine in soil samples from an agricultural farm site that had been previously used for mixing pesticide formulations and washing application equipment. Atrazine catabolic genes and atrazine-degrading bacteria in the soil samples were analyzed by molecular methods.

Materials and methods

Biomineralization of atrazine was measured in soil samples with a [U-ring-¹⁴C]-atrazine biometer technique in soil samples. Enrichment cultures growing with atrazine were derived from soil samples and they were analyzed for bacterial diversity by constructing 16S rDNA clone libraries and sequencing. Bacterial isolates were also obtained and they were screened for atrazine catabolic genes.

Results and discussion

The soils contained active atrazine-metabolizing microbial communities and both aerobic and anaerobic biomineralization of [U-ring-¹⁴C]-atrazine to ¹⁴CO₂ was demonstrated. In contrast to aerobic incubations, anaerobic biometers displayed considerable differences in the kinetics of atrazine mineralization between duplicates. Sequence analysis of 16S rDNA clone libraries constructed from the enrichment cultures revealed a preponderance of Variovorax spp. (51 %) and Schlesneria (16 %). Analysis of 16S rRNA gene sequences from pure cultures (n?=?12) isolated from enrichment cultures yielded almost exclusively Arthrobacter spp. (83 %; 10/12 isolates). PCR screening of pure culture isolates for atrazine catabolic genes detected atzB, atzC, trzD, trzN, and possibly atzA. The presence of a complete metabolic pathway was not demonstrated by the amplification of catabolic genes among these isolates.

Conclusions

The soils contained active atrazine-metabolizing microbial communities. The anaerobic biometer data showed variable response of atrazine biomineralization to external electron acceptor conditions. Partial pathways are inevitable in soil microbial communities, with metabolites linking into other catabolic and assimilative pathways of carbon and nitrogen. There was no evidence for the complete set of functional genes of the known pathways of atrazine biomineralization among the isolates.

     

The impact of a bio-fertilizer on the soil organic matter status and carbon sequestration—results from a field-scale study

Purpose

The application of bio-fertilizers is one of the management practices that can help to maintain or increase the content of organic matter (OM) and improve soil fertility in arable soils. While some results have been obtained in relation to the influence of bio-fertilizers on organic matter content, less in known about the fractional composition of humus.

Materials and methods

The aim of this study was to determine the effects of the bio-fertilizer UGmax on soil total organic carbon (TOC), dissolved organic carbon (DOC), and the fractional composition of organic matter (C of humic acids (CHAs), C of fulvic acids (CFAs), and C in humins) in the humus horizon of an arable field. Measurements were taken in 2005 before the application of UGmax and in 2008, 3 years after its application, which was done in 2005, 2006, and 2007. Forty soil samples were taken in 2005 (the control year without UGmax), while 20 samples were taken after UGmax treatment and 20 from the control in 2008. Samples were always collected after the plants were harvested.

Results and discussion

After the 3-year period of the experiment, the TOC content was 6.3 % higher in plots on which UGmax was applied in comparison to the control, while the DOC content was 0.19 percentage points lower after 3 years of bio-fertilizer use as compared to the initial year of the experiment. The contribution of DOC to TOC decreased significantly after the application of UGmax in comparison with the control. The content of CFAs and its contribution in the TOC pools in soil without UGmax was higher at the end of the experiment compared to the beginning, while there was an inverse relationship in the soil with the bio-fertilizer. In comparison with the control, organic matter in the soil treated with UGmax had a higher content of C of humic acids, C in humins, and higher CHAs/CFAs ratio.

Conclusions

We conclude that the use of a bio-fertilizer that increases the stable fractions of organic matter provides evidence of an increase in the soil OM stability. In turn, the contribution of the organic matter fractions that are more resistant to decomposition is crucial for increasing soil carbon sequestration.

     

Assessing chemical soil tests for predicting nitrogen mineralization in paddy soils of the Dongting Lake region in China

Purpose

Developing routine methods that accurately predict soil nitrogen (N) mineralization is essential for fertilization recommendation; thus, chemical soil testing has received worldwide attention. However, the optimal chemical soil test for predicting soil N mineralization is region specific. This study aimed to determine suitable chemical soil tests for predicting N mineralization in paddy soils of the Dongting Lake region, China.

Materials and methods

Composite surface samples (0–20 cm) of soils (n?=?30) with diverse inherent properties were collected from representative paddy fields across the region. The benchmark indices for soil N mineralization were the net mineralization rate of soil N in a 112-day anaerobic incubation under waterlogged conditions (NMRN₁₁₂) and N mineralization potential (N _o ) estimated using a modified double exponential model. Laboratory-based measurements of soil labile organic N (SLON) were conducted using chemical fractionation methods including 0.01 M NaHCO₃ extraction, hot 2 M KCl hydrolysis, phosphate-borate (PB) buffer hydrolysis, acidic KMnO₄ oxidation, and alkaline KMnO₄ oxidation. These were compared with the benchmark indices to assess their suitability for use as indicators for N mineralization.

Results and discussion

Acidic KMnO₄-oxidative organic N (acidic KMnO₄-N) and PB buffer-hydrolysable organic N (PB_HYDR-N) correlated strongly with NMRN₁₁₂ and N _o (r?=?0.825–0.884, P?<?0.001, n?=?30). Grouping of soils based on soil texture generally provided no improvement in the relationships of chemical soil tests with NMRN₁₁₂ and N _o . Multiple stepwise regression analysis indicated that combining acidic KMnO₄-N and PB_HYDR-N yielded the best prediction of soil N mineralization, explaining 86.1 and 85.5 % of the variation in NMRN₁₁₂ and N _o , respectively, of the 30 tested paddy soils.

Conclusions

The results of acidic KMnO₄-N and PB_HYDR-N as indicators for soil N mineralization were promising, and the operations of acidic KMnO₄ oxidation and PB buffer hydrolysis procedures are simple and cost-effective. Therefore, a combination of acidic KMnO₄-N and PB_HYDR-N shows promise in predicting N mineralization in paddy soils of the Dongting Lake region. However, further calibration through field studies is required and the chemical characteristics of acidic KMnO₄-N and PB_HYDR-N needs to be further clarified.

     

Trends in Dissolved Gaseous Mercury in the Tahquamenon River Watershed and Nearshore Waters of Whitefish Bay in the Michigan Upper Peninsula

A field study was conducted in June of 1998 to characterize the dynamics of dissolved gaseous mercury (DGM) in the TahquamenonRiver watershed and nearshore waters of Whitefish Bay in the Upper Michigan Peninsula. We found that over a transect acrossthe watershed, DGM levels increased generally from a creek (mean = ～12 pg L^-1), passing through the watershed, to the nearshore surface waters of the bay (mean = ～29 pg L^-1). DGM levels in nearshore surface waters of the bayranged from ～15 to ～50 pg L^-1 and peaked generally around noontime, exhibiting diurnal trends. A significant DGM decline from ～32 pg L^-1 in the early morning to ～15 pg L^-1 during the day was observed in these surface waters following passage of a coldfront, probably caused by wind-induced mixing and decrease insolar radiation associated with the frontal passage.     

Incorporating LASSO effects into a mixed model for quantitative trait loci detection

The identification of quantitative trait loci (QTL) can be viewed as a subset selection problem. In a simulation study the least absolute selection and shrinkage operator (LASSO) is shown to be a useful and powerful tool for QTL identification. LASSO effects are embedded into a mixed model allowing simultaneous modeling of genetic and experimental effects. This provides the flexibility to model the experiment in conjunction with the power of LASSO QTL identification. Estimation is performed using an approximation to the restricted likelihood and modified Gaussian elimination. The extended mixed model is used to analyze a cattle gene mapping dataset.     

Arsenic,lead, and uranium concentrations on sediments deposited in reservoirs in the Rio Grande Basin,USA–Mexico border

Purpose

The El Granero reservoir is the last reservoir of the Rio Conchos before it joins the Rio Grande at the Mexico–USA border. This reservoir, together with the San Marcos reservoir, is located in the arid region of Chihuahua, Mexico. High, naturally occurring radioactivity levels, as well as high arsenic (As) concentrations, have been found in both reservoirs. The main goal of this research was to establish the spatial and temporal distribution of trace and radioactive elements in surface sediments and cores collected from these reservoirs.

Materials and methods

Sediment cores were dated using ²¹⁰Pb and ¹³⁷Cs measurements and applying the constant rate of supply (CRS) model. Major, trace, and radioactive elements were determined in surface samples and three sediment cores. Radioactive elements were determined by both alpha and gamma spectrometry. Major and trace elements were determined by inductively coupled plasma optical emission spectrometry (ICP-OES) using the EPA 3051a method. Enrichment factors (EF), contamination factors (CF), and pollution load indexes (PLI) were calculated in order to identify the human impact in both reservoirs, whereas the chemical index weathering (CIW) was used to assess differences in the degree of weathering.

Results and discussion

High uranium (U) enrichment (EFs?=?24.9–54.7) was observed in core layers at the San Marcos reservoir, while in surface sediments, this enrichment was lower. The high variability of lead (Pb) and As in sediment cores from the Granero reservoir was attributed to human influence. Arsenic and Pb enrichment differences between entry and exit sediment cores were explained by the filtering capabilities of the elongated shape, the topography, and the presence of plants on the reservoir’s bed. The highest PLI was found at the entrance core of the Granero reservoir.

Conclusions

The natural element concentration levels of As, Pb, and U were established at the Granero reservoir. High EFs for As and Pb suggest an anthropogenic origin of these pollutants at specific time intervals. High U concentrations in the San Marcos area are explained as naturally occurring. The concentrations of As in most of the studied sediments could pose a risk to human health by As ingestion, since they are above the probable effect level (PEL).

     

Thermal and water regime studied in a thin soil layer of green roof systems at early stage of pedogenesis

Purpose

The potential heat load and stormwater reduction of the anthropogenic, lightweight soil systems, such as green roofs, are valuable to heat island effect mitigation and to urban water management. Benefits of extensive green roofs, as widely used vegetated roof system with very thin soil layer, could be threatened by temporal changes of the soil structure.

Materials and methods

Green roof raised beds filled with two different anthropogenic soils (artificially constructed stripped topsoil with admixed crushed bricks and a commercial mixture of a technogenic substrate) were built to investigate the benefits of such systems in a temperate climate. These two soils were chosen with the intent to compare their thermal and water regime. One soil is expected to be favorable for hydrological functioning, whereas the other one for the thermal performance. Temperature and water balance measurements complemented with meteorological observations and knowledge of physical properties of the soil substrates provide the basis for detailed analysis of a thermal and hydrological regime in green roof raised beds. Moreover, the state of pedogenesis was studied on undisturbed soil samples by means of X-ray computed tomography.

Results and discussion

The water balance of green roof raised beds was calculated for a whole vegetation season and individual rainfall events. Runoff from raised beds was 38 and 63 % of received rainfall. On the basis of a detailed analysis of individual rainfall events, rainfall-runoff dependency was found for both raised beds. The difference between measured actual evapotranspiration and calculated potential evapotranspiration was discussed on the period with contrasting conditions in terms of moisture stress. Thermal characteristics of soil substrates result in a highly contrasting diurnal variation of soil temperatures. Analysis of X-ray computed tomography-derived macroporosity profiles reveals significant temporal changes in the soil comprised of the stripped topsoil with admixed crushed bricks.

Conclusions

Both green roof systems were able to reduce heat load of roof construction when comparing with the concrete roof construction. Similarly, received rainfall was significantly reduced. The extent of rainfall reduction mainly depends on soil, vegetation status, and experienced weather patterns. Methods used for non-invasive imaging proved to be beneficial for studying of soil structure changes.

     

The practical use of semiparametric models in field trials

This article examines the practical use of semiparametric models in the analysis of field trials—that is, models with parameterized treatment effects and additive terms derived by a data-driven approach using a locally weighted running line smoother (loess). We discuss graphical methods to identify spatial structure in the data and model selection procedures to choose the degree of smoothing. Once the spatial part of the model has been chosen, hypotheses about the treatment effects may be tested. Semiparametric models are used to analyze two barley field trials exhibiting spatial trends. The first has a single experimental treatment and a row-column design. The second has a split-plot design, and we use a semiparametric model which accounts for the randomization at the different strata of this design. We compare the semiparametric analyses with classical analyses of variance and with alternative spatial models. We find that semiparametric models give a good insight into spatial variation in the field and can improve the precision of parameter estimates.     

Latent Process Modelling of Threshold Exceedances in Hourly Rainfall Series

Two features are often observed in analyses of both daily and hourly rainfall series. One is the tendency for the strength of temporal dependence to decrease when looking at the series above increasing thresholds. The other is the empirical evidence for rainfall extremes to approach independence at high enough levels. To account for these features, Bortot and Gaetan (Scand J Stat 41:606–621, 2014) focus on rainfall exceedances above a fixed high threshold and model their dynamics through a hierarchical approach that allows for changes in the temporal dependence properties when moving further into the right tail. It is found that this modelling procedure performs generally well in analyses of daily rainfalls, but has some inherent theoretical limitations that affect its goodness of fit in the context of hourly data. In order to overcome this drawback, we develop here a modification of the Bortot and Gaetan model derived from a copula-type technique. Application of both model versions to rainfall series recorded in Camborne, England, shows that they provide similar results when studying daily data, but in the analysis of hourly data the modified version is superior.     

Genetic variation of the durum wheat landrace Haurani from different agro-ecological regions

The durum wheat landrace Haurani (Triticum durum Desf.) is grown under contrasting climatic regions of Syria from Deir Ezzor, in the North-East (230 m altitude, 150 mm mean annual rainfall), to Qunaytra, in the South-West (1060 m altitude, 825 mm mean annual rainfall). In order to assess the genetic variation between and within Haurani populations, samples from eight provinces of Syria (Daraa, Damascus, Qunaytra, Deir Ezzor, Hassakeh, Aleppo, Homs and Hama) were analysed by RFLPs and seed storage proteins of glutenin subunits as markers. The analyses showed the presence of genetic polymorphisms in all populations with the highest values in those from Homs and Hassakeh. Moreover, the results point out differences in genetic distances between populations; some populations were further apart, such as Damascus and Aleppo, whereas others were closer to each other, for instance Homs and Hama. Cluster analysis identified two distinct groups of populations, characterized by geographical proximity, with similar rainfall and altitude. It is suggested that the similarity of landraces at locations close to each other might be the result of more frequent seed exchanges between farmers or of gene flow due to 5% estimated outcross rate of Haurani.