Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons

Soil contamination with petroleum, especially in the area of oil wells, is a serious environmental problem. Restoring soil subjected to long-term pollution to its original state is very difficult. Under such conditions, unique bacterial communities develop in the soil that are adapted to the contaminated conditions. Analysis of the structure and function of these microorganisms can be a source of valuable information with regard to bioremediation. The aim of this study was to evaluate structural and functional diversity of the bacterial communities in soils with long-term impacts from petroleum. Samples were taken from the three oldest oil wells at the Crude Oil Mine site in Węglówka, Poland; the oldest was established in 1888. They were collected at 2 distances: (1) within a radius of 0.5 m from the oil wells, representing soil strongly contaminated with petroleum; and (2) 3 m from the oil wells as the controls. The samples were analyzed by 16S rRNA sequencing and the community level physiological profiling (CLPP) method in order to better understand both the genetic and functional structure of soil collected from under oil wells. Significant differences were found in the soil samples with regard to bacterial communities. The soils taken within 0.5 m of the oil wells were characterized by the highest biodiversity indexes. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria were strongly correlated with biological activity in these soils. Families of Alphaproteobacteria were also dominant, including: Bradyrhizobiaceae, Rhizobiaceae, Rhodobacteraceae, Acetobacteraceae, Hyphomicrobiaceae, and Sphingomonadaceae. The study showed that the long term contamination of soil changes bacterial communities and their metabolic activity. Even so, natural bioremediation leads to the formation of specific groups of bacteria that actively grow at the site of contamination in the soil

Assessment of Pesticide Residue Content in Polish Agricultural Soils

Pesticides belong to a group of xenobiotics harmful to humans and wildlife, whose fate and activity depends on their susceptibility to degradation. Therefore, the monitoring of their residue level in agricultural soils is very important because it provides very valuable information on the actual level of soil contamination and environmental risk resulting from their application. The aim of this study was to evaluate contemporary concentrations of organochlorine (OCPs) and non-chlorinated pesticides (NCPs) in arable soils of Poland as an example of Central and Eastern European countries. The results were assessed in relation to Polish regulations, which are more restrictive compared to those of other European countries. The sampling area covered the territory of arable lands in Poland (216 sampling points). The distribution of sampling points aimed to reflect different geographical districts, conditions of agricultural production, and various soil properties. The collected soil samples were extracted with organic solvents in an accelerated solvent extractor (ASE 2000). The OCPs, including α-HCH, β-HCH, γ-HCH, and p,p’DDT, p,p’DDE, and p,p’DDD, were extracted with a hexane/acetone mixture (70:30 v/v) and determined by gas chromatography with an electron capture detector (GC-μECD). NCPs included atrazine, carbaryl, and carbofuran were extracted with a dichloromethane/acetone mixture (50:50 v/v), while maneb was extracted by intensive shaking the sample with acetone (1:1 v/v) and ethylenediamine-tertraacetic acid. The NCPs were identified by a dual mass- spectrometry (GC-MS/MS). The total content of individual OCPs ranged from 0.61 to 1031.64 µg kg−1, while the NCP concentrations were significantly lower, from 0.01 to 43.92 µg kg−1. DDTs were detected in all soils samples (p,p’DDD (23.60 µg kg−1) > p,p’DDT (18.23 µg kg−1) > p,p’DDE (4.06 µg kg−1), while HCHs were only in 4% of the analyzed samples (β-HCH (339.55 µg kg−1) > α-HCH (96.96 µg kg−1) > γ-HCH (3.04 µg kg−1)), but in higher values than DDTs. Among NCPs, higher concentration was observed for carbaryl (<0.01–28.07 µg kg−1) and atrazine (<0.01–15.85 µg kg−1), while the lower for carbofuran (<0.01–0.54 µg kg−1). Maneb was not detected in analyzed soils. Assessment of the level of soil pollution based on Polish regulations indicated that several percentages of the samples exceeded the criterion for OCPs, such as ∑3DDTs (14 samples; 6.5% of soils) and HCH congeners (α-HCH in one sample; 0.5% of soils), while NCP concentration, such as for atrazine, carbaryl and carbofuran were below the permissible levels or were not detected in the analyzed soils, e.g., maneb. The obtained results indicated that residues of the analyzed pesticides originate from historical agricultural deposition and potentially do not pose a direct threat to human and animal health. The behavior and persistence of pesticides in the soils depend on their properties. Significantly lower NCP concentration in the soils resulted from their lower hydrophobicity and higher susceptibility to leaching into the soil profile. OCPs are characterized by a high half-life time, which affect their significantly higher persistence in soils resulting from affinity to the soil organic phase

Enzymatic activity in soil treated with exogenous organic matter

The content of organic matter affects the quality and productivity of agricultural soils. Due to the shortage of manure as the basic source of organic matter for agricultural soils, al- ternative and commonly available exogenous sources of organic matter, such as sewage sludge and bottom sediments, are taken into account. The aim of the study was to evaluate the effect of the addition of various types of manure, municipal sewage sludge and bottom sediments on the enzymatic activity of soils (dehydrogenases, acidic and alkaline phosphatases). Manure and sludge were applied to the soil in two doses, corresponding to 20 and 40 tons of dry matter of material per ha. The control was soil fertilized with ammonium nitrate in the amount corresponding to 170 kg N per ha. The experiment included 2 different variants of the same fertilization combinations: without plants and with a test plant (Sinapis alba L.). The greenhouse experiment showed the stimulating effect of one of the municipal sewage sludge and poultry manure. On the other hand, the introduction of bottom sediments to the soil limited its enzymatic activity

Sorption of Organic Contaminants by Stable Organic Matter Fraction in Soil

Soil organic matter (SOM) and its heterogeneous nature constitutes the main factor determining the fate and transformation of organic chemicals (OCs). Thus, the aim of thus research was to analyze the influence of the molecular chemodiversity of a stable SOM (S-SOM) on the sorption potential of different groups of OCs (organochloride pesticides—OCPs, and non-chlorinated pesticides—NCPs, polycyclic aromatic hydrocarbons—PAHs). The research was conducted as a batch experiment. For this purpose, a S-SOM was separated from six soils (TOC = 15.0–58.7 gkg−1; TN = 1.4–6.6 gkg−1, pH in KCl = 6.4–7.4 and WRB taxonomy: fluvisols, luviosols, leptosols) by alkaline urea and dimethylsulphoxide with sulfuric acid. Isolated S-SOM fraction was evaluated by UV–VIS, FT-IR and EEM spectroscopy to describe molecular diversity, which allowed the assessment of its potential sorption properties regarding OCs. In order to directly evaluate the sorption affinity of individual OCs to S-SOM, the mixture of the 3 deuterated contaminants: chrysene (PAHs), 4,4′DDT (OCPs) atrazine (NCPs) were applied. The sorption experiment was carried out according to the 106 OECD Guidelines. The OCs concentration was analyzed by gas chromatography triple mass spectrometry (GC-MS/MS). OCs were characterized by different sorption rates to S-SOM fractions according to the overall trend: atrazine (87.5–99.9%) > 4,4′DDT (64–81.6%) > chrysene (35.2–79.8%). Moreover, atrazine exhibited the highest saturation dynamic with fast bounding time amounting to 6 h of contact with S-SOM. Proportionally, the chrysene showed the slowest binding time achieving an average of 55% sorption after 78 h. Therefore, S-SOM isolated from different soils demonstrated varying binding capacity to OCs (CoV = 21%, 27% and 33% for atrazine, DDT and chrysene, respectively). Results indicate that each sample contains S-SOM with different degrees of transformation and sorption properties that affect the OCs availability in soil. Spectroscopic analyses have shown that the main component of S-SOM are biopolymers at various stages of transformation that contain numerous aromatic–aliphatic groups with mostly hydrophilic substituents

Diffuse Reflectance Spectroscopy for Black Carbon Screening of Agricultural Soils under Industrial Anthropopressure

Visible and near-infrared spectroscopy (VIS-NIRS) is a fast and simple method increasingly used in soil science. This study aimed to investigate VIS-NIRS applicability to predict soil black carbon (BC) content and the method’s suitability for rapid BC-level screening. Forty-three soil samples were collected in an agricultural area remaining under strong industrial impact. Soil texture, pH, total nitrogen (Ntot) and total carbon (Ctot), soil organic carbon (SOC), soil organic matter (SOM), and BC were analyzed. Samples were divided into three classes according to BC content (low, medium, and high BC content) and scanned in the 350–2500 nm range. A support vector machine (SVM) was used to develop prediction models of soil properties. Partial least-square with SVM (PLS-SVM) was used to classify samples for screening purposes. Prediction models of soil properties were at best satisfactory (Ntot: R2 = 0.76, RMSECV = 0.59 g kg−1, RPIQ = 0.65), due to large kurtosis and data skewness. The RMSECV were large (16.86 g kg−1 for SOC), presumably due to the limited number of samples available and the wide data spread. Given our results, the VIS-NIRS method seems efficient for classifying soil samples from an industrialized area according to BC content level (training accuracy of 77% and validation accuracy of 81%)

Comparison of the Effects of Different Crop Production Systems on Soil Physico-Chemical Properties and Microbial Activity under Winter Wheat

In many areas, organic crop production systems have been shown to contribute to maintaining good soil condition. The organic production system has been recommended as an alternative to conventional agriculture. However, in order to recommend this practice in new regions, it is necessary to obtain information about its effects and consequences in local environmental conditions. The research was completed during 2016–2018 in Osiny (Lublin region, Poland) on a field experiment established 26 years previously in a Haplic Luvisol soil. The research was aimed at comparing the effects of long-term use of tilled soil with organic (ORG) and conventional (CON) crop production systems with those in non-tilled soil under permanent grass (PRG) as a control. This comparison was done on the basis of changes in the values of soil properties as follows: Total porosity (TP), total organic matter (OM), particulate organic matter (POM), humic substances (HS), water-extractable carbon (WEC), microbial biomass carbon pool (MBC) and dehydrogenase activity (DH). Soil samples were collected from experimental fields (each treatment 1 ha) under winter wheat and permanent grass each year from 0–5, 5–10, 15–20 and 30–35 cm depths. Over the three year study period, it was found that permanent grass and the organic crop production system contributed to increased soil OM, POM, HS, WEC and MBC contents and DH activity compared to the CON system, especially in the top soil layer, 0–5 cm. To obtain a clearer picture of soil quality change our study examined for the first time the metabolic potential index (MPI) as a ratio of dehydrogenase activity to the soluble organic carbon content. The MPI values confirmed the increase of metabolism in ORG soil as a consequence of management practices compared with CON soil. The obtained correlations showed strong mutual relationships within properties of the heterogeneous soil complex. The results show the positive effects of the ORG management system causing soil condition improvement which is based on organic fertilization, enriching the soil with a large amount of plant residues in creating positive changes in the soil quality in contrast to the CON system

Characterization of Soil Organic Matter Individual Fractions (Fulvic Acids, Humic Acids, and Humins) by Spectroscopic and Electrochemical Techniques in Agricultural Soils

The objective of this paper was to investigate the molecular characterization of soil organic matter fractions (humic substances (HS): fulvic acids-FAs, humic acids-HAs, and humins-HNs), which are the most reactive soil components. A wide spectrum of spectroscopic (UV–VIS and VIS–nearIR), as well as electrochemical (zeta potential, particle size diameter, and polydispersity index), methods were applied to find the relevant differences in the behavior, formation, composition, and sorption properties of HS fractions derived from various soils. Soil material (n = 30) used for the study were sampled from the surface layer (0–30 cm) of agricultural soils. FAs and HAs were isolated by sequential extraction in alkaline and acidic solutions, according to the International Humic Substances Society method, while HNs was determined in the soil residue (after FAs and HAs extraction) by mineral fraction digestion using a 0.1M HCL/0.3M HF mixture and DMSO. Our study showed that significant differences in the molecular structures of FAs, Has, and HNs occurred. Optical analysis confirmed the lower molecular weight of FAs with high amount of lignin-like compounds and the higher weighted aliphatic–aromatic structure of HAs. The HNs were characterized by a very pronounced and strong condensed structure associated with the highest molecular weight. HAs and HNs molecules exhibited an abundance of acidic, phenolic, and amine functional groups at the aromatic ring and aliphatic chains, while FAs mainly showed the presence of methyl, methylene, ethenyl, and carboxyl reactive groups. HS was characterized by high polydispersity related with their structure. FAs were characterized by ellipsoidal shape as being associated to the long aliphatic chains, while HAs and HNs revealed a smaller particle diameter and a more spherical shape caused by the higher intermolecular forcing between the particles. The observed trends directly indicate that individual HS fractions differ in behavior, formation, composition, and sorption properties, which reflects their binding potential to other molecules depending on soil properties resulting from their type. The determined properties of individual HS fractions are presented as averaged characteristics over the examined soils with different physico-chemical properties

The Effect of Soil Amendments on Trace Elements’ Bioavailability and Toxicity to Earthworms in Contaminated Soils

The aim of this study was to assess the impact of soil amendments, characterized by different sorption properties, on the effectiveness of trace elements’ (Cu, Zn, Pb, Cd, Ni, and Cr) stabilization and bioavailability to earthworms. The study was conducted as a microcosm experiment using soil derived from a heavily contaminated post-industrial area. The Eisenia veneta earthworm was cultured for 4 weeks in soils amended with materials characterized by different properties, origins, and potential effects on limiting the availability of metals in soils: two type of compost (Zabrze compost-ZC; GWDA compost-GC), two types of biosolid (Bełchatów biosolids-BB, Grabów biosolids-GB), calcium phosphate (CP), iron oxide (IO), bentonite (BE), rock waste (RW), and limestone (CC). After the incubation, the biomass and survival numbers of the earthworm species decreased significantly (p < 0.05). The accumulation of metals in the earthworm tissues expressed by the bioaccumulation factor value (BSAF) were dependent on the type of amendment applied to the soil. The highest decrease in the earthworms’ weight and survival rate was caused by compost (72%) and bentonite (33%), while the lowest was caused by the rock waste (10%) and iron oxide (11%). The biosolids exhibited the greatest toxicity, causing the mortality of all the earthworms. The accumulation of metals in earthworm tissues and the BSAF value were dependent on the type of amendment applied to the soil. The BSAF for the contaminated soil by Cd decreased to the greatest extent after the addition of ZC (by 57%), GC (55%), CP (41%), and IO (37%). A similarly positive effect was noted for Pb after IO addition (45% decrease). The Zn, Cr, and Ni concentration in earthworms, contrary to other elements, increased, regardless of the amendment. The results showed that the applied soil amendments were characterized by varying potential for the reduction in the metal bioavailability in the soil, depending on their composition and physicochemical properties. Moreover, earthworms may exhibit a diversified response to soil amendments as a result of the impact of amendment on the metal forms in soils and their direct impact on organisms. Generally, the Cd was easily transferred from the soil into and accumulated in the earthworm tissues. Our study confirms that this element creates the highest risk for the trophic chain in soils affected by the Zn and Pb smelting industry. Moreover, greater Zn supply reduces the accumulation of Cd in animal bodies. This study provides valuable practical knowledge on the short-term biological effects of a range of soil amendments in metal-contaminated soils

Biochar changes in soil based on quantitative and qualitative humus compounds parameters

Due to the indisputable significance of humus in many biochemical processes as well as its increasing deficit particularly in light soils, alternative sources of substrates for the reproduction of this constituent should be sought. The aim of this study was to evaluate the effect of the addition of wheat straw and wheat straw biochar (in four rates) on quantitative and qualitative humus parameters. The following properties were determined in soil: pH, organic carbon, total nitrogen, humic and fulvic acids, carbon in the extract, non-hydrolysing carbon and spectrophotometric indexes for solution of humic acids including A2/6, A2/4, A4/6. After applying 1% and 2% additions of biochar to the soil, the Corg soil content significantly increased compared to the same doses of thermally unconverted straw. After 254 days of incubation, the addition of biochar to soil at higher doses, decreased the share of humic acid carbon (CHA, CFA) in the Corg content compared to treatments without organic additions and WS treatment. The nonhydrolysing carbon soil content was significantly increased by treatments with 1% and 2% additions of WSB, which indicates greater stabilisation of humus compounds and, at the same time, lower CO2 emission. Soil humic acids amended by treatment with biochar, especially at 1% and 2% doses, were characterised by lower A2/6 and A2/4 ratios. Recognition of changes that may occur in the quantitative and qualitative composition of soil humus after the application of biochar may in the future be helpful information for determining appropriate biochar dose

Concentration of Potentially Toxic Elements in Farmed Fallow Deer Antlers Depending on Diet and Age

Deer antlers, usually harvested annually on a farm, are an accessible material used to determine the exposition to potentially toxic elements, PTEs, during growth. Moreover, the study of antlers from animals of different ages allows the assessment of long-term exposition to these elements. The aim of the study was to analyze the concentration of eight potentially toxic elements (Cd, Pb, As, Ba, Ni, Sr, La, Ce) in individual positions of the antlers (first, second, and third position, corresponding to the stages of development and life of these animals) and in the food that the animals consumed during the growth of individual antler fragments, depending on the age of the farmed fallow deer (Dama dama). The mineral composition of samples was analyzed using inductively coupled plasma mass spectrometry (ICP-MS). The analysis included 31 male deer aged 2–8 years old. The average concentration of Pb, Ba, and Ni was higher in the second position of the antler, and As, La, and Ce in the third position. In addition, the oldest individuals showed a higher Cd, Pb, and As concentration in the third position. A significant positive relationship was found between the age of animals and accumulation of As (r = 0.582, p p p p p < 0.05). An increase in the PTEs in the pasture determined the concentration of these components in fallow deer antlers