Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons

Biodegradation of phenol-contaminated soil and plant growth promotion by Myroides xuanwuensis H13

Physicochemical methods for remediating phenol-contaminated soils are costly and inefficient, making biodegradation an environmentally friendly alternative approach. This study aims to screen for potential phenol-degrading bacteria and to verify the removal capacities of a selected strain in a bioaugmentation experiment at the greenhouse level using Brassica chinensis L. (Chinese cabbage) as the model plant and phenol-contaminated soil. In parallel, pot experiments were conducted using a collaborative approach based on this model system. We found that Myroides xuanwuensis strain H13 showed a high degradation capability, with a 97.67% efficiency in degrading 100 mg/L phenol. Under shaking flask conditions, H13 facilitated the solubilization of tricalcium phosphate and potassium feldspar powder. Pot experiments suggested a phenol removal percentage of 89.22% and enhanced availability of soil phosphorus and potassium for plants with H13 inoculation. In this case, the abundance of soil microbes and the activity of soil enzymes significantly increased as well. Furthermore, both photosynthesis and the antioxidant system in Chinese cabbage were enhanced following H13 inoculation, resulting in its increased yield and quality. Partial least squares path modeling revealed that H13 can primarily affect plant root growth, with a secondary impact on photosynthesis. These findings highlight the potential of biodegradation from phenol-degrading bacteria as a promising strategy for efficient phenol removal from soil while promoting plant growth and health.IMPORTANCEThis study is significant for environmental remediation and agriculture by its exploration of a more environmentally friendly and cost-effective bio-strategy in treating phenol-contaminated soil. These findings have essential implications for environmental remediation efforts and sustainable agriculture. By utilizing the biodegradation capabilities of Myroides xuanwuensis strain H13, it is possible to remove phenol contaminants from the soil efficiently, reducing their negative effects. Furthermore, the enhanced growth and health of the Chinese cabbage plants indicate the potential of this approach to promote sustainable crop production.

Biochars assisted phytoremediation of polycyclic aromatic hydrocarbons contaminated agricultural soil: Dynamic responses of functional genes and microbial community

A biochar-intensified phytoremediation experiment was designed to investigate the dynamic effects of different biochars on polycyclic aromatic hydrocarbon (PAH) removal in ryegrass rhizosphere contaminated soil. Maize and wheat straw biochar pyrolyzed at 300 °C and 500 °C were amended into PAH-contaminated soil, and then ryegrass (Lolium multiflorum L.) was planted for 90 days. Spearman's correlations among PAH removal, enzyme activity, abundance of PAH-ring hydroxylating dioxygenase (PAH-RHDα), and fungal and bacterial community structure were analyzed to elucidate the microbial degradation mechanisms during the combined remediation process. The results showed that 500 °C wheat straw biochar had higher surface area and more nutrients, and significantly accelerated the phytoremediation of PAHs (62.5 %), especially for high molecular weight PAH in contaminated soil. The activities of urease and dehydrogenase and the abundance of total and PAH-degrading bacteria, which improved with time by biochar and ryegrass, had a positive correlation with the removal rate of PAHs. Biochar enhanced the abundance of gram-negative (GN) PAH-RHDα genes. The GN PAH-degraders, Sphingomonas, bacteriap25, Haliangium, and Dongia may play vital roles in PAH degradation in biochar-amended rhizosphere soils. Principal coordinate analysis indicated that biochar led to significant differences in fungal community structures before 30 days, while the diversity of the bacterial community composition depended on planting ryegrass after 60 days. These findings imply that the structural reshaping of microbial communities results from incubation time and the selection of biochar and ryegrass in PAH-contaminated soils. Applying 500 °C wheat straw biochar could enhance the rhizoremediation of PAH-contaminated soil and benefit the soil microbial ecology.

Growth of alfalfa in the presence of metabolites from a dark septate endophyte strain Alternaria sp. 17463 cultured with a nonionic surfactant and emulsifier

AIM

Dark septate endophytes (DSE) were widely used in the agriculture and ecological restoration. The objective of this work was to assess the effect of culture media nonionic surfactant and emulsifier on the biomass and metabolites of DSE strain Alternaria sp. 17463.

METHODS AND RESULTS

Changes in the composition of DSE metabolites following the addition of Tween 80 during liquid culture of a DSE fungus were analyzed and used in growth tests of alfalfa.Shaking flask fermentation was carried out and the surfactant was fed to the fungus during the fermentation. The residual sugar content and pH declined significantly in the medium and the biomass of DSE increased by 7.27% over controls with no surfactant. Metabolomic analysis showed that adding the surfactant significantly increased the content of 63 metabolites (P < 0.05). These include lipids and lipid-like molecules, organooxygen compounds, amino acids and organic acids, and flavonoids. Enrichment analysis of metabolic pathways indicates that surfactant addition promoted carbohydrate metabolism and amino acid synthesis. A plant hydroponic experiment indicated that these changes in metabolites altered the root structure of alfalfa seedlings. They also promoted significant increases in root length and root surface area, and increased alfalfa total biomass by 50.2%.

CONCLUSIONS

The addition of the surfactant promoted sugar utilization by the DSE fungus and increased the synthesis of lipids and amino acids, resulting in the ability of the fungal metabolites to change root structure and promote plant growth.

The Usability of Sorbents in Restoring Enzymatic Activity in Soils Polluted with Petroleum-Derived Products

Due to their ability to adsorb or absorb chemical pollutants, including organic compounds, sorbents are increasingly used in the reclamation of soils subjected to their pressure, which results from their high potential in eliminating xenobiotics. The precise optimization of the reclamation process is required, focused primarily on restoring the condition of the soil. This research are essential for seeking materials sufficiently potent to accelerate the remediation process and for expanding knowledge related to biochemical transformations that lead to the neutralization of these pollutants. The goal of this study was to determine and compare the sensitivity of soil enzymes to petroleum-derived products in soil sown with Zea mays, remediated using four sorbents. The study was conducted in a pot experiment, with loamy sand (LS) and sandy loam (SL) polluted with VERVA diesel oil (DO) and VERVA 98 petrol (P). Soil samples were collected from arable lands, and the effects of the tested pollutants were compared with those used as control uncontaminated soil samples in terms of Zea mays biomass and the activity of seven enzymes in the soil. The following sorbents were applied to mitigate DO and P effects on the test plants and enzymatic activity: molecular sieve (M), expanded clay (E), sepiolite (S), and Ikasorb (I). Both DO and P exerted a toxic effect on Zea mays, with DO more strongly disturbing its growth and development and the activities of soil enzymes than P. In sandy clay (SL), P was found to be a significant inhibitor of dehydrogenases (Deh), catalase (Cat), urease (Ure), alkaline phosphatase (Pal), and arylsulfatase (Aryl) activities, while DO stimulated the activity of all enzymes in this soil. The study results suggest that the sorbents tested, mainlya molecular sieve, may be useful in remediating DO-polluted soils, especially when alleviating the effects of these pollutants in soils of lower agronomic value.

Diminishing toxicity of pyrene on photosynthetic performance of soybean using Bacillus subtilis (NCIM 5594)

Polycyclic aromatic hydrocarbons are persistent organic pollutants causing serious environmental problems, being toxic to plants and difficult to remediate. Pyrene is one such extremely dangerous compound that is toxic for the environment. This study suggests the use of Bacillus subtilis (National Collection of Industrial Microorganisms [NCIM] 5594) to overcome inhibitory effects of pyrene on soybean photosynthesis. The toxicity of pyrene to soybean was evident from a significant decrease in seed germination parameters, photosynthetic performance and biomass during growth of soybean in pyrene contaminated soil. Efficiency of performance index, light absorption, trapping and electron transport were reduced in plants grown in pyrene contaminated soil while significant recovery in these parameters was observed in plants grown in pyrene+B. subtilis treated soil. Activity levels of dehydrogenase and lipase enzymes significantly recovered in pyrene+B. subtilis treated soil. After extraction of pyrene from soil and soybean plant, concentration of pyrene was lowered in pyrene+B. subtilis treated soil and plants. These findings suggest efficient degradation of pyrene by B. subtilis . About 70% degradation of pyrene was achieved in soil using B. subtilis ; thus it is a useful strain for crop improvement in pyrene polluted soil.

The Effect of Spring Barley Fertilization on the Content of Polycyclic Aromatic Hydrocarbons, Microbial Counts and Enzymatic Activity in Soil

Soil-dwelling microorganisms play an important role in the environment by decomposing organic matter, degrading toxic compounds and participating in the nutrient cycle. The microbiological properties of soil are determined mainly by the soil pH, granulometric composition, temperature and organic carbon content. In agricultural soils, these parameters are modified by agronomic operations, in particular fertilization. Soil enzymes participate in nutrient cycling and they are regarded as sensitive indicators of microbial activity and changes in the soil environment. The aim of the present study was to determine whether PAH content in soil is associated with the microbial activity and biochemical properties of soil during the growing season of spring barley treated with manure and mineral fertilizers. Soil samples for analysis were collected on four dates in 2015 from a long-term field experiment established in 1986 in Bałcyny near Ostróda (Poland). The total content of PAHs was lowest in August (194.8 µg kg^-1) and highest in May (484.6 µg kg^-1), whereas the concentrations of heavier weight PAHs was highest in September (158.3 µg kg^-1). The study demonstrated that weather conditions and microbial activity induced considerable seasonal variations in PAHs content. Manure increased the content of organic carbon and total nitrogen, the abundance of organotrophic, ammonifying and nitrogen-fixing bacteria, actinobacteria and fungi and enhanced the activity of soil enzymes, including dehydrogenases, catalase, urease, acid phosphatase and alkaline phosphatase.

Printing ink wastewater treatment using combined hydrodynamic cavitation and pH fixation

Printing ink wastewater (PIW) carries a heavy load of pollutants, the composition of which makes treatment difficult, especially when trying to minimize the pollution load. According to the latter, the present study aims to investigate PIW treatment with different various methods and to determine the maximum color, COD (chemical oxygen demand) and TSS (total suspended solids) removal. First, hydrodynamic cavitation (HC) was tested and the effect of hydrogen peroxide dosage (0-10 g L^-1), and pH (3, 5, 8, 10) was examined concerning the removal of PIW initial COD concentrations 4000 and 8000 mg L^-1. Removal was high (more than 81%) only at pH 5 in HC reactor. The second method involved treatment with separate pH fixation of the undiluted PIW (COD 17000 mg L^-1, actual pH 8 ± 0.2). This treatment, maximized removals, reaching reduction of the initial values more than 91%, at pH 5. Finally, PIW was treated with a combination of the above methods, leading to 93-97% removals for 8000 mg L^-1 PIW treatment and 97-99% for 17000 mg L^-1 PIW respectively. Process cost calculations showed that the latter method is an effective and affordable treatment method for PIW streams, while toxicity tests of the treated PIW showed substantial toxicity reduction.

Structural, metabolic, and functional characteristics of soil microbial communities in response to benzo[a]pyrene stress

Understanding the characteristics of soil microbes responding to benzo[a]pyrene (BaP) helps to deepen the knowledge of the risks of BaP to soil ecosystem. In this study, the structural, metabolic, and functional responses of soil microbial communities to BaP (8.11 mg kg^-1) were investigated. Analysis of microbial community structure based on 16 S rRNA and ITS gene sequencing indicated that BaP addition enriched microbes associated with aromatic compound degradation (Sphingomonas, Bacilli, Fusarium) and oligotrophs (Blastocatellaceae, Rokubacteriales), but inhibited Cyanobacteria involved in nitrogen-fixing process. Network analysis showed that the bacterial community enhanced intraspecific cooperation, while fungal community mainly altered the keystone taxa under BaP stress. Biolog EcoPlate assay demonstrated that microbial metabolism of carbon sources, especially nitrogen-containing sources, was stimulated by BaP addition. Functional analysis based on enzyme activity tests, functional gene quantification, and function annotation showed that nitrogen-cycling processes, especially nitrogen fixation, were significantly inhibited. These results suggest that BaP-tolerant microbes may establish cooperative relationships and compete for resources and ecological niches with sensitive microbes, especially those associated with nitrogen cycling, ultimately leading to enhanced carbon source utilization and restricted nitrogen cycling. This study clearly elucidates the adaptation strategies and functional shifts of soil microbial communities to BaP contamination.

Role of Different Material Amendments in Shaping the Content of Heavy Metals in Maize (Zea mays L.) on Soil Polluted with Petrol

Petroleum substances are among the xenobiotics that most often contaminate the natural environment. They have a strong effect on soil, water, and other components of the environment. The aim of this pot experiment has been to determine the effect of different soil material amendments (compost, 3%; bentonite, 2% relative to the soil mass or calcium oxide, in amounts corresponding to one full hydrolytic acidity) on the content of heavy metals in aerial parts of maize (Zea mays L.) grown on soil polluted with petrol (0, 2.5, 5, and 10 cm3 kg−1 of soil). The content of all heavy metals, except copper, in the aerial biomass of maize was positively correlated, but biomass yield negatively correlated, with the increasing doses of petrol. The highest increase in the content of heavy metals was noted for chromium and manganese. Materials used for phytostabilisation (compost, bentonite, and calcium oxide) had a significant effect on the content of heavy metals and biomass yield of maize. They contributed to the modified accumulation of elements, especially chromium, copper, and cobalt in the aerial biomass of maize. In comparison with the control series (without material amendments), the application of calcium oxide proved to be most effective. It had the most evident influence on the chemical composition of maize, limiting the accumulation of lead, zinc, manganese, and iron and increasing biomass yield.

Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics

Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.

Amendments and bioaugmentation enhanced phytoremediation and micro-ecology for PAHs and heavy metals co-contaminated soils

Co-existence of polycyclic aromatic hydrocarbons (PAHs) and multi-metals challenges the decontamination of large-scale contaminated sites. This study aims to comprehensively evaluate the remediation potential of intensified phytoremediation in coping with complex co-contaminated soils. Results showed that the removal of PAHs and heavy metals is time-dependent, pollution-relevant, and plant-specific. Removal of sixteen PAHs by Medicago sativa L. (37.3%) was significantly higher than that of Solanum nigrum L. (20.7%) after 30 days. S. nigrum L. removed higher amounts of Cd than Zn and Pb, while M. sativa L. uptake more Zn. Nevertheless, amendments and microbial agents significantly increased the phytoremediation efficiency of pollutants and shortened the gap between plants. Cd removal and PAHs dissipation reached up to 80% and 90% after 90 days for both plants. Heavy metal stability in soil was promoted after the intensified phytoremediation. Plant lipid peroxidation was alleviated, regulated by changed antioxidant defense systems (superoxide dismutase, peroxidase, catalase). Soil enzyme activities including dehydrogenase, urease, and catalase increased up to 5-fold. Soil bacterial diversity and structure were changed, being largely composed of Proteobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Firmicutes. These findings provide a green and sustainable approach to decontaminating complex-polluted environments with comprehensive improvement of soil health.

Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes

The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.

The combination of biochar and plant roots improves soil bacterial adaptation to PAH stress: Insights from soil enzymes, microbiome, and metabolome

Polycyclic aromatic hydrocarbon (PAH) contamination in agricultural soils poses serious stress to the soil microbiome. With the broad application of biochar, however, the co-effects of biochar and plant roots on the bacterial responses to PAH stress remain unclear. Here, the effects of biochar and the rhizosphere on bacterial community structure and functions were analyzed by coupling enzyme activity tests, high-throughput sequencing, and soil metabolomics. The contents of available nutrients and dissolved organic carbon, enzyme activities, and carbon metabolism functions were improved by biochar and plant roots. With the combined effects of biochar and plant roots, sucrose and starch metabolism was mainly impacted, and the soil metabolite diversity decreased. There was a strong co-occurrence network among soil properties, bacterial members, and metabolites in the biochar-amended and rhizosphere soils, favoring bacterial resistance to PAH stress, and consequently, PAH removal. In light of the above results, we suggest that biochar application can efficiently improve bacterial functions in rhizosphere soil, and our results facilitate the development of in situ remediation programs in soil contaminated with PAHs.

Halo-tolerant plant growth promoting rhizobacteria for improving productivity and remediation of saline soils

Background

The collective impact of climate change and soil salinity is continuously increasing the degraded lands across the globe, bringing agricultural productivity and food security under stress. The high concentration of salts in saline soils impose osmotic, ionic, oxidative and water stress in plants. Biological solutions can be the most reliable and sustainable approach to ensure food security and limit the use of agro-chemicals.

Aim of Review

Halo-tolerant plant growth promoting rhizobacteria (HT-PGPR) are emerging as efficient biological tools to mitigate the toxic effects of high salt concentrations and improve the growth of plants, simultaneously remediating the degraded saline soils. The review explains the role of HT-PGPR in mitigating the salinity stress in plants through diverse mechanisms and concurrently leading to improvement of soil quality.

Key Scientific Concepts of Review

HT-PGPR are involved in alleviating the salinity stress in plants through a number of mechanisms evoking multipronged physiological, biochemical and molecular responses. These include changes in expression of defense-related proteins, exopolysaccharides synthesis, activation of antioxidant machinery, accumulation of osmolytes, maintaining the Na⁺ kinetics and improving the levels of phytohormones and nutrient uptake in plants. The modification of signaling by HT-PGPR inoculation under stress conditions elicits induced systemic resistance in plants which further prepares them against salinity stress. The role of microbial-mechanisms in remediating the saline soil through structural and compositional improvements is also important. Development of novel bioinoculants for saline soils based on the concepts presented in the review can be a sustainable approach in improving productivity of affected agro-ecosystems and simultaneously remediating them.

Carbon dioxide as a carrier gas and mixed feedstock pyrolysis decreased toxicity of sewage sludge biochar

The common use of sewage sludge (SSL)-derived biochar can be limited due to contaminants present in SSL, which may affect SSL-derived biochar toxicity. We propose the reduction of SSL-derived biochar toxicity by it co-pyrolysis with biomass and in CO₂ atmosphere. Ecotoxicity of biochars produced at 500, 600, and 700 °C from SSL and SSL with the addition of willow (at a ratio of SSL:willow - 8:2 and 6:4, w/w) in an atmosphere of N₂ or CO₂ were investigated. The toxicity of aqueous extracts derived from the biochars (Lepidium sativum - Elongation test, Vibrio fischeri - Microtox) or solid-phase toxicity (Lepidium sativum - Phytotoxkit F, Folsomia candida - Collembolan test) was also studied. SSL-derived biochar produced at N₂ atmosphere usually was toxic for all tested organisms. Co-pyrolysis of mixed feedstock reduced the toxicity of the produced biochar. In the case of biochars produced from SSL and willow under N₂ atmosphere decrease in inhibition of F. candida reproduction (from 27 to 58%) or its stimulation (from 7 to 30%) in comparison to SSL alone derived biochar, was observed. Co-pyrolysis of SSL with willow significantly reduced the toxicity of extracts the SSL-derived biochar towards L. sativum. The aqueous extracts obtained from the biochars produced at temperatures of 500 and 600 °C with willow addition were also less toxic to V. fischeri than the biochars produced from SSL alone. The change of carrier gas from N₂ to CO₂, regardless of the feedstock used, in most cases reduced toxicity or positively affected the test organisms. This was probably caused by changes in the physicochemical properties and content of contaminants in the biochars produced in an atmosphere of CO₂, compared to N₂. An exception was root growth inhibition in the solid phase tests where no significant differences were found between biochars produced in N₂ and CO₂.

Impact of Various Grass Species on Soil Bacteriobiome

Today, various grass species are important not only in animal feeding but, increasingly often, also in energetics and, due to esthetic and cultural values, in landscape architecture. Therefore, it is essential to establish the roles various grass species and their functional forms play in modifying soil bacteriobiome and enzymatic activity. To this end, a pot experiment was conducted to examine effects of various fodder grass and lawn grass species on the bacteriobiome and biochemical properties of soil. Nonsown soil served as the control for data interpretation. Analyses were carried out with standard and metagenomic methods. The intensity of effects elicited by grasses depended on both their species and functional form. More favorable living conditions promoting the development of soil bacteria and, thereby, enzymatic activity were offered by fodder than by lawn grass species. Among the fodder grasses, the greatest bacteriobiome diversity was caused by sowing the soil with Phleum pratense (Pp), whereas among lawn grasses in the soil sown with Poa pratensis (Pr). Among the fodder grasses, the highest enzymatic activity was determined in the soil sown with Lolium x hybridum Hausskn (Lh), and among the lawn grasses—in the soil sown with Lolium perenne. Sowing the soil with grasses caused the succession of a population of bacterial communities from r strategy to k strategy.

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics

Polycyclic aromatic hydrocarbons (PAHs), some of the most widespread organic contaminants, are highly toxic to soil microorganisms. Whether long-term polluted soils can still respond to the fresh input of pollutants is unknown. In this study, the soil enzyme activity, soil microbial community structure and function and microbial metabolism pathways were examined to systematically investigate the responses of soil microorganisms to fresh PAH stress. Microbial activity as determined by soil dehydrogenase and urease activity was inhibited upon microbe exposure to PAH stress. In addition, the soil microbial community and function were obviously shifted under PAH stress. Both microbial diversity and richness were decreased by PAH stress. Rhizobacter, Sphingobium, Mycobacterium, Massilia, Bacillus and Pseudarthrobacter were significantly affected by PAH stress and can be considered important indicators of PAH contamination in agricultural soils. Moreover, the majority of microbial metabolic function predicted to respond to PAH stress were affected adversely. Finally, soil metabolomics further revealed specific inhibition of soil metabolism pathways associated with fatty acids, carbohydrates and amino acids. Therefore, the soil metabolic composition distinctively changed, reflecting a change in the soil metabolism. In summary, fresh contaminant introduction into long-term polluted soils inhibited microbial activity and metabolism, which might profoundly affect the whole soil quality.

Effects of benzo [a] pyrene (BaP) on the composting and microbial community of sewage sludge

Benzo [a] pyrene (BaP), the most ubiquitous polycyclic aromatic hydrocarbons (PAHs) found in sludge, can impact the composting processes of sewage sludge as well as the quality of compost produced. In the present study, we investigated the effects of BaP at various concentrations on physicochemical characteristics, heavy metal passivation, and microbial community during the composting processes. The removal efficiency of BaP at 5 and 20 mg kg^-1 after composting was 51.1% and 74.2%, respectively. In comparison with the control, the content of residual Cu, Pb, Cr and Ni in 5 mg kg^-1 BaP contained system declined dramatically on the second day of composting, while such content in 20 mg kg^-1 BaP system significantly decreased on the 8th day. Regardless of the presence of BaP in the sludge, composting process had a positive passivation effect on Cu, Pb, Cr and Ni. A stronger inhibitory effect of BaP at higher concentration was observed on microorganism, which reduced microbial abundance and species in the composting, and influenced microbial diversity. Besides, microbial communities in BaP-containing composting would improve the transformation of silicates and minerals, increase the concentration of humus and extend the passivation time of heavy metals. As these results verified, composting process could remove BaP from the sludge effectively, and BaP had a significant impact on heavy metal passivation and abundance and composition of microbial community during the composting process.

Responses of soil microbial community and enzymes during plant-assisted biodegradation of di-(2-ethylhexyl) phthalate and pyrene

A pot experiment was conducted to explore the plant-assisted degradation efficiency of di-(2-ethylhexyl) phthalate (DEHP) and pyrene. Three plant species: Ceylon spinach, sunflower, and leaf mustard were cultivated in co-contaminated soils under three contamination levels: control (T0), 20 mg kg^-1 (T20), and 50 mg kg^-1 (T50). The results showed that a higher DEHP and pyrene degradation efficiency was observed evidently in planted cases, increasing from 42 to 53-59% (T0), 61 to 65-76% (T20) and 52 to 68-78% (T50) for DEHP, and from 22 to 30-49% (T0), 58 to 62-72% (T20), and 54 to 57-70% (T50) for pyrene. Under T20 contamination level, soil phospholipid fatty-acid analysis depicted the increased microbial biomass in rhizosphere, especially the arbuscular mycorrhizal fungus that is effective for the degradation of organic pollutants. The study also revealed that the activities of dehydrogenase, acid phosphomonoesterase, urease, and phenol oxidase negatively correlated with pollutant concentration. In general, the removal rate of DEHP and pyrene was highest in the soil planted with leaf mustard for each contamination level considered. For soils at T20 level, sunflower and leaf mustard appeared as interesting phytoremediation plants due to the improved removal rates of organic pollutants and the soil microbial activity.

Content of PAHs in soil of a hazel orchard depending on the method of weed control

PAHs belong to persistent organic pollutants (POPs) found in the natural environment. They eventually accumulate in the highest quantities in soil. The purpose of this study has been to determine quantities of PAHs in soil depending on the method applied to control weeds in rows of a 4-year plantation of hazel (mulch fabric, bark chips, sawdust, manure compost, bare fallow, chemical fallow, grass sward). The highest concentration of PAHs (16 PAHs) was found in soil kept as bare fallow. The second most abundant concentration of these compounds was determined in soil under grass sward, followed by soil under sawdust, chemical fallow, and fabric. Less of these compounds accumulated in soil mulched with bark chips. The best method for protection of orchard soil against the accumulation of unwanted and toxic PAHs was mulching with manure compost. In most cases, lower concentrations of PAHs (total 16) were found in the subsoil (30-60 cm) than in the topmost soil layer, except the soil covered with mulch fabric, where fourfold more PAHs accumulated.

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Biochar based remediation of water and soil contaminated by phenanthrene and pentachlorophenol

Phenanthrene (Phe) and pentachlorophenol (PCP) are classified as persistent organic pollutants and represent serious concern for the environment as they are toxic and ubiquitous. Biochar based remediation is an emerging technology used in water and soil contamination. In this study we used poplar (BP) and conifer (BC) biochars to remediate water and soil contaminated by Phe and PCP. BP and BC were able to remove completely either Phe or PCP from contaminated water within one to three days. When biochar was confined in a porous membrane, BC and BP maintained their sorption efficiency for several remediation cycles. However, in these conditions BC allowed faster Phe removal. In soil remediation experiments, addition of two biochar rates, i.e. 2.5 and 5 mg g^-1, strongly reduced Phe extractability (up to 2.7% of the initially added Phe with the larger BC dose). This was similar to the behavior observed when compost was applied in order to verify the role of soil organic matter in the fate of both contaminants. PCP extractability was reduced only up to 75% (in average) in all samples including those with compost amendment. Only larger amount of biochar (20 and 50 mg g^-1) allowed reduction of the extractable PCP and nullified phytotoxicity of the contaminant.

Resistance of aerobic microorganisms and soil enzyme response to soil contamination with Ekodiesel Ultra fuel

This study determined the susceptibility of cultured soil microorganisms to the effects of Ekodiesel Ultra fuel (DO), to the enzymatic activity of soil and to soil contamination with PAHs. Studies into the effects of any type of oil products on reactions taking place in soil are necessary as particular fuels not only differ in the chemical composition of oil products but also in the composition of various fuel improvers and antimicrobial fuel additives. The subjects of the study included loamy sand and sandy loam which, in their natural state, have been classified into the soil subtype 3.1.1 Endocalcaric Cambisols. The soil was contaminated with the DO in amounts of 0, 5 and 10 cm³ kg^-1. Differences were noted in the resistance of particular groups or genera of microorganisms to DO contamination in loamy sand (LS) and sandy loam (SL). In loamy sand and sandy loam, the most resistant microorganisms were oligotrophic spore-forming bacteria. The resistance of microorganisms to DO contamination was greater in LS than in SL. It decreased with the duration of exposure of microorganisms to the effects of DO. The factor of impact (IF_DO) on the activity of particular enzymes varied. For dehydrogenases, urease, arylsulphatase and β-glucosidase, it had negative values, while for catalase, it had positive values and was close to 0 for acid phosphatase and alkaline phosphatase. However, in both soils, the noted index of biochemical activity of soil (BA) decreased with the increase in DO contamination. In addition, a positive correlation occurred between the degree of soil contamination and its PAH content.

Functional Diversity of Fungal Communities in Soil Contaminated with Diesel Oil

The widespread use and consumption of crude oil draws the public's attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R) and Shannon-Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2-3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD) and Eco-physiological Diversity (EP) indices] is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterization of the consequences of a long-term impact of diesel oil on soil fungi.

The role of artificial root exudate components in facilitating the degradation of pyrene in soil

Root exudates play an important role in the phytoremediation of soils contaminated by organic pollutants, but how root exudate components affect the remediation process is not well understood. In this study, we explored the effects and mechanisms of the major root exudates, including glucose, organic acids, and serine, in the rhizoremediation of pyrene-contaminated soil. The results showed that glucose increased the degradation of pyrene (54.3 ± 1.7%) most significantly compared to the organic acids (45.5 ± 2.5%) and serine (43.2 ± 0.1%). Glucose could significantly facilitate the removal of pyrene in soil through promoting dehydrogenase activity indicated by a positive correlation between the removal efficiency of pyrene and the soil dehydrogenase activity (p < 0.01). Furthermore, root exudates were able to change soil microbial community, particularly the bacterial taxonomic composition, thereby affecting the biodegradation of pyrene. Glucose could alter soil microbial community and enhance the amount of Mycobacterium markedly, which is dominant in the degradation of pyrene. These findings provide insights into the mechanisms by which root exudates enhance the degradation of organic contaminants and advance our understanding of the micro-processes involved in rhizoremediation.

Enhanced bioremediation of lead-contaminated soil by Solanum nigrum L. with Mucor circinelloides

Strain selected from mine tailings in Anshan for Pb bioremediation was characterized at the genetic level by internal transcribed spacer (ITS) sequencing. Results revealed that the strain belongs to Mucor circinelloides. Bioremediation of lead-contaminated soil was conducted using Solanum nigrum L. combined with M. circinelloides. The removal efficacy was in the order microbial/phytoremediation > phytoremediation > microbial remediation > control. The bioremediation rates were 58.6, 47.2, and 40.2% in microbial/phytoremediation, microbial remediation, and phytoremediation groups, respectively. Inoculating soil with M. circinelloides enhanced Pb removal and S. nigrum L. growth. The bioaccumulation factor (BF, 1.43), enrichment factor (EF, 1.56), and translocation factor (TF, 1.35) were higher than unit, suggesting an efficient ability of S. nigrum L. in Pb bioremediation. Soil fertility was increased after bioremediation according to change in enzyme activities. The results indicated that inoculating S. nigrum L. with M. circinelloides enhanced its efficiency for phytoremediation of soil contaminated with Pb.

Chemical and ecotoxicological evaluation of biochar produced from residues of biogas production

Analyses were carried out for biochars produced at three temperatures of pyrolysis (400, 600 and 800°C) from solid residue from biogas production (RBP). Separated and non-separated RBP from biogas plants employing different biogas production conditions were pyrolyzed. The contents of heavy metals and polycyclic aromatic hydrocarbons (PAHs) (16 PAH US EPA) were analyzed in biochars. The analyses showed that with an increased pyrolysis temperature, there was an increase in the contents of PAHs and of certain heavy metals (Cr, Cu, Cd, Pb and Mn). In the ecotoxicological tests, it was noted that the effect depended on the temperature of pyrolysis and on the feedstock from which the biochar was produced. The least harmful effect on the test organisms was from biochar produced by separated RBP in a biogas plant operating in mesophilic conditions. The most negative effect on the test organisms was characteristic of biochar produced from non-separated mesophilic RBP. This study shows that the main factors determining the level of toxicity of biochars produced from RBP towards various living organisms are both the method of feedstock production and the temperature at which the process of pyrolysis is conducted.

The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth

Fungicides are considered to be effective crop protection chemicals in modern agriculture. However, they can also exert toxic effects on non-target organisms, including soil-dwelling microbes. Therefore, the environmental fate of fungicides has to be closely monitored. The aim of this study was to evaluate the influence of the Falcon 460 EC fungicide on microbial diversity, enzyme activity and resistance, and plant growth. Samples of sandy loam with pHKCl 7.0 were collected for laboratory analyses on experimental days 30, 60 and 90. Falcon 460 EC was applied to soil in the following doses: control (soil without the fungicide), dose recommended by the manufacturer, 30-fold higher than the recommended dose, 150-fold higher than the recommended dose and 300-fold higher than the recommended dose. The observed differences in the values of the colony development index and the eco-physiological index indicate that the mixture of spiroxamine, tebuconazole and triadimenol modified the biological diversity of the analyzed groups of soil microorganisms. Bacteria of the genus Bacillus and fungi of the genera Penicillium and Rhizopus were isolated from fungicide-contaminated soil. The tested fungicide inhibited the activity of dehydrogenases, catalase, urease, acid phosphatase and alkaline phosphatase. The greatest changes were induced by the highest fungicide dose 300-fold higher than the recommended dose. Dehydrogenases were most resistant to soil contamination. The Phytotoxkit test revealed that the analyzed fungicide inhibits seed germination capacity and root elongation. The results of this study indicate that excessive doses of the Falcon 460 EC fungicide 30-fold higher than the recommended dose to 300-fold higher than the recommended dose) can induce changes in the biological activity of soil. The analyzed microbiological and biochemical parameters are reliable indicators of the fungicide's toxic effects on soil quality.