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Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.

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The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-016-0837-2) contains supplementary material, which is available to authorized users.

Soil microbial communities play an important role in the biodegradation of different petroleum derivates, including hydrocarbons. Also other biological factors such as enzyme and respiration activities and microbial abundance are sensitive to contamination with petroleum derivates. The aim of this study was to evaluate the response of autochthonic microbial community and biological parameters (respiration, dehydrogenase and catalase activities, total microorganisms count) on contamination with car fuels and engine oils. The surface layer (0–20 cm) of Mollic Gleysol was used for the experiment. In laboratory conditions, soil was contaminated with the following petroleum substances: car fuels (petrol, diesel) and car engine oils (new and waste—after 10,000 km). The results demonstrated that, among the investigated hydrocarbon substances, petrol addition seemed to be the most toxic for the microbial activity of the investigated soil. The toxicity of the used hydrocarbon substances to microorganisms might be summarized as follows: diesel > new oil > waste oil > petrol. Species belonging to the genera Micrococcus and Rhodococcus were noted as the major autochthonic bacteria being present in soil contaminated with new automobile oil, whereas species of the genera Bacillus sp. and Paenibacillus sp. were identified in the combination treated with waste oil.

The main goal of the study was to determine the biodiversity of bacteria and their metabolic profile in the rhizosphere of four winter wheat (Triticum aestivum L.) varieties (Hondia, Nordkap, Rotax, Tytanika) cultivated in Haplic Podzol soil in a no-tillage system. Two techniques, i.e., next generation sequencing (NGS, meta-barcoding of 16S rRNA community) and community level physiological profiling (CLPP), were applied to obtain a holistic picture of biodiversity. The basic soil chemical parameters (acidity, redox potential, carbon content, forms of nitrogen, and phosphorus) were also determined. It was found that the rhizospheric microbiome (at the genus level) of cv. Hondia and Rotax were significantly different from that present in the other cultivars studied. The CLPP technique demonstrated that microbial metabolic activity depended on both the type of substrate and wheat cultivars. Carbohydrates and carboxylic acids were the most easily utilized compounds in all rhizospheric soils. The principal component analysis (PCA) evidenced that the rhizospheric soils of Rotax and Nordkap were characterized by a higher functional activity (strong correlation with the Shannon-Wiener index, the Richness index, and utilization of hydrocarbons) than those of Hondia and Tytanika.