Effect of organic farming on soil microbiological parameters

All over the world, including Poland, interest in the organic farming is growing. It is based on an attempt to minimize human impact on the environment while maintaining the natural functionality and productivity of the agricultural system. At the same time, every human activity in the natural environment results in greater or lesser changes in the soil ecosystem. Organic farming also has an impact on physical and chemical parameters and soil biological activity. These changes should be monitored and considered in the context of long-term land management. This review focuses on the impact of the organic farming system on soil biological activity and diversity of soil microorganisms

The Molecular‐Based Methods Used for Studying Bacterial Diversity in Soils Contaminated with PAHs (The Review)

Soil contamination could adversely affect microbial diversity, and perhaps also above‐ and below‐ground ecosystem functioning. It is important to study microbial diversity not only for basic scientific research, but also to understand the link between diversity and community structure and function in the pollution site. The study of microbial diversity and their function in contaminated soil creates a serious problem because they observed significant limitations in methodology and taxonomy of this group. Methodology for the determination of bacterial diversity does not include their function in the soil and other environment areas. Microbes are known for their catabolic activity in bioremediation, but changes in microbial communities are still unpredictable. The bioremediation of a pollutant and its rate depend on the environmental conditions, number and type of the microorganisms, nature and chemical structure of the chemical compound being degraded. However, molecular methods have been used to study soil bacterial communities. While many anthropogenic activities, such as city development, agriculture, and use of pollution, can potentially affect soil microbial diversity, it is unknown how changes in microbial diversity can influence below‐ground and above‐ground ecosystems. There are problems associated with studying bacterial diversity in soil. These arise not only from methodological limitations, but also from a lack of taxonomic knowledge. Methods to measure microbial diversity in soil can be categorized into two groups: biochemical‐based techniques and molecular‐based techniques. But more common for studying microbial diversity in soil contaminated with polycyclic aromatic hydrocarbons are the molecular methods

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment

The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5–21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles

Ecchordosis physaliphora – opis przypadku i omówienie patologicznych pochodnych struny grzbietowej

Some notochord cells remain along the axis of the vertebral column after embryogenesis. These ‘notochordal remnants’ have some similarities, but their biological behaviour varies considerably. They can give rise to benign lesions such as ecchordosis physaliphora (EP) and ‘benign notochordal cell tumour’ (BNCT), or aggressive ones like chordoma. We review the problems of the differential diagnosis of notochordal remnants apropos of a case of the incidental autopsy finding of EP in a 78-year-old man, who died due to heart infarction. The 6-mm asymptomatic gelatinous lesion was fixed to the basilar artery on its ventral aspect. Small EPs can be easily overlooked in autopsy. Ecchordosis physaliphora and intradural chordoma share some similarities that may be misleading and may even result in the wrong diagnosis and therapy. The recently reported new entity BNCT poses a similar problem. We review the literature illustrating the most important features of notochord-derived lesions and discuss the relationships between these lesions with regard to molecular genetics.Podczas formowania się jąder miażdżystych na pozostałościach komórek struny grzbietowej rozwijają się zmiany podobne do siebie, mające jednak różny przebieg kliniczny. Niektóre z nich, takie jak ecchordosis physaliphora (EP) i notochordal benign cell tumour (NBCT), mają charakter łagodny, inne (np. struniak) – agresywny. Celem pracy jest przegląd najważniejszych cech zmian wywodzących się ze struny grzbietowej i ich diagnostyka różnicowa na podstawie przypadku EP stwierdzonego podczas autopsji mózgu 78-letniego mężczyzny zmarłego na atak serca. Galaretowaty guz o największym wymiarze 6 mm, przytwierdzony do brzusznej części tętnicy podstawnej nie dawał żadnych objawów. Ecchordosis physaliphora to zazwyczaj mały, bezobjawowy guzek, łatwy do przeoczenia podczas autopsji. Struniak i EP wywodzą się z tych samych komórek, lecz ze względu na podobieństwa mogą być ze sobą mylone, co skutkuje niewłaściwym rozpoznaniem i ewentualnym leczeniem. Podobny problem występuje w przypadku NBCT. W pracy poruszono również kwestię ich wzajemnego związku na podstawie badań genetycznych

"Ecchordosis physaliphora" : opis przypadku i omówienie patologicznych pochodnych struny grzbietowej

Podczas formowania się jąder mia¿d¿ystych na pozostałościach komórek struny grzbietowej rozwijają się zmiany podobne do siebie, mające jednak różny przebieg kliniczny. Niektóre znich, takie jak ecchordosis physaliphora (EP) i notochordal benign cell tumour(NBCT), mają charakter łagodny, inne (np. stru- niak) - agresywny. Celem pracy jest przegląd najważniejszych cech zmian wywodzących się ze struny grzbietowej iich dia­gnostyka różnicowa na podstawie przypadku EP stwierdzo­nego podczas autopsji mózgu 78-letniego mężczyzny zmarłego na atak serca. Galaretowaty guz o największym wymiarze 6 mm, przytwierdzony do brzusznej części tętnicy podstaw- nej nie dawał żadnych objawów. Ecchordosis physaliphora to zazwyczaj mały, bezobjawowy guzek, łatwy do przeoczenia podczas autopsji. Struniak iEP wywodzą się z tych samych komórek, lecz ze względu na podobieństwa mogą być ze sobą mylone, co skutkuje niewła­ściwym rozpoznaniem i ewentualnym leczeniem. Podobny problem występuje w przypadku NBCT. W pracy poruszo­no również kwestię ich wzajemnego związku na podstawie badań genetycznych.Some notochord cells remain along the axis of the vertebral column after embryogenesis. These ‘notochordal remnants’ have some similarities, but their biological behaviour varies considerably. They can give rise to benign lesions such as ecchordosis physaliphora (EP) and ‘benign notochordal cell tumour’ (BNCT), or aggressive ones like chordoma. We review the problems of the differential diagnosis of notochordal remnants apropos of a case of the incidental autopsy finding of EP in a 78-year-old man, who died due to heart infarction. The 6-mm asymptomatic gelatinous lesion was fixed to the basilar artery on its ventral aspect. Small EPs can be easily overlooked in autopsy. Ecchordosis physaliphora and intradural chordoma share some similarities that may be misleading and may even result in the wrong diagnosis and therapy. The recently reported new entity BNCT poses a similar problem. We review the literature illustrating the most important features of notochord-derived lesions and discuss the relationships between these lesions with regard to molecular genetics

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