GFP-tagged multimetal-tolerant bacteria and their detection in the rhizosphere of white mustard

The introduction of rhizobacteria that tolerate heavy metals is a promising approach to support plants involved in phytoextraction and phytostabilisation. In this study, soil of a metal-mine wasteland was analyzed for the presence of metal-tolerant bacterial isolates, and the tolerance patterns of the isolated strains for a number of heavy metals and antibiotics were compared. Several of the multimetal-tolerant strains were tagged with a broad host range reporter plasmid (i.e. pPROBE-NT) bearing a green fluorescent protein marker gene (gfp). Overall, the metal-tolerant isolates were predominately Gram-negative bacteria. Most of the strains showed a tolerance to five metals (Zn, Cu, Ni, Pb and Cd), but with differing tolerance patterns. From among the successfully tagged isolates, we used the transconjugant Pseudomonas putida G25 (pPROBE-NT) to inoculate white mustard seedlings. Despite a significant decrease in transconjugant abundance in the rhizosphere, the gfp-tagged cells survived on the root surfaces at a level previously reported for root colonisers

A comparative study of biodegradation of vinyl acetate by environmental strains

Four Gram-negative strains, E3_2001, EC1_2004, EC3_3502 and EC2_3502, previously isolated from soil samples, were subjected to comparative studies in order to select the best vinyl acetate degrader for waste gas treatment. Comparison of biochemical and physiological tests as well as the results of fatty acids analyses were comparable with the results of 16S rRNA gene sequence analyses. The isolated strains were identified as Pseudomonas putida EC3_2001, Pseudomonas putida EC1_2004, Achromobacter xylosoxidans EC3_3502 and Agrobacterium sp. EC2_3502 strains. Two additional strains, Pseudomonas fluorescens PCM 2123 and Stenotrophomonas malthophilia KB2, were used as controls. All described strains were able to use vinyl acetate as the only source of carbon and energy under aerobic as well as oxygen deficiency conditions. Esterase, alcohol dehydrogenase and aldehyde dehydrogenase were involved in vinyl acetate decomposition under aerobic conditions. Shorter degradation times of vinyl acetate were associated with accumulation of acetic acid, acetaldehyde and ethanol as intermediates in the culture fluids of EC3_2001 and KB2 strains. Complete aerobic degradation of vinyl acetate combined with a low increase in biomass was observed for EC3_2001 and EC1_2004 strains. In conclusion, P. putida EC1_2004 is proposed as the best vinyl acetate degrader for future waste gas treatment in trickle-bed bioreactors

Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

<p>Abstract</p> <p>Background</p> <p>The influence of diet on intestinal microflora has been investigated mainly using conventional microbiological approaches. Although these studies have advanced knowledge on human intestinal microflora, it is imperative that new methods are applied to facilitate scientific progress. Culture-independent molecular fingerprinting method of Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) has been used to study microbial communities in a variety of environmental samples. However, these protocols must be optimized prior to their application in order to enhance the quality and accuracy of downstream analyses. In this study, the relative efficacy of four commercial DNA extraction kits (Mobio Ultra Clean^®Fecal DNA Isolation Kit, M; QIAamp^®DNA Stool Mini Kit, Q; FastDNA^®SPIN Kit, FSp; FastDNA^®SPIN Kit for Soil, FSo) were evaluated. Further, PCR-DGGE technique was also assessed for its feasibility in detecting differences in human intestinal bacterial fingerprint profiles.</p> <p>Method</p> <p>Total DNA was extracted from varying weights of human fecal specimens using four different kits, followed by PCR amplification of bacterial 16S rRNA genes, and DGGE separation of the amplicons.</p> <p>Results</p> <p>Regardless of kit, maximum DNA yield was obtained using 10 to 50 mg (wet wt) of fecal specimens and similar DGGE profiles were obtained. However, kits FSp and FSo extracted significantly larger amounts of DNA per g dry fecal specimens and produced more bands on their DGGE profiles than kits M and Q due to their use of bead-containing lysing matrix and vigorous shaking step. DGGE of 16S rRNA gene PCR products was suitable for capturing the profiles of human intestinal microbial community and enabled rapid comparative assessment of inter- and intra-subject differences.</p> <p>Conclusion</p> <p>We conclude that extraction kits that incorporated bead-containing lysing matrix and vigorous shaking produced high quality DNA from human fecal specimens (10 to 50 mg, wet wt) that can be resolved as bacterial community fingerprints using PCR-DGGE technique. Subsequently, PCR-DGGE technique can be applied for studying variations in human intestinal microbial communities.</p

Interactive and Single Effects of Ectomycorrhiza Formation and Bacillus cereus on Metallothionein MT1 Expression and Phytoextraction of Cd and Zn by Willows

Single and joint ectomycorrhizal (+ Hebeloma mesophaeum) and bacterial (+ Bacillus cereus) inoculations of willows (Salix viminalis) were investigated for their potential and mode of action in the promotion of cadmium (Cd) and zinc (Zn) phytoextraction. Dual fungal and bacterial inoculations promoted the biomass production of willows in contaminated soil. Single inoculations either had no effect on the plant growth or inhibited it. All inoculated willows showed increased concentrations of nutritional elements (N, P, K and Zn) and decreased concentrations of Cd in the shoots. The lowest biomass production and concentration of Cd in the willows (+ B. cereus) were combined with the strongest expression of metallothioneins. It seems that biotic stress from bacterial invasion increased the synthesis of these stress proteins, which responded in decreased Cd concentrations. Contents of Cd and Zn in the stems of willows were combination-specific, but were always increased in dual inoculated plants. In conclusion, single inoculations with former mycorrhiza-associated B. cereus strains decreased the phytoextraction efficiency of willows by causing biotic stress. However, their joint inoculation with an ectomycorrhizal fungus is a very promising method for promoting the phytoextraction of Cd and Zn through combined physiological effects on the plant

Isolation of nucleic acids from the environment - the first step in metagenome analysis

Recently, increasing interest in ecology of microorganisms has been associated with the possibility of direct analysis of microbial community structure due to application of molecular methods based on isolated metagenome DNA. The metagenome approach can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil or water microbial communities. However, the crucial step in this approach is efficient extraction of high-quality total DNA representing the metagenome of a habitat. The DNA extraction methods for soil habitats are grouped into two major types, i.e. indirect based on the recovery of microbes (e.g. bacterial cells) and their subsequent lysis, and direct lysis of cells in the sample followed by DNA purification. The direct extraction of total DNA from an environmental sample presumably better represents its bacterial or fungal metagenome; hence, this approach has been used more often than the fractionation methods. Although direct extraction of DNA is less labour-intensive and yield more DNA, the recovered DNA fragments are usually smaller than those obtained by the indirect approach are. The fractionation method is advantageous for soil samples containing higher amounts of organic matter or other substances that interfere with DNA isolation. This method is also applied for DNA extraction from water samples. Microbial ecologists currently use different commercially available kits for total DNA isolation from soil or water. However, it would appear that the most efficient method of DNA extraction from environmental samples is still far from being established

Maps of the potential of shallow geothermal energy: purposes of preparation, types and examples from Poland and Europe

Mapy potencjału geotermii niskotemperaturowej (pot. płytkiej) stanowią nowoczesny sposób prezentacji warunków termicznych podłoża skalnego i mogą być używane, po uwzględnieniu innych uwarunkowań geologicznych i środowiskowych, jako narzędzie planistyczne dla regionalnego i lokalnego wykorzystania odnawialnych źródeł energii oraz indywidualnej oceny efektywności energetycznej pomp ciepła z otworowym wymiennikiem ciepła. Mapy geotermiczne, o charakterze jakościowym lub ilościowym (ukazujące rozkład średniej wartości przewodnictwa cieplnego skał lub wskaźnika mocy cieplnej do określonej głębokości) są powszechnie stosowane w krajach Europy zachodniej. Pierwsze przykłady ich opracowania w Polsce powinny stać się zachętą dla ich szerszego zastosowania, zwłaszcza w kontekście przygotowywania (lub zmiany) planów rozwoju OZE lub planów ochrony powietrza i zwalczania „niskiej emisji”.Maps of the potential of low-temperature (shallow) geothermal energy represent a modern way of presenting thermal conditions of bedrock and can be used, taking other geological and environmental conditions into account, as a planning tool for local and regional use of renewable energy sources as well as for an individual assessment of the energy efficiency of ground source heat pumps. Geothermal maps, qualitative or quantitative (showing the distribution of the average value of the thermal conductivity of rocks or the heat extraction ratio to a specified depth) are widely used in Western Europe. The first examples of similar studies in Poland should become an incentive for their wider use, especially in the context of the preparation (or changes) of plans for RES development and air quality protection schemes aimed to combat “low emission”

Practicing childhood at the Care and Education Centre in Żmiąca belonging to the Rupert Mayer Children's Aid Foundation in Kraków

W niniejszej pracy autorka skupia się na instytucji prowadzonej przez Fundację Dzieło Pomocy Dzieciom im. Ruperta Mayera w Krakowie, która zajmuje się opieką nad dziećmi, a mianowicie na ośrodku opiekuńczo-wychowawczym w Żmiącej. Celem badań było uchwycenie i zrozumienie tego, co jest tworzone przez dzieci, czemu nadają znaczenie, i w jakim stopniu może to stanowić formę praktykowania dzieciństwa. Zostało scharakteryzowane dzieciństwo idealne, przypisując mu określone cechy, a następnie nastąpiła analiza dzieciństwa realnego w kontekście wybranych problemów społecznych. Została opisana Fundacja Dzieło Pomocy Dzieciom imienia Ruperta Mayera. Przedstawiona została geneza jej powstania oraz struktura. W czwartym rozdziale, znajduje się analiza badań. Szczegółowo przedstawiono zadania badawcze oraz ich interpretacje naukowe, które stanowią wprowadzenie do refleksji autorki, będących rezultatem prowadzonej obserwacji, a także (z)budowanej relacji z dziećmi.In this study, the author focuses on an institution run by the Rupert Mayer Children's Aid Foundation in Krakow, which provides care for children, namely the care and education center in Zmiąca. The aim of the research was to capture and understand what is created by children, what they give meaning to, and to what extent this can be a form of practicing childhood. An ideal childhood was characterized, attributing certain characteristics to it, followed by an analysis of real childhood in the context of selected social problems. The Rupert Mayer Children's Aid Foundation was described. The genesis of its establishment and structure are presented. In the fourth chapter, there is an analysis of the research. The research tasks and their scientific interpretations are presented in detail, which serve as an introduction to the author's reflections, which are the result of her observations, as well as the (z)built relationship with children

Planning the location and optimization of performance of ground heat pumps installation in closed-loop systems with the support of geothermal mapping. Results of the TransGeoTherm project

Artykuł prezentuje wyniki badań projektu TransGeoTherm – Energia geotermalna dla transgranicznego rozwoju regionu Nysy. Projekt pilotażowy, zrealizowanego przez Państwowy Instytut Geologiczny–Państwowy Instytut Badawczy oraz Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie. Celem projektu było wsparcie wykorzystania płytkiej, niskotemperaturowej energii geotermalnej za pomocą ogólnodostępnych map geotermicznych. Po analizie danych z 5146 otworów geologicznych i hydrogeologicznych oraz danych geofizycznych dla obszaru o powierzchni około 1000 km2 położonego na pograniczu Polski i Saksonii, w rejonie Zgorzelca i Görlitz wykonano geologiczny model podłoża 3D w oprogramowaniu GOCAD® do głębokości około 200 m. W obrębie 75 jednostek wydzielonych na podstawie klasyfikacji litostratygraficznej i właściwości hydrogeologicznych obliczono wartości współczynnika przewodności cieplnej λ. W efekcie opracowano 12 map geotermicznych w cięciach głębokościowych do: 40, 70, 100 i 130 m, ukazujących rozkład przestrzenny średniej wartości współczynnika mocy cieplnej [W/m] i średniej wartości przewodności cieplnej skał λ [W/m∙K], które stanowią pomoc w lokalizacji i optymalizacji wydajności instalacji gruntowych pomp ciepła.This paper presents the results of the TransGeoTherm – Geothermal Energy for transboundary development of the Nysa Region. Pilot project, implemented by the Polish Geological Institute–National Research Institute and the Saxon State Agency for Environment, Agriculture and Geology for the area of about 1000 km2, within the Polish-Saxon transboundary region nearby Zgorzelec and Görlitz. This aimed at enhancing the use of shallow geothermal energy with the support of publically available geothermal maps. The analysis of geological and hydrogeological data of 5,146 boreholes and geophysical data allowed, for the construction of a 3D geological model up to the depth of about 200 m with help of the GOCAD® software. The values of the thermal conductivity λ were determined for 75 units based on their lithostratigraphic classification and hydrogeological parameters. In effect 12 geothermal maps for the depths up to 40, 70, 100 and 130 meters, showing spatial variation of an average heat extraction rate (thermal power coefficient) [W/m] and an average value of thermal conductivity of the rocks λ [W/m∙K] were produced. Those provide valuable support to place and optimize performance of the ground source heat pumps