Template-Type: ReDIF-Article 1.0 Author-Name: P. Poltronieri Author-Workplace-Name: Consiglio Nazionale delle Ricerche, Instituto di Scienze delle Produzioni Alimentari, Lecce, Italy Author-Name: M.D. de Blasi Author-Workplace-Name: Consiglio Nazionale delle Ricerche, Instituto di Scienze delle Produzioni Alimentari, Lecce, Italy Author-Name: O.F. D'Urso Author-Workplace-Name: Biotecgen, Ecotekne, Lecce, Italy Title: Detection of Listeria monocytogenes through real-time PCR and biosensor methods Abstract: Listeria monocytogenes is a foodborne pathogen causing listeriosis, especially in sensitive individuals such as children, pregnant women and persons with compromised immune systems. This pathogen has been isolated from different food products, but milk products surely play a major role in the epidemiology of this foodborne disease. Identification traditionally involved culture methods based on selective enrichment and plating followed by the characterization of Listeria spp. based on colony morphology, sugar fermentation and haemolytic properties. These methods are the gold standard, but in the last years more rapid tests were developed based on antibodies (ELISA) or molecular techniques (PCR or DNA hybridization). More recently, molecular methods were developed that target RNA rather than DNA, such as RT-PCR, real time PCR or nucleic acid sequence-based amplification (NASBA). In this review, real-time PCR assays, protein chip methods and label-free SPR immunosensors were compared for their application in bacterial detection. Keywords: Listeria monocytogenes, real-time PCR, protein arrays, surface plasmon resonance Journal: Plant, Soil and Environment Pages: 363-369 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/139/2009-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/139/2009-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0001.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:139-2009-PSE Template-Type: ReDIF-Article 1.0 Author-Name: P. Baldrian Author-Workplace-Name: Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Prague, Czech Republic Title: Microbial enzyme-catalyzed processes in soils and their analysis Abstract: Currently, measuring enzyme activities in soils or other lignocellulose-based materials is technically feasible; this measurement is particularly suitable for evaluating soil processes of biopolymer (cellulose, hemicelluloses, lignin, chitin and others) degradation by microbes and for assessing cycling and mobilization of principal nutrients including nitrogen, phosphorus and sulfur. With some considerations, assay methods can provide reliable information on the concentration of enzymes in soil or the rates of enzyme-catalyzed processes. Enzyme analyses in recent studies demonstrated a high level of spatial variability of soil enzyme activity both in depth and in space. The vertical gradients of enzyme activities are most developed in forest soils. Furthermore, enzyme activity in soils is regulated by seasonally-dependent variables such as temperature, moisture and the input of fresh litter. While several enzymes are widely produced by different groups of soil microorganisms, some of them can be used as indicators of the presence or activity of specific microbial taxa. Keywords: Keywords: assay methods, ecology, extracellular enzymes, fungi, lignocellulose, litter, soil microorganisms Journal: Plant, Soil and Environment Pages: 370-378 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/134/2009-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/134/2009-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0002.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:134-2009-PSE Template-Type: ReDIF-Article 1.0 Author-Name: M. Kyselková Author-Workplace-Name: Universitéde Lyon, F-69622, Lyon, France Author-Workplace-Name: UniversitéLyon 1, Villeurbanne, France Author-Workplace-Name: CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France Author-Name: J. Kopecký Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Author-Name: M. Ságová-Marečková Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Author-Name: G.L. Grundmann Author-Workplace-Name: Universitéde Lyon, F-69622, Lyon, France Author-Workplace-Name: UniversitéLyon 1, Villeurbanne, France Author-Workplace-Name: CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France Author-Name: Y. Moënne-Loccoz Author-Workplace-Name: Universitéde Lyon, F-69622, Lyon, France Author-Workplace-Name: UniversitéLyon 1, Villeurbanne, France Author-Workplace-Name: CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France Title: Oligonucleotide microarray methodology for taxonomic and functional monitoringof microbial community composition Abstract: Microarray analysis is a cultivation-independent, high-throughput technology that can be used for direct and simultaneous identification of microorganisms in complex environmental samples. This review summarizes current methodologies for oligonucleotide microarrays used in microbial ecology. It deals with probe design, microarray manufacturing, sample preparation and labeling, and data handling, as well as with the key features of microarray analysis such as specificity, sensitivity and quantification potential. Microarray analysis has been validated as an effective approach to describe the composition and dynamics of taxonomic and functional microbial communities, in environments including soil, compost, sediment, air or humans. It is now part of the technical arsenal available to address key issues in microbial community ecology, ranging from biogeography to ecosystem functioning. Keywords: Keywords: oligonucleotide microarray, taxonomic microarray, functional microarray, microbial community Journal: Plant, Soil and Environment Pages: 379-388 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/140/2009-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/140/2009-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0003.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:140-2009-PSE Template-Type: ReDIF-Article 1.0 Author-Name: P. Štursa Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Name: O. Uhlík Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Workplace-Name: Institute of Organic Chemistry and Biochemistry CAS, Prague, Czech Republic Author-Name: V. Kurzawová Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Name: J. Koubek Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Name: M. Ionescu Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Name: M. Strohalm Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Workplace-Name: Laboratory of Molecular Structure Characterization, Institute of Microbiology CAS, Prague, Czech Republic Author-Name: P. Lovecká Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Name: T. Macek Author-Workplace-Name: Institute of Organic Chemistry and Biochemistry CAS, Prague, Czech Republic Author-Name: M. Macková Author-Workplace-Name: Department of Biochemistry and Microbiology, Institute of Chemical Technology in Prague, Prague, Czech Republic Author-Workplace-Name: Institute of Organic Chemistry and Biochemistry CAS, Prague, Czech Republic Title: Approaches for diversity analysis of cultivable and non-cultivable bacteriain real soil Abstract: Until recently, investigators had no idea how accurately cultivated microorganisms represented the overall microbial diversity. The cultivation-dependent approach is limited by the fact that the overwhelming majority of microorganisms present in soil cannot be cultivated under laboratory conditions. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. There is a vast amount of information held within the genomes of cultivable and non-cultivable microorganisms, and new methods based on analysis of DNA allow to investigate this potential. In this work we show some aspects, advantages and disadvantages of classical and new approaches in taxonomical and functional description of bacteria present in natural microbial assemblages on the example of cultivable bacteria isolated from rhizosphere of plants, tobacco and black nightshade, planted in PCB contaminated soil. Biochemical analysis of isolates showed 8 different bacterial species. This identification was compared by discrimination using MALDI-TOF mass spectrometry and identity evaluation after sequencing of 16S rDNA. Six strains from original number of 8 were positively identified after 16S rDNA sequencing and their phylogenetic relations were compared. These analyses confirmed closed relations of all species (two of isolates exhibited the same characteristics and were discriminated as the same species Pseudomonas stutzeri) and also of Burkholderia xenovorans LB 400, a well-known PCB degrader. Nevertheless, only two isolates gave a positive reaction after amplification of the biphenyl dioxygenase gene and exhibited potential to degrade PCB. These results indicate that only a subset of the recovered molecular information, derived from active population based on molecular and functional analysis is relevant to microbial ecology. Keywords: microbial diversity, cultivable bacteria, non-cultivable bacteria, SIP, DGGE, TGGE, T-RFLP, MALDI-TOF mass spectrometry Journal: Plant, Soil and Environment Pages: 389-396 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/136/2009-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/136/2009-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0004.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:136-2009-PSE Template-Type: ReDIF-Article 1.0 Author-Name: J. Kopecký Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Author-Name: G. Novotná Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Author-Name: M. Ságová-Marečková Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Title: Modification of the terminal restriction fragment length polymorphism analysisfor assessment of a specific taxonomic group within a soil microbial community Abstract: A double color terminal restriction fragment length polymorphism analysis was applied for the diversity assessment of a complex bacterial community in a deciduous forest soil. Application of the second label was used to project a specific taxonomic group of bacteria, actinomycetes in our case, to the universal fingerprint. The diversity of actinomycetes was evaluated directly as a percentage of the whole bacterial community by comparing the corresponding terminal fragments of the same length. Keywords: bacterial community, Actinobacteria, terminal restriction fragment length polymorphism Journal: Plant, Soil and Environment Pages: 397-403 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/1012-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/1012-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0005.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:1012-PSE Template-Type: ReDIF-Article 1.0 Author-Name: W. Ripl Author-Workplace-Name: Technische Universität Berlin, Teltow, Germany Author-Name: M. Eiseltová Author-Workplace-Name: Crop Research Institute, Prague, Czech Republic Title: Sustainable land management by restoration of short water cycles and preventionof irreversible matter losses from topsoils Abstract: Sustainable land management requires that water and matter (nutrients and base cations) are efficiently recycled within ecosystems so that irreversible losses of matter from topsoils are minimised. Matter losses are connected to water flow. The division of water into evapotranspiration that is loss-free, and seepage to groundwater or surface water flow that both carry material losses, is decisive in determining total losses of dissolved matter in a given catchment. Investigations of areal matter losses confirmed the instrumental role of vegetation cover. Areal matter losses measured in agricultural catchments in Germany were on average between 1-1.5 tons of dissolved matter per ha per year, i.e. some 50 to 100 times higher than those from unmanaged land in a virgin forest. Such high losses continuously reduce soil fertility and can hardly be compensated by fertilisation. Some suggestions on how to achieve sustainable management of agricultural land and maintain high soil fertility are presented - the priority is to close water and matter cycles through the incorporation of more natural vegetation cover into our landscapes and to restore the energy-dissipative properties of ecosystems. Keywords: agriculture, energy dissipation, irreversible matter losses, soil fertility, sustainable land management, water dynamics Journal: Plant, Soil and Environment Pages: 404-410 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/133/2009-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/133/2009-PSE.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/pse-200909-0006.txt Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:133-2009-PSE Template-Type: ReDIF-Article 1.0 Author-Name: Václav Stejskal Author-Workplace-Name: Czech University of Life Sciences Prague, Kamýcká 957, 165 21 Prague 6-Suchdol, Czech Republic Author-Name: Pavel Tlustoš Author-Workplace-Name: Czech University of Life Sciences Prague, Kamýcká 957, 165 21 Prague 6-Suchdol, Czech Republic Title: Introduction of Scientific Committee on Phytosanitary and Environment Journal: Plant, Soil and Environment Pages: 411-412 Volume: 55 Issue: 9 Year: 2009 DOI: 10.17221/2793-PSE File-URL: http://pse.agriculturejournals.cz/doi/10.17221/2793-PSE.html File-Format: text/html Handle: RePEc:caa:jnlpse:v:55:y:2009:i:9:id:2793-PSE