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Použití specifických aktinomycetových PCR primerů k charakterizaci bakteriálních společenstev exkrementů žížal
Hill, P. ; Krištůfek, Václav ; Feijoo, A. M. ; Gallego, G.
Tropical geophageous earthworms stimulate soil bacterial activity in soil that they ingest; it is uncertain if they affect the whole bacterial population or only subgroups. We sampled .i.Martiodrillus heterostichon, Polypheretima elongata./i. and bulk soil from a Bamboo plantation near Cali, Colombia. Pots of 1500 g of an adjacent tobacco field soil were brought to field capacity and two worms of each species placed in each pot. .i.Martiodrillus./i. gut contents and wormcasts from the soil surface and within tunnels were sampled after three months. The soil was maintained at field capacity for a further five months during which the worms continued to produce casts. Worm cast Amplified ribosomal DNA restriction analysis ARDRA (using Tag I) with actinomycete specific primers gave two strong bands at approximately 750 and 370 bp. ARDRA patterns from the three bamboo grove and four field soils had several additional bands notably at 140 and 126 bp.
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Ovlivňuje obsah buněčných mastných kyselin a enzymů jeskynních bakterií potravní preferenci .i.Enchytraeus crypticus./i. (Oligochaeta, Enchytraeidae)?
Krištůfek, Václav ; Elhottová, Dana ; Šustr, Vladimír ; Lasák, R. ; Kováč, L. ; Mock, A. ; Luptáčik, P.
Cellular fatty acid screening (MIDI System) of 93 bacterial strains isolated from the Domica Cave in the Slovak Karst region ( Slovakia) showed that three bacterial strains (.i.Chryseobacterium./i. sp., .i.Enterobacter amnigenus, Rhodococcus./i. sp.) produce polyunsaturated fatty acids (PUFA) 18:3w6 and 20:4w6. These species (along with a non PUFA producer, .i.Rhizobium./i. sp.) were isolated from the gut content or body surface of .i.Mesoniscus graniger./i. (Frivaldsky, 1865) (Crustacea: Isopoda). Bacterial strains were tested for activity of nine saccharolytic enzymes. .i.Chryseobacterium./i. sp. showed amylase, maltase and cellobiase activity, other bacterial species only had amylase activity. As PUFA and enzymes may be essential for animal growth and development, colonies of the four strains were grown for further use in laboratory food selection and reproduction experiments with .i.E. crypticus./i..
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Analýza bakteriálních izolátů a DNA ze společenstva ze čtyř různých sukcesních ploch na území po těžbě hnědého uhlí
Chroňáková, Alica ; Halbritter, A. ; Krištůfek, Václav ; Biró, B.
Microbial communities of 4 different stages (initial [0 years after heaping of the excavated material], early [10], middle [20] and late [42] of primary succession process were studied. They were characterized by genotyping methods: ARDRA - Amplified ribosomal DNA restriction analyses and box-PCR - genomic fingerprinting using specific primer for boxA-element. Box-PCR method was chosen for comparison of methodological approaches used for characterization of heterotrophic bacterial communities. ARDRA patterns of eubacterial communities were so complex and there weren´t shown any differences among individual communities on different stages of primary succession process. Actinomycetes communities were analyzed using two sets of primers: Actinomycetes 1. (243F-1378R, Heuer et al. 1997) and Actinomycetes 2. (243F-A3R; Monciardini et al. 2002). Fingerprints, which were obtained using both of actinomycetes specific primers, showed differences between communities on the early and later stages of primary succession process. Boy-PCR analysis is still in data processing and will be published later
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Charakteristika různorodých půd a sedimentů užitím specifických aktinomycetových r-DNA PCR primerů
Hill, P. ; Krištůfek, Václav ; Caballero, S. ; Kroetsch, D. J. ; Rauch, Ota
Most molecular biological studies of the soil characterise a few soils or sediments under a range of treatments or over a limited time. It is difficult to compare results between studies due to variations in DNA extraction method and PCR conditions. High diversity of the soil bacterial population means that it is impossible to characterise many soils through cloning and sequencing and that finger prints are often blurred and difficult to interpret. We compare a broad range of soils and zoo/anthropogenic sediments with actinomycete specific primers. ARDRA and cloning showed that these primers amplified mainly verrucomicrobia from tropical, temperate and sub-arctic soils and actinomycetes from biologically active and urban street sediments. We found two new groups that were broadly distributed in soils: a new actinomycete family and the AD-3 candidate division that was found in acid tropical and sub-arctic soils
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Použití metody Sherlock MIS System pro identifikaci bakteriálních izolátů z lesního opadu – předběžné výsledky
Jirout, Jiří ; Petrásek, Jiří ; Elhottová, Dana ; Krištůfek, Václav ; Nováková, Alena ; Rusek, Josef
This work has been related to the effect of climatic changes (especially warming) on communities of forest litter bacteria. We simulated this effect with use of litter bags with beech and/or oak litter transported to beech and spruce forest. After 2, 6 and 12 months of exposition we collected and analysed the samples. We measured quantitative and qualitative characteristics of bacteria and micromycetes community structure in all variants of forest/litter combinations (number of CFU, description of bacterial morphotypes, identification of dominant bacterial morphotypes with MIDI Sherlock Microbial Identification System). We found out that there were differencies in diversity in all variants in exposition time. From the first to the third sampling the CFU bacterial number has decreased whereas CFU micromycetes number has increased. Multivariate comparison (PCA based on relative distribution of bacterial morphotypes in samples) separated the oak litter bacterial community in spruce forest soil as the most different variant among the others.
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Metodické aspekty studia biodiverzity v půdě
Šimek, Miloslav ; Krištůfek, Václav
Soil has many ecological and human-linked functions which can be fulfilled mostly due to the presence of countless living creatures - soil biota. Diversity of soil organisms is often linked to other important soil attributes, e.g. fertility, productivity, resilience, quality and health, as well as soil degradation. In this paper, concept of soil biodiversity is analysed and traditional and current methodological approaches in studying soil biodiversity are listed and briefly discussed
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