Monitoring of microbial indicator groups in caves through the use of RIDA®COUNT kits

RIDA®COUNT kitsMeasurements of microbiological parameters are not currently widely used for protection, monitoring and preservation of caves although they indicate very well the recent human impact. Here we present a commercially available microbiological kit for cave ecologists, the RIDA®COUNT test kit (R-Biopharm AG, Germany), as a supplementary tool for research and show examples. Simultaneously, lists of microbial indicator groups and cave microhabitats, where this methodology may be applied, are presented. Indicators include certain clinically important human-associated microbes such as Escherichia coli, Salmonella spp. and Staphylococcus aureus that are easy to quantify with basic cultivation methodology. Relatively higher bacterial counts compared to yeast and moulds on RIDA®COUNT test plates indicate recent and pronounced human impact. Swab samples allow detection of gradients of surface microbial colonization and determination of the microbial load on footprints and fingerprints in caves. In our tests, RIDA®COUNT plates for enumeration of yeast and moulds revealed a similar microbial load between unwashed caving boots and human fingerprints on a metal fence. Similarly, total bacterial counts were comparable between these two surfaces, 5,890 CFU/100 cm2 for unwashed boots and 4,340 CFU/100 cm2 for fingerprints on metal fence. Bacterial counts on walking surfaces in show caves can exceed 10,000 CFU/100 cm2 (Postojna Cave). These examples show that quantification of microbial indicator groups revealed increased microbial load and possible biohazard in the underground. This procedure may be widely adopted as a part of a regular monitoring programme in caves

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

BACKGROUND: Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings. RESULTS: Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots. CONCLUSIONS: Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth

Ovlivňuje obsah buněčných mastných kyselin a enzymů jeskynních bakterií potravní preferenci .i.Enchytraeus crypticus./i. (Oligochaeta, Enchytraeidae)?

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.

Culture Collection of Soil Actinomycetes in the Institute of Soil Biology BC ASCR, v.v.i. České Budějovice

The Culture Collection of Actinomycetes in České Budějovice (CCACB) was established in 2006 that serves as a depository for cultures of soil actinomycetes. The cultures can be used for research, industrial applications, education and general scientific interest. Cultures are preserved mainly in glycerol or freeze-dried conserves. CCACB will offer strains of actinomycetes, namely streptomycetes (more than 900 cultures at the present moment), in catalogue of cultures www.upb.cas.cz, www.actinomycetes.cz

Detection of microorganisms in the soil using CARD-FISH (Catalyzed Reporter Deposition - Fluorescence in situ hybridization)

CARD-FISH protocol (Catalyzed Reporter Deposition - Fluorescence in situ Hybridization) for detection of soil microbial community composition was successfully established in the Institute of Soil Biology. CARD-FISH is the relatively new molecular biology tool permitting to quantify distinct groups of microorganisms by hybridization of specific oligonucleotide probes. Compared to classic FISH-protocol the probe-attached enzyme amplifies the fluorescent signal and enables to detect nearly all microorganisms in soil or in organic compounds. As the first, we used this method to determine the bacterial community composition of a dated layer of guano-heap from Domica Cave (Slovak Carst National Park, Slovakia). We quantified the percentuel composition of Archaea, Eubacteria (.i.Planktomycetales, Verrucomicrobiales./i. included) and major bacterial groups (Actinobacteria, proteobacteria, .i.Cytophaga-Flavobacter./i.-Bacteroidetes, Sphingobacteria)

The effects of cultivation conditions on polyphenol compounds levels in potato tubers periderm in varieties differing in their susceptibility to common scab

Field and glasshouse trials were performed in 2000 and 2001 to estimate total polyphenol contents in 15 potato cultivars from two sites that differed in the level of scab incidence. Polyphenol content was determined spectrophotometrically by Folin-Ciocalteau reagent at a wavelength 765 nm in tuber peelings of cultivars less and more susceptible to common scab. The polyphenol content of tuber peeling was influenced by cultivar, site, year and age of tuber periderm and was not influenced by maturity. The highest polyphenol content was observed in potato cultivars less susceptible to the scab. Regression analysis showed that negative relation occurs between polyphenol content and potato scab incidence (P=0,006). The polyphenol content significantly decreased during vegetative period