). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl 2 purification and in 93% of cases by the method based on CaCO 3 pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.

The objective of this study was to investigate the effects of 11 active compounds of essential oils (ACEO) on rumen fermentation characteristics and methane production. Two trials were conducted. In trial 1, ACEO (eugenol, carvacrol, citral, limonene, 1,4-cineole, p-cymene, linalool, bornyl acetate, α-pinene, and β-pinene) at a dose of 1,000 μL/L were incubated for 24 h in diluted rumen fluid with a 70:30 forage:concentrate substrate (16.2% crude protein; 36.6% neutral detergent fiber). Three fistulated Holstein cows were used as donors of rumen fluid. The reduction in methane production was observed with nine ACEO (up to 86% reduction) compared with the control (p<0.05). Among these, only limonene, 1,4-cineole, bornyl acetate, and α-pinene did not inhibit volatile fatty acid (VFA) production, and only bornyl acetate produced less methane per mol of VFA compared with the control (p<0.05). In a subsequent trial, the effects on rumen fermentation and methane production of two concentrations (500 and 2,000 μL/L) of bornyl acetate, the most promising ACEO from the first trial, were evaluated using the same in vitro incubation method that was used in the first trial. In trial 2, monensin was used as a positive control. Both doses of bornyl acetate decreased (p<0.05) methane production and did not inhibit VFA production. Positive effects of bornyl acetate on methane and VFA production were more pronounced than the effects of monensin. These results confirm the ability of bornyl acetate to decrease methane production, which may help to improve the efficiency of energy use in the rumen.

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.

Members of the Actinobacteria are among the most important litter decomposers in soil. The site of a waterlogged deciduous forest with acidic soil was explored for actinobacteria because seasonality of litter inputs, temperature, and precipitation provided contrasting environmental conditions, particularly variation of organic matter quantity and quality. We hypothesized that these factors, which are known to influence decomposition, were also likely to affect actinobacterial community composition. The relationship between the actinobacterial community, soil moisture and organic matter content was assessed in two soil horizons in the summer and winter seasons using a 16S rRNA taxonomic microarray and cloning-sequencing of 16S rRNA genes. Both approaches showed that the community differed significantly between horizons and seasons, paralleling the changes in soil moisture and organic matter content. The microarray analysis further indicated that the actinobacterial community of the upper horizon was characterized by high incidence of the genus Mycobacterium. In both horizons and seasons, the actinobacterial clone libraries were dominated (by 80%) by sequences of a separate clade sharing an ancestral node with Streptosporangineae. This relatedness is supported also by some common adaptations, for example, to soil acidity and periodic oxygen deprivation or dryness.

A group of 240-day-old Ross cockerels were used in a 4-week experiment to assess the effect of the fat type on the intestinal digestibility of fatty acids (FAs), the FA profiles of breast meat and abdominal fat, and the mRNA expression of six hepatic lipid-related genes. Experimental diets were supplemented with rapeseed oil, pork lard or palm oil at 60 g/kg. In the control diet, wheat starch was substituted for the fat source. The highest ileal digestibility of the fat and all FAs (except stearic acid) was observed in chickens fed lard. The content of fat in the breast meat of chickens was not significantly influenced by the fat supplements. The FA profiles of breast meat and abdominal fat reflected the FA composition of the diet. In the meat of chickens fed rapeseed oil, oleic acid was the predominant FA. Palmitic acid was the most abundant FA in the meat of chickens fed lard or palm oil. Oleic acid was the most abundant FA in the abdominal fat of all chickens. The highest mRNA expression of desaturases (Δ5-, Δ6- and Δ9-) was observed in chickens fed palm oil. The mRNA expression of hepatic FA synthase was higher in chickens fed palm oil or lard than in chickens fed rapeseed oil. The expression of HMG-CoA reductase was higher in chickens fed palm oil than in those fed rapeseed oil or lard. It can be concluded that rapeseed oil and lard are better sources of lipids than palm oil. These former two sources contain more digestible fatty acids and provide a lower concentration of SFAs in the meat and fat of chickens.