INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2011
A Gram-negative-staining, short-rod-shaped, floc-forming bacterium, designated strain RB3-7(T), w... more A Gram-negative-staining, short-rod-shaped, floc-forming bacterium, designated strain RB3-7(T), was isolated from a laboratory-scale activated sludge system treating coke plant effluent. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate was distantly related (≤ 95.8 % similarity) to Ottowia thiooxydans K11(T) within the family Comamonadaceae. Strain RB3-7(T) was catalase- and oxidase-positive and non-motile. The predominant fatty acids were C₁₆:₀, cyclo C₁₇:₀, C₁₈:₁ω7c and C₁₆:₁ω7c, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain RB3-7(T) was 68.5 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain RB3-7(T) is considered to represent a novel species of the genus Ottowia, for which the name Ottowia pentelensis sp. nov. is proposed. The type strain is RB3-7(T) ( = DSM 21699(T) = NCAIM B 02336(T)).
The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the p... more The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing in Mangalica pigs where the exclusion probability is 0.999115 if one parent is known and the probability of identity is 1.54×10 -23 .
... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bott... more ... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bottles as supplementary substrates. ... In the HS-MOLA microcosms, a slow but steady decrease of sulfate concentration was observed. ...
Each step of a molecular environmental microbiology study is prone to errors, though the qualitat... more Each step of a molecular environmental microbiology study is prone to errors, though the qualitative and quantitative biases of PCR amplification could result in the most serious biases. One has to be aware of this fact, and well-characterized PCR biases have to be avoided by using target-optimized PCR protocols. The most important tasks are primer and thermal profile optimization. We have shown that primer mismatches, even in the case of universal primers, can cause almost complete missing of common taxa from clone libraries, for example. Similarly high annealing temperatures can drastically distort community composition of the sample in the PCR product. Strategies of primer selection and PCR thermal profile design are discussed in detail.
The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by t... more The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora. Actinobacteria and Bacilli [4,, but plating at higher Microb Ecol
International Biodeterioration & Biodegradation, 2006
... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bott... more ... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bottles as supplementary substrates. ... In the HS-MOLA microcosms, a slow but steady decrease of sulfate concentration was observed. ...
DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) w... more DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) was isolated from the background smear rather than from discrete bands of the DGGE gel. The ''interband'' region was considered as a potential source of less dominant members of natural microbial communities. Surprisingly, instead of detecting new bands from the re-amplified PCR products, patterns very similar to the original ones were obtained regardless of the position of the ''interband'' region. The results suggest that the separation of amplicons by DGGE may not be perfect and band re-amplification based sequence analyses need careful interpretation. (M. Nikolausz). www.fems-microbiology.org FEMS Microbiology Letters 244 (2005) 385-390
In the attempt to explore complex bacterial communities of environmental samples, primers hybridi... more In the attempt to explore complex bacterial communities of environmental samples, primers hybridizing to phylogenetically highly conserved regions of 16S rRNA genes are widely used, but differential amplification is a recognized problem. The biases associated with preferential amplification of multitemplate PCR were investigated using 'universal' bacteria-specific primers, focusing on the effect of primer mismatch, annealing temperature and PCR cycle number. The distortion of the template-to-product ratio was measured using predefined template mixtures and environmental samples by terminal restriction fragment length polymorphism analysis. When a 1 : 1 genomic DNA template mixture of two strains was used, primer mismatches inherent in the 63F primer presented a serious bias, showing preferential amplification of the template containing the perfectly matching sequence. The extent of the preferential amplification showed an almost exponential relation with increasing annealing temperature from 47 to 61 1C. No negative effect of the various annealing temperatures was observed with the 27F primer, with no mismatches with the target sequences. The number of PCR cycles had little influence on the template-to-product ratios. As a result of additional tests on environmental samples, the use of a low annealing temperature is recommended in order to significantly reduce preferential amplification while maintaining the specificity of PCR.
In the present study, the species composition and potential metabolic activities of bacterial com... more In the present study, the species composition and potential metabolic activities of bacterial communities of reed Phragmites australis (Cav.) (Trin. ex Steudel) periphyton from Lake Velencei were studied by cultivation-based and metabolic fingerprinting methods. Serially diluted spring biofilm samples were used to test the community-level physiological profiling (CLPP) using BIOLOG microplates, and for plating onto different media. On the basis of their morphological, biochemical, and physiological test results, 173 strains were clustered by numerical analysis. Representatives of amplified ribosomal DNA restriction analysis (ARDRA) groups were identified by their 16S rDNA sequence comparison. Based on the results of the CLPP investigations, regional differences were detected among the utilized substrate numbers and types, parallel with the increase in incubation time. The phenotypic test results of the strains showed considerable variability with respect to the sampling sites and the media used for cultivation. The most frequently isolated strains were identified as members of genera Agrobacterium, Pseudomonas (P. anguilliseptica, P. marginalis, P. alcaligenes, P. fragi) with aerobic or facultative anaerobic respiratory metabolism, and the species Aeromonas sobria and A. veronii with strong facultative fermentative metabolism. Other strains were identified as Gram-positive Arthrobacter, Bacillus, and Kocuria species. The rarely isolated strains were members of b-Proteobacteria
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2011
A Gram-negative-staining, short-rod-shaped, floc-forming bacterium, designated strain RB3-7(T), w... more A Gram-negative-staining, short-rod-shaped, floc-forming bacterium, designated strain RB3-7(T), was isolated from a laboratory-scale activated sludge system treating coke plant effluent. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate was distantly related (≤ 95.8 % similarity) to Ottowia thiooxydans K11(T) within the family Comamonadaceae. Strain RB3-7(T) was catalase- and oxidase-positive and non-motile. The predominant fatty acids were C₁₆:₀, cyclo C₁₇:₀, C₁₈:₁ω7c and C₁₆:₁ω7c, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain RB3-7(T) was 68.5 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain RB3-7(T) is considered to represent a novel species of the genus Ottowia, for which the name Ottowia pentelensis sp. nov. is proposed. The type strain is RB3-7(T) ( = DSM 21699(T) = NCAIM B 02336(T)).
The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the p... more The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing in Mangalica pigs where the exclusion probability is 0.999115 if one parent is known and the probability of identity is 1.54×10 -23 .
... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bott... more ... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bottles as supplementary substrates. ... In the HS-MOLA microcosms, a slow but steady decrease of sulfate concentration was observed. ...
Each step of a molecular environmental microbiology study is prone to errors, though the qualitat... more Each step of a molecular environmental microbiology study is prone to errors, though the qualitative and quantitative biases of PCR amplification could result in the most serious biases. One has to be aware of this fact, and well-characterized PCR biases have to be avoided by using target-optimized PCR protocols. The most important tasks are primer and thermal profile optimization. We have shown that primer mismatches, even in the case of universal primers, can cause almost complete missing of common taxa from clone libraries, for example. Similarly high annealing temperatures can drastically distort community composition of the sample in the PCR product. Strategies of primer selection and PCR thermal profile design are discussed in detail.
The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by t... more The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora. Actinobacteria and Bacilli [4,, but plating at higher Microb Ecol
International Biodeterioration & Biodegradation, 2006
... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bott... more ... Five hundred mg L −1 (dry weight) whey (WHEY) and molasses (MOLA) were added to adequate bottles as supplementary substrates. ... In the HS-MOLA microcosms, a slow but steady decrease of sulfate concentration was observed. ...
DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) w... more DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) was isolated from the background smear rather than from discrete bands of the DGGE gel. The ''interband'' region was considered as a potential source of less dominant members of natural microbial communities. Surprisingly, instead of detecting new bands from the re-amplified PCR products, patterns very similar to the original ones were obtained regardless of the position of the ''interband'' region. The results suggest that the separation of amplicons by DGGE may not be perfect and band re-amplification based sequence analyses need careful interpretation. (M. Nikolausz). www.fems-microbiology.org FEMS Microbiology Letters 244 (2005) 385-390
In the attempt to explore complex bacterial communities of environmental samples, primers hybridi... more In the attempt to explore complex bacterial communities of environmental samples, primers hybridizing to phylogenetically highly conserved regions of 16S rRNA genes are widely used, but differential amplification is a recognized problem. The biases associated with preferential amplification of multitemplate PCR were investigated using 'universal' bacteria-specific primers, focusing on the effect of primer mismatch, annealing temperature and PCR cycle number. The distortion of the template-to-product ratio was measured using predefined template mixtures and environmental samples by terminal restriction fragment length polymorphism analysis. When a 1 : 1 genomic DNA template mixture of two strains was used, primer mismatches inherent in the 63F primer presented a serious bias, showing preferential amplification of the template containing the perfectly matching sequence. The extent of the preferential amplification showed an almost exponential relation with increasing annealing temperature from 47 to 61 1C. No negative effect of the various annealing temperatures was observed with the 27F primer, with no mismatches with the target sequences. The number of PCR cycles had little influence on the template-to-product ratios. As a result of additional tests on environmental samples, the use of a low annealing temperature is recommended in order to significantly reduce preferential amplification while maintaining the specificity of PCR.
In the present study, the species composition and potential metabolic activities of bacterial com... more In the present study, the species composition and potential metabolic activities of bacterial communities of reed Phragmites australis (Cav.) (Trin. ex Steudel) periphyton from Lake Velencei were studied by cultivation-based and metabolic fingerprinting methods. Serially diluted spring biofilm samples were used to test the community-level physiological profiling (CLPP) using BIOLOG microplates, and for plating onto different media. On the basis of their morphological, biochemical, and physiological test results, 173 strains were clustered by numerical analysis. Representatives of amplified ribosomal DNA restriction analysis (ARDRA) groups were identified by their 16S rDNA sequence comparison. Based on the results of the CLPP investigations, regional differences were detected among the utilized substrate numbers and types, parallel with the increase in incubation time. The phenotypic test results of the strains showed considerable variability with respect to the sampling sites and the media used for cultivation. The most frequently isolated strains were identified as members of genera Agrobacterium, Pseudomonas (P. anguilliseptica, P. marginalis, P. alcaligenes, P. fragi) with aerobic or facultative anaerobic respiratory metabolism, and the species Aeromonas sobria and A. veronii with strong facultative fermentative metabolism. Other strains were identified as Gram-positive Arthrobacter, Bacillus, and Kocuria species. The rarely isolated strains were members of b-Proteobacteria
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