Search results for " 16S"
showing 10 items of 336 documents
Diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater
1999
Chlorophenol-degrading bacteria from a long-term polluted groundwater aquifer were characterized. All isolates degraded 2,4,6-trichlorophenol and 2,3,4,6-tetrachlorophenol at concentrations detected in the contaminated groundwater (10 mg 1(-1)). Pentachlorophenol was degraded by three isolates when present alone. In two gram-positive isolates, 2,3,4,6-tetrachlorophenol was required as an inducer for the degradation of pentachlorophenol. The gram-positive isolates were sensitive to pentachlorophenol, with an IC50 value of 5 mg/l. Isolates belonging to the Cytophaga/Flexibacter/Bacteroides phylum had IC50 values of 25 and 63 mg/l. Isolates belonging to alpha-, beta- and gamma-Proteobacteria g…
Streptococcus lactarius sp. nov., isolated from breast milk of healthy women.
2011
Three strains of a hitherto-unknown, Gram-stain-positive coccus were recovered from the milk of three non-related healthy women. The isolates shared 99% 16S rRNA gene sequence similarity with sequences from uncultured members of the Lactobacillales and Streptococcus. The closest sequence corresponding to a defined species was that of Streptococcus peroris GTC 848T, with a similarity of 98%. A partial sequence (488 bp) of the tuf gene also showed 97% similarity with that of S. peroris CCUG 39814T. The combined 16S rRNA/tuf-based phylogeny revealed that all the isolates grouped in a statistically well-supported cluster separate from S. peroris. Enzyme activity profiles as well as fermentation…
Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.
2013
Four strains (M15∅_3, M17(T), M49 and R37(T)) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF…
Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB sequences of type and clinical strains suggests the cla…
2010
Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ≥2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous. However, more than one distinct rpoB clade could be defined among strains belonging to the species Proteus vulgaris (two clades), Providencia alcalifaciens (two clades) and Pro…
Molecular analysis of the dominant lactic acid bacteria of chickpea liquid starters and doughs and propagation of chickpea sourdoughs with selected W…
2020
Abstract Fermented chickpea liquid is used as a leavening agent in chickpea bread production. In the present study, traditional chickpea liquid starter and dough samples were collected from bakeries in Turkey and microbiologically investigated. Culture-independent analysis for microbiota diversity, performed by MiSeq Illumina, identified Clostridium perfringens as major group in all samples, while Weissella spp. Dominated LAB community. A culture-dependent methodology was applied and 141 isolates were confirmed to be members of the LAB group based on 16s rRNA gene sequence analysis. In particular, 11 different LAB species were identified confirming the high frequency of isolation of weissel…
Occurrence of rhizobia in the gut of the higher termite Nasutitermes nigriceps
2006
Wood-eating termites feed on a diet highly deficient in nitrogen. They must complement their diet with the aid of nitrogen-fixing bacteria. Nitrogen fixation in the gut has been demonstrated, but information about nitrogen-fixing bacteria in pure culture is scarce. From the higher termite Nasutitermes nigriceps the symbiotic bacterial strain M3A was isolated, which thrives in the hindgut contents. The Gram-negative strain exhibited similarities to the species of the genus Ensifer (including Sinorhizobium) on the basis of morphological and physiological/biochemical features. The 16S rRNA gene analysis showed the highest sequence similarity of the isolate M3A to Ensifer adhaerens (>99%; ATCC …
Identification of Beijerinckia fluminensis strains CIP 106281T and UQM 1685T as Rhizobium radiobacter strains, and proposal of Beijerinckia doeberein…
2009
During the course of a research project with free-living, nitrogen-fixing bacteria, we determined the 16S rRNA gene sequence of Beijerinckia fluminensis strains UQM 1685T and CIP 106281T and discovered that they were only 90.6–91.2 % similar to the sequences of strains of other Beijerinckia species and subspecies. Moreover, the highest similarity to these sequences (99.7 %) corresponded to strains of Rhizobium radiobacter (including Agrobacterium tumefaciens). Other diagnostic features confirmed that the two strains have the same origin but do not descend from the nomenclatural type. At the same time, B. fluminensis LMG 2819 was characterized and it was found that its properties also do not…
Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodologic…
2001
ABSTRACT Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extracti…
DNA extraction from soils: old bias for new microbial diversity analysis methods.
2001
ABSTRACT The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure o…
Shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to Hg(II) spiking in soil.
2003
In a previous experiment [Ranjard et al. (2000) FEMS Microbiol Ecol 31:107–115], the spatial heterogeneity of a mercury impact on soil bacterial community was revealed by an increase of mercury-resistant (HgR) bacterial numbers in the outer fraction and the sand fractions when compared to those in the silt fractions. The objectives of the present study were (i) to investigate whether mercury exposure affects the diversity and the distribution within the various fractions of the HgR populations and (ii) to evaluate the contribution of the HgR populations to the overall community adaptation. A total of 236 strains isolated before (104 isolates) and 30 days (132 isolates) after spiking were ch…