Standardized procedures must be followed when characterizing, officially describing, and validly naming novel bacteria. For species descriptions, DNA-DNA hybridization still is needed for ...whole-genome comparisons between close relatives, but many established hybridization methods have drawbacks, such as requiring labeled or large amounts of DNA. We evaluated a new technique based on the spectrophotometric method in which renaturation rates are used for calculating the degree of binding, which estimates relatedness. In this new approach, DNA is denatured and reassociated in a real-time PCR thermal cycler and the process monitored fluorimetrically using SYBR Green I dye that selectively binds to double-stranded DNA. We investigated the effects of different parameters on the renaturation rates, such as the quantities of DNA and SYBR Green I used. Then using this technique, we calculated the percent binding for pairs of selected bacterial species representing different taxonomic groups and compared our results with published values. We demonstrated that the SYBR Green I method is useful for describing new species and as a screening tool to quickly identify the relatedness of uncharacterized isolates with similar 16S rRNA gene sequences.
A Gram-negative ultramicrobacterium (designated strain UMB49(T)) was isolated from a 120,000-year-old, 3,042 m deep Greenland glacier ice core using a 0.2 mum filtration enrichment procedure. ...Phylogenetic analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Herminiimonas of the family Oxalobacteraceae of the class Betaproteobacteria. Strain UMB49(T) was most closely related to Herminiimonas saxobsidens (99.6 % sequence similarity), Herminiimonas arsenicoxydans (98.4 %), Herminiimonas aquatilis (97.6 %) and Herminiimonas fonticola (97.9 %). Genomic DNA-DNA hybridization showed low levels of relatedness (below 57 %) to H. saxobsidens and H. arsenicoxydans. Cells of strain UMB49(T) were small thin rods with a mean volume of 0.043 mum(3) and possessed 1 or 2 polar and/or 1-3 lateral very long flagella. The original colony pigmentation was brown-purple but after recultivation the colonies were translucent white to tan coloured. Strain UMB49(T) grew aerobically and under microaerophilic conditions. The strain produced catalase and oxidase, but did not reduce nitrate. Sole carbon sources included citrate, succinate, malate, lactate and alanine. The strain produced acid from l-arabinose, d-arabinose, l-xylose, d-xylose and d-ribose. The DNA G+C content was 59.0 mol%. Based on differential characteristics of strain UMB49(T) and recognized Herminiimonas species, it was concluded that strain UMB49(T) represents a novel species of the genus Herminiimonas, for which the name Herminiimonas glaciei sp. nov. is proposed. The type strain is UMB49(T) (=ATCC BAA-1623(T)=DSM 21140(T)).
A novel, psychrophilic, gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented ...colonies, had an optimal growth temperature of 18 degrees C and grew on a variety of media between -2 and 21 degrees C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest. The G + C content of the genomic DNA was approximately 62 mol%. The cell walls contained ornithine as the diamino acid. The major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. Cells grown at -2 degrees C contained significant amounts of anteiso-C15:1. The major menaquinones found in strain LV3T were MK-11 and MK-12. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain LV3T was a member of the family Microbacteriaceae and related to, but distinct from, organisms belonging to the genera Agreia, Leifsonia and Subtercola. In addition, alignments of 16S rRNA sequences showed that the sequence of strain LV3T contained a 13 bp insertion that was found in only a few related sequences. Based on the low growth temperature, unusual cell shape, distinct 16S rRNA gene sequence and structure and cell-wall amino acid and menaquinone compositions, Rhodoglobus vestalii gen. nov., sp. nov. is proposed, with the type strain LV3T (= ATCC BAA-534T = CIP 107482T).
A small cryptic Lactobacillus helveticus plasmid, pLBL4, was able to reveal restriction fragment length polymorphism in different bacterial species including Lactobacillus species, Bacillus species, ...and Escherichia coli when used as a DNA probe. The observed polymorphism was a result of the combined hybridization of several microsatellite sequences. The 6-bp sequence (TTGTTT) was repeated 12 times, seven of which were concentration within the region between 1791 and 1997 bp of the plasmid sequence. The polymorphic patterns generated with pLBL4 differed from those obtained with M13 DNA in the larger number of bands observed. The results presented here open the possibility of using pLBL4 as a new broad-spectrum polymorphic DNA probe for fingerprint analysis.
The growth of some locally isolated Lactobacillus strains forming D(-) or L(+) lacticacid, Lactobacillus helveticus ATCC 15009 and Lactobacillus del- brueckii subsp. bulgaricus ATCC 11842 was ...examined in different media. L. helveticus and Lactobacillus LBL strains formed atypical protoplast-like cells in LAPT medium, sensitive to SDS and proteinase. Specific morphological changes in the cell wall structure of these variants were revealed by transmission and scanning electron microscopy. The effect of glucose and various salts on their appearance was investigated. The prevalent role of metal cations, especially of Mg(2+), was established.
A small cryptic
Lactobacillus helveticus plasmid, pLBL4, was able to reveal restriction fragment length polymorphism in different bacterial species including
Lactobacillus species,
Bacillus species, ...and
Escherichia coli when used as a DNA probe. The observed polymorphism was a result of the combined hybridization of several microsatellite sequences. The 6-bp sequence (TTGTTT) was repeated 12 times, seven of which were concentrated within the region between 1791 and 1997 bp of the plasmid sequence. The polymorphic patterns generated with pLBL4 differed from those obtained with M13 DNA in the larger number of bands observed. The results presented here open the possibility of using pLBL4 as a new broad-spectrum polymorphic DNA probe for fingerprint analysis.
Cold environments represent the majority of the biosphere on Earth and have been successfully colonized by psychrophilic microorganisms that are able to thrive at low temperatures and to survive and ...even maintain metabolic activity at subzero temperatures. These microorganisms play key ecological roles in their habitats and include a wide diversity of representatives of all three domains (
Bacteria,
Archaea,
Eukarya). In this review, we summarize recent knowledge on the abundance, on the taxonomic and functional biodiversity, on low temperature adaptation and on the biogeography of microbial communities in a range of aquatic and terrestrial cold environments.
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