Comparison of the 16S rRNA gene sequence determined for Chitinophaga pinensis showed that this species is most closely related to Flexibacter filiformis in the Flexibacter-Bacteroides-Cytophaga phylum. These two chitinolytic bacteria, which are characterized by transformation into spherical bodies on ageing, belong to a strongly supported lineage that also includes Cytophaga arvensicola, Flavobacterium ferrugineum and Flexibacter sancti. The lineage is distinct from the microcyst-forming species Sporocytophaga myxococcoides.
The phylogenetic relationships among the species of Caulobacter, Asticcacaulis and Brevundimonas were studied by comparison of their 16S rDNA sequences. The analysis of almost complete sequences confirmed the early evolutionary divergence of the freshwater and marine species of Caulobacter reported previously [Stahl, D. A., Key, R., Flesher, B. & Smit, J. (1992). J Bacteriol 174, 2193-2198]. The freshwater species formed two distinct clusters. One cluster contained the species Caulobacter bacteroides, Caulobacter crescentus, Caulobacter fusiformis and Caulobacter henricii. C. bacteroides and C. fusiformis are very closely related (sequence identity 99.8%). The second cluster was not exclusive and contained the species Caulobacter intermedius, Caulobacter subvibrioides and Caulobacter variabilis, as well as Brevundimonas diminuta and Brevundimonas vesicularis. The marine species Caulobacter halobacteroides and Caulobacter maris were very closely related, with a sequence identity of 99.7%. These two species were most closely but distantly related to the marine hyphal/budding bacteria Hyphomonas jannaschiana and Hirschia baltica, which formed a deep phylogenetic line with Rhodobacter sphaeroides and Rhodobacter capsulatus. Caulobacter leidyia is unrelated to the other species of Caulobacter and belongs to the alpha-4 subclass of the Proteobacteria, forming a distinct cluster with Asticcacaulis excentricus and Asticcacaulis biprosthecium. The taxonomic implications of the polyphyletic nature of the genus Caulobacter and the absence of a type culture for the type species of the genus, Caulobacter vibrioides, are discussed.
Sequence heterogeneities of variable positions located at regions V1 and V6 56 cloned 16S rRNA genes were determined from six Escherichia coli strain These nucleotides were involved in secondary structure base-pairing of stem-loops. Compensatory and single mutations have occurred but seconat structure was conserved. Eight different sequences were found in the stem a region V1 indicating that in these sites mutation rates are higher than those homogenization processes. Region V6 showed two different structures (V6-I and V6-II) although heterogeneities were determined in nine sites. Strains ECOR52 and ECOR56 only showed the V6-I sequence, ECOR35 showed V6-II, whereas clones from ECOR42 and ECOR49 showed both types of V6 structre Results were confirmed by PCR using V6 sequence-specific probes. Stem V6-I was also found in 16S rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6 seems to be homogenized in all rrn operons of the multigene family of strai ECOR35 producing effects of distortion in the molecular clock, similar to tho that homoplasies could produce. V6 sequence-specific probes were applied to the 72 ECOR strains: half showed both V6-I and V6-II, and the rest had one or another. Only strain ECOR24 did not yield products in the PCR test and sequencing of 12 cloned 16S rRNA genes revealed a third form, V6-III, also found in the RDP. Concerted evolution by homogenization of the rRNA fami may induce chronometric distortions responsible for a loss of ultrametricity phylogenetic trees, particularly, of very closely related micro-organisms.
The membrane lipids of Listeria innocua, Listeria monocytogenes, Listeria seeligeri and Listeria welshimeri were fractionated on DEAE-cellulose and purified by chromatography on silica gel and/or preparative TLC. The lipid structures were elucidated by chemical and chromatographic means. The polar lipid composition of the four listeria species was similar. Phospholipids predominated. They consisted of phosphatidylglycerol, L-lysylphosphatidylglycerol, cardiolipin [bis(phosphatidyl)glycerol] and L-lysylcardiolipin. A phospholipid more polar than cardiolipin, possibly two L-lysyl derivatives of it, sn-glycero-1-phosphoglycolipid, its D-alanyl derivative, and polyprenol phosphate were also detected. Towards the end of exponential growth, the relative amounts of cardiolipin and L-lysylcardiolipin increased, approaching 47-78% lipid phosphorus with a ratio of L-lysylcardiolipin to cardiolipin of 0.25-1.6. As shown by fast atom bombardment-mass spectrometry, cardiolipin and L-lysylcardiolipin consisted of five molecular species due to various fatty acid combinations. L-Lysylcardiolipin has so far not been found in nature. It belongs to the recently discovered class of substituted cardiolipins. Its occurrence in the four listeria species tested shows that it is a characteristic lipid component of the L. monocytogenes line of descent. Further studies on the lipid pattern of members of the other descent line are required to decide whether lysylcardiolipin can serve as a genus-specific chemotaxonomic marker for listeriae.
The 16S rDNA sequences of 20 novel isolates of members of the order Planctomycetales were compared to those of the type strains of described planctomycete species and 22 planctomycete isolates for which the 16S rDNA sequences had been previously determined. The novel isolates could be assigned to several phylogenetically broad groups, four of which are defined by the genera Gemmata, Isosphaera, Planctomyces and Pirellula. To evaluate polyamines as a chemotaxonomic marker within this order, the polyamine pool was determined for six planctomycete reference species and for 20 planctomycete isolates. All analysed members of the order Planctomycetales contained significant amounts of polyamines. sym-Homospermidine (HSPD) is present in all strains except Planctomyces limnophilus and related strains, which had high amounts of putrescine (PUT) as the dominant polyamine component. The distribution of PUT, HSPD and spermidine reflects the phylogenetic diversity within the Planctomycetales as closely related representatives of the phylogenetic groups defined by described species and novel isolates exhibit similar polyamine patterns. Determination of the DNA base composition revealed G+C contents of >60 mol% for members of Gemmata and Isosphaera whereas, except for two isolates, strains which are phylogenetically associated with Planctomyces and Pirellula had G+C contents of 51-57 mol%.
The nucleotide sequences of the 16S rRNA gene (rDNA) in 38 taxa of the genus Staphylococcus were compared phylogenetically. Based on phylogenetic tree analysis, staphylococcal species were divided into 12 cluster groups. These cluster groups were in very good agreement with species groups determined by DNA-DNA reassociation studies. These genealogical classifications were consistent with the results of the production of coagulase or oxidase and with resistance to novobiocin. These suggest that the phylogenetic relationship of the genus Staphylococcus is accurately represented by the results obtained from the sequence analysis of 16S rDNA.