More than 20 Synechococcus and Cyanobium isolates were obtained from central European subalpine lakes and sequenced for their 16S rRNA gene and part of the phycocyanin operon (cpc), specifically the intergenic spacer (IGS) between cpcB and cpcA, and corresponding flanking regions (cpcBA-IGS). Maximum-likelihood analyses revealed the existence of at least six to seven clusters of nonmarine picocyanobacteria within the picophytoplankton clade and support the conjecture of global dispersal for some closely related picocyanobacterial genotypes.

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Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.Microdiversity of prokaryotes, i.e., the genetic diversity within species-like (Ͼ97% similarity of 16S rRNA genes) phylogenetic groups, receives increasing attention in microbial ecology (1,5,18,19,24,28); however, the ecological significance of this diversity is still unknown. The coexistence of different bacterial genotypes belonging to the same species-like phylogenetic group is well documented for marine (1,18,19,35,45) and freshwater habitats (8,9,10,11,27,30,43). Recently, Acinas et al. (1) demonstrated by the construction and analysis of 16S rRNA clone libraries that a coastal bacterioplankton community contained a very high diversity of ribotypes, the vast majority of which fell into phylogenetically microdiverse sequence clusters (Ͻ1% divergent 16S rRNA sequences). Similarly, extensive microdiversities were also observed in populations of sulfate-reducing bacteria inhabiting a salt marsh (29) and in a Vibrio splendidus population from coastal bacterioplankton (42). The V. splendidus population consisted of at least a thousand distinct genotypes, which demonstrated a high variability in genome size and allelic composition (42).The major aim of the study presented here was the investigation of the intraspecific structure (microdiversity) of a bacterial p...

Seven strains with identical 16S rRNA genes affiliated with the Luna2 cluster (Actinobacteria) were isolated from six freshwater habitats located in temperate (Austria and Australia), subtropical (People's Republic of China), and tropical (Uganda) climatic zones. The isolates had sequence differences at zero to five positions in a 2,310-nucleotide fragment of the ribosomal operon, including part of the intergenic spacer upstream of the 16S rRNA gene, the complete 16S rRNA gene, the complete 16S-23S internal transcribed spacer (ITS1), and a short part of the 23S rRNA gene. Most of the few sequence differences found were located in the internal transcribed spacer sequences. Two isolates obtained from habitats in Asia and Europe, as well as two isolates obtained from different habitats in the People's Republic of China, had identical sequences for the entire fragment sequenced. In spite of minimal sequence differences in the part of the ribosomal operon investigated, the strains exhibited significant differences in their temperature response curves (with one exception), as well as pronounced differences in their temperature optima (25.0 to 35.6°C). The observed differences in temperature adaptation were generally in accordance with the thermal conditions in the habitats where the strains were isolated. Strains obtained from temperate zone habitats had the lowest temperature optima, strains from subtropical habitats had intermediate temperature optima, and a strain from a tropical habitat had the highest temperature optimum. Based on the observed temperature responses, we concluded that the strains investigated are well adapted to the thermal conditions in their home habitats. Consequently, these closely related strains represent different ecotypes adapted to different thermal niches.Many free-living bacterial, archaeal, and protist species have a cosmopolitan distribution and differ in this trait from almost all macroorganisms (9). Closely related strains of several microbial species have been detected in distant habitats (4,6,8,10,12,26). For some free-living bacteria and archaea, restricted geographical distributions have been demonstrated for strains inhabiting rare, extreme environments (e.g., hot springs) (17, 24). These distributions might be a result of isolation of populations due to limited dispersal potential resulting from small population sizes combined with the rare occurrence of appropriate habitats separated by wide distances. In the case of free-living microorganisms inhabiting nonextreme environments, the existence of a restricted geographical distribution has rarely been demonstrated (6). For free-living microbes easy dispersal and frequent population of appropriate habitats are assumed (2, 9). Intensive gene flux between habitats should prevent the isolation of populations. On the other hand, local adaptation of populations may prevent colonization of a habitat by less adapted competitors originating from an ecologically different habitat. It is not known, however, if free-living cosmopolitan mic...

Summary 26Bacterial strains affiliated to the phylogenetically shallow subcluster C (PnecC) of the Polynucleobacter cluster, which is characterized by a minimal 16S rRNA gene sequence 28 similarity of approx. 98.5%, have been reported to occur as obligate endosymbionts of ciliates (Euplotes spp.), as well as to occur as free-living cells in the pelagic zone of 30 freshwater habitats. We investigated if these two groups of closely related bacteria represent