Identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Germany

AIMS: The identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Mainz (Germany) during the year 2002. METHODS AND RESULTS: Total counts varied between 3.5 x 103 and 2.2 x 104 cells ml-1, viable counts were approximately between 8.1 x 102 and 3.3 x 103 cells ml-1. After cultivation on different nutrient media (R2A, DEV, PCA, Endo, Standard) <1% appeared to be culturable on the media used. After denaturating gradient gel electrophoreses, up to 24 different bacterial species were detected in the ground water. With the aid of 16S rDNA isolation, amplification and sequencing, the isolated organisms and clones could be identified. CONCLUSIONS: The isolated and cultured organisms mainly belonged to the Proteobacteria (alpha, beta and gamma), Flavobacteria or Actinobacteria. However, most of the noncultured micro-organisms were beta-Proteobacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study in which the identification of all culturable and nonculturable bacteria in a ground water has been attempted.     

The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLP

AIMS: To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. METHODS AND RESULTS: Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. CONCLUSIONS: Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1-16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. SIGNIFICANCE AND IMPACT OF THE STUDY: This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment.     

Genome-wide identification of NBS genes in<Emphasis Type="Italic"> japonica</Emphasis> rice reveals significant expansion of divergent non-TIR NBS-LRR genes

A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativa L. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at .)Communicated by R. HagemannThe first three authors contributed equally to this work     

Genetic Diversity Between Japanese and Chinese Threeline Grunt (<Emphasis Type="Italic">Parapristipoma trilineatum</Emphasis>) Examined by Microsatellite DNA Markers

Threeline grunt (Parapristipoma trilineatum) distributes around the southwestern coast of Japan and the east coast of China. The Chinese P. trilineatum was imported by Japan as an aquacultural seed because of its rapid growth compared with that of the Japanese P. trilineatum. The Japanese P. trilineatum differs from the Chinese P. trilineatum in some quantitative traits, and it has been suggested that these two P. trilineatum populations are genetically different. In order to identify the population structures around Japan and China, 5 local populations of the Japanese P. trilineatum and 2 local populations of the Chinese P. trilineatum were analyzed using 4 microsatellite DNA markers. Significant differences were detected between Japanese and Chinese P. trilineatum and among samples of Chinese P. trilineatum; however, among the samples of Japanese P. trilineatum, no significant differences were detected. These results suggest that care must be taken to prevent the escape of the Chinese P. trilineatum from culture cages around the Japanese coast, in order to preserve the genetically different population structures of Japanese and Chinese P. trilineatum.     

Dorsal telencephalon-specific expression of Cre recombinase in PAC transgenic mice

The ability to restrict gene expression or disruption to specific regions of the brain would enhance understanding of the molecular basis for brain development and function. For this purpose, brain region-restricted promoters are essential. Here we report the isolation of a DNA fragment containing the Emx1 gene promoter, which is responsible for dorsal telencephalon-specific expression. The Cre recombinase gene was inserted into a mouse PAC (P1-derived artificial chromosome) Emx1-locus clone (PAC-Emx1#1 clone) and utilized to generate three transgenic mouse lines. In all three lines, especially Tg3, Cre-mediated recombination was highly restricted to Emx1-expressing cell lineages, from embryonic stages to adulthood. Immunohistochemical analyses showed that Cre protein is expressed in the dorsal telencephalon in all three lines in adulthood. Thus, the PAC-Emx1#1 clone contains essentially all regulatory elements necessary for Emx1 gene expression. Our results suggest that Emx1-Cre Tg3 mice and the PAC-Emx1#1 clone constitute powerful tools for dorsal telencephalon-specific gene manipulation.     

Effects of habitat fragmentation on the genetic structure of the monophagous butterfly Polyommatus coridon along its northern range margin

Population genetic patterns of species at their range margin have important implications for species conservation. We performed allozyme electrophoresis of 19 loci to investigate patterns of the genetic structure of 17 populations (538 individuals) of the butterfly Polyommatus coridon, a monophagous habitat specialist with a patchy distribution. The butterfly and its larval food plant Hippocrepis comosa reach their northern distribution margin in the study region (southern Lower Saxony, Germany). Butterfly population size increased with host plant population size. The genetic differentiation between populations was low but significant (FST = 0.013). No isolation-by-distance was found. Hierarchical F-statistics revealed significant differentiation between a western and an eastern subregion, separated by a river valley. The combination of genetic and ecological data sets revealed that the expected heterozygosity (mean: 18.5%) decreased with increasing distance to the nearest P. coridon population. The population size of P. coridon and the size of larval food plant population had no effect on the genetic diversity. The genetic diversity of edge populations of P. coridon was reduced compared to populations from the centre of its distribution. This might be explained by (i). an increasing habitat fragmentation towards the edge of the distribution range and/or (ii). a general reduction of genetic variability towards the northern edge of its distribution.     

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within-population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter-patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.     

Genetic diversity across a vertebrate species' range: a test of the central-peripheral hypothesis

Although it has been long presumed that population genetic variability should decrease as a species' range margin is approached, results of empirical investigations remain ambiguous. Sampling strategies employed by many of these studies have not adequately sampled the entire range. Here we present the results of an investigation of population genetic diversity in a vertebrate species, the Italian agile frog, Rana latastei, sampled comprehensively across its entire range. Our results show that genetic variability is not correlated with population location with respect to the range periphery. Instead, the model that best explains the genetic variation detectable across the range is based on an east-to-west gradient of declining diversity. Although we cannot state definitively what has led to this distribution, the most likely explanation is that the range of Rana latastei expanded postglacially from a Balkan refugium.     

太白红杉群落物种多样性与环境因子的关系

定量研究了太白红杉群落物种多样性与环境因子的关系,结果表明:(1)海拔与物种丰富度和种间相遇机率呈极显著的负相关;与Shannon指数、Simpson指数和Pielou指数表现为"中间高度膨胀"的规律,即中等海拔高度上多样性高而低海拔和高海拔多样性较低。(2)岩石裸露度与物种丰富度呈显著的负相关。(3)土壤含水量与物种丰富度呈极显著的正相关;与种间相遇机率呈先降后升的趋势。(4)环境因子与物种多样性逐步回归结果是:海拔和岩石裸露度与物种丰富度关系密切,其回归方程为:S=90.62-0.02E-14.14B(r=0.769,P<0.05)。     

Estimation of the proportion of genetically unbalanced spermatozoa in the semen of boars carrying chromosomal rearrangements using FISH on sperm nuclei

Many chromosomal rearrangements are detected each year in France on young boars candidates for reproduction. The possible use of these animals requires a good knowledge of the potential effect of the rearrangements on the prolificacy of their mates. This effect can be estimated by an accurate determination of the rate of unbalanced spermatozoa in the semen of boars which carry the rearrangements. Indeed, these spermatozoa exhibiting normal fertilizing ability are responsible for an early embryonic mortality, and then, for a decrease of the litter sizes. The "spermFISH" technique, i.e. fluorescent in situ hybridization on decondensed sperm heads, has been used on several occasions in Man, in this perspective. In livestock species, this method was formerly used mainly for semen sexing purposes. We used it, for the first time, to estimate the rates of imbalance in the semen of four boars carrying chromosomal rearrangements: two reciprocal translocations, rcp(3;15)(q27;q13) and rcp(12;14)(q13;q21), as well as two independent cases of trisomy 18 mosaicism. The rates of unbalanced gametes were relatively high for the two reciprocal translocations (47.83% and 24.33%, respectively). These values differed from the apparent effects of the rearrangements estimated using a limited number of litters: a decrease in prolificacy of 23% (estimation obtained using the results of 6 litters) and 39% (57 litters), respectively for the 3/15 and 12/14 translocations. The imbalance rates were much lower for the trisomy mosaics (0.58% and 1.13%), suggesting a very moderate effect of this special kind of chromosomal rearrangement.