A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4-V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8-V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G؉C DNA content and to the SSU rDNA of ␥-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

A culture independent survey of the microbial community dynamics during the composting of organic waste in an industrial composting process was conducted by sequence analysis of (1) universal clone coding for small-subunit rRNA-genes libraries and, in parallel, with electrophoresis and sequencing of PCR-amplified 16S rDNA fragments based on DNA single strand-conformation polymorphism (SSCP). Samples were taken from a force aerated module composting system during a two week dynamic process. In addition, to examine the beginning maturation phase, one sample was taken from force-aerated compost piles. In the initial composting stage, where a starting temperature of 41°C was recorded, a number of Enterobacteriaceae and members of the genus Lactobacillus were still detected, while different members of the low-G+C Gram-positive bacteria formed the dominant fraction of the bacterial community during the hot composting phase with temperatures fluctuating between 55 and 70°C. During the initial curing phase, where temperature had declined to 50°C, the microbial community changed accompanied by an increasing number of sequences affiliated with the Bacteroides-Cytophaga-Flexibacter group. The combined results of 16S rRNA sequence analysis demonstrated that both approaches, cloning and SSCP, have their specific advantages and limitations, but both methods were capable to detect the predominating taxa and have proved useful for the analysis of microbial community successions during composting.

JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org.. Mycological Society of America is collaborating with JSTOR to digitize, preserve and extend access to Mycologia.Abstract: Undifferentiated plant cells may be used in simplified systems for studying the interactions between plants and fungi. We used plant calli for investigating the interactions between three endophytic fungi (Coniothyrium palmarum, Geniculosporium sp. and Phomopsis sp.) and their host and nonhost plants (Lamium purpureum and Teucrium scorodonia), showing that growth of these endophytes was specifically enhanced by calli of the host. Substance(s) secreted by the host calli were responsible for this growth response. The endophytes also secreted metabolites into the medium. These were toxic to the plant calli, irrespective of whether it was a host or nonhost interaction. Further tests demonstrated the nonspecific herbicidal nature of these substances.

Background: Bacteriochlorophyll biosynthesis is fundamental for the photosynthetic capture of solar energy by photosynthetic bacteria. Results: 3-Hydroxyethyl chlorophyllide a was identified as a novel substrate of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC). Conclusion:The broadened substrate specificity of BchC would allow for a novel branched pathway for bacteriochlorophyll a biosynthesis. Significance: The observed plasticity of the pathway might be relevant for the engineering of photosynthetic organisms.