Effects of calcium cyanamide on soil microbial communities and Fusarium oxysporum f. sp. cucumberinum.

Calcium cyanamide (CaCN(2)) has been one of the potential candidates as soil disinfectant since the restriction of methyl bromide in soil fumigation due to its ecological risk. However, little information is available on effects of CaCN(2) on soil microbial community. In this study, the soil microbial communities and the fate of pathogen Fusarium oxysporum (Schlechtend, Fr) f. sp. cucumberinum (Owen) Snyder and Hansen (F.O. f. sp. cucumberinum) in response to CaCN(2) treatment was evaluated. F.O. f. sp. cucumberinum population in soil treated with CaCN(2) at rates of 80 and 200 gm(-2) was suppressed by 88.7 and 92.2% after 15 d of CaCN(2) application. Bacterial, fungal, and actinomycete populations were also greatly decreased after 3 d of CaCN(2) application, but they recovered to the control level by 15 d. The variation in functional diversity of soil microbes characterized by principal component analysis, diversity and evenness indices based on Biolog data followed a similar trend. Meanwhile, the band number from the DGGE of soil 16S rDNA fragments increased from 9 for the non-CaCN(2)-treated soil to 10 or 12 after different rates of CaCN(2) application at 15 d, indicating the increase of abundant rDNA types in the community. The results suggest that CaCN(2) application had only a short-term and transitory impact on the indigenous soil microbial community in contrast to the long-term suppression of the F.O. f. sp. cucumberinum population. It is feasible to reduce Fusarium wilt without significant impact on microbial community by application of CaCN(2) at reasonable doses.

The yeast rDNA locus: a model system to study DNA repair in chromatin.

Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.

Acetobacter intermedius, sp. nov.

Strains of a new species in the genus Acetobacter, for which we propose the name A. intermedius sp. nov., were isolated and characterized in pure culture from different sources (Kombucha beverage, cider vinegar, spirit vinegar) and different countries (Switzerland, Slovenia). The isolated strains grow in media with 3% acetic acid and 3% ethanol as does A. europaeus, do, however, not require acetic acid for growth. These characteristics phenotypically position A. intermedius between A. europaeus and A. xylinus, DNA-DNA hybridizations of A. intermedius-DNA with DNA of the type strains of Acetobacter europaeus, A. xylinus, A. aceti, A. hansenii, A. liquefaciens, A. methanolicus, A. pasteurianus, A. diazotrophicus, Gluconobacter oxydans and Escherichia coli HB 101 indicated less than 60% DNA similarity. The important features of the new species are described. Acetobacter intermedius strain TF2 (DSM11804) isolated from the liquid phase of a tea fungus beverage (Kombucha) is the type strain.