Using a widely used commercial DNA extraction kit and a newly modified direct DNA extraction method proposed in this report, soil DNA was extracted from arable land in diverse geological locations in Japan and the quality and quantity of the DNA were examined. A modified direct DNA extraction method was developed, consisting of one-step extraction and two-step purification using potassium acetate and a DEAE-cellulose column, respectively, and designated as a DSPD (Differential Salt Precipitation and DEAE-cellulose) method. The total time needed to process six soil samples with this method was less than two hours, including the time taken to set up the DEAE-cellulose columns. Other advantages of our DSPD method are the use of non-hazardous reagents and running costs only 5-10% of the commercial kits currently used in soil microbiological research. This DSPD method was tested using 24 soil samples collected from diverse locations in Japan and showed that it is a reliable technique for DNA extraction from a wide range of soil types when compared with commercial DNA extraction kits. This DSPD method will therefore contribute to the molecular and genomic analyses of microbial populations and ecosystems that require numerous samples of soil DNA.Key words: agricultural ecosystem, DEAE-cellulose column, DSPD method, potassium acetate precipitation, soil DNA The microbial community plays an indispensable and unique role in both the function and sustainability of diverse ecosystems. The development and application of nucleic acid-based techniques in ecology has made a huge contribution to our understanding of microbial community dynamics and activities in natural environments, as these analyses go beyond culture-dependent methodological approaches 1) . Recently, environmental genomic approaches have also provided significant insights into the biological properties of individual species within microbial populations 24) . These molecular and genomic analyses strongly depend on how nucleic acids are extracted and purified from environmental samples. The improvement and optimization of DNA extraction and purification methodology is therefore crucial in the advance of these approaches.In the last two decades, methods to extract DNA from soil samples have been explored as key techniques to facilitate a better understanding of soil microbiology at the molecular level. To date, two different approaches, direct and indirect extraction, have been proposed for soil DNA preparation. Torsvik and Goksoyr 22) first described an indirect DNA extraction method that involved the separation of bacterial cells from soil particles by differential centrifugation, followed by cell lysis, DNA recovery and several DNA purification steps. Subsequently, Ogram et al. 12) developed a direct DNA extraction method that involved the release of DNA from cells by physical disruption without separating the cells from the soil matrix, followed by alkaline extraction and a series of purification steps. Holben et al. 7) and other groups have proposed that ind...

A survey of hydrothermal activity along the superfast-spreading (approximately 150 millimeters per year) East Pacific Rise shows that hydrothermal plumes overlay approximately 60 percent of the ridge crest between 13 degrees 50' and 18 degrees 40'S, a plume abundance nearly twice that known from any other rige portion of comparable length. Plumes were most abundant where the axial cross section is inflated and an axial magma chamber is present. Plumes with high ratios of volatile ((3)He, CH(4), and H(2)S) to nonvolatile (Mn and Fe) species marked where hydrothermal circulation has been perturbed by recent magmatic activity. The high proportion of volatile-rich plumes observed implies that such episodes are more frequent here than on slower spreading ridges.

Evolutionary studies are generating increasing numbers of phylogenies which, in turn, sometimes result in changes to hierarchical organization and therefore changes in taxonomic nomenclature. A three-layered data model for a nomenclature database has been developed in order to elucidate the information structure in nomenclature and as a means to organize and manage a large, dynamic knowledge-base. In contrast to most other taxonomic databases, the model is publication-oriented rather than taxon-oriented and dynamic rather than static, in order to mimic the processes that taxonomists use naturally. The three-layered structure requires data integrity localized to each publication, instead of global data integrity, which relaxes constraints common to taxonomic databases and permits multiple taxonomic opinions: taxon names are made available as metadata within the model. Its prototype implementation, written in C + + , has an autonomous self-identification mechanism to avoid spurious data-inflation in a publication-oriented data model. Self-identification is also desirable for distributed implementations of the nomenclature database. Publication-oriented design also will make maintenance easier than for taxon-oriented databases, much of the maintenance workload being amenable t o automation. The three-layered data model was designed for use by taxonomists, but is also able to provide concise, reduced expression for non-experts required in biodiversity research, for example.

Microbial diversity in forage crop seeds was examined using culture-independent methods. Environmental DNA samples were extracted from the surface of the seeds, and the intergenic spacer region between small subunit and large subunit RNA genes was then amplified by ribosomal intergenic spacer analysis (RISA) for the profiling of microbial community structures. The results suggested the presence of stable microbial communities in seeds and sequencing of the RISA amplicons identified a total of 33 unique microbial sequences in 1.6 g of seed material from Italian ryegrass (Lolium multiflorum) and timothy (Phleum pretense). These included several sequences showing high similarity to known plant-associated microbes, such as Pseudomonas fluorescens and Clavibacter michiganensis, the Cladosporium and Dioszegia group of fungi, and also several uncultured bacteria.

Soil microbial community analysis is one of the most important elements in the environmental risk assessment of transgenic plants. Recent technical advances in this area now enable us to assess the impact of plant genotypes on soil microbial communities with rapid, simple and less biased molecular techniques than the previously used conventional microbiological methodologies. We review the use of these modern molecular techniques from the aspect of environmental assessments of transgenic plants.