Assessing and tracking the functional diversity of forest soil microbes in coastal British Columbia, Canada.Winder Richard, Dale Phyllis
Natural Resources Canada / Canadian Forest Service Pacific Forestry Centre 506 West Burnside Rd. V8Z1M5 Victoria B.C. Canada
In the coastal Douglas-fir forests of Canada, several projects are underway to understand the dynamics of microbial communities in forest soils. We are gathering information concerning the dynamics of microbial communities (e.g. nitrogen cycling bacteria, methanotrophic bacteria, fungi) responding to ‘baseline’ variables such as the degree of tree retention after harvest, the seral stage of the site, or the productivity of the site. Using denaturing gradient gel electrophoresis (DGGE), we have detected fragments corresponding to the methane monooxygenase gene (pmoA2) of the so-called “uncultured forest soil methanotrophs”. Several fragments corresponded to different site types or seasons. However, no significant differences in overall diversity of this group were observed. DGGE was also used to assay bacteria containing the nitrogen reductase (nifH) gene. Of 46 positive signals detected with DGGE, subsequent incorporation into microarray tests found that 28 were actually ubiquitous, nine were seasonally variable in control and clear-cut plots, four were variable with respect to spatial distribution, and three (a Paenibacillus species, an unnamed member of the Intrasporangiaceae, and an unnamed N-fixing bacterial species) were specific to clear-cuts. Again, differences in the overall diversity were not significant. Regarding the impacts of forest management methods, we have examined fungal diversity among plots with different levels of tree retention, age, and N-fertilization using 18S rDNA primers and DGGE. We found no statistically significant differences in fragment distribution across the different sites; however, other functional groups continue to be evaluated. We have also examined the impact of a fungal biological control agent (Chondrostereum purpureum), using both universal and nifH primers-specific for Frankia, Azospirillum, Herbaspirillum, and nitrogen-fixers in the Rhizobiales family. There were no significant differences in the number of nifH DGGE bands between the treatments, suggesting that any negative effects from the different vegetation-management treatments on nitrogen-fixing community were transient. In conjunction with the field work, we have developed a database named the Edaphic Indicator Research Tool (EdIRT); the purpose of the database is to correlate microbial indicators with environmental conditions and impacts, linking microbial genetic sequences and other signals with details concerning the environment of origin.