Canadian Forest Service Publications

Development of a microbial indicator database for validating measures of sustainable forest soils. 2010. Winder, R.S.; Dale, P.L.; Greer, C.W.; Levy-Booth, D.J. Pages 81-89 in V.V.S.R. Gupta, M. Ryder, and J. Radcliffe, editors. The Rovira Rhizosphere Symposium. Celebrating 50 years of Rhizosphere Research, August 15, 2008, SARDI Plant Research Centre, Waite Campus, Adelaide. The Crawford Fund, Deakin ACT, Austrailia.

Year: 2010

Issued by: Pacific Forestry Centre

Catalog ID: 31915

Language: English

CFS Availability: Not available through the CFS (click for more information).

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Abstract

EdIRT (Edaphic Indicator Research Tool) is a database of microbial indicators of soil status, designed to assist in the validation of forest soil conservation efforts. The database prototype was developed using Microsoft Inc. (MS) Access, with regular migration to an open-source version using a structured query language (MySQL). To enable future web access, a browser-accessible interface was developed for the MySQL version of the database, using a mixture of personal home page language (PHP), cascading style sheet language (CSS), and hyper-text markup language (HTML). To enable queries for genetic sequences, a ‘Pattern Recognition Algorithm for Microbes’ (PRAM) was developed by modifying the Boyer-Moore algorithm. The database catalogs source information, genetic features, biochemical and physiological attributes, and functional significance of microbial indicators. EdIRT currently comprises a relatively modest dataset of 105 genetic sequences for microbial indicators of site productivity and tree loss in coastal Douglas-fir forests of British Columbia (BC). When 46 indicator sequences from EdIRT were used to re-evaluate source soils using molecular microarrays, 28 were actually ubiquitous, nine varied with season, four varied with site productivity, and three (a Paenibacillus sp., an unidentified member of the Intrasporangiaceae, and an unidentified diazotrophic bacterial species) were indicators of clear-cutting. Taxonomic analysis of sequences in EdIRT revealed some clustering of diazotrophic bacteria sequences related to the level of tree removal and season. Further expansion of EdIRT will allow for increased utility of the dataset in validating forest soil conservation efforts.