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The effects of stumping and tree species composition on the soil microbial community in the interior cedar-hemlock zone, British Columbia Modi, Dixi


Stump removal (stumping) is an effective forest management practice used to reduce the mortality of trees affected by fungal pathogen-mediated root diseases such as Armillaria root rot, but its impact on soil microbial community structure has not been ascertained. This study investigated the long-term impact of stumping and tree species composition on the abundance, diversity and taxonomic composition of soil fungal and bacterial communities in a 48-year-old trial at Skimikin, British Columbia. We used DNA metabarcoding targeting the fungal internal transcribed spacer (ITS) marker and the bacterial 16S rRNA gene to decipher the microbiomes. A total of 108 samples were collected from the FH (fermented and humus layers), 0-10 cm (A horizon) and 10-20 cm (B horizon) layers in 36 plots, 18 stumped and 18 unstumped, that were planted with pure stands and admixtures of Douglas-fir, western redcedar and paper birch. Fungal α-diversity in the A horizon increased with stumping regardless of tree species composition and had a tendency to increase in the FH and B horizons. In the FH horizon, the relative abundance of the saprotrophic fungal community declined while that of ectomycorrhizal (ECM) fungal community increased with stumping. Bacterial α-diversity in the B horizon declined with stumping, irrespective of tree species, and also tended to decrease in the A horizon. The B horizon of stumped plots was significantly enriched with potential plant growth-promoting bacteria (PGPR), such as rhizobia. Similarly, Pseudomonadales, known for their antagonistic role against pathogens, increased significantly in all three soil horizons with stumping and was especially observed in association with birch and its admixtures. The culture-based assessment focused on 16S rDNA substantiated the dominance of potential PGPRs in the stumped plots. Furthermore, molecular characterization of Armillaria using translation elongation factor-1 alpha (tef-1) and ITS revealed the occurrence of A. gallica, reported for the first time at this site. Overall, we conclude that stumping along with plantation of resistant tree species with susceptible ones, led to a healthy fungal community structure and promotion of a beneficial bacterial microbiome, thus proves as a potent practice for the suppression of Armillaria root rot and promotion of forest health.

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