A statistical method was developed to test for equivalence of microbial communities analysed by next-generation sequencing of amplicons. The test uses Bray-Curtis distances between the microbial community structures and is based on a two-sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high-throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants.

Department for Biometry and Medical Informatics Otto von Guericke University Magdeburg Magdeburg Germany

Department of Biosafety in Plant Biotechnology Julius Kühn Institut Federal Research Centre for Cultivated Plants Quedlinburg Germany

Department of Epidemiology and Pathogen Diagnostics Julius Kühn Institut Federal Research Centre for Cultivated Plants Braunschweig Germany

Laboratory of Environmental Microbiology Institute of Microbiology of the CAS Prague Czech Republic

Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren Germany

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