Bacteroidetes as a sensitive biological indicator of agricultural soil usage revealed by a culture-independent approach

• Agricultural practices and soil genesis are essential factors for Bacteroidetes abundance.
• Flavobacteriaceae and Flavobacterium OTUs are dominating in all types of Polish soils.
• Bacteroidetes abundance significantly decreased in arable soils than in wastelands.
• The sensitivity of Bacteroidetes phylum on agricultural soil usage was evidenced.

The aim of the study was to determine the Bacteroidetes community structure in arable soils versus wastelands in order to assess their sensitivity to agricultural soil usage. Twelve arable soils (A) and the same number of wastelands, serving as controls (C), were grouped on the basis of the soil origin as: autogenic (AG) − formed from loess material, represented by Albic Luvisols, Haplic Luvisols, and Brunic Arenosols, hydrogenic (HG) − formed under the influence of stagnant water, represented by Haplic Chernozem, Mollic Gleysol, and Gleyic Umbrisol and lithogenic (LG) − formed from limestone, represented by Calcaric Cambisols. Additionally, the soils were classified into orders (Luvisols, Arenosols, Chernozems, Cambisols) according to the WRB classification rules. Statistical analyses were performed to gain the knowledge about soil chemical factors directly affecting the operational taxonomic units (OTUs) of Bacteroidetes in the soil environment. The composition of Bacteroidetes was analysed with the next generation sequencing Ion Torrent™ technology. The sequences were clustered into OTUs based on a 99% similarity threshold. An average of 2516 OTUs belonging to Bacteroidetes per C soil and 1568 OTUs per A soils were evidenced. It was found that Flavobacterium was the dominant genus in both C and A soils; however, its numbers significantly decreased in A soils, which proves its sensitivity to agricultural practices. Pedobacter and Mucilaginibacter were subdominants. Our results emphasised that, besides agricultural practices, soil genesis is an essential factor for the abundance of Bacteroidetes. They were found to prefer colonising the non-cultivated AG and HG soils rather than the LG soils. Importantly, the sensitivity to agricultural soil usage was similar irrespective of the soil classification system (genesis or orders), as reduction of Bacteroidetes OTUs in arable soils was revealed in both cases. Therefore, we recommend the Bacteroidetes phylum a sensitive biological indicator of agricultural soil usage.