Changes in bacterial and fungal abundance in the soil during the process of anaerobic soil disinfestation

Anaerobic soil disinfestation (ASD) has potential to reduce soilborne plant pathogens as a sustainable alternative for chemical or energy-demanding steam treatments. It involves adding a labile carbon source, irrigating the soil to stimulate decomposition of organic material and then covering the soil with air-tight plastic to limit gas exchange. During ASD, many by-products of anaerobic metabolism (e.g., various organic acids and gases) are produced, which are thought to affect soil-borne plant pathogens negatively. However, effects of ASD vary, and therefore our goal was to study the microbial processes occurring during ASD in more detail. We designed a lab-scale experiment and studied the effects of ASD on six soils by incubating soil mixed with a commercially available organic amendment (Herbie; Thatchtec BV, The Netherlands) at 20°C. Changes in biotic and abiotic soil parameters were followed by destructive samplings over the course of 28 days of incubation. In this paper, we present the results of analysis of soil microbial communities and their relation to chemical parameters of the studied soils. After three days of incubation, the number of total bacteria and fungi were significantly higher in soil treated with ASD compared with controls. However, there was no significant difference in bacterial numbers at the end of the incubation period. The relative abundance of Firmicutes (spore-forming bacteria) increased significantly in ASD soils. This means that anaerobic bacteria, which survive in aerobic soil as spores, became active. Numbers of sulphate-reducing bacteria (SRB) increased significantly during incubation in four out of six ASD treated soils, and in the controls. In ASD soils, the abundance of SRB was positively correlated with increasing concentration of organic acids