High-Resolution Taxonomic Assessment Using PacBio 16S rRNA Sequencing of Farm Animal Slurry, Broiler Waste and Anaerobically Digested Wastewater Treatment Sludge and Description of Soil Microbiota

The application of organic wastes as fertilisers is important for sustainable agriculture, provided that resulting changes in microbial communities do not disrupt nutrient cycling or soil fertility. To the authors’ knowledge, this study was the first to use PacBio 16S rRNA sequencing to characterise soil microbiota changes following waste application to land. This technology provides high taxonomic resolution, improving the characterisation of complex soil microbial communities. To assess the microbiota of five organic wastes and describe soil microbiota following field application, 18 plots received each waste in triplicate at nitrogen-equivalent rates simulating band spreading. Soil cores were collected at 0, 1, 3, 6, and 10 weeks post-application. The primary genera in pre-application soil were Niallia (7.6%) and Unclassified_type_III (7.3%). Following waste application, the dominant genera included UCG-001 (13.3%) and DMER64 (8.8%) in bovine-treated soil, Candidatus_Udaeobacter (8.5%) and unclassified_Xanthobacteraceae (7.9%) in ovine, Niallia (6.1%) and Candidatus_Udaeobacter (5.8%) in pig, Staphylococcus (27.3%) and Brachybacterium (26.7%) in poultry, and unclassified_Anaerolineaceae (25.8%) and Thiopseudomonas (14.2%) in anaerobically digestated wastewater treatment sludge (DWWTS). The time required for soil to return to its pre-application microbiota ranged from 0 to 6 weeks. Organic waste type strongly influenced disturbance magnitude and duration, with prolonged shifts potentially affecting microbial diversity, nutrient cycling and soil fertility.