Liming induces growth of a diverse flora of ammonia-oxidising bacteria in acid spruce forest soil as determined by SSCP and DGGE

The autotrophic ammonia-oxidising bacterial (AOB) community composition was studied in acid coniferous forest soil profiles at a site in southwestern Sweden 6 years after liming. Liming caused a significant increase in pH in the organic horizons, while the mineral soil was unaffected. The AOB communities were studied by single-strand conformation polymorphism (SSCP) in parallel with denaturing gradient gel electrophoresis (DGGE) analysis of partial 16S rRNA genes amplified by PCR using primers reported to be specific for β-Proteobacteria AOB, followed by nucleotide sequencing. High genetic diversity of Nitrosospira-like sequences was found in the limed soil profiles, whereas no AOB-like sequences were detected in the control soil at any depth, according to both the SSCP and DGGE analyses. This clearly showed that liming induced growth of a diverse flora of AOB at this forest site. Both Nitrosospira cluster 2 and cluster 4 sequences were present in the limed soil profiles, regardless of soil pH, but we found a higher number of sequences affiliated with cluster 4. The high lime dose seemed to affect the AOB community more than the low dose, and its effects reached deeper into the soil profile. Seven different Nitrosospira-like sequences were found 10 cm under the litter layer in the soil limed with the high dose, but only two in the soil amended with the low lime dose.