Clear-cutting affects the ammonia-oxidising community differently in limed and non-limed coniferous forest soils

The effects of clear-cutting on the ammonia-oxidising bacterial community were studied in the soil of limed and non-limed spruce forest plots located in the central part of southern Sweden. The communities were studied using denaturing gradient gel electrophoresis (DGGE) profiling after polymerase chain reaction (PCR) amplification from total DNA with primers reported to be specific for beta-subgroup ammonia-oxidising bacteria. The bands on the DGGE were sequenced and each unique sequence was interpreted as representing one ammonia-oxidising population. The relative abundance of each population was determined by measuring the fluorescence of the respective DGGE bands. In both limed and non-limed soil, the same two Nitrosospira populations were found, one belonging to cluster 2 (NScl2) and one to cluster 4 (NScl4). However, while NScl4 first appeared a year after the clear-cutting in the non-limed plot, it was present both before and after the cutting in the limed plot. Irrespective of previous liming, clear-cutting caused a shift in the ammonia-oxidiser community, from dominance by the NScl2 population to a community with approximately equal relative abundance of NScl2 and NScl4. In both plots the total size of the community increased after clear-cutting (based on increased DGGE band intensity), most likely due to increased NH4+ availability, but the growth response was faster in the limed plot. Hence, the prior liming increased the responsiveness of the ammonia-oxidisers to the changes caused by cutting. This is the first study to report the effects of clear-cutting on the ammonia-oxidising community, and the results show a clear correlation between increased potential nitrification and a shift in the ammonia-oxidiser community.