Investigation of nitrification and denitrificationbacterial community structure in vermicompost appliedsoil by culture-independent molecular techniques

The improving and maintaining soil fertility depends on improving the physical, chemical and biological properties of the soil and keeping them at the desired levels. In addition to the traditional organic fertilizers used for this purpose, vermicompost has emerged as an important alternative in recent years. Studies investigating the effects of vermicompost on soil microorganisms have generally been limited to certain parameters representing the biological activity in the soil. Although these parameters are considered to be good indicators of the biological status of the soil, they alone may not be sufficient. In particular, detailed examination of community structure and diversity of microorganism groups that take part in important nutrient cycles by DNA-based "culture-independent" molecular techniques is very important to understand the biological dynamics in the soil. Nitrifying and denitrifying bacteria, which take part in the nitrogen cycle, are at the forefront of the microbial groups that need to be investigated. However, there is no detailed molecular ecological study on the effect of vermicompost on community structure and diversity of nitrification and denitrification bacteria in soil. In this study, the aim was to find an answer to the question of how nitrification and denitrification bacterial community structure and diversity in soil (rhizosphere soil and bulk soil) is affected to find out the relationships between community structure and other biochemical parameters in the soil. For this purpose, the effects of vermicompost application on bulk soil and rhizosphere soil were investigated in a field experiment carried out in two consecutive growth seasons and compared with animal manure and chemical fertilizer. The phylogenetic data from molecular analysis showed that the community structure of ammonia-oxidizing bacteria and denitrifying bacteria changed depending on time and applications. Especially, changes in ammonia-oxidizing bacterial community were more visible in the phylogenetic tree. It was observed that Nitrosospira cluster 3 was dominant in the experiment soils and the changes that occurred were generally within this group. In addition, it was possible to identify and monitor clones similar to aerobic denitrifying bacteria and denitrifying ammonia-oxidizing bacteria. The observation that the clones obtained from vermicompost contain different groups shows that this fertilizer can make significant contributions to the bacterial diversity in the soil. Even though, the relationship of these changes with other biological and chemical parameters was not clear, it can still be said that the ammonium oxidizing bacteria population interacts positively with the nitrifying bacterial number and total N, and the denitrifying bacteria population with the nitrification activity, ammonium and total N. The results showed that organic fertilizers applied to the soil, especially vermicompost, can directly or indirectly affect the nitrification and denitrification community structure and diversity. However, longer-term studies are needed to better understand these effects and interactions.