In this special focus, we wanted to draw attention to the involvement of microorganisms in biogeochemical element cycling, and here specifically to their nitrogen metabolism. In soils, both root associated and free-living bacteria are involved in nitrogen fixation providing nutritional input for plant growth. Hence, during re-vegetation of disturbed areas, the role of nitrogen-fixing bacteria cannot be overestimated. Here, an article deals with nitrogen fixation in soils degenerated because of salt contamination. However, not only nitrogen-fixing proteobacteria are involved in nitrogen cycling. The entire microbial community changes involved in nitrogen turnover was addressed in a second contribution where ammonia oxidizing communities were addressed. The title image shows archaeal communities with respect to ammonia oxidation in a degenerated soil that was re-vegetated. Ammonia from manure fertilization may also lead to community changes and changes between bacterial and archaeal contribution, which was addressed in a paddy soil. And, finally, the influence of microbes in remediation with respect to nitrate contamination was addressed in a short communication. Erika Kothe Editor-in-Chief