Investigating the diversity of viruses infecting Nitrospira across different ecosystems

Nitrogen serves as a vital element in all living organisms and acts as the primary nutrient that restricts life on Earth in all known ecosystems. Its biological availability is determined by a variety of microbial-driven transformations, known as the nitrogen cycle. Various microorganisms participate in the nitrogen cycle, making them key to global biogechemistry and making viral infection of nitrogen cyclers an ecological process of global relevance. One phylum of these microorganisms is Nitrospira, which can be found in various ecosystems where they are often involved in of nitrification. Here, we investigated the unexplored diversity of Nitrospira-infecting viruses and their ecological impact on nitrification in diverse ecosystems. We conducted genomic analyses on 20 publicly available metagenomes from a range of environments, including activated sludge, bioreactors, lakes, and groundwater, where Nitrospira presence was detected. Additionally, we incorporated metagenomes from a mesocosm experiment simulating streams and from a sedimentation basin. We identified CRISPR-Cas systems in different Nitrospira MAGs that were matching unrecognized viral particles, indicating either past or current viral infections. This allowed for the reconstruction of viral infection histories of Nitrospira across various ecosystems. We further explore potential differences between viruses infecting Nitrospira engaged in complete ammonia oxidation (COMAMMOX) and those involved solely in nitrite oxidation. We hypothesize that viruses significantly influence impactthe ecological functions of Nitrospira within these ecosystems, thereby exerting a direct impact on the global nitrogen cycle.