Identity, infection strategy, and biogeochemical impact of nitrifier-infecting viruses

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Environmental viruses heavily influence the genetic diversity and ecology of microbial communities and thus exert control on biogeochemical cycling. This has been exemplified for the carbon cycle in concepts like the viral shunt and the viral shuttle. However, very little is known how viruses modulate N-cycling microbial communities and in turn the nitrogen cycle. Here, we propose to study the effect viruses have on the virocell metabolism of nitrifying microorganisms, in particular ammonia oxidizing archaea (AOA) and bacteria (AOB). We hypothesize that viruses affect the rate and resilience of nitrification differently depending on their infection strategy and the interconnected dominating ammonia oxidizing population. Environmentally relevant microorganisms, such as AOA and AOB, are often difficult to culture including very low cell yields and in addition do not grow on plates. This is the main reason why knowledge on nitrifier-infecting viruses is mainly based on a few bioinformatics-based studies. This year, we established a plaque-free isolation method of nitrifier-infecting viruses in our laboratory and successfully isolated the first lytic phage of AOB. Using this strategy, we propose to study the identity, infection strategy, and biogeochemical impact of nitrifier-infecting viruses. This work will be performed in two work packages (WP). In WP1, we aim to establish a comprehensive catalogue of model virus-nitrifier pairs spanning from archaeal to bacterial hosts. The existing DSMZ collection of AOAs and AOBs will be used as bait organisms to obtain nitrifier-infecting viruses from viral filtrates spanning the range of oligotrophic to eutrophic environments (lakes, soils, and wastewater treatment plants). Selected archaeal and bacterial nitrifier-infecting viruses will be studied in detail concerning their phylogeny, genetic make-up, and infection strategy. Building upon this knowledge, we will study the biogeochemical impact of nitrifier-infecting viruses in WP2. Viruses isolated in WP1 that differ in their infection strategies, e.g., lytic vs. chronic infections, will guide WP2. Nitrifying enrichments will be challenged with viruses isolated from the same habitat. The impact of viral infection will be quantified by nitrification activity changes. In addition, the impact on microbial community dynamics and transcriptional activity in respect to energy metabolism and viral defense will be assessed using state-of-the-art molecular techniques. The proposed project will directly contribute to Research Area C of the priority program SPP2330: Viral impact on microbial communities. It will establish important links between novel viruses and environmentally relevant hosts and thus provide benefit to other SPP proposals dealing, e.g., with computational (machine learning-based) predictions of virus-host pairs from metagenomes or modeling approaches to understand virus-host interactions.