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

环境病毒严重影响微生物群落的遗传多样性和生态，从而控制生物地球化学循环。这已经在碳循环的概念中得到了例证，比如病毒分流和病毒穿梭。然而，人们对病毒如何调节氮循环微生物群落，进而调节氮循环所知甚少。在此，我们拟研究病毒对硝化微生物，特别是氨氧化古菌（AOA）和细菌（AOB）的病毒细胞代谢的影响。我们假设病毒对硝化速率和恢复力的影响不同，这取决于它们的感染策略和相互关联的主导氨氧化种群。与环境相关的微生物，如AOA和AOB，通常难以培养，包括细胞产量非常低，而且不能在平板上生长。这就是为什么关于硝化病毒的知识主要是基于少数生物信息学研究的主要原因。今年，我们在实验室建立了一种无菌斑分离硝化感染病毒的方法，成功分离出首个AOB裂解噬菌体。利用这一策略，我们建议研究硝化感染病毒的身份、感染策略和生物地球化学影响。这项工作将在两个工作包（WP）中进行。在WP1中，我们的目标是建立从古细菌到细菌宿主的模型病毒-硝化菌对的综合目录。现有的DSMZ收集的aoa和aob将被用作诱饵生物，从病毒滤液中获得硝化感染病毒，这些病毒滤液横跨贫营养到富营养环境（湖泊、土壤和废水处理厂）的范围。选定的古细菌和细菌硝化细菌感染病毒将详细研究其系统发育，基因组成和感染策略。在此基础上，我们将研究硝化感染病毒对WP2的生物地球化学影响。在WP1中分离的感染策略不同的病毒，例如溶性感染与慢性感染，将指导WP2。从同一生境分离出的病毒将对硝化富集造成挑战。病毒感染的影响将通过硝化活性的变化来量化。此外，在能量代谢和病毒防御方面对微生物群落动态和转录活性的影响将使用最先进的分子技术进行评估。该项目将直接资助优先项目SPP2330的研究领域C：病毒对微生物群落的影响。它将建立新型病毒与环境相关宿主之间的重要联系，从而为其他SPP提案提供好处，例如，从宏基因组中对病毒-宿主对进行计算（基于机器学习）预测或建模方法以了解病毒-宿主相互作用。

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.