Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173 kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.

中文翻译：

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感染土壤硝化剂的新型病毒家族的活性与宿主生态位分化是相伴的


化学自养硝化器是连接系统发育、进化和生态生理学的模型组。氨氧化菌 （AOB） 通常在高铵态氮供应率下主导氨氧化的第一步，氨氧化古细菌 （AOA） 和完全氨氧化硝基螺藻 （comammox） 通常在较低的供应速率或 AOB 不活跃期间活跃，亚硝酸盐氧化菌 （NOB） 完全经典硝化。土壤病毒群落是动态的，但对功能过程的贡献在很大程度上尚未确定。此外，表征感染相对丰度低的宿主（例如硝化剂）的病毒可能会受到巨大病毒多样性、部分基因组恢复和宿主连锁困难的限制。在这里，我们描述了一项靶向孵化研究，旨在确定土壤中不同硝化者组的生长是否与活跃的病毒种群有关，以及以过程为中心的分析是否有助于表征高质量的病毒基因组。感染不同硝化剂基团的 dsDNA 病毒通过差异宿主抑制原位富集。每个硝化组的生长与预测的抑制曲线一致，并伴随着其病毒的丰度。其中包括 61 个长度为 35-173 kb 的高质量/完整病毒基因组，与经过验证的家族的相似性最小。AOA 病毒缺乏在海洋 AOA 病毒中发现的氨单加氧酶亚基 C （amoC） 基因，但一些编码 AOA 特异性多铜氧化酶 1 型 （MCO1），以前与铜的获取有关，并表明在支持土壤 AOA 的能量代谢中发挥作用。 研究结果表明，重点孵化研究有助于表征与土壤 AOA、AOB 和 NOB 的特定过程相关的活跃宿主-病毒相互作用，并且病毒是动态的，并可能影响氮循环过程。