Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions
Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions
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DOI：
10.1016/j.soilbio.2018.09.032
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发表时间：
2018-12-01
影响因子：
9.7
通讯作者：
Mason-Jones, Kyle
中科院分区：
文献类型：
--
作者：
Kuzyakov, Yakov;Mason-Jones, Kyle
病毒在自然界中无处不在，具有多种生态功能。尽管土壤中的病毒丰度很高(高达10(10)克(-1))，但迄今为止发表的少数几项描述性研究仍未引起人们的注意。在这篇综述中，我们重点介绍了病毒在土壤中的可能功能及其对微生物生命和周转的影响，碳(C)和养分的生物地球化学循环的相关机制，以及C的长期稳定。我们利用了有限的土壤文献，来自水生生态系统和沉积物的更丰富的知识，以及来自纯培养研究的证据。来自土壤和其他生态系统的证据表明，绝大多数土壤细菌在任何时候都会被噬菌体感染。因此，我们引入并调整了五个概念来描述噬菌体在土壤中的作用：(1)病毒分流，(2)‘永远年轻’，(3)EXOMET的病毒调控门，(4)微生物坏死体稳定的C封存，(5)C/N/P化学计量学的微尺度差异。噬菌体(即使没有土壤动物-微生物环概念)解释了细菌死亡率和容易获得的C和养分的释放，从而加速了土壤中的生物地球化学循环。“永远年轻”的概念假定病毒感染在年轻时保持活跃的细菌种群，因为感染和裂解会导致较短的预期寿命。我们对这一概念进行了有争议的讨论，这些假设涉及(1)大多数土壤微生物的休眠，(2)微生物的维持能量，以及(3)它们的高碳利用效率。我们通过细胞内酶和代谢物的抒情释放，统一了先前提出但未解释的‘调节门’和‘EXOMET’的概念。由于噬菌体的元素组成，感染导致微观尺度上的化学计量比C/N/P失衡，从而导致宏观尺度上的磷限制。本文从病毒裂解和细胞碎片在纳米孔中“埋藏”的新视角讨论了最近发展起来的“C固存”概念，即土壤中的C来自于微生物的坏死体，但很少有人研究土壤中的病毒，因此所有的研究方向都是开放、重要和引人入胜的。最迫切的是阐明病毒的功能、它们对微生物生命的后果和生态相关性，并确认(或拒绝)提出的概念。亡灵驱动力在纳米尺度上运行非常迅速，控制着土壤中的微生物生命和从微观到生态系统尺度的生物地球化学周转。
Viruses are ubiquitous in nature and have various ecological functions. Despite their very high abundance (up to 10(10) g(-1)), viruses in soil remain disregarded with just a few, mostly descriptive studies published to date. With this review we focus on the probable functioning of viruses in soil and the consequences for microbial life and turnover, related mechanisms of biogeochemical cycling of carbon (C) and nutrients, and long-term C stabilization. We draw on the limited literature for soil, the richer knowledge from aquatic ecosystems and sediments, and evidence from pure culture studies.Evidence from soil and other ecosystems indicate that the vast majority of soil bacteria are infected by phages at any time. Consequently, we introduce and adapt five concepts for the role of phages in soil: (1) Viral Shunt, (2) 'Forever Young', (3) Viral Regulatory Gate of EXOMET, (4) C sequestration by microbial necromass stabilization, and (5) Microscale divergence of C/N/P stoichiometry.The 'Viral Shunt' accounts for the short-circuiting of trophic C and nutrient transfers by virus-induced mortality. Phages (even without soil animals - the Microbial Loop concept) explain bacterial death rates and the release of easily available C and nutrients, consequently accelerating biogeochemical cycles in soil. The concept 'Forever Young' postulates that viral infection maintains the active bacterial population at a young age, because infection and lysis lead to a short life expectancy. We controversially discuss this concept in relation to hypotheses such as (1) the dormancy of most soil microorganisms, (2) maintenance energy for microorganisms, and (3) their high C use efficiency. We unify the previously suggested but unexplained concepts of 'Regulatory Gate' and 'EXOMET' through the lyric release of intracellular enzymes and metabolites. Due to the elemental composition of phages, infection results in Stoichiometric C/N/P Imbalances at the microscale, with consequences for P limitation at macroscales. The recently developed concept of 'C Sequestration by Necromass Stabilization', i.e., that C sequestered in soil derives from microbial necromass, is discussed from the new perspective of viral lysis and "entombment" of cell fragments in nano-pores.Very few studies have investigated viruses in soil, so all research directions are open, important and fascinating. The most urgent are those elucidating virus functions, their consequences for microbial life, and ecological relevance, and to confirm (or to reject) the proposed concepts. Functioning very fast at the nano-scale, the undead drivers govern microbial life in soil and biogeochemical turnover from micro to ecosystem scales.