摘要
病毒是由蛋白质外壳包被内含遗传物质,必须寄生在活细胞内才能进行增殖的非细胞型生物实体,它是地球上数量最多的生物实体之一。土壤是病毒的重要储藏库,其中以侵染原核生物的噬菌体为主。土壤病毒在调控宿主群落结构、驱动种群进化以及参与土壤元素循环等方面发挥着重要的生态功能。深入理解这些功能及其作用机制,不仅有助于揭示病毒在土壤生态系统中的重要角色,还为高效管理土壤环境的健康发展提供科学依据。本文概括了土壤噬菌体通过选择生存策略调控微生物组成和多样性,同时影响宿主的生存能力和毒力;介导基因水平转移以及与宿主的相互作用,影响微生物种群的进化;通过病毒分流(viral shunt)和携带辅助代谢基因介导元素循环;以及病毒对植物、动物和人体健康的广泛影响。基于上述分析,展望了土壤病毒生态学功能未来研究的重点。
土壤是一个具有高度异质性空间结构的复合生态系统,拥有广泛的生态位,成为细菌、真菌、古菌等微生物的主要栖息地,而这些微生物均受病毒的侵染,因此土壤也是病毒最主要的分布场
研究表明,病毒侵染对水生生态系统产生重大影
1 土壤病毒调控宿主群落结构与功能
根据病毒的生存策略,可将病毒分为烈性病毒、溶源性病毒和慢性病毒三大
1.1 土壤病毒影响微生物组成和多样性
越来越多的研究表明,病毒是影响微生物群落组成(物种相对丰度)的关键因
噬菌体除了通过直接作用影响宿主种群,也会通过间接作用影响土壤中其他微生物群落。研究发现噬菌体通过感染和裂解宿主细胞,显著影响宿主细胞的密度,从而改变微生物群落内的竞争动
病毒对微生物群落产生影响,反过来,微生物也会对病毒群落产生影响,两者存在紧密的相互作用。研究发现细菌多样性的显著下降可能通过减少噬菌体的潜在宿主范
1.2 土壤病毒影响宿主的生存能力
土壤病毒能够通过改变生存策略(溶原转化)或者引入特定的功能基因到宿主细胞,从而增强宿主的感染能力或生存能力。溶源性噬菌体使细菌能够在广泛的资源波动范围内共存,提高细菌的生存能
1.3 土壤病毒影响宿主菌株毒力
土壤病毒通过溶原转换、基因水平转移(如抗菌性基因或毒力基因)或与宿主细胞相互作用而产生某种效应(如协同效应),影响宿主菌株的致病性或毒力。在溶原转换方面,研究发现β-棒状杆菌(β-Corynebacterium)噬菌体通过溶原转换使白喉棒状杆菌(Corynebacterium diphtheriae)获得毒力,成为致病菌,对农业生产造成不利影
噬菌体已经成为农业、食品、动物和人类抗细菌性疾病最有前途和最安全的生物制剂之
2 土壤病毒介导土壤元素循环
作为最丰富的生物实体,病毒越来越被认为是全球生物地球化学营养循环的主要驱动

图1 土壤病毒介导土壤营养元素循环
Figure 1 Soil viruses mediate the cycles of soil nutrient elements.
2.1 通过病毒分流影响土壤元素循环
研究表明,绝大多数土壤细菌都会受到噬菌体的感
噬菌体在土壤有机碳矿化过程发挥重要作用。相比于细菌,噬菌体(如T4噬菌体)可更好地预测有机碳矿
2.2 通过携带辅助代谢基因间接参与土壤元素循环
辅助代谢基因(AMGs)起源于细菌细胞,但由噬菌体携带,以增强噬菌体自身和宿主的适应性。噬菌体编码的AMGs种类繁多,例如抗生素抗性基因(antibiotic resistance genes, ARGs),且不同AMGs之间具有一定的互补功
由于土壤病毒影响复杂有机物的降解,例如病毒通过富集参与降解复杂化合物的微生物类群[如假单胞菌属(Pseudomonas)、厌氧柱状菌属(Anaerocolumna)和柄杆菌属(Caulobacter)],从而促进碳的矿
不同的土壤环境条件影响土壤病毒所携带基因的丰度以及种类。虽然底层土壤病毒的密度较低,但其含有AMGs的丰度是表层土壤病毒组的16倍,表明底层土壤病毒高度调控微生物的代谢过
3 土壤病毒影响土壤微生物种群的进化
噬菌体除了影响细菌种群的组成,也成为细菌进化的重要驱动因素,因为它们不仅通过侵染对宿主施加高选择压力,而且通过溶原转化、转导(transduction)和宿主基因破坏等机制将自身基因整合到细菌基因组
3.1 土壤病毒介导基因水平转移
病毒侵染宿主时向宿主细胞引入新的基因,从而引起宿主细胞基因重组的过程称为病毒介导的HGT,即转
目前,关于病毒介导HGT的研究主要集中在抗性基因。土壤生态系统是环境中抗性基因的重要源和
土壤病毒除了作为HGT的载体,其裂解宿主细胞后释放的DNA也具有HGT的能力。病毒侵染裂解宿主细胞,释放裸露的DNA到环境中,成为胞外游离DNA。只有当感受态细菌存在时游离的DNA才能被自然感受态细胞吸收和整合,这种方式称为转化,此方式会引起微生物发生遗传变异,进而推动微生物种群进
3.2 土壤病毒与宿主细菌的相互作用
土壤病毒与土壤微生物耦合关系的研究在揭示土壤生态功能方面发挥着重要的作
4 土壤病毒影响植物、动物和人类健康
目前,微生物活动在驱动生物地球化学循环和促进植物健康方面发挥重要作用的热点研究区是根
土壤病毒是人类健康的危害之
5 总结与展望
土壤噬菌体由于较高的丰度和多样性以及独特的生活策略等,对生态系统的功能产生深远影响。土壤噬菌体通过生存策略的选择或调节宿主的代谢过程影响微生物的组成、生存能力和毒力水平,同时其丰度的高低影响这些方面作用的强度。在介导土壤营养物质循环方面,病毒通过裂解宿主导致大量营养物质释放到外界环境,进而影响这些营养物质的循环过程,或者病毒通过将自身携带的AMGs基因载入宿主细胞,调节宿主细胞对营养物质的代谢水平。此外,土壤病毒能够在细胞水平或基因水平上推动微生物种群进化历程。另外,在农业生产上,依据噬菌体对宿主微生物的作用开发了一种安全的防治农作物细菌性疾病的生物制剂,但该技术对土壤微生态环境的健康稳定的研究仍非常有限,亟待体系化开展相关方面的研究。由于土壤的异质性和复杂性,以及病毒自身的复杂特性,目前对土壤病毒生态功能研究的广度和深度仍非常有限,今后对土壤病毒生态功能的研究,可重点关注如下几个方面。
(1) 提升宏病毒组学精度并强化宏基因组整合,解析病毒功能基因与宿主互作机制,进一步发掘病毒在土壤生态系统的新功能。由于宏病毒组学对病毒测序长度和质量有限,导致宏病毒组学的精确性偏低,以及病毒基因数据库信息有限,使测定基因信息与数据库的比对成功率和功能基因的鉴定结果非常有限,因此亟待通过延长测序长度和提高测序质量提高病毒测序技术的精确度。同时,通过与目前较成熟的宏基因组结合,和基于已有的病毒与宿主相互作用理论知识,推断并鉴定出病毒新的功能基因,不断扩充基因数据库。
(2) 提高病毒-宿主关联预测技术水平,结合转录组学深入理解病毒与宿主相互作用的机制。由于大多数土壤病毒尚未被培养,其信息仅来源于宏基因组重叠群或宏基因组组装基因组,病毒与宿主的相互作用通常只能通过计算模拟进行预
(3) 强化与现代科学技术的结合,将有利于改变研究土壤病毒的维度和实现突破性的发现。有研究利用人工智能(artificial intelligence, AI)大语言模型助力破解病毒蛋白功能,显著提高注释准确
(4) 加强利用宏基因组稳定同位素探测,揭示土壤病毒参与元素循环的过程,同时可结合实时荧光定量PCR跟踪(或定量)宿主和病毒对元素输入的动态响应,从而实现全面了解病毒影响土壤元素循环过程,甚至实现定量评估土壤病毒在生物地球化学循环的潜力。目前,稳定同位素标记主要集中应用于土壤病毒参与碳和氮循环的研究,而对磷和其他元素循环的研究较缺乏。其中,磷元素是病毒结构组成的重要元素,而病毒颗粒对保留土壤磷元素具有非常重要的作用,因此,病毒参与磷循环的研究将是未来的重要研究方向。
作者贡献声明
陈紫婷:论文撰写、绘图和修改;魏亮:参与讨论部分写作;祝贞科:负责对纳入文献进行深度分析;鲁顺保:论文指导和审阅;葛体达:论文指导和审阅;王双:综述选题、论文框架构思和确定、论文审阅和修订、获取基金和项目管理。
利益冲突
作者声明不存在任何可能会影响本文所报告工作的已知经济利益或个人关系。
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