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地球科学进展, 2018, 33(3): 225-235
doi: 10.11867/j.issn.1001-8166.2018.03.0225
病毒对海洋细菌代谢的影响及其生物地球化学效应
Influence of Virus upon the Marine Bacterial Metabolism and Its Biogeochemical Effects
卢龙飞1,, 张锐1, 徐杰2, 焦念志1,*,
1.厦门大学海洋与地球学院, 近海海洋环境科学国家重点实验室, 海洋微型生物与地球圈层研究所, 福建 厦门 361102
2.中国科学院南海海洋研究所, 广东 广州 510301
Lu Longfei1,, Zhang Rui1, Xu Jie2, Jiao Nianzhi1,*,
1.Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen 361102, China;
2.South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
 引用本文:
卢龙飞, 张锐, 徐杰, 焦念志. 病毒对海洋细菌代谢的影响及其生物地球化学效应[J]. 地球科学进展, 2018, 33(3): 225-235, doi:10.11867/j.issn.1001-8166.2018.03.0225
Lu Longfei, Zhang Rui, Xu Jie, Jiao Nianzhi. Influence of Virus upon the Marine Bacterial Metabolism and Its Biogeochemical Effects[J]. Advances in Earth Science, 2018, 33(3): 225-235, doi:10.11867/j.issn.1001-8166.2018.03.0225

摘要:

病毒是海洋生态系统中丰度最高的生命形式,其中超过90%属于浮游细菌(细菌和古菌)病毒,是海洋生态系统的重要参与者和海洋生物地球化学循环的重要驱动力。作为海洋浮游细菌主要的致死因子之一,病毒通过裂解宿主释放出大量的有机物和营养盐,调控宿主群落的代谢行为,进而影响生物地球化学循环。同时,伴随侵染的发生,病毒挟持宿主细胞的代谢系统完成自身的生命周期,从而改变宿主胞内的代谢途径和代谢产物。概述了病毒在个体层面和群落层面对海洋浮游细菌代谢的影响,及其对海洋元素循环的作用,评估了气候变化、环境因子对病毒调控细菌代谢的潜在影响,有助于人们对微生物参与的海洋生物地球化学循环的全面认识。

关键词: 海洋病毒 ; 海洋细菌 ; 代谢 ; 病毒—宿主相互作用;

Abstract:

Viruses are by far the most abundant entities in marine environments, and are mainly phages that infect bacteria and archaea, which also are a significant component of marine ecosystem and a major force behind marine biogeochemical cycles. As a major source of mortality, viral lysis can release highly labile cellular components, both organic matters and inorganic nutrients, regulating the metabolism of its hosts and influencing the biogeochemical cycles. During infection, viruses could hijack the metabolic system of hosts for its own propagation, thereby changing the metabolism and metabolites of host cells. This paper summarized the effects of viruses on the metabolism of marine bacterioplankton at both the cellular and community level, and its influence on the cycling of ocean elements. Then, the potential impact of environmental factors was assessed on the influence of viruses upon bacterial metabolism. This paper will contribute to a comprehensive understanding of the role of microbes within marine biogeochemical cycles.

Key words: Marine virus ; Marine bacteria ; Metabolism ; Virus-host interaction.
1 海洋病毒

海洋是地球上最广阔的水体,约占地球表面积的71%。海洋也是地球上最大的恒化器,孕育着数量庞大、形态多样的各式生物。海洋微生物是海洋生态系统中最重要的组成部分,其生物量约占海洋总生物量的90%以上,是全球海洋物质能量循环的重要驱动者和主导者[1,2]。在众多微生物中,海洋病毒是一类寄生的、非细胞结构的超微型有机体,其个体微小、结构简单,主要由蛋白质外壳和包裹在外壳内的遗传物质(DNA或RNA)所组成[3]。海洋病毒是海洋生态系统中丰度最高的微生物,可达1010个/L,是海洋细菌丰度的5~25倍,其生物量仅次于海洋细菌,位居第二[4]。90%以上的海洋病毒属于侵染细菌的病毒,即噬菌体。病毒是海洋生态系统中重要的致死者,每天可以裂解10%~20%的海洋生物,藉此每年能够释放出大概3 Gt的有机碳[1,2,4,5]。通过侵染和裂解宿主,病毒对海洋生态系统和生物地球化学循环产生重要影响,被称为“全球尺度过程的纳米尺度驱动者”[6]

2 海洋细菌及其代谢

海洋细菌(包括分类学意义上的细菌和古菌)作为海洋生态系统的重要组分,其总生物量在海洋生物中最高,丰度可达105~106 cells/mL。海洋细菌代谢快,生长繁殖迅速,能够快速应对外界环境的变化。Azam等[7,8]提出了微食物环(Microbial loop)的概念,指出海洋细菌在海洋碳循环中发挥着关键的作用。一方面,海洋细菌可以把周围环境中的有机碳(包括颗粒有机碳和溶解有机碳,Particle Organic Carbon and Dissolved Organic Carbon,POC and DOC)水解,并吸收转化为自身的生物量,即同化作用或合成代谢,就是细菌的生产力(Bacterial Production,BP)。整合到细菌中的有机碳,一部分经原生动物等的捕食作用向更高营养级传递到经典食物链[7,8],另一部分通过主动分泌和病毒的裂解作用以溶解有机碳的形式重新释放到环境中。另一方面,海洋细菌扮演着分解者的角色,将有机碳(包括POC和DOC)矿化,转化为无机营养盐和CO2,即异化作用或分解代谢[9],代表指标是细菌呼吸作用(Bacterial Respiration,BR),这也是海洋有机碳矿化的主要途径之一。这2个重要指标(细菌生产力和细菌呼吸)对研究海洋细菌在海洋碳循环和物质能量流动中的作用十分重要。通过细菌生产力和细菌呼吸还可以计算细菌的生长效率(Bacterial Growth Efficiency,BGE,BGE=BP/(BP+BR)),用来表征被细菌吸收的有机碳中用于合成自身组分的碳的百分含量。细菌生长效率是表征细菌功能和生态角色的重要参数,也是评价细菌群落碳收支的关键指标,细菌生长效率与细菌的生长状态密切相关,能够反应其生长环境的变化[10,11,12]。细菌生产力、呼吸以及生长效率一般均呈现从近岸到开阔大洋、从表层到底层逐渐降低的趋势[13,14,15,16,17]。在开阔大洋,细菌碳的需求量(Bacterial Carbon Demand,BCD,BCD=BP+BR)约占初级生产力的65%(在部分寡营养海域甚至超过初级生产力)[13,17],其中,细菌生产力约占10%,细菌呼吸作用约占50%[13,18,19]

3 病毒对海洋细菌胞内代谢的影响

病毒的生命周期一般分为吸附、入侵、复制、装配和释放等阶段。病毒没有自己的代谢系统,需要依靠宿主的系统来进行自身的代谢活动。在入侵宿主细胞后,海洋病毒会利用宿主的资源并接管宿主的代谢系统,一方面抑制宿主细胞基因的表达,另一方面大量表达病毒自身的基因,以完成子代病毒的复制[20,21,22,23,24]。Hagay等[24]对全球海洋调查(Global Ocean Survey,GOS)获得的数据库进行了分析总结,发现病毒侵染后增强的主要是嘌呤和嘧啶代谢相关的基因,说明病毒在侵染宿主后操控了宿主的代谢途径以降解宿主的DNA和RNA,并用以合成病毒复制所需的核酸。病毒颗粒是由蛋白和核酸所构成的,其氮/磷(N/P)含量的相对比例要高于其他微生物[2],病毒颗粒携带的N/P可以通过不同的生态过程进入生物地球化学循环[25,26]。同时,宿主细胞遗传物质的降解并不能完全满足病毒复制的需求,所以病毒的大量复制需要被侵染细胞从环境中吸收更多的N/P[27]

许多海洋病毒还携带与宿主代谢相关的基因,即代谢辅助基因(Auxiliary Metabolic Genes,AMGs)。这类基因可以调控宿主的光合作用[20,21,28]、碳代谢[22]、核酸合成[24,29]以及营养物质的摄取等[30]。基因组的比对分析表明AMGs在全球海洋病毒基因组中大量存在[31,32]。在病毒侵染宿主细胞后,AMGs一般能够大量表达,用以辅助由于病毒侵染而导致的宿主表达的抑制作用。针对噬藻体(侵染蓝细菌的病毒)的研究发现,在病毒侵染宿主细胞后,宿主细胞几乎所有的基因(包括光系统的相关基因)表达均显著降低[33],而噬藻体携带的光合AMGs(包括psbA,psbDhli基因)却能够大量表达,以满足子代病毒合成的能量需求。宏组学的分析表明全球海洋表层水中60%的psbA基因源自噬藻体[34],并且,噬藻体合成的光系统蛋白比宿主自身合成的活性更高[35]。Zeng 等[30]调查发现,在磷限制的条件下,被病毒侵染的细胞中与磷吸收相关的病毒基因(phosphate-binding protein gene和alkaline phosphatase gene,pstSphoA)的表达量明显增加,这2个基因是细胞同化磷的重要基因,在磷限制的状态下能够增强磷酸盐的吸收。此外,在海洋极端环境下,也发现病毒AMGs基因的存在。从深海热液喷口获得的宏基因组数据中,Anantharaman等[23]拼装出能够侵染硫氧化细菌的18株病毒基因组,其中15株包含rdsr基因(reverse dissimilatory sulfite reductase)。rdsr基因能够表达一类含有硫氧化酶活性的蛋白,在病毒侵染宿主后rdsr基因能大量表达,为病毒的复制提供能量。宏组学的比较分析发现,含有此类AMGs基因的病毒在热液喷口、缺氧区以及其他海域广泛分布,且相对丰度很高,说明其在全球硫循环中潜在的重要作用[33]

近几年,质谱相关技术的应用,让研究人员可以更好地检测细菌代谢产物(包括胞内和胞外)在病毒侵染后的变化。Ankrah等[36]利用质谱检测技术发现,在病毒侵染亚硫酸杆菌(Sulfitobacter sp. 2047)后,宿主细胞内的代谢途径未发生显著变化,而约71%的代谢产物的浓度显著提高;同时,大于70%的可鉴别培养基组分显著降低,说明被病毒侵染的宿主细胞从培养基中吸收了更多的营养物质,其整体的表达作用也显著提升。De Smet等[37]探究了在6株不同病毒侵染后假单胞菌(Pseudomonas aeruginosa)的胞内代谢产物的变化情况,发现在病毒侵染后嘧啶和核苷酸糖相关的代谢产物浓度显著增加;在侵染过程中病毒AMGs的代谢产物大量积累。上述研究均表明,海洋病毒在侵染细菌后,在相当程度上影响了宿主细胞的代谢、表达以及营养物质的吸收。在不同病毒侵染的条件下胞内代谢产物的明显差异也说明海洋环境中病毒侵染所导致的宿主胞内代谢的改变可能是多样化的。

4 病毒对海洋细菌群落代谢的影响

细菌的群落代谢指细菌群落宏观的代谢表征。在海洋生态系统中,代表性的细菌群落代谢指标即为细菌生产力和细菌呼吸。任何能够调控细菌丰度和活性的因素,都可能影响海洋细菌在海洋生物地球化学循环中的作用[38]。作为海洋细菌的重要致死者,海洋病毒每天可以杀死20%~40%的海洋细菌,与原生动物的捕食作用相当[39],从而影响海洋细菌的群落代谢[1,2,38]。生态模型分析的结果也表明病毒裂解对细菌在海洋碳循环的作用具有显著的影响[39,40]。近几年,涉及海洋病毒对细菌群落代谢调控的相关研究逐渐增多[41,42,43]。目前,在海洋生态系统中检测海洋病毒对细菌生产力、细菌呼吸和细菌生长效率的影响,主要采用2种方法:①通过分离纯化的病毒—宿主体系,结合环境群落建立有无病毒条件下的培养体系[44,45];②通过切向流系统或者不同粒径的滤膜,采用小体积的培养体系以探究海洋病毒的添加、富集、灭活或减少对原位细菌群落所产生的影响[41~43,46~50],具体研究及结果见表1

表1

涉及海洋病毒对细菌群落代谢影响的已发表研究总结

Table 1

Summary of published studies used to investigate the effects of marine virus upon bacterial community metabolism

大部分的实验结果均表明海洋病毒的存在能够提升细菌群落的呼吸,并降低细菌群落的生长效率。在病毒侵染过程中,病毒的存在一方面迫使被侵染宿主消耗额外的能量来进行自身的复制,另一方面裂解细胞后释放细胞碎片,而大部分裂解产物均需要其他未被侵染的细菌细胞分泌酶类(消耗额外的能量)来降解[17,41,47],并且未被侵染的细胞也需要花费能量来抵御病毒的侵染,从而增加细菌总体的呼吸作用[51]。然而,部分实验结果则展现出相反的趋势[41,43,48,50]。这可能是由于病毒的裂解能够导致宿主细胞的大量死亡,降低了细菌群落的总丰度;同时,在环境营养物质相对丰富的情况下,病毒裂解宿主产生的营养物质对未侵染宿主的刺激作用不强,导致群落呼吸降低。将细菌分离株同海水环境中的病毒群落共培养的实验结果,也证实病毒可以显著降低其宿主菌的呼吸和单细菌呼吸作用[45]

此外,病毒对细菌生产力的影响也存在差异。通过模型预测的结果表明,病毒的存在有利于提升细菌的生产力[39],但已有的调查结果却表明,海洋病毒对细菌生产力的影响差异较大,包括促进作用[46,49]、无显著影响[44]以及抑制作用[41,45,47],这也与淡水环境下的调查结果类似[12,52~54]。宿主自身携带的营养物质一般很难满足海洋病毒复制的需求,病毒在侵染过程会促进宿主细胞吸收更多的营养物质以合成子代病毒[36];大部分的裂解产物活性较高,能够被其他细菌迅速吸收利用,尤其寡营养区域[1],上述过程均可能提升细菌生产力和单细菌生产力。然而,病毒会倾向于侵染活性高、体积较大的细菌类群[43,45,50],而这部分细菌一般是细菌生产力的重要贡献者[50],其大量的裂解会降低整体细菌的生产力[4]。Liu等[45]采用无细菌海水培养4株细菌分离株(2 Psychrobacter 和 2 α-proteobacterium),发现病毒的存在能够显著抑制4株细菌的生产力和单细胞生产力。此外,部分实验结果表明,病毒裂解产物在被其他细菌吸收后,大部分转化为细菌的呼吸作用,而不是合成细胞结构,这也可能导致细菌生产力的降低[1,39,55,56]

调查结果的不一致也可能与环境的营养程度相关。在富营养条件下,环境中的有机物足够支撑生境内细菌的生长需求。病毒更多的是发挥“捕食者”的作用,优先侵染活性高的细菌,而不是促进营养的循环,这时病毒的裂解产物对其他细菌的刺激作用并不显著[43]。此时,病毒的影响可能仅限于被侵染的较为活性的细菌,这部分细菌的生产力、呼吸会被抑制。而这部分细菌是整体细菌生产力和呼吸作用的主要贡献者,对应的,病毒的侵染则可能降低整体细菌的生产力和呼吸作用。在寡营养条件下,细菌的生长受营养物质的限制,大部分的细菌活性较低,此时病毒的裂解作用除了降低其宿主的生产力并提升呼吸作用外,其裂解产物也能迅速被其他细菌吸收利用,从而促进其他细菌的生长,即未被侵染细菌生产力的增加。虽然病毒裂解产物相对较为活性,但细菌只能限制利用小于700 Da的低分子量的有机物[17],所以仍需要消耗能量来降解吸收裂解产物,也就提升了其呼吸作用。

5 病毒调控细菌代谢对海洋生物地球化学循环的影响

海洋不仅是地球上面积最大的水体,也是巨大的有机碳库,海洋的总有机碳库可达到662 Pg C, 与大气含量(600 Pg C)基本相当[57,58]。海洋也是全球重要的碳汇,可以大量吸收人类活动排放的CO2[59]。海洋吸收并储存大气CO2的方式主要有4种:溶解度泵(solubility pump)、碳酸盐泵(carbonate pump)、海洋生物介导的生物泵(Biological Carbon Pump,BCP)[60,61]和微型生物碳泵(Microbial Carbon Pump,MCP)[62,63]。在BCP和MCP这2种机制中,海洋细菌以及海洋病毒都发挥着不可替代的作用。尤其在MCP过程中,细菌的主动分泌以及病毒的裂解作用都对海洋惰性有机碳(Recalcitrant DOC,RDOC)的产生具有重要作用[62]。据估计,流经病毒的碳量约占海洋初级生产力总量的25%[39],考虑到病毒的生命周期短、丰度高、对宿主致死率高,病毒裂解作用对RDOC产生的贡献不可忽略。

Fuhrman[39]构建的模型表明,在没有病毒存在的情况下,通过细菌生产力整合的50%的有机碳可通过原生动物的捕食向上传递,另外的50%则通过细菌的呼吸作用转化为CO2;在病毒存在的情况下,其裂解作用可以将细菌细胞中的碳重新释放到环境中,大大降低了向经典食物链的传递,减少比例为33%。一般认为,原生动物的捕食作用有利于无机营养盐的释放,促进其他细菌、浮游植物的生长,而病毒的裂解作用则有助于有机碳在海洋碳库中的停留与再循环[52,53,54]。虽然二者都有利于将细菌的有机碳转化为无机碳,但少部分的病毒裂解产物属于相对惰性的有机碳[62],所以在长时间尺度上,后者将更有利于RDOC的产生。病毒的存在也能够促进海洋微型生物群落多样性的提高[2,5,6,64],因此细菌群落可利用的底物种类相应可能提高,半活性溶解有机碳和半惰性溶解有机碳(Semi-Labile Dissolved Organic Carbon/Semi- Refractory Dissolved Organic Carbon,SLDOC/SRDOC)的被利用概率也就可能提高[62]

虽然海洋可以大量吸收大气中的CO2,但固碳并不等于储碳[62],在通过海洋初级生产力固定的碳中,最终只有不到1%被储存在海洋里[14]。影响某海域属于碳源或者碳汇的关键之一就是该海域的初级生产力和呼吸代谢的强弱。在大洋,海洋细菌是群落总呼吸最重要的承担者,即使在浮游植物较多的真光层,细菌呼吸也可以贡献群落总呼吸的50%~90%[16,65]。病毒裂解宿主细胞释放的有机碳,大部分可通过呼吸和光降解最终转化为C O 2 1,39,55,56,66 。在海洋细菌群落中,病毒一般倾向于侵染活性较高的细菌,而这部分细菌是细菌群落代谢的主要承担者,尤其在河口、近岸等富营养海域。病毒的倾向性裂解作用,能够显著控制富营养环境中这部分细菌的生产力、呼吸作用和生长效率[45]。这也将影响该区域的碳循环,例如在河口区域,病毒对高活性细菌的裂解作用,能够降低河口细菌对河源性DOC的分解作用,从而有利于河源性DOC向外海的扩散[50];而这部分细菌的大量裂解,也能够显著降低细菌呼吸作用,从而减少对氧气的消耗和有机碳的矿化作用[45]。可见,病毒群落、活性的波动极可能对海洋部分、整体碳汇/源的格局、程度产生重要的影响。

此外,病毒的裂解作用可以释放出大量的活性氮/磷营养盐[66],是海洋生态系统中重要的N/P的来源,也能够促进海洋浮游植物、海洋细菌的生长,尤其是面积广大的寡营养大洋[66,67]。海洋真光层的细菌生产力为26~70 Pg C/a[14],按照10%~20%的病毒裂解致死率,以及细菌细胞的C: N: P为69: 16: 1[2,68],则通过病毒裂解作用可以在真光层产生0.60~3.25 Pg N/a ,以及0.038~0.20 Pg P/a。海洋的初级生产力约为49.3 Pg C/a[14],对应为7.4 Pg N/a和0.47 Pg P/a(Redfield ratio,106C: 16N: 1P),病毒的裂解作用则可以为初级生产力提供7%~38%的N,以及8%~43%的P。病毒裂解也可以释放铁元素[69,70]。铁元素是限制世界大部分海洋初级生产的关键元素,例如在高氮低叶绿素的大西洋,外界补充的铁元素只能够满足初级生产力4%~20%的需求[69],而病毒裂解海洋细菌后释放的铁量,可以支撑生境内浮游植物生长90%的铁需求[69,70]。相比裂解产物中的C,N/P/Fe等元素含量高的化合物,更容易被吸收利用[2],这也将导致裂解产物中C的积累和保存[25]

6 病毒调控细菌代谢的影响因素

海洋生态系统复杂多变,对海洋生物可以产生影响的因素主要包括:非生物因素(物理化学因子)和生物因素(竞争、共生、捕食和寄生等)。其中,能够影响细菌生长、病毒活性的因素都可能直接或者间接影响病毒的生理作用,进而影响病毒—宿主间的相互作用。

(1)温度。可以直接影响病毒在海洋中的丰度、分布以及生活策略,例如温度升高可以增加病毒的降解率[71]和生产力[72],降低病毒的溶源性[73]等。不同的病毒对温度的耐受性不尽相同,即使同一株病毒侵染不同宿主的温度范围也存在差异[74]。据统计,病毒的温度耐受性一般高于其宿主,这能够赋予病毒相对更强的温度适应性,有利于病毒颗粒在相对更广温度范围内的存活及成功侵染[75]。此外,温度对宿主生长状态(如细胞膜脂的弹性)的改变也可以间接影响病毒的生活策略、复制过程以及病毒—宿主间的作用[76,77]

(2)光照。在太阳光中,紫外线对病毒的损伤较大,包括降解病毒的蛋白质,改变衣壳结构,损害DNA,阻断病毒的复制等[78,79,80]。由于紫外线对DNA的损伤主要是形成嘧啶二聚体,所以G+C含量较低(拥有更多的潜在嘧啶二聚体位点)的病毒对紫外线尤为敏感[80]。同时,紫外线也能诱导溶源性病毒向裂解性生活史的转换,这也导致了大洋的溶源性病毒比例要低于近岸海域[75]。可见光在一定程度上能够促进病毒的降解[81],同时也能够提升病毒的生产力[82]。部分海洋病毒还存在光周期性,例如噬藻体在夜间的侵染性和生产力均要高于白天[82,83]。此外,光照的差异也可以体现在海洋不同的深度上,海洋下层的病毒通过上升流转移到表层后,降解率显著提高[84]。为应对自然光照,细菌细胞一般具有自我修复的能力,但大部分病毒只能在成功侵染宿主后依靠宿主的体系来进行修复[85,86,87],游离的病毒则不具备修复的能力。光照的差异以及病毒—细菌对光照不同的应对策略均可能导致病毒—细菌交互作用的多样化。

(3)盐度。海洋病毒一般都需要特定的离子环境来维持其结构的稳定性和侵染性,病毒的衣壳结构维持着一定的渗透压,当外界环境的离子强度突然剧烈改变时,可能直接导致病毒的失活、吸附的不成功或者核酸注入的失败[88]。其中,被脂膜包裹的病毒对盐度的敏感性更高[89]。盐度也可以改变病毒的生命周期,Zachary[90]发现在盐度低于18‰时,噬菌体的潜伏期增长,裂解量降低。此外,不适宜的盐度变化也能够影响海洋细菌的生长,间接促进病毒溶源性的发生[91]。在自然环境中,尤其在河口环境下,盐度的剧烈变化可以直接或间接影响病毒和细菌间的相互关系,影响病毒对细菌群落代谢的调节,进而影响细菌在海洋碳循环中的作用[50]

(4)营养盐以及各元素比例。由于病毒颗粒是由蛋白衣壳包裹的遗传物质,其N和P的相对含量(C: N: P为20: 6: 1,7株病毒分离株平均值[25])相比其他海洋微生物(海洋浮游植物的C: N: P平均比例为106: 16: 1;浮游细菌,69: 16: 1)要高很多[2,25],病毒的复制也就需要相对更多的N和P。已有研究表明,P的缺乏能够显著降低病毒基因组的表达[30],促进病毒生活史从裂解性向溶源性/假溶源性转化[92,93],而形成的溶源状态的宿主则更具生存优势(表现为高的细菌生产力和呼吸)。而且,环境中不同的C: N: P也可能会导致病毒代谢(裂解量、潜伏期等)的差异[56,94],进而影响病毒—宿主间的相互作用。

(5)溶解有机碳(Dissolved Organic Carbon,DOC)。Carlson等[17]提出细菌的呼吸作用与DOC的质量(即可利用程度)紧密联系,环境中DOC的可利用程度降低会提升细菌的呼吸作用[43,95]。当环境中可利用的DOC较多时,细菌的生长速度可能超过病毒,摆脱病毒的控制,Motegi等[42]提出当营养充足的时候,细菌可能有足够的代价来改变病毒—细菌受体、合成限制酶等来抵御病毒的侵染。同时,当营养充足时,细菌生长迅速,胞外酶的分泌也对应增加,导致病毒的衣壳结构被破坏,病毒的降解率也对应提高[96,97]。此外,外源DOC的输入也可能影响病毒—细菌间的相互作用[43]。值得一提的是,在目前的研究中,不少是采用的切向流膜包技术(表1),而通过切向流膜包在浓缩病毒的同时,也浓缩了30/100 kDa-0.22 μm的高分子量有机物(属于比较易于利用的活性有机物)[43]。这部分活性有机物的引入能够促进细菌的生长,表现为细菌生产力的提升。但细菌只能利用小于700 Da的低分子量的有机物[17],也就需要额外的能量来酶解吸收30/100 kDa-0.22 μm的组分,也就相对提升了细菌的呼吸作用。所以,上述实验中单纯以灭活病毒为参照的探究,除了病毒有无的变量外,也引入了DOC(30/100 kDa-0.22 μm)的差异,从而可能导致结果的不确定性[49]

(6)其他的环境参数。涉及CO2浓度对病毒—宿主相互关系的报道较少,相关结果并不一致。部分研究表明CO2浓度的升高对海洋病毒丰度的影响不显著[98,99,100],但也有报道表示高荧光病毒(High Fluorescence Virus,HFV)的丰度随着CO2 浓度的升高而降低[101]。但一般认为,CO2是通过对宿主细胞产生作用进而间接改变病毒的特性、病毒—宿主间的关系等[102]

7 结论和展望

病毒是海洋生态系统中丰度最高的生命形式。海洋病毒每天可以裂解10%~20%的海洋生物,是海洋生态系统中重要的致死者,对海洋的生物地球化学循环产生重要影响。通过侵染和裂解宿主,病毒对海洋细菌的代谢行为具有显著的调控作用。在细胞水平上,海洋病毒侵染细菌后接管了宿主的代谢系统,改变了宿主的代谢和表达以完成自身的生命周期。在群落水平上,海洋病毒能够影响细菌的群落代谢表现,即细菌生产力、呼吸以及生长效率,进而影响细菌在海洋生物地球化学循环中的作用。病毒对细菌代谢的调控作用也受多种环境因素的影响,例如温度、盐度、光照、营养盐以及DOC等。但到目前为止,针对上述情景的研究仅限于极个别的细菌—病毒体系,为数不多的野外调查也分布在有限范围的海域内,很难量化海洋病毒在全球尺度上对细菌代谢的调控作用。这极大限制了我们全面了解病毒—细菌体系在海洋生态系统中的作用。针对目前的研究现状,作者提出以下几点研究方向:

(1) 胞内代谢层面:当前对病毒胁迫细菌代谢系统的认识主要源于病毒—细菌分离株的基因组和宏组学的分析研究,针对性的培养实验受限于以蓝细菌、硫酸杆菌、假单胞菌菌株为代表的极个别细菌类群。为更好地跟踪病毒对细菌胞内代谢的影响,迫切需要纳入更多的病毒—细菌体系,尤其是具有代表性的模式菌株,如SAR11,玫瑰杆菌等。此外,需要将现有的基因水平的研究提升到转录组和代谢组水平上,并与生态系统层面建立更直接的链接。

(2) 群落代谢层面:截止目前,相关的野外生态调查和培养实验主要集中在地中海、北美近岸以及中国香港周边等海域,代表性不强,也缺少时间尺度上的探究,难以在全球尺度上量化病毒对细菌群落代谢表现的影响。为此,我们需要补充进行更广范围的生态调查和现场试验,尤其是典型海洋环境下的时间尺度上的跟踪观测,例如寡营养大洋、深海及极地等环境,以全面探究病毒对细菌代谢调控的时空变化规律,并定量分析海洋病毒在全球尺度上对细菌群落代谢的调控作用。

(3) 全球气候变化引发了一系列的海洋环境改变,例如升温、海洋酸化和低氧区扩大等。而在逐渐改变的海洋背景下,针对病毒对细菌代谢调控的相关研究非常少,这极大地阻碍了我们对未来海洋病毒—细菌相互作用的认识。因而,我们需要模拟未来的海洋环境建立单一环境参数变化下、或者多个参数同步改变下的中宇宙培养实验,跟踪不同时间尺度下病毒与细菌代谢的相互关系,以厘清海洋病毒在新环境下对细菌代谢的调控作用,并评估病毒—细菌在未来海洋中所发挥的生物地球化学作用。

致 谢:感谢厦门大学近海海洋环境科学国家重点实验室李雪静博士在文章撰写过程中给予的帮助。

The authors have declared that no competing interests exist.

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氨基糖作为海洋环境中一类具有重要地球化学特征的有机质,其在海水、颗粒物和沉积物中的含量和组成等信息能够有效反映有机质的来源、降解过程及成岩状态。从氨基糖的来源与组成、海洋环境中的分布特征和影响因素,以及其作为生物标志物对有机质来源和降解状态的指示作用等方面,系统总结了海洋环境中氨基糖的研究进展。结果表明,氨基糖的活性受其大分子形态、环境中溶解氧、营养盐水平和沉积环境的影响。葡萄糖胺/半乳糖胺(Glc N/GalN)和总可水解氨基酸/总可水解氨基糖(THAA/THAS)对有机质来源和降解状态的指示具有一致性,较高的Glc N/GalN和THAA/THAS值可反映浮游生物来源的新鲜有机质,其比值的降低表明有机质逐渐向细菌有机质转化。氨基糖的碳、氮归一化含量对二者的指示具有差异性,其比例的升高和降低取决于有机质降解程度和来源影响的相对贡献大小。胞壁酸可用于估算较为新鲜的细菌有机质对总有机质的贡献,但由于其快速循环而导致在溶解有机质中的含量极低,不适合应用在溶解有机质中。今后的工作应进一步加强不同微生物对海洋环境中氨基糖的贡献,区分有机质来源和降解对氨基糖的影响以及转化和归宿研究。
[本文引用: 1]
[10]
Smith E M, Prairie Y T.Bacterial metabolism and growth efficiency in lakes: The importance of phosphorus availability[J]. Limnology and Oceanography, 2004, 49(1): 137-147.
DOI:10.4319/lo.2004.49.1.0137 URL
We investigated bacterial responses to variations in dissolved organic carbon (DOC) and nutrient availability by a comparative analysis of bacterial metabolism in lakes ranging from oligotrophic to eutrophic. Bacterial growth, respiration, and growth efficiency were quantified in lake water dilution cultures performed in 20 lakes located in eastern Quebec, Canada, which varied with respect to both DOC and nutrient concentrations. Intrinsic growth rates of the bacteria ranged from 0.1 to $1.4\ \text{d}^{-1}$ bacterial cell-specific respiration rates ranged from 0.4 to 7.2 fg C $\text{cell}^{-1}\ \text{h}^{-1}$, and growth efficiencies ranged from 6.7% to 51.6%. These variations were unrelated to bulk DOC concentrations. Instead, growth rate and efficiency were positively related to total phosphorus concentrations. Specific respiration rate, on the other hand, decreased with increasing phosphorus concentrations, and the magnitude of respiration, on a per-cell basis, strongly influenced observed growth efficiencies. In a series of substrate enrichment experiments, additions of glucose alone failed to stimulate a response in growth rate, mean cell biovolume, or the potential biomass yield in dilution cultures, but all responded positively to phosphorus additions. Our results show that bacterial metabolism and the fate of DOC input to lake microbial communities are strongly dependent on phosphorus availability, rather than total carbon availability. Extreme oligotrophy appears to place high respiratory demands on the bacterioplankton, resulting in very low bacterial growth efficiencies and consequently greater DOC flow to CO2 than to biomass available for transfer to higher trophic levels.
[本文引用: 1]
[11]
Kritzberg E S, Cole J J, Pace M M, et al. Does autochthonous primary production drive variability in bacterial metabolism and growth efficiency in lakes dominated by terrestrial inputs[J]. Aquatic Microbial Ecology, 2005, 38(2): 103-111.
DOI:10.3354/ame038103 URL
During the past 20 yr, aquatic microbiologists have reported 2 strong patterns which initially appear contradictory. In pelagic systems, bacterial growth and biomass is well correlated with the growth and biomass of primary producers. However, bacterial respiration often exceeds net primary production, which suggests that bacteria are subsidized by external inputs of organic matter. We hypothesize that bacterial growth efficiency (BGE) varies systematically between autochthonous and allochthonous carbon (C) sources and that this variation resolves the above conundrum. To test these ideas, we examined the ecological regulation of bacterial secondary production (BP), bacterial respiration (BR) and BGE in a series of lakes dominated by terrestrial (allochthonous) C inputs. BP was correlated with autochthonous C sources (chlorophyll a) even though the lakes were net heterotrophic (i.e. heterotrophic respiration consistently exceeded primary production). The results were simulated by a simple steady-state model of bacterial utilization of autochthonous and allochthonous dissolved organic C. A higher preference and greater growth efficiency of bacteria on autochthonous C may explain why BP is coupled to autochthonous production also in net heterotrophic ecosystems where the use of allochthonous C by bacteria is high. These results suggest that little of the allochthonous C assimilated by bacteria is likely to reach higher consumers.
[本文引用: 1]
[12]
Maurice C F, Bouvier T, Comte J, et al. Seasonal variations of phage life strategies and bacterial physiological states in three northern temperate lakes[J]. Environmental Microbiology, 2010, 12(3): 628-641.
DOI:10.1111/j.1462-2920.2009.02103.x PMID:20002137 URL
Summary The current consensus concerning the prevalence of lytic and lysogenic phage life cycles in aquatic systems is that the host physiological state may influence viral strategies, lysogeny being favoured when hosts have reduced metabolic rates. We explored this hypothesis, by following phage cycle dynamics, host physiological state and metabolic activity over an annual cycle in three lakes subjected to strong seasonal fluctuations, including 4–5months of ice cover. We observed marked seasonal dynamics of viral and bacterial communities, with low bulk and cell-specific bacterial metabolism in winter, and a dramatic increase in injured bacteria under the ice cover in all lakes. This period was accompanied by contrasting patterns in the proportion of lysogenic cells. In the eutrophic lake, times of low bacterial metabolic rates and high proportion of damaged cells corresponded to highest levels of lysogeny, supporting the notion that hosts are a ‘refuge’ for viruses. In the two unproductive lakes, peaks of injured cells corresponded to a minimum of lysogeny, suggesting an ‘abandon the sinking ship’ response, where the prophage replicates before the loss of genome. We suggest that these diverging responses to the host physiological state are not contradictory, but rather that there may be thresholds of cell stress and metabolic activity leading to one or the other response.
[本文引用: 2]
[13]
Cole J J, Findlay S, Pace M L.Bacterial production in fresh and saltwater ecosystems: A cross-system overview[J]. Marine Ecology Progress Series, 1988, 43: 1-10.
DOI:10.3354/meps043001 URL
The influx of extraterrestrial matter to the Earth is dominated by two size-fractions: sub-millimeter interplanetary dust and impacting asteroids and comets. Over geologic time the major contribution of extraterrestrial matter is from the largest impactors. Interplanetary dust is largely vaporized by atmospheric entry, but some surviving material is found in sediments as cosmic spherules. Impacting asteroids and comets can produce fallout layers either regionally or globally which may contain a significant fraction of meteoritic material as well as shock-metamorphosed and shock-melted terrestrial material. Iridium is a sensitive tracer of extraterrestrial matter. Although high concentrations of Ir in marine sediments probably have an extraterrestrial origin, they do not necessarily indicate the presence of a major impact event. Of the thousands of impact horizons which must be resolvable in the sedimentary record, to date only seven probable impact horizons have been identified in the entire Phanerozoic. The marine geochemistry and occurrence of Ir is still poorly understood, but the thousands of Ir analyses performed in the last several years have demonstrated that the global occurrence high Ir (> 10 ng/g) concentrations in Cretaceous-Tertiary boundary sediments is a truly anomalous phenomenon.
[本文引用: 3]
[14]
Ducklow H W, Carlson C A.Oceanic bacterial production[M]∥Marshall K C, ed. Advances in Microbial Ecology. Boston, MA: Springer, 1992: 113-181.
[本文引用: 4]
[15]
del Giorgio P A, Cole J J. Bacterial growth efficiency in natural aquatic ecosystems[J]. Annual Review of Ecology and Systematics, 1998, 29: 503-541.
[本文引用: 1]
[16]
Biddanda B, Ogdahl M, Cotner J.Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters[J]. Limnology and Oceanography, 2001, 46(3): 730-739.
DOI:10.4319/lo.2001.46.3.0730 URL
Heterotrophic bacteria are a key component driving biogeochemical processes in aquatic ecosystems. In 1998, we examined the role of heterotrophic bacteria by quantifying plankton biomass and bacterial and planktonic respiration across a trophic gradient in several small Minnesota lakes as well as Lake Superior. The contribution of bacteria ($<$l-m fraction) to total planktonic respiration ranged from 鈭10 to 90%, with the highest contribution occurring in the most oligotrophic waters. The bacterial size fraction constituted a substantial reservoir of planktonic carbon, nitrogen, and phosphorus (14-58%, 10-49%, and 14-48%, respectively), being higher in oligotrophic than in eutrophic waters. However, we saw no clear evidence for the selective enrichment of either nitrogen or phosphorus in the bacteria size fraction relative to total plankton. Carbon: nitrogen and carbon: phosphorus ratios in both the total particulate matter and$<$1-m fractions were similar and above Redfield values in oligotrophic waters, but approached them in eutrophic waters. Carbon-based bacterial growth efficiencies (BGE) were variable (4-40%) but were lowest in oligotrophic systems and increased in eutrophic systems. BGE varied negatively with carbon: nitrogen: phosphorus ratios, suggesting increased maintenance costs in low-nutrient waters. In oligotrophic waters most of the organic matter is dissolved, supporting a predominantly microbial food web, whereas in eutrophic waters there is an increased abundance of particulate organic matter supporting a food web consisting of larger autotrophs and phagotrophic heterotrophs
[本文引用: 2]
[17]
Carlson C A, Giorgio P D, Herndl G J.Microbes and the dissipation of energy and respiration: From cells to ecosystems[J]. Oceanography, 2007, 20(2): 89-100.
DOI:10.5670/oceanog.2007.52 URL
An accurate estimation of scour depth around piles is important for coastal and ocean engineers involved in the design of marine structures. Owing to the complexity of the problem, most conventional approaches are often unable to provide sufficiently accurate results. In this paper, an alternative attempt is made herein to develop adaptive neuro-fuzzy inference system (ANFIS) models for predicting scour depth as well as scour width for a group of piles supporting a pier. The ANFIS model provides the system identification and interpretability of the fuzzy models and the learning capability of neural networks in a single system. Two combinations of input data were used in the analyses to predict scour depth: the first input combination involves dimensional parameters such as wave height, wave period, and water depth, while the second combination contains nondimensional numbers including the Reynolds number, the Keulegan-Carpenter number, the Shields parameter and the sediment number. The test results show that ANFIS performs better than the existing empirical formulae. The ANFIS predicts scour depth better when it is trained with the original (dimensional) rather than the nondimensional data. The depth of scour was predicted more accurately than its width. A sensitivity analysis showed that scour depth is governed mainly by the Keulegan-Carpenter number, and wave height has a greater influence on scour depth than the other independent parameters. (c) 2006 Elsevier Ltd. All rights reserved.
[本文引用: 6]
[18]
Kirchman D L.Processes in Microbial Ecology[M]. Oxford: Oxford University Press, 2012.
[本文引用: 1]
[19]
Hansell D A, Carlson C A.Biogeochemistry of Marine Dissolved Organic Matter Second edition[M]. London: Academic Press, 2014.
[本文引用: 1]
[20]
Mann N, Cook A, Millard A, et al. Marine ecosystems: Bacterial photosynthesis genes in a virus[J]. Nature, 2003, 424(6 950): 741.
DOI:10.1038/424741a PMID:12917674 URL
Cyanobacteria contribute to the overall photosynthetic production of oxygen in the oceans, but they are susceptible to infection by viruses and also to photo-inhibition when sunlight is too intense. Here we show that the genomic sequence of one such virus, a bacteriophage known as S-PM2, encodes the D1 and D2 proteins that are key components of one of the photosynthetic reaction centres (photosystem II, PSII), which are crucial sites of damage in photo-inhibition. The presence of this virus, and others like it, in the ocean may ensure that photo-inhibition is prevented in infected cells, allowing photosynthesis to continue and therefore provide the energy needed by the virus for its replication.
[本文引用: 2]
[21]
Sharon I, Battchikova N, Aro E, et al. Comparative metagenomics of microbial traits within oceanic viral communities[J]. ISME Journal, 2011, 5(7): 1 178-1 190.
DOI:10.1038/ismej.2011.2 PMID:21307954 URL
Abstract Viral genomes often contain genes recently acquired from microbes. In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication. In this study, using a unique search strategy on the Global Ocean Survey (GOS) metagenomes in combination with marine virome and microbiome pyrosequencing-based datasets, we characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities. A total of 34 microbial gene families were detected on 452 viral GOS scaffolds. The majority of auxiliary metabolic genes found on these scaffolds have never been reported in phages. Host genes detected in viruses were mainly divided between genes encoding for different energy metabolism pathways, such as electron transport and newly identified photosystem genes, or translation and post-translation mechanism related. Our findings suggest previously undetected ways, in which marine phages adapt to their hosts and improve their fitness, including translation and post-translation level control over the host rather than the already known transcription level control.
[本文引用: 2]
[22]
Thompson L, Zeng Q, Kelly L, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(39): E757-E764.
[本文引用: 2]
[23]
Anantharaman K, Duhaime M, Breier J, et al. Sulfur oxidation genes in diverse deep-sea viruses[J]. Science, 2014, 344(6 185): 757-760.
DOI:10.1126/science.1252229 PMID:24789974 URL
Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary effects of viruses on marine phototrophs are well recognized, little is known about their impact on ubiquitous marine lithotrophs. Here, we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the 伪 and 纬 subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans.
[本文引用: 2]
[24]
Hagay E, Mandel-Gutfreund Y, Béj O.Comparative metagenomics analyses reveal viral-induced shifts of host metabolism towards nucleotide bio-sysnthesis[J]. Microbiome, 2014, 2(1): 9.
DOI:10.1186/2049-2618-2-9 PMID:24666644 URL
Background Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction. Results In this study, we searched for enriched viral auxiliary genes and mapped them to metabolic pathways. To initially identify enriched auxiliary genes, we analyzed metagenomic microbial reads from the Global Ocean Survey (GOS) dataset that were characterized as viral, as well as marine virome and microbiome datasets from the Line Islands. Viral-enriched genes were mapped to a ???global metabolism network??? that comprises all KEGG metabolic pathways. Our analysis of the viral-enriched pathways revealed that purine and pyrimidine metabolism pathways are among the most enriched pathways. Moreover, many other viral-enriched metabolic pathways were found to be closely associated with the purine and pyrimidine metabolism pathways. Furthermore, we observed that sequential reactions are promoted in pathways having a high proportion of enriched genes. In addition, these enriched genes were found to be of modular nature, participating in several pathways. Conclusions Our na??ve metagenomic analyses strongly support the well-established notion that viral auxiliary genes promote viral replication via both degradation of host DNA and RNA as well as a shift of the host metabolism towards nucleotide biosynthesis, clearly indicating that comparative metagenomics can be used to understand different environments and systems without prior knowledge of pathways involved.
[本文引用: 3]
[25]
Jover L F, Effler T C, Buchan A, et al. The elemental composition of virus particles: Implications for marine biogeochemical cycles[J]. Nature Reviews Microbiology, 2014, 12(7): 519-528.
DOI:10.1038/nrmicro3289 PMID:24931044 URL
In marine environments, virus-mediated lysis of host cells leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling on a global scale. However, efforts to characterize the effects of viruses on nutrient cycles have overlooked the geochemical potential of the virus particles themselves, particularly with respect to their phosphorus content. In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. By extrapolating particle-scale estimates to the ecosystem scale, we propose that, under certain circumstances, marine virus populations could make an important contribution to the reservoir and cycling of oceanic phosphorus.
[本文引用: 4]
[26]
Zhang R, Wei W, Cai L.The fate and biogeochemical cycling of viral elements[J]. Nature Reviews Microbiology, 2014, 12: 850-851.DOI:10.1038/nrmicro3384.
DOI:10.1038/nrmicro3384 PMID:25396723 URL
The article discusses a study suggesting that the chemical elements, particularly phosphorus, within the viral particles could make a considerable contribution to marine elemental reservoirs. The importance of the elements that are bound in virus articles has been highlighted. The marine virioplankton, which adds knowledge of the biogeochemical cycling of the elements that are present in the viral particles in the ocean is also discussed.
[本文引用: 1]
[27]
Middelboe M.Bacterial growth rate and marine virus-host dynamics[J]. Microbial Ecology, 2000, 40(2): 114-124.
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[28]
Philosof A, Battchikova N, Aro E, et al. Marine cyanophages: Tinkering with the electron transport chain[J]. ISME Journal, 2011, 5(10): 1 568-1 570.
DOI:10.1038/ismej.2011.43 PMID:21509045 URL
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
[本文引用: 1]
[29]
Dwivedi B, Xue B, Lundin D, et al. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes[J]. BMC Evolutionary Biology, 2013, 13: 33.
DOI:10.1186/1471-2148-13-33 PMID:3653736 URL
Background Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively. Results RNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host???s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage. Conclusions This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.
[本文引用: 1]
[30]
Zeng Q, Chisholm S W.Marine viruses exploit their host’s two-component regulatory system in response to resource limitation[J]. Current Biology, 2012, 22(2): 124-128.
DOI:10.1016/j.cub.2011.11.055 PMID:22244998 URL
Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [1-4] and its viruses (cyanophages). As in other bacteria, in Prochlorococcus these genes are regulated by the PhoR/PhoB two-component regulatory system that is used to sense and respond to P availability and is typical of signal transduction systems found in diverse organisms. Replication of cyanophage genomes requires a significant amount of P, and therefore these phages could gain a fitness advantage by influencing host P acquisition in P-limited environments. Here we show that the transcription of a phage-encoded high-affinity phosphate-binding protein gene (pstS) and alkaline phosphatase gene (phoA)-both of which have host orthologs-is elevated when the phages are infecting host cells that are P starved, relative to P-replete control cells. We further show that the phage versions of these genes are regulated by the host's PhoR/PhoB system. This not only extends this fundamental signaling mechanism to viruses but is also the first example of regulation of lytic phage genes by nutrient limitation in the host. As such, it reveals an important new dimension of the intimate coevolution of phage, host, and environment in the world's oceans.
[本文引用: 3]
[31]
Williamson S, Rusch D, Yooseph S, ,et al. The sorcerer II global ocean sampling expedition: Metagenomic characterization of viruses within aquatic microbial samples[J]. PloS ONE. The sorcerer II global ocean sampling expedition: Metagenomic characterization of viruses within aquatic microbial samples[J]. PloS ONE, 2008, 3(1): e1 456.
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Crummett L T, Puxty R J, Weihe C, et al. The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses[J]. Virology, 2016, 499: 219-229.
DOI:10.1016/j.virol.2016.09.016 PMID:27693926 URL
Viruses of marine cyanobacteria frequently contain auxiliary metabolic genes (AMGs) that augment host metabolism during infection, but little is known about their adaptive significance. We analyzed the distribution and genomic context of 33 AMGs across 60 cyanomyovirus genomes. Similarity in AMG content among cyanomyoviruses was only weakly correlated with phylogenetic relatedness; however, AMG content was generally conserved within the same operational taxonomic unit (OTU). A virus鈥 AMG repertoire was also correlated with its isolation host and environment (coastal versus open ocean). A new analytical method based on shared co-linear blocks revealed that variation in the genomic location of an AMG was negatively correlated with its frequency across the genomes. We propose that rare AMGs are more frequently gained or lost as a result of fluctuating selection pressures, whereas common AMGs are associated with stable selection pressures. Finally, we describe a unique cyanomyovirus (S-CAM7) that lacks many AMGs including the photosynthesis gene psbA .
[本文引用: 1]
[33]
Lindell D, Jaffe J D, Johnson Z I, et al. Photosynthesis genes in marine viruses yield proteins during host infection[J]. Nature, 2005, 438(7 064): 86-89.
DOI:10.1038/nature04111 PMID:16222247 URL
Cyanobacteria, and the viruses (phages) that infect them, are significant contributors to the oceanic 'gene pool'. This pool is dynamic, and the transfer of genetic material between hosts and their phages probably influences the genetic and functional diversity of both. For example, photosynthesis genes of cyanobacterial origin have been found in phages that infect Prochlorococcus and Synechococcus, the numerically dominant phototrophs in ocean ecosystems. These genes include psbA, which encodes the photosystem II core reaction centre protein D1, and high-light-inducible (hli) genes. Here we show that phage psbA and hli genes are expressed during infection of Prochlorococcus and are co-transcribed with essential phage capsid genes, and that the amount of phage D1 protein increases steadily over the infective period. We also show that the expression of host photosynthesis genes declines over the course of infection and that replication of the phage genome is a function of photosynthesis. We thus propose that the phage genes are functional in photosynthesis and that they may be increasing phage fitness by supplementing the host production of these proteins.
[本文引用: 2]
[34]
Sharon I, Tzahor S, Williamson S, et al. Viral photosynthetic reaction center genes and transcripts in the marine environment[J]. ISME Journal, 2007, 1(6): 492-501.
DOI:10.1038/ismej.2007.67 PMID:18043651 URL
Abstract Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photosynthetic productivity in the open ocean. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages that infect these cyanobacteria suggests new paradigms for the regulation, function and evolution of photosynthesis in the vast pelagic ecosystem. Reports on the prevalence and expression of phage photosynthesis genes, and evolutionary data showing a potential recombination of phage and host genes, suggest a model in which phage photosynthesis genes help support photosynthetic activity in their hosts during the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psbA genes in surface water along the global ocean sampling transect are of phage origin, and that the phage genes are undergoing an independent selection for distinct D1 proteins. Furthermore, we show that different viral psbA genes are expressed in the environment.
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[35]
Mann N H, Clokie M R J, Millard A, et al. The genome of S-PM2, a ‘photosynthetic’ T4-type bacteriophage that infects marine Synechococcus[J]. Journal of Bacteriology, 2005, 187(9): 3 188-3 200.
DOI:10.1128/JB.187.9.3188-3200.2005 PMID:15838046 URL
Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle.
[本文引用: 1]
[36]
Ankrah N Y D, May A L, Middleton J L, et al. Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition[J]. ISME Journal, 2014, 8(5): 1 089-1 100.
DOI:10.1038/ismej.2013.216 PMID:3996693 URL
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
[本文引用: 2]
[37]
De Smet J, Zimmermann M, Kogadeeva M, et al. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection[J]. ISME Journal, 2016, 10(8): 1 823-1 835.
DOI:10.1038/ismej.2016.3 PMID:26882266 URL
Abstract Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomonas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology. However, a large fraction of the profound effect on host metabolism could not be attributed to the phage-encoded AMGs. We suggest a potentially crucial role for small, 'non-enzymatic' peptides in metabolism take-over and hypothesize on potential biotechnical applications for such peptides. The highly phage-specific nature of the metabolic impact emphasizes the potential importance of the 'phage diversity' parameter when studying metabolic interactions in complex communities.The ISME Journal advance online publication, 16 February 2016; doi:10.1038/ismej.2016.3.
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Azam F, Malfatti F.Microbial structuring of marine ecosystems[J]. Nature Reviews Microbiology, 2007, 5(10): 782-791.
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Fuhrman J A.Marine viruses and their biogeochemical and ecological effects[J]. Nature, 1999, 399(6 736): 541-548.
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Weitz J S, Stock C A, Wilhelm S W, et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes[J]. ISME Journal, 2015, 9(6): 1 352-1 364.
DOI:10.1038/ismej.2014.220 PMID:25635642 URL
Abstract Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.
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Bonilla-Findji O, Malits A, Lefèvre D, et al. Viral effects on bacterial respiration, production and growth efficiency: Consistent trends in the Southern Ocean and the Mediterranean Sea[J]. Deep-Sea Research Part II:Topical Studies in Oceanography, 2008, 55(5): 790-800.
DOI:10.1016/j.dsr2.2007.12.004 URL
To investigate the potential effects of viruses on bacterial respiration (BR), production (BP) and growth efficiency (BGE), experiments were performed using natural microbial communities from the coastal Mediterranean Sea, from a typical high-nutrient low-chlorophyll (HNLC) region in the Southern Ocean and from a naturally iron (Fe)-fertilized algal bloom above the Kerguelen Plateau (Southern Ocean). Seawater was sequentially filtered and concentrated to produce a bacterial concentrate, a viral concentrate and a virus-free ultrafiltrate. The combination of all three fractions served as treatments with active viruses. Heating or microwaving was used to inactivate viruses for the control treatments. Despite the differences in the initial trophic state and community composition of the study sites, consistent trends were found. In the presence of active viruses, BR was stimulated (up to 113%), whereas BP and BGE were reduced (up to 51%). Our results suggest that viruses enhance the role of bacteria as oxidizers of organic matter, hence as producers of CO 2 , and remineralizers of CO 2 , N, P and Fe. In the context of Fe-fertilization, this has important implications for the final fate of organic carbon in marine systems.
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Motegi C, Nagata T, Miki T, et al. Viral control of bacterial growth efficiency in marine pelagic environments[J]. Limnology and Oceanography, 2009, 54(6): 1 901-1 910.
DOI:10.4319/lo.2009.54.6.1901 URL
ABSTRACT We tested the hypothesis that viruses can control bacterial growth efficiency (BGE) in marine pelagic environments. In the Bay of Villefranche, Northwestern Mediterranean, three experiments were conducted on different months to determine bacterial and viral variables in seawater cultures. In December, phosphorus (P) addition enhanced bacterial growth 6–9-fold with concomitant increase in viral production (4–15-fold), but little enhancement of bacterial respiration (BR). In other months, P enrichment increased BR 2–6-fold and viral production 2–5-fold, but did not increase in bacterial abundance (Aug, Feb) or growth (Feb). BGE depended on the fraction of bacterial production destroyed by viruses (shunting efficiency, v; i.e., when v was low, nutrient enrichment enhanced BGE, whereas when v was high, nutrient enrichment mainly led to low BGE). Viral production and bacterial production and respiration in the Western North Pacific and other data from the literature showed that BGE was negatively correlated with shunting efficiency. Predictions from a carbon flow model were consistent with the above results showing that decreased BGE over a broad range of values (from 0.7 to 0.001) could be largely explained by viral-induced conversion of bacterial biomass to dissolved organic carbon. Viruses exert the major influence on patterns in carbon fluxes mediated by bacteria in marine pelagic environments.
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Xu J, Jing H, Sun M, et al. Regulation of bacterial metabolic activity by dissolved organic carbon and viruses[J]. Journal of Geophysical Research: Biogeosciences, 2013, 118(4): 1 573-1 583.
DOI:10.1002/2013JG002296 URL
The regulation of bacterial metabolic activity by viruses and dissolved organic carbon (DOC) was examined using natural microbial communities in three treatments (active viruses, inactive viruses, and virus free) at two contrasting coastal sites (pristine vs. eutrophic) with substantial differences in environmental conditions during the wet and dry seasons. Our results showed that net growth rates and production of bacterioplankton were reduced primarily by viruses via repressing metabolically active bacteria with high nucleic acid (HNA) content which had a high capacity for incorporating carbon, while bacterial respiration was primarily regulated by DOC lability. The quality of organic matter played a more important role in regulating bacterial growth efficiency (BGE) than the supply of organic matter in eutrophic coastal waters. The lack of HMW-DOC and high carbon demand in the virus-free treatment resulted in a significant increase in cell-specific bacterial respiration, which was responsible for the lowest bacterial growth efficiency among the three treatments. The presence of viruses did not necessarily lower bacterial growth efficiency since virus-induced mortality alleviated bacterial carbon demand and enhanced carbon cycling. Virus-induced mortality was greater in relatively pristine waters than eutrophic waters, likely since the high supply of substrates alleviated the pressure of viral infection, through extracellular proteases produced by bacteria, which might result in the hydrolytic destruction or modification of viral capsids. An important implication of our results was that the input of riverine DOC and nutrients improved bacterial metabolic activity by alleviating virus-induced mortality of bacteria in estuarine and coastal waters.
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Middelboe M, Jørgensen N O G, Kroer N. Effects of viruses on nutrient turnover and growth efficiency of noninfected marine bacterioplankton[J]. Applied and Environmental Microbiology, 1996, 62(6): 1 991-1 997.
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Liu H, Yuan X, Xu J, et al. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters[J]. Scientific Reports, 2015, 5: 14 217.
DOI:10.1038/srep14217 URL
Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.
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Noble R T, Middelboe M, Fuhrman J A.The effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton[J]. Aquatic Microbial Ecology, 1999, 18(1): 1-13.
DOI:10.3354/ame018001 URL
The direct effects of viral enrichments upon natural populations of marine viruses and bacteria were studied in seawater from Santa Monica Bay, CA, USA. Active virus concentrates, or control additions (ultrafiltered seawater or autoclaved virus concentrate) were added to 2 1 incubations of protist-free seawater, and the effects were monitored for about 3 d. At the beginning of the experiments, the virus numbers reflected the expected addition of intact virus particles as determined by transmission electron microscopy (TEM). Subsequently, the mean frequency of visibly infected bacteria (FVIB; % bacteria which were visibly infected with 5 or more virus-like particles) was greater in the enriched incubations than in the controls. In controls, the estimated percent of bacteria that were infected remained constant at about 5 to 10 % of the total bacterial population, but with active enrichment, 10 to 35 % of the total bacterial population was infected at a given time. Therefore, by increasing the concentration of active viruses in seawater incubations we were able to increase the amount of bacterial mortality attributed to virus infection. Even with the presumed increase in bacterial mortality, the net increases in bacterial abundance in the samples that were enriched with active virus concentrate were higher than those seen in the controls. The vital abundance in bottles that were enriched with the active virus concentrate was significantly higher than that in the controls in Expts 2 and 3 (p < 0.05), but by the end of the experiments, viral abundances in the enriched incubations approached control levels. In Expts 1 and 2, rates of DOP hydrolysis were higher in the samples enriched with the active virus concentrate, and may have been due to an increase in the incidence of viral lysis. However, overall analysis of DCAA, DFAA, and DOP hydrolysis were quite variable and difficult to interpret. Results indicate that viral enrichment increased the incidence of bacterial infection and consequently stimulated the growth of subpopulations of non-infected heterotrophic bacterioplankton.
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Middelboe M, Lyck P G.Regeneration of dissolved organic matter by viral lysis in marine microbial communities[J]. Aquatic Microbial Ecology, 2002, 27(2): 187-194.
DOI:10.3354/ame027187 URL
The influence of viruses on bacterial net growth and respiration was investigated in batch cultures with natural assemblages of marine bacterioplankton, which were manipulated with respect to abundance of natural virioplankton. In 1 set of cultures (-virus), a virus-free water sample (0.02 m filtered) was inoculated with a bacterioplankton concentrate, and in a parallel set of cultures (control) a virus-containing water sample (0.2 pm filtered) was inoculated with the bacterioplankton concentrate. The 0.02 pm filtration procedure reduced viral abundance by 62 to 92 % in the -virus cultures relative to the parallel control cultures with the natural density of viruses (i.e. the fraction of natural viruses <0.2 m). This approach allowed us to examine the effects of reduced viral densities on the production of natural assemblages of bacteria and viruses and on the distribution of added
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Eissler Y, Quiñones R A.The effect of viral concentrate addition on the respiration rate of Chaetoceros gracilis cultures and microplankton from a shallow bay (Coliumo, Chile)[J]. Journal of Plankton Research, 2003, 25(8): 927-938.
DOI:10.1093/plankt/25.8.927 URL
Abstract. Experiments were conducted to test the possible effects of viral concentrate additions on the respiration rates of both Chaetoceros gracilis and a na
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Malits A, Weinbauer M G.Effect of turbulence and viruses on prokaryotic cell size, production and diversity[J]. Aquatic Microbial Ecology, 2009, 54(3): 243-254.
DOI:10.1016/j.sysconle.2005.12.002 URL
A factorial design was used to assess the roles of turbulence and viral infection in prokaryotic production and diversity in a spring phytoplankton bloom experiment in the Bay of Ville-franche, France, Several consistent trends were observed in 2 experiments: (1) turbulence stimulated prokaryotic production, (2) prokaryotic cell length increased in experimental turbulence and virus treatments, and (3) organic micro-aggregates with attached prokaryotes formed only in the turbulence treatments and seemed to be reduced in the presence of viruses. We conclude that turbulence likely influenced prokaryotes indirectly by affecting micro-aggregate formation and nutrient availability, Turbulence and viruses had only small influences on the number of bacterial and archaeal bands detected by 16S rRNA gene denaturing gradient gel electrophoresis. However, taking into account presence versus absence of specific bands and their intensities, we detected strong effects in the experiments. We not only detected a negative effect of viruses, but also found that some bands increased in intensity in the presence of active viruses, e.g. one of 3 phylotypes affiliated with the Rhodobacteriaceae. In both experiments, several consistent patterns were found: (1) a phylotype affiliated with Roseobacter was negatively affected (in terms of band intensity) by viruses and turbulence, (2) the relative band intensity of a Rhodobacter increased in the turbulence treatments, and (3) a phylotype related to Oceanospirillum was detected only in the turbulence treatment. We suggest that turbulence and viruses play a significant and previously neglected role in shaping prokaryotic diversity, aggregation and production.
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Xu J, Sun M, Shi Z, et al. Response of bacterial metabolic activity to riverine dissolved organic carbon and exogenous viruses in estuarine and coastal waters: Implications for CO2 emission[J]. PloS ONE, 2014, 9(7): e102490.
DOI:10.1371/journal.pone.0102490 PMID:25036641 URL
A cross-transplant experiment between estuarine water and seawater was conducted to examine the response of bacterial metabolic activity to riverine dissolved organic carbon (DOC) input under virus-rich and virus-free conditions, as well as to exogenous viruses. Riverine DOC input increased bacterial production significantly, but not bacterial respiration (BR) because of its high lability. The bioavailable riverine DOC influenced bulk bacterial respiration in two contrasting ways; it enhanced the bulk BR by stimulating bacterial growth, but simultaneously reduced the cell-specific BR due to its high lability. As a result, there was little stimulation of the bulk BR by riverine DOC. This might be partly responsible for lower CO2 degassing fluxes in estuaries receiving high sewage-DOC that is highly labile. Viruses restricted microbial decomposition of riverine DOC dramatically by repressing the growth of metabolically active bacteria. Bacterial carbon demand in the presence of viruses only accounted for 7鈥12% of that in the absence of viruses. Consequently, a large fraction of riverine DOC was likely transported offshore to the shelf. In addition, marine bacteria and estuarine bacteria responded distinctly to exogenous viruses. Marine viruses were able to infect estuarine bacteria, but not as efficiently as estuarine viruses, while estuarine viruses infected marine bacteria as efficiently as marine viruses. We speculate that the rapid changes in the viral community due to freshwater input destroyed the existing bacteria-virus relationship, which would change the bacterial community composition and affect the bacterial metabolic activity and carbon cycling in this estuary.
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[51]
Bratbak G, Heldal M, Norland S, et al. Viruses as partners in spring bloom microbial trophodynamics[J]. Applied and Environmental Microbiology, 1990, 56(5): 1 400-1 405.
DOI:10.1007/BF01200945 PMID:16348190 URL
Population sizes of algae, bacteria, heterotrophic flagellates, and viruses were observed through the 1989 spring diatom bloom in Raunefjorden in western Norway. The culmination of the diatom bloom was followed by a peak in the concentration of bacteria and an increase in the concentration of heterotrophic flagellates, a pattern consistent with the concept of a food chain from photosynthetically produced organic material, through bacteria, to bacterivorous flagellates. The concentration of viruses varied through the spring bloom from 5 x 10 in the prebloom situation to a maximum of 1.3 x 10 viruses ml 1 week after the peak of the diatom bloom. Coinciding with the collapse in the diatom bloom, a succession of bacteria and viruses was observed in the mucous layer surrounding dead or senescent diatoms, with an estimated maximum of 23% of the total virus population attached to the diatoms. The dynamic behavior observed for the virus population rules out the possibility that it is dominated by inactive species, and the viruses are suggested to be active members of the microbial food web as agents causing lysis in parts of the bacterial population, diverting part of the bacterial production from the predatory food chain.
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Pradeep Ram A S, Colombet J, Perriere F, et al. Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments[J]. FEMS Microbial Ecology, 2015, 91(2): 1-12.
DOI:10.1093/femsec/fiv002 PMID:25764557 URL
Abstract In aquatic systems, limited data exists on the impact of mortality forces such as viral lysis and flagellate grazing when seeking to explain factors regulating prokaryotic metabolism. We explored the relative influence of top-down factors (viral lysis and heterotrophic nanoflagellate grazing) on prokaryotic mortality and their subsequent impact on their community metabolism in the euphotic zone of 21 temperate freshwater lakes located in the French Massif Central. Prokaryotic growth efficiency (PGE, index of prokaryotic community metabolism) determined from prokaryotic production and respiration measurements varied from 5 to 74% across the lakes. Viral and potential grazer-induced mortality of prokaryotes had contrasting impact on PGE. Potential flagellate grazing was found to enhance PGE whereas viral lysis had antagonistic impacts on PGE. The average PGE value in the grazing and viral lysis dominated lake water samples was 35.4% (卤15.2%) and 17.2% (卤8.1%), respectively. Selective viral lysis or flagellate grazing on prokaryotes together with the nature of contrasted substrates released through mortality processes can perhaps explain for the observed variation and differences in PGE among the studied lakes. The influences of such specific top-down processes on PGE can have strong implications on the carbon and nutrient fluxes in freshwater pelagic environments. 漏 FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Pradeep Ram A S P, Colombet J, Perriere F, et al. Viral regulation of prokaryotic carbon metabolism in a hypereutrophic freshwater reservoir ecosystem (Villerest, France)[J]. Frontiers in Microbiology, 2016, 7: 81.
DOI:10.3389/fmicb.2016.00081 PMID:4746248 URL
The current consensus concerning the viral regulation of prokaryotic carbon metabolism is less well studied, compared to substrate availability. We explored the seasonal and vertical distribution of viruses and its relative influence on prokaryotic carbon metabolism in a hypereutrophic reservoir, Lake Villerest (France). Flow cytometry and transmission electron microscopy analyses to determine viral abundance (range = 6.1 - 63.5 x 107 ml-1) and viral infection rates of prokaryotes (range = 5.3 - 32%) respectively suggested that both the parameters varied more significantly with depths than with seasons. Prokaryotic growth efficiency (PGE, considered as a proxy of prokaryotic carbon metabolism) calculated from prokaryotic production and respiration measurements (PGE = prokaryotic production/[prokaryotic production + prokaryotic respiration] x 100) varied from 14 to 80% across seasons and depths. Viruses through selective lyses had antagonistic impacts on PGE by regulating key prokaryotic metabolic processes (i.e. production and respiration). Higher viral lysis accompanied by higher respiration rates and lower PGE in the summer (mean = 22.9 卤 10.3%) than other seasons (mean = 59.1 卤 18.6%), led to significant loss of carbon through bacterial-viral loop and shifted the reservoir system to net heterotrophy. Our data therefore suggests that the putative adverse impact of viruses on the growth efficiency of the prokaryotic community can have strong implications on nutrient flux patterns and on the overall ecosystem metabolism in anthropogenic dominated aquatic systems such as Lake Villerest.
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Pradeep Ram A S, Palesse S, Colombet J, et al. Variable viral and grazer control of prokaryotic growth efficiency in temperate freshwater lakes (French Massif Central)[J]. Microbial Ecology, 2013, 66(4): 906-916.
DOI:10.1007/s00248-013-0289-x PMID:24061344 URL
The effects of viral lysis and heterotrophic nanoflagellate grazing (top down forces) on prokaryotic mortality and their subsequent impact on their metabolism were estimated in the upper euphotic and deeper aphotic depth of 11 freshwater lakes located in the French Massif Central. The standing stocks of viruses (VA) and heterotrophic nanoflagellate (HNF) varied significantly ( p 65<650.05) with sampled depth. VA was substantially (twofold on an average) and significantly higher ( p 65<650.03) at the aphotic compared to euphotic depth, whereas the reverse was true ( p 65<650.02) for HNF. Among the prokaryote subgroup, high nucleic acid content prokaryotes explained for significant variability in the total VA and served as principle host target for viral proliferation. Like standing stocks, flagellate grazing and viral infection rates also followed similar patterns. In the investigated lakes, the mechanism for regulating prokaryotic production varied with sampled depth from grazing control in the euphotic to control due to viral lysis in the aphotic. We also tested the hypothesis of top down control on prokaryotic growth efficiency (PGE, which we used as an index of prokaryotic physiological and energetic status at the community level) at both depths. Overall, among the studied lakes, PGE varied widely (4–5102%) with significantly ( p 65<650.05) lower values in the aphotic (mean65=651865±65402%) than euphotic depth (mean65=653265±65902%). Contrasting observations on the top down control of PGE between sampled depths were observed. The presence of grazers was found to stimulate PGE at the euphotic, whereas viruses through their lytic infection had a strong negative impact on PGE at the aphotic depth. Such observed differences in PGE and the mechanism controlling prokaryotic production with depth could eventually have strong implication on carbon and nutrient flux patterns in the studied lakes.
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Wilhelm S W, Suttle C A.Viruses and nutrient cycles in the sea[J]. Bioscience, 1999, 49(10): 781-788.
DOI:10.2307/1313569 URL
ABSTRACT Few of us may ever live on the sea or under it, but all of us are mak-ing increasing use of it either as a source of food and other materi-als, or as a dump. As our demands upon the ocean increase, so does our need to understand the ocean as an ecosystem. Basic to the un-derstanding of any ecosystem is knowledge of its food web, through which energy and materials flow. (Pomeroy 1974, p. 499)
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Abstract Marine dissolved organic carbon (DOC) exhibits a spectrum of reactivity, from very fast turnover of the most bioavailable forms in the surface ocean to long-lived materials circulating within the ocean abyss. These disparate reactivities group DOC by fractions with distinctive functions in the cycling of carbon, ranging from support of the microbial loop to involvement in the biological pump to a hypothesized major source/sink of atmospheric CO(2) driving paleoclimate variability. Here, the major fractions constituting the global ocean's recalcitrant DOC pool are quantitatively and qualitatively characterized with reference to their roles in carbon biogeochemistry. A nomenclature for the fractions is proposed based on those roles.
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Containing as much carbon as the atmosphere, marine dissolvedorganic matter is one of Earth鈥檚 major carbon reservoirs. With invigoration ofscientific inquiries into the global carbon cycle, our ignorance of its role in oceanbiogeochemistry became untenable. Rapid mobilization of relevant research twodecades ago required the community to overcome early false leads, but subsequentprogress in examining the global dynamics of this material has been steady.Continuous improvements in analytical skill coupled with global ocean hydrographicsurvey opportunities resulted in the generation of thousands of measurementsthroughout the major ocean basins. Here, observations and model results provide newinsights into the large-scale variability of dissolved organic carbon, its contribution tothe biological pump, and its deep ocean sinks.
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Using inorganic carbon measurements from an international survey effort in the 1990s and a tracer-based separation technique, we estimate a global oceanic anthropogenic carbon dioxide (CO2) sink for the period from 1800 to 1994 of$118 \pm 19$petagrams of carbon. The oceanic sink accounts for ~48% of the total fossil-fuel and cement-manufacturing emissions, implying that the terrestrial biosphere was a net source of CO2to the atmosphere of about$39 \pm 28$petagrams of carbon for this period. The current fraction of total anthropogenic CO2emissions stored in the ocean appears to be about one-third of the long-term potential.
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Jiao N, Herndl G J, Hansell D A, et al. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean[J]. Nature Reviews Microbiology, 2010, 8(8): 593-599.
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The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.
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[焦念志, 李超, 王晓雪. 海洋碳汇对气候变化的响应与反馈[J]. 地球科学进展, 2016, 31(7): 668-681.]
Jiao Nianzhi, Li Chao, Wang Xiaoxue.Response and feedback of marine carbon sink to climate change[J]. Advances in Earth Science, 2016, 31(7): 668-681.
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海洋碳汇对气候变化的响应与反馈是一个系统的科学命题,也是当前国际地球系统科学领域的前沿热点问题,需要通过微观与宏观结合、古今链接、多学科交叉融合进行深入研究。在我国科学家发起的海洋生物地球化学&#x0201c;戈登科学前沿论坛&#x0201d;(Gordon Research Conferences,GRC)首届论坛上,以海洋生物泵(Biological Pump,BP)、微型生物碳泵(Microbial Carbon Pump, MCP)以及碳酸盐泵(Carbonate Counter Pump,CCP)等海洋储碳机制为核心,深入研讨了海洋碳汇的过程与效应,起到了引领国际海洋学科发展方向的作用。国内学界也积极行动起来,在第四届地球系统科学大会上组织了海洋碳汇专题,从古海洋碳汇、现代海洋碳循环及海洋碳汇的生物海洋学过程3个方面开展研讨。海洋微型生物生态学过程与海洋碳汇以海洋浮游植物、细菌、古菌、病毒以及不同微型生物间的互作为切入点,探讨了微型生物的储碳和固碳作用的过程及其与全球气候变化的关系。古海洋碳汇方向的报告在时间尺度上跨越了从18~8亿年前的中元古代到距今2.5 Ma的第四纪,涵盖了包括古海洋碳汇形成的古海洋环境、古海洋碳汇的生态环境效应等前沿科学问题;古海洋碳汇的报告为现代海洋碳汇研究提供了有益的借鉴,并有助于本领域科学家对海洋碳汇的历史演化观的认识。现代海洋碳循环过程方面,专题报告结合时间梯度和空间梯度,以南海珊瑚礁碳循环源汇争议为代表,探讨了碳循环中的初级生产力、溶解有机碳的来源与有机碳的降解等过程,对现代海区和全球变化背景下海洋的源汇评估提出了新的想法与研究方向。
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Weinbauer M G, Rassoulzadegan F.Are viruses driving microbial diversification and diversity?[J]. Environmental Microbiology, 2004, 6(1): 1-11.
DOI:10.1046/j.1462-2920.2003.00539.x PMID:14686936 URL
Abstract Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.
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Rivkin R B, Legendre L.Biogenic carbon cycling in the upper ocean: Effects of microbial respiration[J]. Science, 2001, 291(5 512): 2 398-2 400.
DOI:10.1126/science.291.5512.2398 PMID:11264533 URL
Abstract Food-web processes are important controls of oceanic biogenic carbon flux and ocean-atmosphere carbon dioxide exchange. Two key controlling parameters are the growth efficiencies of the principal trophic components and the rate of carbon remineralization. We report that bacterial growth efficiency is an inverse function of temperature. This relationship permits bacterial respiration in the euphotic zone to be computed from temperature and bacterial production. Using the temperature-growth efficiency relationship, we show that bacterial respiration generally accounts for most community respiration. This implies that a larger fraction of assimilated carbon is respired at low than at high latitudes, so a greater proportion of production can be exported in polar than in tropical regions. Because bacterial production is also a function of temperature, it should be possible to compute euphotic zone heterotrophic respiration at large scales using remotely sensed information.
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[66]
Shelford E J, Middelboe M, Møller E F, et al. Virus-driven nitrogen cycling enhances phytoplankton growth[J]. Aquatic Microbial Ecology, 2012, 66(1): 41-46.
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Middelboe M, Jørgensen N O G. Viral lysis of bacteria: An important source of dissolved amino acids and cell wall compounds[J]. Journal of the Marine Biological Association of the United Kingdom, 2006, 86(3): 605-612.
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Goldman J C, Caron D A, Dennett M R.Regulation of gross growth efficiency and ammonium regeneration in bacteria by substrate C: N ratio[J]. Limnology and Oceanography, 1987, 32(6): 1 239-1 252.
DOI:10.4319/lo.1987.32.6.1239 URL
ABSTRACT Natural assemblages of marine bacteria were cultured on combinations of C and N sources (amino acids, glucose, and NH,') to span a range of substrate C: N ratios from 1.5 : 1 to 10 : 1. Catabolic metabolism of the N component of amino acid substrates led to NH,+ regeneration during exponential growth. The efficiency of this regeneration (RN) and also of the carbon gross growth efficiency (GGE) generally was independent of the sources of C and N, but increased as the C : N ratio of the substrate (C : NJ decrcascd relative to the C : N ratio of the bacterial biomass (C : NJ. The clemental chemical composition (C : N: P ratio) of the bacterial biomass was relatively invariant at about 45 : 9 : 1 and the gross growth efficiency varied from a threshold value of about 40-50% at C : Ns > 6 : 1 up to 94% when C : N, was 1.5 : 1. Hence, R, varied from 00/o when C : N, was 10: 1 up to 86% when C: N, was 1.5 : 1. Inorganic sources of both N and P were taken up only in stoichiometric quantities during this phase of growth. Regeneration of NH,+ during the stationary phase as well as of POd3- occurred, most likely due to endogenous metabolism or cell death, but the magnitude of this regeneration seemed to increase greatly only when C: N, was ~6 : 1. Considering that amino acids frequently do not provide all of the N required and that carbohydrates often are the major C source for growth of marine bacteria, we speculate that C : Ns of available substrates in marine waters is > 10 : 1. Hence, actively growing bacteria may be inef- ficient remineralizers of N.
[本文引用: 1]
[69]
Poorvin L, Rinta-Kanto J M, Hutchins D A, et al. Viral release of iron and its bioavailability to marine plankton[J]. Limnology and Oceanography, 2004, 49(5): 1 734-1 741.
DOI:10.4319/lo.2004.49.5.1734 URL
The biological availability of Fe has been demonstrated to strongly influence both primary and secondary production in pelagic as well as coastal upwelling high-nutrient low-chlorophyll (HNLC) regimes. Although nearly all of the dissolved Fe in marine surface waters is thought to be complexed by organic ligands, the character and origin of these Fe-organic complexes remains a mystery. Here we report that the activity of naturally occurring viral populations in an HNLC coastal upwelling system can regenerate sufficient concentrations of dissolved Fe to support the growth of the native phytoplankton community. When combined with studies that have demonstrated that Fe in virus-mediated lysates of heterotrophic bacteria and cyanobacteria is highly bioavailable to model marine plankton, our data demonstrate that viral activity in this marine system (and potentially others) is critical to the recycling of organically complexed Fe that supports as much as 90% of primary production in HNLC surface waters.
[本文引用: 3]
[70]
Mioni C E, Poorvin L, Wilhelm S W.Virus and siderophore-mediated transfer of available Fe between heterotrophic bacteria: Characterization using an Fe-specific bioreporter[J]. Aquatic Microbial Ecology, 2005, 41(3): 233-245.
DOI:10.3354/ame041233 URL
Although marine chemists can accurately quantify both the concentration of dissolved iron (Fe) and the high-affinity organic ligands which complex Fe in surface waters, tools to characterize the relative bioavailability of such organically bound Fe complexes remain unavailable. In this study, we compared the bioavailability of Fe released from the lysis of the heterotrophic bacterium Vibrio natriegens PWH3a to that of Fe complexed to synthetic chelators (EDTA) and siderophores (including the trihydroxamate desferrioxamine B [DFB] and 2 catecholates isolated from Fe-limited heterotrophic bacterial cultures) using a heterotrophic bioluminescent reporter of Fe availability (Pseudomonas putida FeLux). Using the bioluminescent response of P. putida FeLux, we were able to rank the Fe sources tested here in a decreasing order of bioavailability: lysates > Fe-homologous catecholate (from a P. putida FeLux culture) - Fe-exogenous catecholate (from V. natriegens culture) > inorganic Fe (FeCl
[本文引用: 2]
[71]
Tomaru Y, Tanabe H, Yamanaka S, et al. Effects of temperature and light on stability of microalgal viruses, HaV, HcV, and HcRNAV[J]. Plankton Biology and Ecology, 2005, 52(1): 1-6.
URL
ABSTRACT Viruses infectious to the fish-killing raphidophyte Heterosigma akashiwo (Hada) Hada {Heterosigma akashiwo Virus (HaV)) and the bivalve-killing dinophyte Heterocapsa circularisquama Horiguchi (Heterocapsa circularisquama Virus (HcV} and Heterocapsa circularisquama RNA Virus (HcRNAV)) have recently been isolated and characterized. The discovery of these microalgal viruses allows for their assessment as potential microbial agents for controlling harmful algal blooms (HABs). To assess the possibility of their practical use as anti-HAB agents, however, it is necessary to estimate how stable their infectivity is both in situ and in vitro. In the present study, we measured the effects of light and temperature on the stability of these viruses. All three viruses were susceptible to cool white fluorescent illumination. Although significant loss of infectivity at 4掳C in the dark for one week was detected in HaV and HcV, the infectivity of HcRNAV was stable for more than one year under the same storage conditions. Furthermore, we succeeded in developing cryopreservation methods for HcV and HcRNAV, which would be useful for their long-term storage.
[本文引用: 1]
[72]
Matteson A R, Loar S N, Pickmere S, et al. Production of viruses during a spring phytoplankton bloom in the South Pacific Ocean near of New Zealand[J]. FEMS Microbiology Ecology, 2012, 79(3): 709-719.
DOI:10.1111/j.1574-6941.2011.01251.x PMID:22092871 URL
Abstract Top of page Abstract Introduction Materials and methods Results Discussion Acknowledgements References Lagrangian studies of virus activity in pelagic environments over extended temporal scales are rare. To address this, viruses and bacteria were examined during the course of a natural phytoplankton bloom in the pelagic South Pacific Ocean east of New Zealand. Daily samples were collected in a mesoscale eddy from year days 263–278 (September 19th–October 4th, 2008). The productive bloom transitioned from a diatom to a pico- and nanoplankton-dominated system, resulting in chlorophyll a concentrations up to 2.43μgL 611 . Virus abundances fluctuated c. 10-fold (1.8×10 10 –1.3×10 11 L 611 ) over 16days. The production rates of virus particles were high compared with those reported in other marine systems, ranging from 1.4×10 10 to 2.1×10 11 L 611 day 611 . Our observations suggest viruses contributed significantly to the mortality of bacteria throughout the bloom, with 19–216% of the bacterial standing stock being lysed daily. This mortality released nutrient elements ( N , Fe ) that likely helped sustain the bloom through the sampling period. Parametric analyses found significant correlations with both biotic (e.g. potential host abundances) and abiotic parameters (e.g. nutrient concentrations, temperature). These observations demonstrate that viruses may be critical in the extended maintenance of regeneration-driven biological production.
[本文引用: 1]
[73]
Paul J H.Prophages in marine bacteria: Dangerous molecular time bombs or the key to survival in the seas?[J]. ISME Journal, 2008, 2(6): 579-589.
DOI:10.1038/ismej.2008.35 PMID:18521076 URL
Abstract Bacteriophages are realized to be numerous and important components of oceanic food webs principally because of their lytic capabilities. The subtle changes that temperate phages impart to their hosts in the oceans are far less understood. Occurrences of lysogeny in the oceans correlate well with conditions unfavorable for rapid host growth. In coliphage lambda, phage encoded repressors have been shown to modulate host metabolic gene expression and phenotype, resulting in economizing host energy expenditure. Comparison of lysogenized marine bacteria to the uninfected hosts indicated that prophage acquisition is correlated with host metabolic gene suppression. Screening 113 marine bacterial genomes for prophages yielded 64 prophage-like elements, 21 of which strongly resembled gene transfer agents (GTAs). The remaining 39 putative prophages had a relatively high incidence of transcriptional regulatory and repressor-like proteins (approximately 2/40 kb prophage sequence) compared to lytic marine phages (approximately 0.25/40 kb phage sequence). Here, it has been hypothesized that marine prophages directly contribute to host survival in unfavorable environments by suppression of unneeded metabolic activities. It has been further suggested that such metabolic downshifts are the result of phage-encoded repressors and transcriptional regulators acting directly on host genes. Finally, the widespread occurrence of GTAs may be an efficient mechanism for horizontal gene transfer in the oceans.
[本文引用: 1]
[74]
Delisle A L, Levin R E.Characteristics of three phages infectious for psychrophilic fishery isolates of Pseudomonas putrefaciens[J]. Antonie Van Leeuwenhoek, 1972, 38(1): 1-8.
DOI:10.1007/BF02328071 PMID:4537085 URL
Three phages capable of infecting at 2 C strains of Pseudomonas putrefaciens from fish were isolated and characterized. Two phages were extremely sensitive to 55 C. DNA base composition of the three phages, based on Tm measurements, were 36.4, 40.0 and 48.8% G+C. Only one phage plaqued at a lower efficiency in the presence of citrate, none were inhibited by indole, while the plating efficiency of all three was reduced by oxalate. One phage was found to be obligately psychrophilic on its original propagating host and was unable to plaque at 20 C even though the host grew well up to 27 C.
[本文引用: 1]
[75]
Mojica K D A, Brussaard C P D. Factors affecting virus dynamics and microbial host-virus interactions in marine environments[J]. FEMS Microbiology Ecology, 2014, 89(3): 495-515.
DOI:10.1111/1574-6941.12343 PMID:24754794 URL
Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host-virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.
[本文引用: 2]
[76]
White P A, Kalff J, Rasmussen J B, et al. The effect of temperature and algal biomass on bacterial production and specific growth-rate in fresh-water and marine habitats[J]. Microbial Ecology, 1991, 21(1): 99-118.
DOI:10.1007/BF02539147 PMID:24194204 URL
We analyzed heterotrophic, pelagic bacterial production and specific growth rate data from 57 studies conducted in fresh, marine and estuarine/coastal waters. Strong positive relationships were identified between 1) bacterial production and bacterial abundance and 2) bacterial production and algal biomass. The relationship between bacterial production and bacterial abundance was improved by also considering water temperature. The analysis of covariance model revealed consistent differences between fresh, marine and estuarine/coastal waters, with production consistently high in estuarine/coastal environments. The log-linear regression coefficient of abundance was not significantly different from 1.00, and this linear relationship permitted the use of specific growth rate (SGR in day 鈭1 ) as a dependent variable. A strong relationship was identified between specific growth rate and temperature. This relationship differed slightly across the three habitats. A substantial portion of the residual variation from this relationship was accounted for by algal biomass, including the difference between marine and estuarine/coastal habitats. A small but significant difference between the fresh- and saltwater habitats remained. No significant difference between the chlorophyll effect in different habitats was identified. The model of SGR against temperature and chlorophyll was much weaker for freshwater than for marine environments. For a small subset of the data set, mean cell volume accounted for some of the residual variation in SGR. Pronounced seasonality, fluctuations in nutrient quality, and variation of the grazing environment may contribute to the unexplained variation in specific growth.
[本文引用: 1]
[77]
Wiebe W J, Sheldon W M, Pomeroy L R.Bacterial-growth in the cold-evidence for an enhanced substrate requirement[J]. Applied and Environmental Microbiology, 1992, 58(1): 359-364.
DOI:10.1016/S0065-2164(08)70256-9 PMID:195215 URL
Growth responses and biovolume changes for four facultatively psychrophilic bacterial isolates from Conception Bay, Newfoundland, and the Arctic Ocean were examined at temperatures from - 1.5 to 35 degrees C, with substrate concentrations of 0.15, 1.5, and 1,500 mg of proteose peptone-yeast extract per liter. For two cultures, growth in 0.1, 1.0, and 1,000 mg of proline per liter was also examined. At 10 to 15 degrees C and above, growth rates showed no marked effect of substrate concentration, while at - 1.5 and 0 degrees C, there was an increasing requirement for organic nutrients, with generation times in low-nutrient media that were two to three times longer than in high-nutrient media. Biovolume showed a clear dependence on substrate concentration and quality; the largest cells were in the highest-nutrient media. Biovolume was also affected by temperature; the largest cells were found at the lowest temperatures. These data have implications for both food web structure and carbon flow in cold waters and for the effects of global climate change, since the change in growth rate is most dramatic at the lowest temperatures.
[本文引用: 1]
[78]
Suttle C A, Chen F.Mechanisms and rates of decay of marine viruses in seawater[J]. Applied and Environmental Microbiology, 1992, 58(11): 3 721-3 729.
DOI:10.1002/yea.320081212 PMID:183166 URL
Loss rates and loss processes for viruses in coastal seawater from the Gulf of Mexico were estimated with three different marine bacteriophages. Decay rates in the absence of sunlight ranged from 0.009 to 0.028 h, with different viruses decaying at different rates. In part, decay was attributed to adsorption by heat-labile particles, since viruses did not decay or decayed very slowly in seawater filtered through a 0.2-mum-pore-size filter (0.2-mum-filtered seawater) and in autoclaved or ultracentrifuged seawater but continued to decay in cyanide-treated seawater. Cyanide did cause decay rates to decrease, however, indicating that biological processes were also involved. The observations that decay rates were often greatly reduced in 0.8- or 1.0-mum-filtered seawater, whereas bacterial numbers were not, suggested that most bacteria were not responsible for the decay. Decay rates were also reduced in 3-mum-filtered or cycloheximide-treated seawater but not in 8-mum-filtered seawater, implying that flagellates consumed viruses. Viruses added to flagellate cultures decayed at 0.15 h, corresponding to 3.3 viruses ingested flagellate h. Infectivity was very sensitive to solar radiation and, in full sunlight, decay rates were 0.4 to 0.8 h. Even when UV-B radiation was blocked, rates were as high as 0.17 h. Calculations suggest that in clear oceanic waters exposed to full sunlight, most of the virus decay, averaged over a depth of 200 m, would be attributable to solar radiation. When decay rates were averaged over 24 h for a 10-m coastal water column, loss rates of infectivity attributable to sunlight were similar to those resulting from all other processes combined. Consequently, there should be a strong diel signal in the concentration of infectious viruses. In addition, since sunlight destroys infectivity more quickly than virus particles, a large proportion of the viruses in seawater is probably not infective.
[本文引用: 1]
[79]
Weinbauer M G, Suttle C A.Lysogeny and prophage induction in coastal and offshore bacterial communities[J]. Aquatic Microbial Ecology, 1999, 18(3): 217-225.
DOI:10.3354/ame018217 URL
ABSTRACT: The influence of solar radiation and hydrogen peroxide on induction of lysogens, and the resulting effect on bacteriophage production and bacterial mortality was investigated for coastal and oceanic manne bacterial conlmunities at 6 stations in the western Gulf of Mexico. The percentage of lysogenic cells induced by mitomycin C was also determined. Solar radiation and hydrogen peroxide were not as effective as mitomycin C at inducing phage production. The burst size of cells induced by mitomycin C was estimated by transmission electron microscopy, assuming that cells completely filled with viral particles were on the verge of bursting. The smallest estimates of burst size were associated with oligotrophic oceanic stations and ranged from 15 to 28 viruses produced per lyhc event, whde in more productive coastal waters the estimated burst sizes ranged from 33 to 64. The mitomycin C- induced phage production and burst size were used to estimate the number of lysogenic bacterial cells. On average, the percentage of inducible lysogens was higher at offshore (1.5to 11.4%) than at coastal (0.8 to 2.2 %) stations. However, with the exception of 1 station, less than 5 % of the bacteria could be induced to produce phage, suggesting that lysogens only occasionally comprised a significant compo- nent of these bacterial communities. The proportion of lysogens that could be induced by sunlight, rel- ative to those that could be induced by rnitomycin C, was lower at oceanic than coastal stations. This implies that prophages in optically transparent offshore waters were more resistant to induction by solar radiation, or that most lysogens that could be triggered by sunlight were already induced. Based on a steady-state model, induction of lysogenic bacteria by solar radiation or hydrogen peroxide could result in between 0 and 3 5 % or 0.9 and 3.4 % of the total bacterial mortality, respectively. Our results imply that solar radiation and hydrogen peroxide induced lysogenic phage production were not an ~mportantsource of phage production or bacterial mortality in offshore or coastal waters of the western Gulf of Mexico.
[本文引用: 1]
[80]
Kellogg C A, Paul J H.Degree of ultraviolet radiation damage and repair capabilities are related to G+C content in marine vibriophages[J]. Aquatic Microbial Ecology, 2002, 27(1): 13-20.
DOI:10.3354/ame027013 URL
A key issue in the ecology of viruses in the marine environment is the rate of viral production and decay. The ultraviolet (UV) radiation in sunlight has been found to cause loss of infectivity in marine bacteriophages at rates nearly equal to all other decay mechanisms combined, There are 2 main host-mediated mechanisms that can repair U-V-damaged phage DNA: photoreactivation and excision repair. Both these mechanisms were investigated in 2 marine Vibrio parahaemolyticus hosts as they catalyzed the reactivation of 7 phages. Photoreactivation was the dominant repair mode in all but one case. A significant correlation was found between G+C content of the phage DNAs (16 to 70%) and degree of DNA damage (r = 0.955), indicating a strong relationship between the number of thymine dimer targets and the capability to photoreactivate DNA damage. Evolution of high G+C content may be a strategy for protection from UV damage in marine phages.
[本文引用: 2]
[81]
Traving S J, Clokie M R J, Middelboe M. Increased acidification has profound effect on the interactions between the cyanobacterium Synechococcus sp. WH7803 and its viruses[J]. FEMS Microbiology Ecology, 2014, 87(1): 133-141.
DOI:10.1111/1574-6941.12199 PMID:24003947 URL
Increased anthropogenic CO2 emissions are expected to cause a drop in oceanic pH of c. 0.4 units within this century. According to current assessments, the consequences of this are limited for oceanic Cyanobacteria, and absent for viruses. We investigated the effect of pH on the life history of cyanophage S-PM2 and its host, Synechococcus sp. WH7803, at current pH concentrations and at predicted future concentrations. We identified significant negative effects of decreasing pH on Synechococcus growth rate, with profound negative implications for S-PM2 biogenesis and its infection cycle. The duration of the S-PM2 eclipse period increased significantly with decreasing pH. In contrast, the latent period was shorter at pH 7.6 than at pH 8, coinciding with a reduction in S-PM2 burst size from 20.1 00± 3.2 progeny phages per cell at pH 8 to 5.68 00± 4.4 progeny phages per cell at pH 7.6. At pH 7, there was no detectable progeny release. The extracellular stage of S-PM2 was insensitive to pH changes, but sensitive to light, with significant loss in infectivity (0.350900090.38 day0908081) at relatively low irradiances (&gt; 130 0204mol photon m0908082 s0908081). Overall, the results suggest that pH has significant influence on cyanobacterial growth with important implications for the interactions between Cyanobacteria and their viruses.
[本文引用: 1]
[82]
Jacquet S, Heldal M, Iglesias-Rodriguez D, et al. Flow cytometric analysis of an Emiliana huxleyi bloom terminated by viral infection[J]. Aquatic Microbial Ecology, 2002, 27(2): 111-124.
DOI:10.3354/ame027111 URL
During a field mesocosm experiment conducted in coastal waters off western Norway, 11 m3 enclosures were filled with unfiltered seawater and enriched daily with different nitrate and phosphate concentrations in order to induce a bloom of the coccolithophorid Emiliana huxleyi under different nutrient regimes. Flow cytometry (FCM) analysis was performed 5 times d-1 in order to follow the initiation, development and termination of the bloom as well as the production of large virus-like particles (LVLPs) identified as E. huxleyi viruses (EhV). EhV production was observed first in the enclosure where N was in excess, and P limitation induced a lower burst size compared to nitrate-replete enclosures. These observations suggest a critical role for both P and N in E. huxleyi-EhV interactions. Concomitant to EhV production, a shift was observed between the original population (coccolith-bearing cells) towards a population characterized by the same chlorophyll a (chl a) fluorescence but with lower right angle light scatter values. This population is likely to correspond to either senescent cells losing their coccoliths or cells characterized by a lower production of coccoliths possibly due to viral infection. At the end of experiment, a significant proportion of E. huxleyi had survived after the end of the bloom. This suggests either the presence of a resistant form of the coccolithophorid or a change in the dominance of different host and/or viral strains during the bloom. A periodical pattern in virus production was recorded with virus number decreasing during the second part of the day suggesting that virus production may be synchronized to the daily light cycle. Our results provide new insights towards the understanding of the relationship between a key marine species and its specific virus.
[本文引用: 2]
[83]
Clokie M R J, Mann N H. Marine cyanophages and light[J]. Environmental Microbiology, 2006, 8(12): 2 074-2 082.
DOI:10.1111/j.1462-2920.2006.01171.x PMID:17107549 URL
In contrast to the phages of heterotrophic hosts, light can play a key role in all aspects of the life cycle of phages infecting ecologically important marine unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus. Phage adsorption, replication, modulation of the host cell metabolism, and survival in the environment following lysis, all exhibit light-dependent components. The analysis of cyanophage genomes has revealed the acquisition of key photosynthetic genes during the course of evolution, such as those encoding central components of the light harvesting apparatus. These discoveries are beginning to reveal novel features of the interactions between parasite and host that shape the biology of both.
[本文引用: 1]
[84]
Wilhelm S W, Jeffrey W H, Dean A L, et al. UV radiation induced DNA damage in marine viruses along a latitudinal gradient in the southeastern Pacific Ocean[J]. Aquatic Microbial Ecology, 2003, 31(1): 1-8.
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Furuta M, Schrader J O, Schrader H S, et al. Chlorella virus PBCV-1 encodes a homolog of the bacteriophage T4 UV damage repair gene denV[J]. Applied and Environmental Microbiology, 1997, 63(4): 1 551-1 556.
DOI:10.1089/oli.1.1997.7.125 PMID:168447 URL
Abstract The bacteriophage T4 denV gene encodes a well-characterized DNA repair enzyme involved in pyrimidine photodimer excision. We have discovered the first homologs of the denV gene in chlorella viruses, which are common in fresh water. This gene functions in vivo and also when cloned in Escherichia coli. Photodamaged virus DNA can also be photoreactivated by the host chlorella. Since the chlorella viruses are continually exposed to solar radiation in their native environments, two separate DNA repair systems, one that functions in the dark and one that functions in the light, significantly enhance their survival.
[本文引用: 1]
[86]
Orgata H, Ray J, Toyoda K, et al. Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment[J]. ISME Journal, 2011, 5(7): 1 143-1 151.
DOI:10.1038/ismej.2010.210 PMID:21248859 URL
MutS proteins are ubiquitous in cellular organisms and have important roles in DNA mismatch repair or recombination. In the virus world, the amoeba-infecting Mimivirus, as well as the recently sequenced Cafeteria roenbergensis virus are known to encode a MutS related to the homologs found in octocorals and 蓻-proteobacteria. To explore the presence of MutS proteins in other viral genomes, we performed a genomic survey of four giant viruses ('giruses') (Pyramimonas orientalis virus (PoV), Phaeocystis pouchetii virus (PpV), Chrysochromulina ericina virus (CeV) and Heterocapsa circularisquama DNA virus (HcDNAV)) that infect unicellular marine algae. Our analysis revealed the presence of a close homolog of Mimivirus MutS in all the analyzed giruses. These viral homologs possess a specific domain structure, including a C-terminal HNH-endonuclease domain, defining the new MutS7 subfamily. We confirmed the presence of conserved mismatch recognition residues in all members of the MutS7 subfamily, suggesting their role in DNA mismatch repair rather than DNA recombination. PoV and PpV were found to contain an additional type of MutS, which we propose to call MutS8. The MutS8 proteins in PoV and PpV were found to be closely related to homologs from 'Candidatus Amoebophilus asiaticus', an obligate intracellular amoeba-symbiont belonging to the Bacteroidetes. Furthermore, our analysis revealed that MutS7 and MutS8 are abundant in marine microbial metagenomes and that a vast majority of these environmental sequences are likely of girus origin. Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world.
[本文引用: 1]
[87]
Santini S, Jeudy S, Bartoli J, et al. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(26): 10 800-10 805.
DOI:10.1073/pnas.1303251110 URL
The viral nature of the first “giant virus,” Mimivirus, was realized in 2003, 10 y after its initial isolation from the water of a cooling tower in Bradford, UK. Soon after its genome was sequenced, the mining of the Global Ocean Sampling environmental sequence database revealed that the closest relatives of Mimivirus, only known to infect Acanthamoeba, were to be found in the sea. These predicted marine Mimivirus relatives remained elusive until 2010, with the first genomic characterization of a virus infecting a heterotrophic unicellular eukaryote, the microflagellate grazer Cafeteria roenbergensis. The genome analysis of a virus (PgV) infecting the common unicellular algae Phaeocystis globosa now shows that it is a bona fide member of the Mimivirus family (i.e., the Megaviridae), extending the realm of these giant viruses to abundant blooming phytoplankton species. Despite its smaller genome size (460 kb encoding 434 proteins), PgV exhibits the most intriguing feature of the previously characterized Megaviridae: an associated virophage. However, the 19-kb virophage genome, devoid of a capsid gene, is packaged in the PgV particle and propagated as a “viral plasmid,” the first ever described. The PgV genome also exhibits the duplication of “core genes,” normally present as single copies and a putative new type of mobile element. In a DNA polymerase phylogeny including representatives of the three cellular domains, PgV and the other Megaviridae cluster into their own clade deeply branching between domains Archaea and Eukarya domains, thus exhibiting the topology of a fourth domain in the Tree of Life.
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Cordova A, Deserno M, Gelbart W M, et al. Osmotic shock and the strength of viral capsids[J]. Biophysical Journal, 2003, 85(1): 70-74.
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Kukkaro P, Bamford D H.Virus-host interactions in environments with a wide range of ionic strengths[J]. Environmental Microbiology Reports, 2009, 1(1): 71-77.
DOI:10.1111/j.1758-2229.2008.00007.x PMID:23765723 URL
Although high-salt environments are rich in viruses, virus–host interactions have not been much explored. Here we study the virus–host interactions occurring in a variety of salt environments, up to saturated salinity. We chose viruses from different environments with diverse morphologies that included both bacterial and archaeal viruses. To extend the test virus set five new haloviruses were isolated and initially characterized in this study. We observed adsorption rates that varied over four orders of magnitude among the virus–host cell systems used in this study. Changes in ionic strength affected the adsorption of these viruses to their host cells in a variety of ways. All the studied viruses, regardless from which environment they were isolated, were more resistant to variations in ionic strength conditions than their host cells. Our study provides a glimpse of the early events in virus life cycles for a number of viruses from different environments. We also gained information on viral responses to changing environments, a valuable piece of information in extending our understanding of the viruses in the environment.
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[90]
Zachary A.Physiology and ecology of bacteriophages of the marine bacterium Beneckea natriegens: Salinity[J]. Applied and Environmental Microbiology, 1976, 31(3): 415-422.
PMID:938035 URL
The effects of variation in ionic levels on the stability and replication of two bacteriophages (nt-1 and nt-6) host specific for the marine bacterium Beneckea natriegens were examined. Monovalent cations influenced the adsorption of the nt-1 but not the nt-6 phage; however, one-step growth studies showed that NaCl was required for replication of both phage. The NaCl optimum for nt-1 production was 0.25 M NaCl, the same as the growth optimum for B. natriegens. However, the optimum for nt-6 production was 0.16 M NaCl. These NaCl optima for host and phage are at estuarine rather than oceanic levels. The nt-1 phage was better suited to replicate at NaCl levels typical of higher salinity areas (18-35%) and the nt-6 phage was better suited to replicate at lower salinities (5-18%). The nt phage were more resistant to low NaCl levels than their host bacterium and appeared limited to marine waters by the lower survival salinity of B. natriegens coupled with phage inactivation processes occurring in natural estuarine waters.
[本文引用: 1]
[91]
Williamson S J, Paul J H.Environmental factors that influence the transition from lysogenic to lytic existence in the ϕHSIC/Listonella pelagia marine phage-host system[J]. Microbial Ecology, 2006, 52(2): 217-225.
DOI:10.1007/s00248-006-9113-1 PMID:16897298 URL
Abstract The marine phage varphiHSIC has been previously reported to enter into a pseudolysogenic-like interaction with its host Listonella pelagia. This phage-host system displays behaviors that are characteristic of both pseudolysogeny and lysogeny including a high rate of spontaneous induction and chromosomal integration of the prophage. To determine what parameters may influence the transition from lysogenic to lytic existence in the varphiHSIC/L. pelagia phage-host system, cultures of this organism were incubated under different environmental conditions, while host cell growth and bacteriophage production were monitored. The environmental parameters tested included salinity, temperature, a rapid temperature shift, and degree of culture aeration. The highest titers of phage were produced by HSIC-1a cells grown in high-salinity nutrient artificial seawater media (67 ppt with a natural salinity equivalent of 57 ppt) or those cultured in highly aerated nutrient artificial seawater media (cultures shaken at 300 rpm). Conversely, the lowest titers of phage were produced under low salinity or rate of aeration. In general, conditions that stimulated growth resulted in greater lytic phage production, whereas slow growth favored lysogeny. These results indicate that elevated salinity and aeration influenced the switch from lysogenic to lytic existence for the phage varphiHSIC. These results may have implications for environmental controls of the lysogenic switch in natural populations of marine bacteria.
[本文引用: 1]
[92]
Wilson W H, Carr N G, Mann N H.The effect of phosphate status on the kinetics of cyanophage infection in the oceanic cyanobacterium Synechococcus sp. WH7803[J]. Journal of Phycology, 1996, 32(4): 506-516.
DOI:10.1111/j.0022-3646.1996.00506.x URL
ABSTRACT Phycoerythrin-containing Synechococcus species are considered to be major primary producers in nutrient-limited gyres of subtropical and tropical oceanic provinces, and the cyanophages that infect them are thought to influence marine biogeochemical cycles. This study begins an examination of the effects of nutrient limitation on the dynamics of cyanophage/ Synechococcus interactions in oligotrophic environments by analyzing the infection kinetics of cyanophage strain S-PM2 ( Cyanomyoviridae isolated from coastal water off Plymouth, UK) propagated on Synechococcus sp. WH7803 grown in either phosphate-deplete or phosphate-replete conditions. When the growth of Synechococcus sp. WH7803 in phosphate-deplete medium was followed after infection with cyanophage, an 18-h delay in cell lysis was observed when compared to a phosphate-replete control. Synechococcus sp. WH7803 cultures grown at two different rates (in the same nutritional conditions) both lysed 24 h postinfection, ruling out growth rate itself as a factor in the delay of cell lysis. One-step growth kinetics of S-PM2 propagated on host Synechococcus sp. WH7803, grown in phosphate-deplete and-replete media, revealed an apparent 80% decrease in burst size in phosphate-deplete growth conditions, but phage adsorption kinetics ofS-PM2 under these conditions showed no differences. These results suggested that the cyanophages established lysogeny in response to phosphate-deplete growth of host cells. This suggestion was supported by comparison of the proportion of infected cells that lysed under phosphate-replete and-deplete conditions, which revealed that only 9.3% of phosphate-deplete infected cells lysed in contrast to 100% of infected phosphate-replete cells. Further studies with two independent cyanophage strains also revealed that only approximately 10% of infected phosphate-deplete host cells released progeny cyanophages. These data strongly support the concept that the phosphate status of the Synechococcus cell will have a profound effect on the eventual outcome of phage-host interactions and will therefore exert a similarly extensive effect on the dynamics of carbon flow in the marine environment.
[本文引用: 1]
[93]
Wilson W H, Turner S, Mann N H.Population dynamics of phytoplankton and viruses in a phosphate-limited mesocosm and their effect on DMSP and DMS production[J]. Estuarine Coastal and Shelf Science, 1998, 46(2): 49-59.
DOI:10.1006/ecss.1998.0333 URL
The effect of phosphate limitation on viral abundance, phytoplankton bloom dynamics and production of dimethylsulphoniopropionate (DMSP) and dimethyl sulphide (DMS) was investigated in seawater mesocosm enclosures, in a Norwegian fjord, during June 1995. Daily estimates of viral concentrations, based on transmission electron microscope (TEM) counts, varied on an apparently random basis in each of the enclosures. A large Synechococcus spp. bloom developed in an enclosure which was maintained at a high N:P ratio, simulating phosphate-deplete growth conditions. Following phosphate addition to this enclosure, there was a large increase in estimated virus numbers shortly before an apparent collapse of the Synechococcus bloom. It is tentatively suggested that lysogenic viruses were induced following phosphate addition to the phosphate-limited enclosures, and that these observations add to a growing body of evidence which supports the hypothesis that nutrient availability may be responsible for the switch between lysogeny and lytic production. High DMS concentrations and viral numbers were observed on the demise of the flagellate (predominantly Emiliania huxleyi ) and diatom blooms, but overall there was no significant correlation. Highest concentrations of DMSP were associated with blooms of E. huxleyi , for which an intracellular concentration of 0路5聽pg cell 鈭1 (SD, 0路06) was calculated. Good correlation of DMSP with Synechococcus spp. cell numbers was observed, suggesting that these species of picoplankton may be significant producers of DMSP. No effects of phosphate limitation on DMS and/or DMSP production were evident from the data.
[本文引用: 1]
[94]
Abedon S T, Herschler T D, Stopar D.Bacteriophage latent period evolution as a response to resource availability[J]. Applied and Environmental Microbiology, 2001, 67(9): 4 233-4 241.
DOI:10.1128/AEM.67.9.4233-4241.2001 PMID:93152 URL
Abstract Bacteriophages (phages) modify microbial communities by lysing hosts, transferring genetic material, and effecting lysogenic conversion. To understand how natural communities are affected it is important to develop predictive models. Here we consider how variation between models--in eclipse period, latent period, adsorption constant, burst size, the handling of differences in host quantity and host quality, and in modeling strategy--can affect predictions. First we compare two published models of phage growth, which differ primarily in terms of how they model the kinetics of phage adsorption; one is a computer simulation and the other is an explicit calculation. At higher host quantities (approximately 10(8) cells/ml), both models closely predict experimentally determined phage population growth rates. At lower host quantities (10(7) cells/ml), the computer simulation continues to closely predict phage growth rates, but the explicit model does not. Next we concentrate on predictions of latent-period optima. A latent-period optimum is the latent period that maximizes the population growth of a specific phage growing in the presence of a specific quantity and quality of host cells. Both models predict similar latent-period optima at higher host densities (e.g., 17 min at 10(8) cells/ml). At lower host densities, however, the computer simulation predicts latent-period optima that are much shorter than those suggested by explicit calculations (e.g., 90 versus 1,250 min at 10(5) cells/ml). Finally, we consider the impact of host quality on phage latent-period evolution. By taking care to differentiate latent-period phenotypic plasticity from latent-period evolution, we argue that the impact of host quality on phage latent-period evolution may be relatively small.
[本文引用: 1]
[95]
Apple J K, del Giorgio P A. Organic substrate quality as the link between bacterioplankton carbon demand and growth efficiency in a temperate salt-marsh estuary[J]. ISME Journal, 2007, 1(8): 729-742.
DOI:10.1038/ismej.2007.86 PMID:18059496 URL
Abstract Bacterioplankton communities play a key role in aquatic carbon cycling, specifically with respect to the magnitude of organic carbon processed and partitioning of this carbon into biomass and respiratory losses. Studies of bacterioplankton carbon demand (BCD) and growth efficiency (BGE) frequently report higher values in more productive systems, suggesting these aspects of carbon metabolism may be positively coupled. However, the existence of such a relationship in natural aquatic systems has yet to be identified. Using a comprehensive 2-year study of bacterioplankton carbon metabolism in a temperate estuary, we investigated BCD and BGE and explored factors that may modulate their magnitude and coherence, including nutrient concentrations, dissolved nutrient uptake and source and quality of dissolved organic carbon (DOC). During the course of our study, BCD ranged from 0.4 to 15.9 microg l(-1) h(-1), with an overall mean of 3.8 microg l(-1) h(-1). Mean BGE was similar to that reported for other estuarine systems (0.32) and of comparable range (that is, 0.06-0.68). Initial analyses identified a negative correlation between BCD and BGE, yet removal of the effect of temperature revealed an underlying positive coupling that was also correlated with long-term DOC lability. Whereas BCD was weakly related to ambient DOC concentrations, neither BCD nor BGE showed any relationship with ambient nutrient concentrations or nutrient uptake stoichiometries. We conclude that in this carbon-rich estuary, organic matter source and quality play an important role in regulating the magnitude of carbon metabolism and may be more important than nutrient availability alone in the regulation of BGE.
[本文引用: 1]
[96]
Noble R T, Fuhrman J A.Virus decay and its causes in coastal waters[J]. Applied and Environmental Microbiology, 1997, 63(1): 77-83.
DOI:10.1016/S0065-2164(08)70266-1 PMID:16535501 URL
Abstract Recent evidence suggests that viruses play an influential role within the marine microbial food web. To understand this role, it is important to determine rates and mechanisms of virus removal and degradation. We used plaque assays to examine the decay of infectivity in lab-grown viruses seeded into natural seawater. The rates of loss of infectivity of native viruses from Santa Monica Bay and of nonnative viruses from the North Sea in the coastal seawater of Santa Monica Bay were determined. Viruses were seeded into fresh seawater that had been pretreated in various ways: filtration with a 0.2-(mu)m-pore-size filter to remove organisms, heat to denature enzymes, and dissolved organic matter enrichment to reconstitute enzyme activity. Seawater samples were then incubated in full sunlight, in the dark, or under glass to allow partitioning of causative agents of virus decay. Solar radiation always resulted in increased rates of loss of virus infectivity. Virus isolates which are native to Santa Monica Bay consistently degraded more slowly in full sunlight in untreated seawater (decay ranged from 4.1 to 7.2% h(sup-1)) than nonnative marine bacteriophages which were isolated from the North Sea (decay ranged from 6.6 to 11.1% h(sup-1)). All phages demonstrated susceptibility to degradation by heat-labile substances, as heat treatment reduced the decay rates to about 0.5 to 2.0% h(sup-1) in the dark. Filtration reduced decay rates by various amounts, averaging 20%. Heat-labile, high-molecular-weight dissolved material (>30 kDa, probably enzymes) appeared responsible for about 1/5 of the maximal decay. Solar radiation was responsible for about 1/3 to 2/3 of the maximal decay of nonnative viruses and about 1/4 to 1/3 of that of the native viruses, suggesting evolutionary adaptation to local light levels. Our results suggest that sunlight is an important contributing factor to virus decay but also point to the significance of particles and dissolved substances in seawater.
[本文引用: 1]
[97]
Motegi C, Nagata T.Enhancement of viral production by addition of nitrogen or nitrogen plus carbon in subtropical surface waters of the South Pacific[J]. Aquatic Microbial Ecology, 2007, 48(1): 27-34.
DOI:10.3354/ame048027 URL
We tested the hypothesis that viral production is limited by nutrient availability in oligotrophic subtropical surface waters of the South Pacific. Nutrient (C, N, P) addition experiments were conducted at 2 stations (Stn SX18, 39° 60'S, 169° 60'W; Stn SX22, 19° 60' S, 169° 60'W) to examine the responses of viral production (
[本文引用: 1]
[98]
Rochelle-Newall E, Delille B, Frankignoulle M, et al. Chromophoric dissolved organic matter in experimental mesocosms maintained under different pCO2 levels[J]. Marine Ecology Progress Series, 2004, 272: 25-31.
DOI:10.3354/meps272025 URL
Chromophoric dissolved organic matter (CDOM) represents the optically active fraction of the bulk dissolved organic matter (DOM) pool. Recent evidence pointed towards a microbial source of CDOM in the aquatic environment and led to the proposal that phytoplankton is not a direct source of CDOM, but that heterotrophic bacteria, through reprocessing of DOM of algal origin, are an important source of CDOM. In a recent experiment designed at looking at the effects of elevated pCO2 on blooms of the coccolithophorid alga Emiliania huxleyi, we found that despite the 3 different pCO2 levels tested (190, 414 and 714 ppm), no differences were observed in accumulation of CDOM over the 20 d of incubation. Unlike previous mesocosm experiments where relationships between CDOM accumulation and bacterial abundance have been observed, none was observed here. These results provide some new insights into the apparent lack of effect of pCO2 on CDOM accumulation in surface waters, and question the previously proposed mechanisms and rates of CDOM production in natural phytoplankton blooms.
[本文引用: 1]
[99]
Carreira C, Heldal M, Bratbak G.Effect of increased pCO2 on phytoplankton-virus interactions[J]. Biogeochemistry, 2012, 114(1/3): 391-397.
DOI:10.1007/s10533-011-9692-x URL
Atmospheric carbon dioxide (CO 2 ) has increased since the pre-industrial period and is predicted to continue to increase throughout the twenty-first century. The ocean is a sink for atmospheric CO 2 and increased CO 2 concentration will change the carbonate equilibrium of seawater and result in lower carbonate ion concentration and lower pH. This may affect the entire marine biota but in particular calcifying organisms. In this study we investigated the effect of increased CO 2 on the virus host interaction of Emiliania huxleyi as a calcifying organism and of Phaeocystis poucheti as a non- calcifying organism . Both algae were grown in laboratory controlled conditions under past (280聽ppmv), present (350聽ppmv) and future (700聽ppmv) CO 2 concentrations with and without added virus. Increased CO 2 had a negative effect on the growth rate of P. pouchetii , but not of E. huxleyi . No impact was found on viral lysis of P. pouchetii while increased burst size and slightly delayed lysis was observed for E. huxleyi with increased CO 2 . We conclude that this short time study could not confirm earlier reports and our hypothesis of a negative effect of high CO 2 on E. huxleyi growth and E. huxleyi virus production.
[本文引用: 1]
[100]
Maat D S, Crawfurd K J, Timmermans K R, et al. Elevated CO2 and phosphate limitation favor Micromonas pusilla through stimulated growth and reduced viral impact[J]. Applied and Environmental Microbiology, 2014, 80(22): 3 119-3 127.
DOI:10.1128/AEM.03639-13 PMID:4018922 URL
Growth and viral infection of the marine picoeukaryote Micromonas pusilla was studied under a future-ocean scenario of elevated partial CO2 (pCO2; 750 atm versus the present-day 370 atm) and simultaneous limitation of phosphorus (P). Independent of the pCO2 level, the ratios of M. pusilla cellular carbon (C) to nitrogen (N), C:P and N:P, increased with increasing P stress. Furthermore, in the P-limited chemostats at growth rates of 0.32 and 0.97 of the maximum growth rate (max), the supply of elevated pCO2 led to an additional rise in cellular C:N and C:P ratios, as well as a 1.4-fold increase in M. pusilla abundance. Viral lysis was not affected by pCO2, but P limitation led to a 150% prolongation of the latent period (6 to 12 h) and an 80% reduction in viral burst sizes (63 viruses per cell) compared to P-replete conditions (4 to 8 h latent period and burst size of 320). Growth at 0.32 max further prolonged the latent period by another 150% (12 to 18 h). Thus, enhanced P stress due to climate change-induced strengthened vertical stratification can be expected to lead to reduced and delayed virus production in picoeukaryotes. This effect is tempered, but likely not counteracted, by the increase in cell abundance under elevated pCO2. Although the influence of potential P-limitation-relieving factors, such as the uptake of organic P and P utilization during infection, is unclear, our current results suggest that when P limitation prevails in future oceans, picoeukaryotes and grazing will be favored over larger-sized phytoplankton and viral lysis, with increased matter and nutrient flow to higher trophic levels.
[本文引用: 1]
[101]
Larsen J B, Larsen A, Thyrhaug R, et al. Response of marine viral populations to a nutrient induced phytoplankton bloom at different pCO2 level[J]. Biogeosciences, 2008, 5(2): 523-533.
DOI:10.5194/bg-5-523-2008 URL
During the PeECE III mesocosm experiment in 2005 we investigated how the virioplankton community responded to increased levels of nutrients (N and P) and CO2. We applied a combination of flow cytometry, Pulsed Field Gel Electrophoresis and degenerate PCR primers to categorize and quantify individual viral populations, and to investigate their temporal dynamics. Species specific and degenerate primers enabled us to identify two specific large dsDNA viruses, EhV and CeV, infecting the haptophytes Emiliania huxleyi and Crysochromulina ericina, respectively. Some of the viral populations detected and enumerated by flow cytometry did not respond to altered CO2-levels, but the abundance of EhV and an unidentified dsDNA virus decreased with increasing CO2 levels. Our results thus indicate that CO2 conditions, or the related change in pH, may affect the marine pelagic food web at the viral level. Our results also demonstrate that in order to unravel ecological problems as how CO2 and nutrient levels affect the relationship between marine algal viruses and their hosts, we need to continue the effort to develop molecular markers used to identify both hosts and viruses.
[本文引用: 1]
[102]
[杨芸兰, 蔡兰兰, 张锐. 气候变化对海洋病毒生态特性及其生物地球化学效应的影响[J]. 微生物学报, 2015, 55(9): 1 097-1 104.]
Yang Yunlan, Cai Lanlan, Zhang Rui.Effects of global climate change on the ecological characteristics and biogeochemical significance of marine viruses—A review[J]. Acta Microbiologica Sinica, 2015, 55(9): 1 097-1 104.
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