Faculty of Health and Life Sciences, Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
Faculty of Health and Life Sciences, Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
Appl Environ Microbiol. 2019 Aug 29;85(18). doi: 10.1128/AEM.01003-19. Print 2019 Sep 15.
Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting sp. strain BAL341 () were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, , and One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring "kill-the-winner" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems allow us to understand and study the influence of phages on aquatic ecosystems.
通过非培养方法，水生病毒学领域的知识已经有了很大的提高，但仍迫切需要分离新的噬菌体来鉴定占宏基因组大部分的“未知”，并对噬菌体-宿主相互作用进行详细分析。在这里，从波罗的海海水中分离到了 54 株感染 sp. 株 BAL341()的噬菌体，并通过基因组内容分析和比较基因组学进行了表征。这些噬菌体呈现出类似于肌病毒的形态，属于一个新的属，我们将其命名为 所有噬菌体的基因组大小和基因数量相似（80 到 84 kb；134 到 145 个基因），根据平均核苷酸身份和基因组 BLAST 距离系统发育，噬菌体被分为五个种。噬菌体具有一些参与代谢过程和宿主信号转导的基因，如编码核糖核苷酸还原酶和胸苷酸合酶的基因 ， ，和 一种噬菌体还具有额外的参与吡啶核苷酸回收的代谢基因，这可能通过进一步提高噬菌体的复制效率为其提供了适应优势。将病毒宏基因组序列（2012 年至 2015 年期间的 25 个波罗的海病毒宏基因组）招募到噬菌体基因组中，显示出明显的季节性变化，八月和九月噬菌体的相对丰度增加，与宿主丰度峰值同步，这可以通过 16S rRNA 基因扩增子测序来证明。总的来说，这项研究提供了有关遗传多样性、噬菌体-宿主相互作用以及生态重要的水生噬菌体-宿主系统时间动态的详细信息。噬菌体在水生生态系统中很重要，因为它们通过裂解、基因转移、转录调控和噬菌体代谢基因的表达来影响其微生物宿主。然而，我们对噬菌体如何与其宿主相互作用的了解仍然有限，尤其是在精细尺度上。在这里，我们呈现了一个由高度相似的噬菌体感染单一宿主株系构成的 噬菌体-宿主系统。这种相对有限的多样性以前只在分离出较少数量的噬菌体时出现过，这表明生态限制影响了 噬菌体的多样性。物种之间代谢基因的变异表明存在各种适应优势，为未来的假设检验开辟了可能性。多年来监测的噬菌体-宿主动态表明存在反复的“杀死胜利者”振荡，并且该系统在波罗的海中占据了一个生态位。识别和量化此类噬菌体-宿主模型系统的生态动态使我们能够理解和研究噬菌体对水生生态系统的影响。
