Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA.
Environ Microbiol. 2022 Dec;24(12):6100-6111. doi: 10.1111/1462-2920.16172. Epub 2022 Aug 29.
The relative abundance of N4-like viruses in two temperate estuaries was assessed using four different methods, read mapping to known N4-like virus isolates, read mapping to native viral contigs, reciprocal blast search based on core genes, and read taxonomy classification using Kaiju. Overall, N4-like viruses were found to be of low abundance in the estuarine viromes. When mapping reads to only known N4-like virus genomes, high occurrences of N4-like viruses infecting Roseobacter were found, with their diversity consisting mostly of locally isolated Roseobacter N4-like virus species. Both contig-based methods and Kaiju classification showed similar seasonal patterns for N4-like viruses, and redundancy analysis revealed a negative correlation between N4-like viruses and temperature, suggesting that N4-like viruses may be more abundant in colder water. The discrepancy of relative abundance estimates using different methods indicates that N4-like viruses are best represented by native viral sequences. Our study indicates that N4-like viruses are rare in the marine environment and also provide insight into the importance of including local viral sequences in reference databases.
采用四种不同方法评估了两种温带河口中二价 N4 样病毒的相对丰度：将读取序列映射到已知的二价 N4 样病毒分离株、将读取序列映射到天然病毒连续体、基于核心基因的相互 Blast 搜索以及使用 Kaiju 进行读取分类。总体而言，河口病毒组中二价 N4 样病毒的丰度较低。当仅将读取序列映射到已知的二价 N4 样病毒基因组时，发现感染玫瑰杆菌的二价 N4 样病毒的高发生率，其多样性主要由当地分离的玫瑰杆菌二价 N4 样病毒物种组成。基于连续体的方法和 Kaiju 分类都显示出二价 N4 样病毒具有相似的季节性模式，冗余分析表明二价 N4 样病毒与温度呈负相关，表明二价 N4 样病毒可能在较冷的水中更为丰富。不同方法的相对丰度估计值的差异表明，天然病毒序列最能代表二价 N4 样病毒。我们的研究表明，二价 N4 样病毒在海洋环境中较为罕见，同时也说明了在参考数据库中包含本地病毒序列的重要性。
