Bryson Samuel Joseph, Thurber Andrew R, Correa Adrienne M S, Orphan Victoria J, Vega Thurber Rebecca
Department of Microbiology, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA.
College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA.
Environ Microbiol. 2015 Oct;17(10):3708-21. doi: 10.1111/1462-2920.12758. Epub 2015 Mar 25.
Methane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major-capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Pequeñovirus.
甲烷渗漏微生物群落通过在温室气体甲烷释放到水圈之前将其消耗，发挥着关键的生态系统服务功能，从而将海洋甲烷源对我们气候的影响降至最低。尽管此前的研究已经考察了这些群落的生态学和生物化学，但尚无研究探讨与这些栖息地相关的病毒群落。我们对两个宏基因组文库进行了病毒颗粒纯化、基因组扩增、焦磷酸测序以及基因/基因组重建和注释，其中一个文库用于单链DNA，另一个用于所有DNA，以鉴定甲烷渗漏处的病毒群落。对这些文库（原始文库和组装文库）的相似性分析表明，该群落以噬菌体为主，其中很大一部分与单链DNA噬菌体的微小病毒科相似。我们将这些病毒定义为鳗鱼河流域微小病毒科（ERBM）。对21个ERBM闭合环状基因组进行组装和比较后，鉴定出其中5个属于肠道杆菌噬菌体微小病毒属一个新的姐妹进化枝的成员。与其他宏基因组以及这些微小病毒科主要衣壳序列的比较表明，这一噬菌体进化枝目前在鳗鱼河流域沉积物中是独一无二的。鉴于这个ERBM进化枝与微小病毒科微小病毒属的关系，我们将这个姐妹进化枝定义为候选属“Pequeñovirus”。
