Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
FEMS Microbiol Lett. 2019 Jul 1;366(13). doi: 10.1093/femsle/fnz152.
Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.
海洋微生物在全球能量和营养循环中发挥着重要作用。确定它们多样性和分布的主要方法是通过对环境样本中的 16S 核糖体 RNA 基因进行测序。然而，由于方法上的差异，包括对 16S 可变区的选择不同，感知到的群落组成可能会有很大的差异。本研究通过标签- Illumina 测序，调查了 16S 可变区选择（V4-V5 或 V6-V8）对细菌、古菌和叶绿体的感知群落组成和多样性的影响。我们使用了来自北大西洋斯科舍浅滩光区的 24 个样本，这些样本是在春季浮游植物繁殖期间采集的。分类学分配和群落组成因可变区的选择而有很大差异，而观察到的β多样性模式在可变区之间是可重现的。基于其对古菌的更好识别，V4-V5 被认为是未来研究的首选可变区，因为古菌在繁殖动态中很少受到关注。V6-V8 区捕获了更多的细菌多样性，包括丰富的 SAR11 类群，以及较少的叶绿体。然而，细菌和叶绿体的可变区之间的差异程度小于古菌。
