Milke Felix, Sanchez-Garcia Selene, Dlugosch Leon, McNichol Jesse, Fuhrman Jed, Simon Meinhard, Wagner-Döbler Irene
Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany.
Front Microbiol. 2022 Jun 28;13:895875. doi: 10.3389/fmicb.2022.895875. eCollection 2022.
Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
进行海洋中上层原核生物和真核生物群落的流域尺度生物地理观测，对于理解驱动群落组成的因素以及为监测全球变化提供基线至关重要。rRNA基因的深度测序可提供高分辨率的群落组成信息；然而，尚不清楚引物的选择如何影响生物地理模式。在此，我们使用通用的V4-V5引物，对“极地星号”科考船ANT28-5航次期间在横跨大西洋从南纬52°到北纬47°的纬度断面采集的DNA中的16S rRNA基因进行了重新扩增，并将结果与先前使用V5-V6细菌特异性引物获得的结果进行了比较。为验证我们的结果，我们基于来自相同站位的宏基因组的16S rRNA基因以及来自全球海洋参考基因组（GORG）数据库的单扩增基因组（SAG）推断群落组成。我们发现，通用的V4-V5引物检索到的SAR11进化枝的相对比例与GORG数据库中的相似，而V5-V6引物回收的进化枝丰度差异很大。我们证实了大西洋存在倒钟形的距离-衰减关系和纬度多样性梯度，且该梯度并非随绝对纬度呈线性下降。模式受到采样深度、测序深度、引物选择和丰度过滤的影响。特别是丰富度模式对方法学变化并不稳健。本研究使用一组通用的PCR引物，详细描绘了大西洋微生物组的情况，这些引物能够将来自不同生命域的生物之间的生物地理模式联系起来。
