AUTHOR=Milke Felix , Sanchez-Garcia Selene , Dlugosch Leon , McNichol Jesse , Fuhrman Jed , Simon Meinhard , Wagner-Döbler Irene 

TITLE=Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.895875

DOI=10.3389/fmicb.2022.895875

ISSN=1664-302X

ABSTRACT=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 bacterial-specific primers. For validation of our results, we inferred community composition based on 16S 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 subclades with similar relative proportions as those found in the GORG database while V5-V6 primers showed similar abundances between SAR11 clade I, II & IV. 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 varied with sampling depth, sequencing depth, choice of primers and abundance filtering and 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 allows for the conjunction of biogeographical patterns among organisms from different domains of life.