Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes

Authors

Luke R. Thompson, University of Southern MississippiFollow
Mohamed F. Haroon, King Abdullah University of Science and Technology
Ahmed A. Shibl, King Abdullah University of Science and TechnologyFollow
Matt J. Cahill, King Abdullah University of Science and Technology
David K. Ngugi, King Abdullah University of Science and TechnologyFollow
Gareth J. Williams, Bangor UniversityFollow
James T. Morton, University of California, San DiegoFollow
Rob Knight, University of California San DiegoFollow
Kelly D. Goodwin, Southwest Fisheries Science Center, NOAAFollow
Ulrich Stingl, King Abdullah University of Science and TechnologyFollow

Document Type

Article

Publication Date

7-1-2019

Department

Biological Sciences

School

Biological, Environmental, and Earth Sciences

Abstract

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this “microbial seed bank” hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.

Publication Title

Applied and Environmental Microbiology

Volume

85

Issue

13

First Page

1

Last Page

18

Recommended Citation

Thompson, L. R., Haroon, M. F., Shibl, A. A., Cahill, M. J., Ngugi, D. K., Williams, G. J., Morton, J. T., Knight, R., Goodwin, K. D., Stingl, U. (2019). Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes. Applied and Environmental Microbiology, 85(13), 1-18.
Available at: https://aquila.usm.edu/fac_pubs/18082