Red Sea SAR11 andProchlorococcusSingle-cell Genomes Reflect Globally Distributed Pangenomes
AuthorsThompson, Luke R.
Haroon, Mohamed F.
Shibl, Ahmed A.
Cahill, Matt J.
Ngugi, David K.
Williams, Gareth J.
Morton, James T.
Goodwin, Kelly D.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Marine Science Program
Office of the VP
Red Sea Research Center (RSRC)
Online Publication Date2019-06-17
Print Publication Date2019-04-26
Permanent link to this recordhttp://hdl.handle.net/10754/653034
MetadataShow full item record
AbstractEvidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations upon 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 ocean; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, II) and 5Prochlorococcus(ecotype HLII) cells 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 crypticProchlorococcusecotypes LLII and LLIII. Compared with reference genomes, 1% ofProchlorococcusand 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 could be functional. SearchingTaraOceans 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.
CitationThompson, L. R., Haroon, M. F., Shibl, A. A., Cahill, M. J., Ngugi, D. K., Williams, G. J., … Stingl, U. (2019). Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes. Applied and Environmental Microbiology, 85(13). doi:10.1128/aem.00369-19
SponsorsWe thank Haiwei Luo for assistance building genome trees, Mamoon Rashid for consultation about decontamination methods, Qiyun Zhu for assistance with genome analysis, and Ramunas Stepanauskas and Nicole Poulton for assistance with the single-cell genomics protocol.
PublisherAmerican Society for Microbiology