Ecophysiology of a common unannotated gene transcript in surface water microbial assemblages of the oligotrophic open ocean

Abstract

Metagenomic and metatranscriptomic surveys of open ocean microbial assemblages have revealed a vast number of nucleic acid sequences that are of unknown function or phylogenetic affiliation. We examined metatranscriptomic databases and found several highly expressed, yet unidentified, transcripts which were present across diverse locations in the open ocean. Comparison of the 5 most highly represented transcript contiguous sequences (hRCs) against the Global Ocean Survey (GOS) assembled metagenomic sequence database revealed that 4 of the 5 hRCs had been observed previously in open ocean microbial DNA. Amplification of the hRCs from pelagic microbial DNA yielded 1 amplicon (hRC93). To confirm that hRC93 was syntenous with the nucleotide sequence on a matching GOS contig (JCVI_SCAF_1096627329331), we amplified a 706 bp region between hRC93 and an adjacent gene from pelagic microbial DNA. We further characterized hRC93 by examining its relative frequency in metatranscriptomic libraries and performed quantitative PCR on microbial DNA collected from the equatorial Atlantic Ocean, the Gulf of Maine, and a tropical estuary (Bayboro Harbor). Our data demonstrate that hRC93 is in a rare (~0.1-1% of cells) component of productive tropical surface water microbial assemblages, and that its role in host physiology is not related to photosynthesis or to the expression of adjacent genes on the matching GOS genome fragment. However, the large investment in hRC93 transcription suggests an important role in host ecology. These results highlight the lack of genomic information on rare marine microorganisms, but also suggest that unannotated reads in metagenomic and metatranscriptomic surveys can provide useful information on the ecophysiology of uncultivated microorganisms.