Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the North Pacific Subtropical Gyre

Citation Shi, Yanmei et al. " Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract 1 As part of an ongoing survey of microbial community gene expression in the 2 ocean, we sequenced and compared a total of ~38 Mbp of community transcriptomes 3 and ~157 Mbp of community genomes from four bacterioplankton samples, along a 4 defined depth profile at Station ALOHA in North Pacific subtropical gyre (NPSG). 5 Taxonomic analysis based on rRNA (as well as protein-coding sequences) suggested that 6 the samples were dominated by three taxa: Prochlorales, Consistiales, and Cenarchaeales, 7 that comprised 36-69% and 29-63% of the annotated sequences in the four DNA and four 8 cDNA libraries, respectively. The remaining of the sequences represented a broad 9 diversity of low abundance taxa (33 taxonomic groups detected with relative abundance 10 of ≥ 1% in any of the eight libraries). The relative abundance of major taxonomic groups 11 was sometimes inconsistently represented in the DNA and cDNA libraries. For example, 12 the 125m sample genomic library was dominated by Pelagibacter (~36% of sequence 13 reads), which contributed far fewer sequences to the community transcript pool (~11%). 14 Those data suggest the utility of metatranscriptomics for assessing the relative 15 transcriptional activities per cell for different taxonomic groups. Functional 16 characterization in combination with taxonomic classification for highly expressed genes 17 revealed taxon-specific contributions to active biogeochemical processes such as 18 phototrophy and nitrogen metabolism. Examples included Roseobacter-relatives involved 19 in aerobic anoxygenic phototrophy at 75m, and the unexpected contribution of ammonia 20 oxidation by low abundance crenarchaeal population at 125m. Recruitment of DNA and 21 cDNA reads to reference microbial genomes indicated depth-specific partition of 22 coexisting microbial populations, as highlighted by the transcriptionally active HL-like 23 3 Prochlorococcus population in the bottom of the photic zone. Transcripts that mapped to 1 Pelagibacter genomes suggested that nutrient uptake genes dominated Pelagibacter 2 transcriptomes, with apparent enrichment for certain transporter types (e.g., the C4-3 dicarboxylate transport system) than others (e.g., phosphorus transporters). Collectively, 4 the data support the utility of coupled DNA and cDNA analyses for describing the 5 taxonomic and functional attributes of microbial communities in their natural habitats. 6