Abstract
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs.
Highlights
Metatranscriptomic differential RNA-Seq identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends
We elucidated the composition of the microbial community by 16S rDNA quantification
This analysis demonstrated that reads assigned to Proteobacteria belonged to 12 different families, with relative abundances increasing from 0.72% for uncultured Myxococcales to 6.25% for Rhodospirillaceae (Fig. 2b)
Summary
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. We analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We have applied metatranscriptomic dRNA-Seq (mdRNA-Seq) to the analysis of a sample obtained from a depth of 45 m from Station A at the northern tip of the Gulf (29°28′N 34°55′E, bottom depth ~700 m) during winter deep mixing conditions[32,33]. We chose these conditions to address a highly diverse marine www.nature.com/scientificreports/.
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