Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

Abstract

Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such ‘metatranscriptomic’ studies1,2 have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins. Here we report that a large fraction of cDNA sequences detected in microbial metatranscriptomic data sets are comprised of well-known small RNAs (sRNAs)3, as well as new groups of previously unrecognized putative sRNAs (psRNAs). These psRNAs mapped specifically to intergenic regions of microbial genomes recovered from similar habitats, displayed characteristic conserved secondary structures and were frequently flanked by genes that indicated potential regulatory functions. Depth-dependent variation of psRNAs generally reflected known depth distributions of broad taxonomic groups4, but fine-scale differences in the psRNAs within closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAs derived from predominant planktonic species such as Pelagibacter revealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomic data sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAs in naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition.

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Figure 1: Inventory of RNAs from each depth in the microbial metatranscriptomic datasets.
Figure 2: Abundance, distribution and features of the top twenty most abundant sRNA and psRNA groups identified in the metatranscriptomic data.
Figure 3: Characteristics of psRNA groups consistent with known sRNAs.
Figure 4: Normalized cDNA/DNA ratios of expressed IGRs (eIGRs) on the P. ubique HTCC7211 genome at all four depths.

Accession codes

Data deposits

The sequences reported here have been deposited in GenBank under accession numbers SRA007802.3, SRA000263, SRA007804.3 and SRA007806.3 corresponding to cDNA sequences, and SRA007801.5, SRA000262, SRA007803.3 and SRA007805.4 corresponding to DNA sequences, for 25 m, 75 m, 125 m and 500 m samples, respectively.

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Acknowledgements

We are grateful to the University of Hawaii HOT team, and the captain and crew of the RV Kilo Moana for their expert assistance at sea. We also thank S. Schuster for collaboration and advice on pyrosequencing, J. Eppley for help with computational analyses and discussion, and J. Maresca, A. Martinez, J. McCarren and V. Rich for their comments on this manuscript. We thank S. Giovannoni, J. Tripp and M. Schwalbach for sharing their in press manuscript on Pelagibacter riboswitches, and S. Giovannoni, U. Stingl, the J. Craig Venter Institute and the Gordon and Betty Moore Foundation for the genome sequence of Pelagibacter strain HTCC7211. This work was supported by the Gordon and Betty Moore Foundation, National Science Foundation Microbial Observatory Award MCB-0348001, the Department of Energy Genomics GTL Program, the Department of Energy Microbial Genomics Program, and an NSF Science and Technology award, C-MORE. This article is a contribution from the NSF Science and Technology Center for Microbial Oceanography: Research and Education (C-MORE).

Author Contributions E.F.D. conceived and directed the research, coordinated the sequencing effort and collected the samples. Y.S. prepared samples for sequencing, and made the initial observation of sRNA sequences. E.F.D., Y.S. and G.W.T. developed the concept of the paper together. Y.S. and G.W.T. performed the data analysis. Y.S. wrote the first draft of the paper, which was completed by G.W.T. and E.F.D. together.

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Correspondence to Edward F. DeLong.

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Shi, Y., Tyson, G. & DeLong, E. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459, 266–269 (2009). https://doi.org/10.1038/nature08055

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