Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

Environmental Microbiology Reports
Despina TsementziKonstantinos T Konstantinidis

Abstract

Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead-beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year-round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcripti...Continue Reading

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Citations

Mar 21, 2016·Journal of Microbiological Methods·Antony T VincentSteve J Charette
Jul 1, 2018·Applied and Environmental Microbiology·Minjae KimKonstantinos T Konstantinidis
Mar 5, 2017·Applied and Environmental Microbiology·Yuanqi WangKonstantinos T Konstantinidis
Jun 22, 2014·Applied and Environmental Microbiology·Seungdae OhKonstantinos T Konstantinidis
Apr 15, 2018·Applied and Environmental Microbiology·Minjae KimKonstantinos T Konstantinidis
Jul 17, 2020·Frontiers in Microbiology·Yulia I Gubelit, Hans-Peter Grossart

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