Transcriptomics in the tropics: Total RNA-based profiling of Costa Rican bromeliad-associated communities

Computational and Structural Biotechnology Journal
Shana K GoffrediMohamed F Haroon

Abstract

RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments ('tanks') formed by tropical bromeliads from Costa Rica. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to the specific presence of eukaryotes. Bacteria from 25 phyla appeared to comprise the majority of transcripts in one tank (Wg24), compared to only 14 phyla in the other (Wg25). Conversely, eukaryotes from only 16 classes comprised the majority of transcripts in Wg24, compared to 24 classes in the Wg25, revealing a greater eukaryote diversity in the latter. Given that these bromeliads had tanks of similar size (i.e. vertical oxygen gradient), and were neighboring with presumed similar light regime and acquisition of leaf litter through-fall, it is possible that pH was the factor governing these differences in bacterial and eukaryotic communities (Wg24 had a tank pH of 3.6 and Wg25 had a tank pH of 6.2). Archaeal diversity was similar in both tanks, represented by 7 orders, with the exception of Methanocellales transcripts uniquely recovered from Wg25. Based on measures of FPKG (fragments mapped per kilobase of gene ...Continue Reading

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Citations

Feb 24, 2016·The Science of the Total Environment·Molli M NewmanJoseph W Kloepper
Jun 7, 2016·Environmental Microbiology Reports·Anne-Catherine LehoursJean-François Carrias
May 11, 2017·Environmental Microbiology·Stilianos LoucaVinicius F Farjalla
Jun 21, 2020·The Journal of Eukaryotic Microbiology·Taiz L L SimãoEduardo Eizirik
Oct 18, 2016·Molecular Ecology·Lars GrossmannJens Boenigk
Jan 28, 2021·European Journal of Protistology·Sabine AgathaAlan Warren

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Datasets Mentioned

BETA
SRR1697355
SRR1697356

Methods Mentioned

BETA
nucleic acid extraction
RNA-Seq

Software Mentioned

RiboZero depletion
CLC Genomics Workbench
Prodigal
SortMeRNA
Integrated Microbial Genomes ( IMG ) system
BWA
FASTQC

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