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

Goffredi, Shana K., Jang, Gene E. and Haroon, Mohamed F. (2015) Transcriptomics in the tropics: total RNA-based profiling of Costa Rican bromeliad-associated communities. Computational and Structural Biotechnology Journal, 13 18-23. doi:10.1016/j.csbj.2014.12.001

Author Goffredi, Shana K.
Jang, Gene E.
Haroon, Mohamed F.
Title Transcriptomics in the tropics: total RNA-based profiling of Costa Rican bromeliad-associated communities
Journal name Computational and Structural Biotechnology Journal   Check publisher's open access policy
ISSN 2001-0370
Publication date 2015
Sub-type Article (original research)
DOI 10.1016/j.csbj.2014.12.001
Open Access Status DOI
Volume 13
Start page 18
End page 23
Total pages 6
Place of publication Gothenborg, Sweden
Publisher Research Network of Computational and Structural Biotechnology [Elsevier]
Language eng
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 length), genes involved in methanogenesis, in addition to a spirochaete flagellin gene, were among those most highly expressed in Wg25. Conversely, aldehyde dehydrogenase and monosaccharide-binding protein were among genes most highly expressed in Wg24. The ability to observe specific presence of insect, plant, and fungi-associated RNA-viruses was unexpected. As with other techniques, there are inherent biases in the use of RNA-Seq, however, these data suggest the possibility of understanding the entire community, including ecological interactions, via simultaneous analysis of microbial, eukaryotic, and viral transcripts.
Keyword Bromeliad
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Australian Centre for Ecogenomics
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Created: Wed, 27 Jul 2016, 22:23:26 EST by Mary-Anne Marrington on behalf of Institute for Molecular Bioscience