Agricultural and Biosystems Engineering Publications
Campus Units
Agricultural and Biosystems Engineering
Document Type
Article
Publication Version
Accepted Manuscript
Publication Date
12-2016
Journal or Book Title
Journal of Microbiological Methods
Volume
131
First Page
122
Last Page
129
DOI
10.1016/j.mimet.2016.10.018.
Abstract
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes. We also evaluated various bioinformatics approaches for analyzing our soil metatranscriptome, including annotation of unassembled transcripts, de novo assembly, and aligning reads to known genomes. Further, we evaluated various databases for their ability to provide annotations for our metatranscriptome. Overall, our results emphasize that low activity, highly genetically diverse and relatively stable microbiomes, like soil, requires very deep sequencing to sample the transcriptome beyond the common core functions. We identified several key areas that metatranscriptomic analyses will benefit from including increased rRNA removal, assembly of short read transcripts, and more relevant reference bases while providing a priority set of expressed genes for functional assessment.
Access
Open
Rights
© 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/.
Copyright Owner
Elsevier, B.V.
Copyright Date
2016
Language
en
File Format
application/pdf
Recommended Citation
Garoutte, Aaron; Cardenas, Erick; Tiedje, James; and Howe, Adina, "Methodologies for probing the metatranscriptome of grassland soil" (2016). Agricultural and Biosystems Engineering Publications. 784.
https://lib.dr.iastate.edu/abe_eng_pubs/784
Included in
Agriculture Commons, Bioresource and Agricultural Engineering Commons, Environmental Microbiology and Microbial Ecology Commons
Comments
This is the accepted manuscript of an article published in Journal of Microbiological Methods, 131 (December 2016): 122-129, http://dx.doi.org/10.1016/j.mimet.2016.10.018.