A COMMUNITY-WIDE INTERCOMPARISON OF METATRANSCRIPTOMIC METHODS FOR CHARACTERIZING MICROBIAL EUKARYOTE CONTRIBUTIONS TO THE BIOLOGICAL CARBON PUMP

Microeukaryotes are central players in the biological carbon pump, driving primary production, carbon export, and trophic transfer within the marine food web. Metatranscriptomics, or the sequencing of the total expressed mRNA within a community, has become a broadly used approach in biological oceanography to observe marine assemblages, including their metabolism and ecological functioning. However, critical gaps exist in our understanding of how methodological choices and practices influence downstream biological interpretations, including estimates of community composition and metabolic function. We coordinated a metatranscriptomic intercomparison exercise across a group of 13 labs located in the United States to examine the impact of extraction methods, library preparation, sequencing depth, and bioinformatic approaches on the biological interpretation of marine metatranscriptomic data. Large-volume filters were collected in the deep chlorophyll maximum from the Costa Rica Upwelling Zone and distributed among the labs for extraction and sequencing, resulting in 29 sequenced samples, which varied in extraction methodology and sequencing coverage (from 2 to 113 gigabase pairs). The number of assembled transcripts varied, as did the content of proteins predicted from recovered transcripts. This type of community-led intercomparison effort is a first step in assessing how meta-omic data might be influenced by methodological choices both in the lab and in silico, but work remains to discern sources of variability and improve data interoperability.

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Primary Presenter: Harriet Alexander, Woods Hole Oceanographic Institution (halexander@whoi.edu)

Authors:

Harriet Alexander, Woods Hole Oceanographic Institution  (halexander@whoi.edu)

Natalie Cohen, Skidaway Institute of Oceanography, University of Georgia  (cohen@uga.edu)

Sarah Hu, Texas A&M University  (skhu@tamu.edu)

Adrian Marchetti, University of North Carolina Chapel Hill  (amarchet@email.unc.edu)

Metatranscriptome Consortium, OCB  (ocb_news@whoi.edu)