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Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom

Citation

McCain, J. Scott P.; Allen, Andrew E.; Bertrand, Erin M. (2021), Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom, Dryad, Dataset, https://doi.org/10.5061/dryad.vt4b8gtrz

Abstract

Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.

Methods

Samples were collected at the Antarctic sea ice edge in the Ross Sea, and metagenomic, metatranscriptomic, and metaproteomic analyses were conducted on each sample. Contained in this data submission are the metaproteomic bioinformatic pipeline output, database configurations, metaproteomic simulation output, cofragmentation bias analysis output, targeted proteomics data summaries, and culture proteomic data summaries.

Funding

Natural Sciences and Engineering Research Council of Canada, Award: RGPIN-2015-05009

Simons Foundation, Award: 504183

National Science Foundation

NSF-OCE, Award: 1756884

NSF-ANT, Award: 1043671

Gordon and Betty Moore Foundation, Award: GBMF3828

NSF-OCE, Award: 1756884

NSF-ANT, Award: 1043671