Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Dupont, Chris L.; McCrow, John P.; Valas, Ruben; Moustafa, Ahmed; Walworth, Nathan; Goodenough, Ursula; Roth, Robyn; Hogle, Shane L.; Bai, Jing; Johnson, Zackary I.; Mann, Elizabeth; Palenik, Brian; Barbeau, Katherine A.; Venter, J. Craig; Allen, Andrew E.

doi:10.1038/ismej.2014.198

Title: Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Journal Article · Tue Oct 21 00:00:00 EDT 2014 · The ISME Journal

DOI: https://doi.org/10.1038/ismej.2014.198 · OSTI ID:1346924

Dupont, Chris L. ^[1]; McCrow, John P. ^[2]; Valas, Ruben ^[2]; Moustafa, Ahmed ^[3]; Walworth, Nathan ^[4]; Goodenough, Ursula ^[5]; Roth, Robyn ^[5]; Hogle, Shane L. ^[6]; Bai, Jing ^[2]; Johnson, Zackary I. ^[7]; Mann, Elizabeth ^[8]; Palenik, Brian ^[6]; Barbeau, Katherine A. ^[6]; Venter, J. Craig ^[2]; Allen, Andrew E. ^[9]

J. Craig Venter Inst., La Jolla, CA (United States); Office of Scientific and Technical Information (OSTI)
J. Craig Venter Inst., La Jolla, CA (United States)
American Univ. in Cairo, New Cairo (Egypt)
J. Craig Venter Inst., La Jolla, CA (United States); Univ. of Southern California, Los Angeles, CA (United States)
Washington Univ., St. Louis, MO (United States)
Univ. of California, San Diego, La Jolla, CA (United States)
Nicholas School of the Environment, Beaufort, NC (United States); Duke Univ., Durham, NC (United States)
Skidaway Institute of Oceanography, Savannah, GA (United States)
J. Craig Venter Inst., La Jolla, CA (United States); Univ. of California, San Diego, La Jolla, CA (United States)

Here, transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO₂ uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.

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Research Organization:: J. Craig Venter Inst., La Jolla, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: FC02-02ER63453

OSTI ID:: 1346924

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 5 Vol. 9; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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