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

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 CO 2 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 nuclearmore » 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.« less
Authors:
 [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [4] ;  [5] ;  [1] ;  [6] ;  [7] ;  [5] ;  [5] ;  [1] ;  [8]
  1. J. Craig Venter Inst., La Jolla, CA (United States)
  2. American Univ. in Cairo, New Cairo (Egypt)
  3. J. Craig Venter Inst., La Jolla, CA (United States); Univ. of Southern California, Los Angeles, CA (United States)
  4. Washington Univ., St. Louis, MO (United States)
  5. Univ. of California, San Diego, La Jolla, CA (United States)
  6. Nicholas School of the Environment, Beaufort, NC (United States); Duke Univ., Durham, NC (United States)
  7. Skidaway Institute of Oceanography, Savannah, GA (United States)
  8. J. Craig Venter Inst., La Jolla, CA (United States); Univ. of California, San Diego, La Jolla, CA (United States)
Publication Date:
Grant/Contract Number:
FC02-02ER63453
Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 9; Journal Issue: 5; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Research Org:
J. Craig Venter Inst., La Jolla, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
OSTI Identifier:
1346924

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, and Allen, Andrew E.. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. United States: N. p., Web. doi:10.1038/ismej.2014.198.
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.. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. United States. doi:10.1038/ismej.2014.198.
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, and Allen, Andrew E.. 2014. "Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities". United States. doi:10.1038/ismej.2014.198. https://www.osti.gov/servlets/purl/1346924.
@article{osti_1346924,
title = {Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities},
author = {Dupont, Chris L. and McCrow, John P. and Valas, Ruben and Moustafa, Ahmed and Walworth, Nathan and Goodenough, Ursula and Roth, Robyn and Hogle, Shane L. and Bai, Jing and Johnson, Zackary I. and Mann, Elizabeth and Palenik, Brian and Barbeau, Katherine A. and Venter, J. Craig and Allen, Andrew E.},
abstractNote = {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.},
doi = {10.1038/ismej.2014.198},
journal = {The ISME Journal},
number = 5,
volume = 9,
place = {United States},
year = {2014},
month = {10}
}