Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities
Abstract
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 originmore »
- Authors:
-
- 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)
- Publication Date:
- Research Org.:
- J. Craig Venter Inst., La Jolla, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1346924
- Grant/Contract Number:
- FC02-02ER63453
- Resource 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
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
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., 2014.
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. https://doi.org/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. Tue .
"Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities". United States. https://doi.org/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 = {Tue Oct 21 00:00:00 EDT 2014},
month = {Tue Oct 21 00:00:00 EDT 2014}
}
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- Limnology and Oceanography: Methods, Vol. 17, Issue 3
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
journal, March 2017
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The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions
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Designer diatom episomes delivered by bacterial conjugation
journal, April 2015
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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
journal, March 2019
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Metatranscriptome analyses indicate resource partitioning between diatoms in the field
journal, April 2015
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- Proceedings of the National Academy of Sciences, Vol. 112, Issue 17
Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean
journal, October 2015
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- Proceedings of the National Academy of Sciences, Vol. 112, Issue 44
Pervasive iron limitation at subsurface chlorophyll maxima of the California Current
journal, December 2018
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- Proceedings of the National Academy of Sciences, Vol. 115, Issue 52
Control of bacterial population density with population feedback and molecular sequestration
posted_content, November 2017
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- BioRxiv
Shifting metabolic priorities among key protistan taxa within and below the euphotic zone: Depth-related protistan metatranscriptomes
journal, July 2018
- Hu, Sarah K.; Liu, Zhenfeng; Alexander, Harriet
- Environmental Microbiology, Vol. 20, Issue 8
Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system: Seasonality of small eukaryotes in surface waters
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Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network
journal, May 2018
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Genomes of Abundant and Widespread Viruses from the Deep Ocean
journal, July 2016
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Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters
journal, September 2017
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DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017
- Goodwin, Kelly D.; Thompson, Luke R.; Duarte, Bernardo
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Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics
journal, February 2018
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Analysis of the Genomic Basis of Functional Diversity in Dinoflagellates using a Transcriptome-Based Sequence Similarity Network
posted_content, October 2017
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- Molecular Ecology
Pervasive iron limitation at subsurface chlorophyll maxima of the California Current
text, January 2018
- Hogle, Shane; Dupont, Chris; Hopkinson, Brian
- EarthArXiv
Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
journal, March 2019
- Sieradzki, Ella T.; Ignacio-Espinoza, J. Cesar; Needham, David M.
- Nature Communications, Vol. 10, Issue 1
Pervasive iron limitation at subsurface chlorophyll maxima of the California Current
journal, December 2018
- Hogle, Shane L.; Dupont, Christopher L.; Hopkinson, Brian M.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 52
Genomes of Abundant and Widespread Viruses from the Deep Ocean
journal, July 2016
- Mizuno, Carolina Megumi; Ghai, Rohit; Saghaï, Aurélien
- mBio, Vol. 7, Issue 4
DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017
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- Frontiers in Marine Science, Vol. 4
Differential Responses of Eukaryotic Phytoplankton to Nitrogenous Nutrients in the North Pacific Subtropical Gyre
journal, March 2018
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Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea
journal, June 2016
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Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae
journal, July 2017
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Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli
journal, June 2018
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