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

Journal Article · · The ISME Journal
 [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)
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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.

Research Organization:
J. Craig Venter Inst., La Jolla, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
FC02-02ER63453
OSTI ID:
1346924
Journal Information:
The ISME Journal, Vol. 9, Issue 5; ISSN 1751-7362
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 75 works
Citation information provided by
Web of Science

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Lysogeny in nature: mechanisms, impact and ecology of temperate phages journal March 2017
The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions journal April 2017
Designer diatom episomes delivered by bacterial conjugation journal April 2015
Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes journal March 2019
Metatranscriptome analyses indicate resource partitioning between diatoms in the field journal April 2015
Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean journal October 2015
Pervasive iron limitation at subsurface chlorophyll maxima of the California Current journal December 2018
Control of bacterial population density with population feedback and molecular sequestration posted_content November 2017
Shifting metabolic priorities among key protistan taxa within and below the euphotic zone: Depth-related protistan metatranscriptomes journal July 2018
Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system: Seasonality of small eukaryotes in surface waters journal August 2018
Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network journal May 2018
Genomes of Abundant and Widespread Viruses from the Deep Ocean journal July 2016
Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters journal September 2017
DNA Sequencing as a Tool to Monitor Marine Ecological Status journal May 2017
Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics journal February 2018
Analysis of the Genomic Basis of Functional Diversity in Dinoflagellates using a Transcriptome-Based Sequence Similarity Network posted_content October 2017
Pervasive iron limitation at subsurface chlorophyll maxima of the California Current text January 2018
Differential Responses of Eukaryotic Phytoplankton to Nitrogenous Nutrients in the North Pacific Subtropical Gyre journal March 2018
Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea journal June 2016
Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae journal July 2017
Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli journal June 2018

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