title: Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.
abstract: 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.
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: Chris L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: McCrow
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: Ruben
authors.initials: R
authors.lastname: Valas
authors.affiliation: Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Moustafa
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Walworth
authors.affiliation: Department of Biology, Washington University, St Louis, MO, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Goodenough
authors.affiliation: Department of Biology, Washington University, St Louis, MO, USA.
authors.forename: Robyn
authors.initials: R
authors.lastname: Roth
authors.affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Shane L
authors.initials: SL
authors.lastname: Hogle
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Bai
authors.affiliation: 1] Marine Laboratory, Nicholas School of the Environment, Beaufort, NC, USA [2] Biology Department, Duke University, Durham, NC, USA.
authors.forename: Zackary I
authors.initials: ZI
authors.lastname: Johnson
authors.affiliation: Skidaway Institute of Oceanography, Savannah, GA, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Mann
authors.affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Palenik
authors.affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Barbeau
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.affiliation: 1] Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA [2] Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
mesh_terms: D059001:Aquatic Organisms / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D002140:California; D002245:Carbon Dioxide / Q000737:chemistry; D002734:Chlorophyll / Q000032:analysis*; D000077194:Chlorophyll A; D015870:Gene Expression; D020869:Gene Expression Profiling; D014644:Genetic Variation; D016680:Genome, Bacterial; D058087:Haptophyta / Q000235:genetics; D008027:Light; D056186:Metagenomics; D009566:Nitrates / Q000737:chemistry; D010140:Pacific Ocean; D048929:Prochlorococcus / Q000235:genetics*; D012623:Seawater / Q000382:microbiology*; D046940:Synechococcus / Q000235:genetics; D059467:Transcriptome
chemical_list: D009566:Nitrates; D002734:Chlorophyll; D002245:Carbon Dioxide; D000077194:Chlorophyll A