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ISME J. 2019 Nov;13(11):2817-2833. doi: 10.1038/s41396-019-0472-2. Epub 2019 Jul 18.

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Author information

1
Scripps Institution of Oceanography, University of California, San Diego, CA, 92093, USA.
2
Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, 92037, USA.
3
Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
4
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
5
Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt.
6
Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA.
7
Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, Kiel, DE, Germany.
8
Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA.
9
Scripps Institution of Oceanography, University of California, San Diego, CA, 92093, USA. aallen@jcvi.org.
10
Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, 92037, USA. aallen@jcvi.org.

Abstract

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.

PMID:
31320727
DOI:
10.1038/s41396-019-0472-2
Free PMC Article

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