Karl David M.

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David M.

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  • Article
    Microbial sources of exocellular DNA in the ocean
    (American Society for Microbiology, 2022-03-21) Linney, Morgan D. ; Eppley, John ; Romano, Anna ; Luo, Elaine ; DeLong, Edward F. ; Karl, David M.
    Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism.
  • Article
    Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA : a case study of summer 2012
    (John Wiley & Sons, 2015-08-13) Wilson, Samuel T. ; Barone, Benedetto ; Ascani, Francois ; Bidigare, Robert R. ; Church, Matthew J. ; del Valle, Daniela A. ; Dyhrman, Sonya T. ; Ferroon, Sara ; Fitzsimmons, Jessica N. ; Juranek, Laurie W. ; Kolber, Zbigniew S. ; Letelier, Ricardo M. ; Martinez-Garcia, Sandra ; Nicholson, David P. ; Richards, Kelvin J. ; Rii, Yoshimi M. ; Rouco, Monica ; Viviani, Donn A. ; White, Angelicque E. ; Zehr, Jonathan P. ; Karl, David M.
    Time-series observations are critical to understand the structure, function, and dynamics of marine ecosystems. The Hawaii Ocean Time-series program has maintained near-monthly sampling at Station ALOHA (22°45′N, 158°00′W) in the oligotrophic North Pacific Subtropical Gyre (NPSG) since 1988 and has identified ecosystem variability over seasonal to interannual timescales. To further extend the temporal resolution of these near-monthly time-series observations, an extensive field campaign was conducted during July–September 2012 at Station ALOHA with near-daily sampling of upper water-column biogeochemistry, phytoplankton abundance, and activity. The resulting data set provided biogeochemical measurements at high temporal resolution and documents two important events at Station ALOHA: (1) a prolonged period of low productivity when net community production in the mixed layer shifted to a net heterotrophic state and (2) detection of a distinct sea-surface salinity minimum feature which was prominent in the upper water column (0–50 m) for a period of approximately 30 days. The shipboard observations during July–September 2012 were supplemented with in situ measurements provided by Seagliders, profiling floats, and remote satellite observations that together revealed the extent of the low productivity and the sea-surface salinity minimum feature in the NPSG.