Microbial sources of exocellular DNA in the ocean

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Date
2022-03-21
Authors
Linney, Morgan D.
Eppley, John
Romano, Anna
Luo, Elaine
DeLong, Edward F.
Karl, David M.
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DOI
10.1128/aem.02093-21
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Keywords
Bbacteriophage
Bacterioplankton
EDNA
Exocellular DNA
Free DNA
Metagenomics
Microbial ecology
Microbial oceanography
Open ocean
Vesicle
Abstract
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.
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© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Linney, M. D., Eppley, J. M., Romano, A. E., Luo, E., DeLong, E. F., & Karl, D. M. Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology, 88(7), (2022): e02093-21, https://doi.org/10.1128/aem.02093-21.
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Linney, M. D., Eppley, J. M., Romano, A. E., Luo, E., DeLong, E. F., & Karl, D. M. (2022). Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology, 88(7), e02093-21.
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