Abstract
Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria. The average quantity of double-stranded DNA and size distribution of DNA fragments released within vesicles varies among different taxa. Although some vesicles contain sufficient DNA to be visible following staining with the SYBR fluorescent DNA dyes typically used to enumerate viruses, this represents only a small proportion (<0.01–1%) of vesicles. Thus DNA is packaged heterogeneously within vesicle populations, and it appears that vesicles are likely to be a minor component of SYBR-visible particles in natural sea water compared with viruses. Consistent with this hypothesis, chloroform treatment of coastal and offshore seawater samples reveals that vesicles increase epifluorescence-based particle (viral) counts by less than an order of magnitude and their impact is variable in space and time.
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Acknowledgements
We thank Katya Frois-Moniz, Phil Arevalo, Madeline Williams and Keven Dooley for laboratory assistance, and Stefan Bertilsson for isolating the Salinicola and Thalassospira strains. E. coli was a gift from Christopher Corzett, and phage PM2 and its host strain were kindly provided by Dennis Bamford. Tony Greco helped with electron microscopy, and Anni Djurhuus and Enrique Montes collected field samples from the West Florida Shelf and Florida Keys. SJB and SWC were supported by grants to SWC from the National Science Foundation (OCE-1356460) and the Simons Foundation (grant 337262, and SCOPE Award ID 329108 to SWC). This work was also supported by grants to MB from the National Science Foundation (IOS-1456301) and NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’ funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM and NASA). This is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE).
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Biller, S., McDaniel, L., Breitbart, M. et al. Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates. ISME J 11, 394–404 (2017). https://doi.org/10.1038/ismej.2016.134
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DOI: https://doi.org/10.1038/ismej.2016.134
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