DeepDOM – Study of DOM composition in South Atlantic Ocean (R/V Knorr 2013)

Erin participated in a 7-week research cruise from Montevideo, Uruguay to Barbados on board the R/V Knorr from March to April 2013. The DeepDOM cruise aimed to take a uniquely detailed and integrated look at the chemistry and biology of the western Atlantic Ocean in order to gain a better understanding of three critical ocean characteristics:Diversity and function of organic matter and biological communities across the ocean depths and over a wide latitude ; Interactions between surface- and deep-ocean processes; Movement of water and organic material from land to the ocean and among large oceanic water masses (taken from the project website. Erin sampled viruses along the transect and performed virus counts by SYBR Green I epifluorescence microscopy. Taken from the project website:

“In the ocean, viruses are so abundant that they outnumber bacteria by at least a factor of ten. They are obligate parasites, meaning they rely on a host to reproduce. The more hosts that are present, like bacteria and zooplankton, the more viruses can replicate. Some viruses hijack the cellular machinery of their host to replicate their genetic material, and then emerge from the host, resulting in the host’s death. These events lead to die-offs in host populations, increased viral abundance, and also a release of nutrients and dissolved organic matter. My goal on this research expedition is to characterize the viral populations and capture their dynamics in the deep ocean.

Who’s there?
Due to limitations in culturing hosts and their viruses, we use nucleic acids to identify viral populations in water samples. To do this, we pre-filter water to capture the bacterial size fraction, which we can use to look at particle-associated viruses, and viruses themselves, which we capture on a filter with very small pore size.

Once back on land, we will extract these nucleic acids and, using a molecular amplification technique, quantitatively track different viral types in the samples. In addition, we will characterize the overall diversity of viruses using a viral metagenomic approach. For this I will use viral concentrate to assess all viruses present in water from six major water depths (Antarctic Bottom Waters, North Atlantic Deep Water, Antarctic Intermediate Water, mesopelagic, deep chlorophyll maximum and surface waters).

How many viruses are produced?
 In addition to investigating what types of viruses are present, we want to get a sense of how viral abundance and community structure change over time. This involves diluting or concentrating viruses through tangential flow filtration and then adding either viral concentrate or virus-free water to ambient water. With these studies I can look at both natural viral production and induced viral production, which we trigger using the chemical Mitomycin C, as well as viral numbers and their effect on host organisms.

One unique aspect of this research expedition has been collaboration between many research groups. The Kujawinski research group has taken samples to analyze organic matter at timepoints for some of my incubations. Using these measurements I will be able to assess the impact viruses have on dissolved organic matter. In collaboration with Harriet Alexander I will assess viral abundance and community composition in a diatom bloom. Combining my data with data of other research groups on board, I will begin to piece together the story of viruses and the role they play in Atlantic Ocean waters.”

Publications from this expedition:

Eggleston EM, Hewson I (2016) “Abundance of two Pelagibacter ubique bacteriophage genotypes along a latitudinal transect in the North and South Atlantic Oceans”. Froniters in Microbiology. 10.3389/fmicb.2016.01534