Date of Award


Degree Type


Degree Name

Master of Science in Oceanography



First Advisor

Ted Durbin


The northern krill, Meganyctiphanes norvegica, is an important member of North Atlantic shelf ecosystems, serving both as prey for whales, fish and seabirds, and as a predator on phytoplankton and other zooplankton. However, understanding in-situ krill feeding is technically challenging; incubations may not be representative of krill feeding in-situ, while biomarkers and microscopic examination of gut contents suffer from limited prey type resolution and have a limited range of detectible prey. Analyzing DNA in gut contents may offer insight into M norvegica feeding in-situ unobtainable using other methodologies. The major technical difficulty in using DNA as a marker of gut contents is the overwhelming quantity of predator DNA; two approaches are taken here to exclude predator DNA from analysis, firstly the use of species specific primers, and secondly the use of a krill-specific peptide nucleic acid probe. Species specific primers were used to sequence and quantify known phytoplankton prey (Thalassiosira weissflogii and Rhodomonas sp.) from the guts of captive krill, showing that even low abundance prey items can be successfully detected using DNA in gut contents. A krill-specific peptide nucleic acid (PNA) probe was used to sequence all non-krill I 8S DNA present in the guts of krill collected in-situ in the Gulf of Maine. PNA is a synthetic, uncharged, DNA analog which binds strongly and specifically to complimentary DNA, and thus inhibits PCR amplification of the target sequence. Including a krill-specific PNA probe in a PCR using universal I 8S primers allowed for amplification of all eukaryotes present in the krill fore-gut. Gut contents amplicons were sequenced from a clone library and compared with known sequences to determine their identity. The most common prey item, found in M norvegica guts at every station, was an uncultured and poorly known protist, which previous studies suggest represents a novel kingdom of eukaryotes, and may suggest krill feeding on the sediment interface. M norvegica in the Gulf of Maine also consumed the copepod Calanus finmarchicus at 7 of the 8 stations samples, in agreement with results found using other methods. Additionally, Centropages sp., 4 other protists, another copepod, 5 phytoplankton and the salp Thalia democratica were found as gut contents. In addition to providing interesting information about M norvegica feeding in-situ in the Gulf of Maine, these results demonstrate the utility of the PNA-PCR clone library approach to gut contents analysis, elucidating prey, such as protists and T. democratica, which would have been difficult or impossible to detect with other methodologies.