Fall\/Winter 2022<\/p>\n\n\n\n
Scene: the future. Vincent Freeman (played by Ethan Hawke) desperately wants to go to space but has been relegated to menial labor by a society that profiles and pigeonholes individuals based on their genetics. In order to assume another man\u2019s genetic identity and realize his dream, Freeman uses a tiny vacuum device to remove all traces of his own DNA from his computer keyboard. Drama ensues.<\/p>\n\n\n\n
Sound familiar? This is the classic sci-fi movie \u201cGattaca,\u201d which envisions a future of DNA surveillance and profiling. For some scientists studying microscopic aquatic life, that future is here. These genetic traces are increasingly being used by CEOAS researchers to gain a wealth of information about unseen organisms, from bacteria to plankton. The resulting analyses help scientists figure out the composition, function and ecology of microbial and planktonic communities, leading to wider inferences about how aquatic ecosystems work.<\/p>\n\n\n\n
Ghost DNA and what it reveals<\/h3>\n\n\n\n
Like Vincent Freeman, organisms of all kinds leave traces of DNA behind wherever they\u2019ve been, originating from sloughed-off skin cells, fecal matter, mucus and other sources. Scientists can collect water samples and analyze these DNA ghosts to determine what species are or have been in an area of ocean. CEOAS oceanographer Maria Kavanaugh<\/a> is chasing this so-called eDNA, or environmental DNA, one new component of her work on defining seascapes.<\/p>\n\n\n Maria Kavanaugh<\/em><\/p>\n\n\n\n Kavanaugh\u2019s work on seascape ecology, inspired by the idea of landscape ecology, involves mapping regions in the ocean that have unique physical and biological characteristics and following how they change over time. Ultimately, an understanding of the gears that grind in a given habitat or seascape could improve our ability to predict and therefore manage marine resources.<\/p>\n\n\n\n With research partners at NOAA\u2019s Northwest Fisheries Science Center, Kavanaugh is undertaking studies in the northern California Current ecosystem off the Oregon coast to contribute to seascape maps in the region, part of a global effort led by the Marine Biodiversity Observation Network. While eDNA can reveal the presence of any kind of organism, from microbes to whales, Kavanaugh would like to use it to focus on the planktonic animals and plants at the base of the food web.<\/p>\n\n\n\n There are two benefits, Kavanaugh says, to collecting and analyzing eDNA over other methods. \u201cBigger organisms, like some fish or krill, can be really patchy, so when we put out our nets, we may or may not capture what\u2019s there, or what has been there. For the smaller stuff that I study, the genomic information [gathered from eDNA] can help us get to a higher taxonomic resolution than traditional oceanographic methods,\u201d she says. In other words, eDNA offers the promise of creating a more complete picture of \u201cwho\u201d is in a habitat by increasing both the likelihood of finding evidence of their presence and the ability to identify them to species level.<\/p>\n\n\n\n Kavanaugh and her team use DNA probes to determine what organisms contribute to the DNA soup in their water samples. Probes are short pieces of single-stranded DNA or RNA with a known sequence that search out their complementary piece in the sample and bind to it. Then the sample sequences are compared to massive databases of known organisms so individual species can be identified. Each taxonomic group requires its own set of analyses. If it sounds labor-intensive, Kavanaugh comments that it is not nearly as difficult as putting every water sample under a microscope to determine which species of plankton are present.<\/p>\n\n\n\n Coupled with other types of data collection, the species lists revealed by eDNA analysis will be able to help Kavanaugh map seascapes by showing where there are discontinuities in assemblages of species, meaning that sampling has crossed a \u201cborder\u201d between one habitat and another. Species lists in a given area can be correlated with physical and chemical characteristics of the habitat to start to understand how ocean conditions may be impacting the base of the food web.<\/p>\n\n\n\n Some CEOAS researchers are most interested in which species are present at the time that a water sample is collected, determined by extracting DNA from living organisms in that sample. When the research involves looking at the entire set of genomes present in a sample that contains many organisms, this technique is referred to as metagenomics.<\/p>\n\n\n\n![\"Maria](\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/5785\/files\/2022\/11\/Maria-Kavanaugh_800x500.jpg\")
<\/figure>\n<\/div>\n\n\nWho’s there?<\/h3>\n\n\n\n
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