{"id":17416,"date":"2016-12-07T12:05:38","date_gmt":"2016-12-07T17:05:38","guid":{"rendered":"https:\/\/college.unc.edu\/?p=17416"},"modified":"2024-07-02T16:30:07","modified_gmt":"2024-07-02T16:30:07","slug":"sequencing-the-sea","status":"publish","type":"post","link":"https:\/\/collegearchive.unc.edu\/?p=17416","title":{"rendered":"Sequencing the sea"},"content":{"rendered":"<figure id=\"attachment_17417\" aria-describedby=\"caption-attachment-17417\" style=\"width: 765px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-17417\" src=\"\/\/casdev.unc.edu\/collegearchive\/wp-content\/uploads\/sites\/44\/2016\/12\/IMG_0806_edited-smaller2-1024x683.jpg\" alt=\"UNC scientists are taking a new, cutting-edge approach to understanding exactly what\u2019s going on in the water with fish kills and pollution on the Neuse River. (photo by Mary Lide Parker)\" width=\"765\" height=\"510\" srcset=\"https:\/\/collegearchive.unc.edu\/wp-content\/uploads\/sites\/21\/2016\/12\/IMG_0806_edited-smaller2-1024x683.jpg 1024w, https:\/\/collegearchive.unc.edu\/wp-content\/uploads\/sites\/21\/2016\/12\/IMG_0806_edited-smaller2-300x200.jpg 300w, https:\/\/collegearchive.unc.edu\/wp-content\/uploads\/sites\/21\/2016\/12\/IMG_0806_edited-smaller2-768x512.jpg 768w, https:\/\/collegearchive.unc.edu\/wp-content\/uploads\/sites\/21\/2016\/12\/IMG_0806_edited-smaller2.jpg 1500w\" sizes=\"auto, (max-width: 765px) 100vw, 765px\" \/><figcaption id=\"caption-attachment-17417\" class=\"wp-caption-text\">UNC scientists are taking a new, cutting-edge approach to understanding exactly what\u2019s going on in the water with fish kills and pollution on the Neuse River. (photo by Mary Lide Parker)<\/figcaption><\/figure>\n<p>An offensive stench fills the salty air above the lower part of the Neuse River Estuary near downtown New Bern. It\u2019s the type of smell that hits you slowly \u2013 and then all at once, stinging the inside of your nose.<\/p>\n<p>While the smell invades your olfactory senses, the cackles of birds rings through your ears. Hundreds of seagulls zoom in circles just above the surface of the water.<\/p>\n<p>\u201cSure sign of a fish kill,\u201d says Jeremy Braddy, a researcher from the UNC Institute of Marine Sciences, staring at the mass of birds swarming like vultures.<\/p>\n<p>\u201cHow often does this happen?\u201d asks Weida Gong, another UNC researcher, who just moved here from China.<\/p>\n<p>We\u2019re zooming down the Neuse on a small fishing boat\u2014fortunately we\u2019re not here to fish\u2014the boat is packed full of water quality testing equipment. \u201cFirst you see the seagulls, and then the smell hits you. \u00a0Just wait for it.\u201d<\/p>\n<p>\u201cA couple times a year,\u201d Braddy says.<\/p>\n<p>Fish kills are one repercussion of a phenomenon called eutrophication. When too much nitrogen enters a water body, algae blooms form, producing a suffocating effect on the water and the fish in it. A textbook example is the Neuse River\u2014part of the Albemarle-Pamlico estuary system which serves as a nursery for 90 percent of commercial seafood caught in North Carolina, according to the NC Division of Tourism.<\/p>\n<p>Neuse River. Pollution. Fish kills. You\u2019ve heard this before. For the past several decades, environmentalists have voiced concerns about it, journalists have reported on it, and marine scientists have looked for answers to why and how this happens.<\/p>\n<p>But now some scientists are taking a new, cutting-edge approach to understanding exactly what\u2019s going on in the water.<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<figure id=\"attachment_17418\" aria-describedby=\"caption-attachment-17418\" style=\"width: 300px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-17418\" src=\"\/\/casdev.unc.edu\/collegearchive\/wp-content\/uploads\/sites\/44\/2016\/12\/IMG_0875_edited-smaller-300x200.jpg\" alt=\"The Neuse River is part of the Albemarle-Pamlico estuary system that serves as a nursery for 90 percent of commercial seafood caught in North Carolina. (photo by Mary Lide Parker)\" width=\"300\" height=\"200\" \/><figcaption id=\"caption-attachment-17418\" class=\"wp-caption-text\">The Neuse River is part of the Albemarle-Pamlico estuary system that serves as a nursery for 90 percent of commercial seafood caught in North Carolina. (photo by Mary Lide Parker)<\/figcaption><\/figure>\n<p><strong>Collecting new information from the same water <\/strong><\/p>\n<p>Weida Gong, a PhD student from the department of marine sciences, is also on board the boat today. Both Gong and Braddy will collect dozens of water samples from 11 different stations along the\u00a0estuary, but they will employ different methods to study them\u2014and ultimately produce two very different data sets. Braddy, a member of the Paerl lab at the UNC Institute of Marine Sciences, will measure parameters like temperature, salinity, nutrients, chlorophyll concentrations and pH \u2014 the same measurements get taken every two weeks throughout the spring, summer, and fall. \u201cEstuaries are so dynamic and they change from year to year,\u201d Braddy says. \u201cThis routine monitoring allows us to determine trends.\u201d<\/p>\n<p>Gong, on the other hand, will use his samples to determine what\u2019s happening inside the tiny\u00a0microscopic organisms known as plankton that inhabit this water\u2014on a molecular level.<\/p>\n<p>\u201cWe are combining traditional methods with molecular level approaches,\u201d Gong explains. \u201cTo do this, we\u2019re using lab work and computers together.\u201d<\/p>\n<p>Gong isn\u2019t talking about measurements that can be performed in most science labs or on your average laptop. To sequence genetic information from the environment, he will take his samples from the lab to the <a href=\"http:\/\/www.med.unc.edu\/genomics\">UNC High-Throughput Sequencing Facility (HTSF)<\/a> on the main campus of UNC-Chapel Hill to be sequenced using new, cutting-edge technologies. He will then require the use of one of the largest computer clusters in the US made for UNC researchers by UNC Research Computing to analyze these sequences.<\/p>\n<p>While the measurements collected by researchers in the Paerl lab illustrate the overall quality of the water, they don\u2019t provide as much information about specific types of plankton that are present in a given area \u2014 and those specific groups may have important ecological consequences, according to <a href=\"http:\/\/marchettilab.web.unc.edu\/\">Adrian Marchetti<\/a>, a UNC expert on the genomics of marine phytoplankton.<\/p>\n<p>\u201cBefore these new molecular approaches, it was just sort of this big black box,\u201d he says. \u201cSo the nutrients go in to the microbes but we have no idea what happens from there. Now, with molecular sequencing, we\u2019re shedding light on that box and we\u2019re seeing the insides of the different plankton cells and what they\u2019re doing in response to taking up nutrients.\u201d<\/p>\n<p>Say a scientist wants to find out if the phytoplankton in the water column are growth-limited by nitrogen. To test that, he or she would add nitrogen, and then wait for a growth response. \u201cFor example, if you think your plants don\u2019t have enough water, you add water and see if they grow,\u201d Marchetti says. \u201cIt\u2019s the same with nutrients or other parameters with phytoplankton. The nice thing about sequencing is if we learn what the microorganisms are telling us through the genes they express, we can get that information just from the sequences without having to alter their environment.\u201d<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<p><strong>From Taihu to the Neuse<\/strong><\/p>\n<p>Gong, originally from China, became interested in water quality during his undergraduate studies at Xiamen University \u2014 where he studied zebra fish in the estuaries of China\u2019s Fujian province. While there, he became fascinated by the harmful algae blooms within the estuaries, as well as Lake Taihu, the country\u2019s third-largest freshwater lake. \u201cThese blooms affect the drinking water for millions of people and really hurts the economy,\u201d Gong says.<\/p>\n<p>Lake Taihu is another location where Hans Paerl conducts research.\u00a0 His foundational research paired with the lake\u2019s environmental conditions make it an ideal place for Marchetti and his team to do a study. If they can obtain funding, learning about this lake could be very useful, Marchetti points out.<\/p>\n<p>For Gong, studying Lake Taihu on a molecular level would bring his research full-circle. \u201cI want to understand phytoplankton\u2019s behavior under a bloom condition so that we can pinpoint what triggers the bloom and figure out how to end it or even prevent it,\u201d he says.\u00a0 \u201cBecause, whether it\u2019s in China or in North Carolina, it affects the world.\u201d<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<figure id=\"attachment_17419\" aria-describedby=\"caption-attachment-17419\" style=\"width: 300px\" class=\"wp-caption alignleft\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-17419\" src=\"\/\/casdev.unc.edu\/collegearchive\/wp-content\/uploads\/sites\/44\/2016\/12\/IMG_1012_edited-smaller-300x200.jpg\" alt=\"Members of the Paerl lab at the UNC Institute of Marine Sciences, are measuring parameters like temperature, salinity, nutrients, chlorophyll concentrations and pH of the Neuse River water. (photo by Mary Lide Parker)\" width=\"300\" height=\"200\" \/><figcaption id=\"caption-attachment-17419\" class=\"wp-caption-text\">Members of the Paerl lab at the UNC Institute of Marine Sciences, are measuring parameters like temperature, salinity, nutrients, chlorophyll concentrations and pH of the Neuse River water. (photo by Mary Lide Parker)<\/figcaption><\/figure>\n<p><strong>Translating a new language\u00a0 <\/strong><\/p>\n<p>\u201cFrom phytoplankton cells to human cells, the universal language of all life is the genetic code,\u201d Marchetti says. \u201cIt\u2019s all made up of DNA and expressed as genes made up of RNA.\u201d<\/p>\n<p>Sequencing enables researchers like Gong and Marchetti to look at these organisms from a new perspective. \u201cThe patterns in taxonomy we obtain through genetic sequencing are very consistent with what people see when they look down a microscope,\u201d Marchetti says. While molecular sequencing provides a sort of universal alphabet, interpreting the sequences of a dinoflagellate (a particular group of plankton well known for their ability to form harmful algal blooms) is similar to interpreting a foreign language.<\/p>\n<p>\u201cIt\u2019s not clear cut,\u201d Marchetti says.\u201d You have to really understand the organisms to be able to interpret what the genes are telling you.\u201d<\/p>\n<p>Dinoflagellates are somewhat unique in that their genomes are large and can be much greater than that of the human genome. \u201cThey have massive genomes with what is believed to be a lot of junk DNA,\u201d Marchetti explains. \u201cSo in order to filter through that, we work at the level of RNA\u2014it\u2019s only when they decide to express a gene, they transcribe it into RNA, which means it\u2019s probably important.\u201d<\/p>\n<p>Humans are diploid, meaning we have two copies of our genome, which contains 23 chromosomes. But most dinoflagellates are thought to be polyploid\u2014they have many copies of their genome\u2014that\u2019s one reason they\u2019re so large.<\/p>\n<p>Scientists aren\u2019t sure exactly why that is, but they think it may be a \u201cquantity over quality\u201d evolutionary approach to survival. \u201cThey\u2019re probably creating a lot of genes that don\u2019t function, but they just keep copying and copying in hopes that every once in a while they\u2019ll produce a beneficial mutation. And then, all of a sudden, that could become the gene that they actually use for some sort of function in their genome.\u201d<\/p>\n<p>This is what these microorganisms have to do in order to constantly keep evolving. \u201cBecause they live in this very complex environment that is always changing, but also because of the interactions they have with all kinds of different organisms in this environment,\u201d Marchetti says. \u201cThey constantly try to modify newly produced genes and if they screw up, it doesn\u2019t matter\u2014they have back-up copies.\u201d<\/p>\n<p>&nbsp;<\/p>\n<p><strong>Monitoring on the molecular level<\/strong><\/p>\n<p>Approximately 4,000 miles from the Neuse River Estuary, off the coast of Oregon and Washington, 500 miles of cable runs along the ocean floor, powering a robust array of scientific instrumentation. \u00a0A massive project of the <a href=\"http:\/\/oceanobservatories.org\/\">Ocean Observatories Initiative<\/a>, the <a href=\"http:\/\/oceanobservatories.org\/array\/cabled-array\/\">Cabled Array<\/a> is the first U.S. ocean observatory to span a tectonic plate (the Juan de Fuca plate) and in many ways, it represents the future of oceanographic research.<\/p>\n<p>A group of researchers from the Monterey Bay Research Institute are developing environmental sample processors that can plug into the Cabled Array and work in real time. They are able to take in cells from the water column, extract DNA, and see whether certain\u00a0microorganisms, like harmful algae species, are present using molecular probes. \u201cThen that information is transmitted from the mooring to a satellite to a computer where the researcher can see it in real time\u2014straight from the water,\u201d Marchetti explains.<\/p>\n<p>Engineering instrumentation that can withstand prolonged periods of time in the open ocean is a challenge that researchers are still dealing with. And while Marchetti\u2019s lab is not working on that particular problem, he hopes that when that data is delivered in real-time, straight from the ocean, he and his team will be ready to translate it.<\/p>\n<p>As time goes on, sequencing genes of organisms in their environment will become more and more common, allowing researchers to have information in real time, meaning they will be able to see when particular harmful algae species are present and whether they are growing. \u201cWe can have all different kinds of sensors looking at the ocean,\u201d Marchetti says. \u201cThis will finally give scientists the ability to predict when blooms are going to happen before they do.\u201d<\/p>\n<p><em>Adrian Marchetti is an assistant professor in the Department of Marine Sciences in the College of Arts and Sciences. Weida Gong is a Ph.D. candidate in the Marchetti lab.<\/em><\/p>\n<p><strong><em>See also: Researchers use genes as early warning system for harmful algae blooms<\/em><\/strong><\/p>\n<p><a href=\"http:\/\/endeavors.unc.edu\/sequencing-the-sea\/\" target=\"_blank\" rel=\"noopener\"><em>By Mary Lide Parker, Endeavors magazine<\/em><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Marine scientists at UNC are taking a new approach to figuring out why and how microalgae blooms occur in the Neuse River Estuary.<\/p>\n","protected":false},"author":4,"featured_media":17417,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"categories":[17,21],"tags":[1878,24,1879,286,1880,1881,36,38,39,40],"class_list":["post-17416","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-natural-sciences-mathematics","category-news","tag-adrian-marchetti","tag-carolina","tag-fish-kills","tag-marine-sciences","tag-neuse-river","tag-pollution","tag-unc","tag-unc-college-of-arts-and-sciences","tag-unc-chapel-hill","tag-university-of-north-carolina-at-chapel-hill"],"_links":{"self":[{"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/posts\/17416","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=17416"}],"version-history":[{"count":1,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/posts\/17416\/revisions"}],"predecessor-version":[{"id":47946,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/posts\/17416\/revisions\/47946"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=\/wp\/v2\/media\/17417"}],"wp:attachment":[{"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17416"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17416"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/collegearchive.unc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17416"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}