• Dr. Smith and co-authors from San Diego State University, the Getty Research Institute, and the Scripps Institution of Oceanography recently published a paper in PeerJ entitled: ‘Can we measure beauty? […]

  • A new paper, written by Susan Kram and co-authors, was recently accepted for publication in the ICES Journal of Marine Science themed article set on Ocean Acidification. The paper, “Variable responses of temperate […]

  • Jill’s new paper, written with Jen and Levi, came out recently in the Marine Ecology Progress Series. Their paper, Quantifying scales of spatial variability in algal turf assemblages on coral reefs, describes how […]

  • skram wrote a new post, Adventures in Chagos, on the site Coral Reef Ecology 2 years ago

    ThumbnailBy Samantha Clements.

    This year, during the months of March and April, I conducted coral reef benthic surveys for the Khaled bin Sultan Living Oceans Foundation (KSLOF) in Chagos. Chagos is the largest […]

  • By Jill Harris

    Jill’s new paper, written with Jen and Levi, was recently accepted for publication in the Marine Ecology Progress Series. Their paper, Quantifying scales of spatial variability in algal turf […]

  • ThumbnailBy Niko Kaplanis

    In April of 2006, during a survey for the Channel Islands Research Program (CIRP), renowned scientists Kathy Ann Miller and John Engle discovered an established population of the invasive alga […]

  • ThumbnailBy Samantha Clements

    Algae, often referred to as “seaweed,” are underwater “plants” that, unlike land plants, lack a vascular system. Algae live underwater and obtain water, nutrients, and sunlight directly […]

  • ThumbnailBy Mike Fox
     

    Last week I traveled south to Puerto Morelos, Mexico to participate in an intensive 3-week course about Light and Photosynthesis on Coral Reefs. Hosted by Dr. Roberto Iglesias-Prieto and the […]

  • ThumbnailBy Niko Kaplanis

    In a recent collaboration with the Paul Jensen Lab here at Scripps, I travelled to the Northern Channel Islands to assist with collections for their research. The Jensen lab focuses on […]

  • Jeffery B. Graham Perspectives on Ocean Science Lecture Series presents Dr. Jenner Smith

    Check out Dr. Smith’s presentation here!  http://www.ucsd.tv/search-details.aspx?showID=28675

    Understanding how humans impact marine ecosystems is crucial to developing successful conservation strategies that protect the health of our ocean.  Discover how Scripps marine ecologist Jennifer Smith and her team are conducting research relevant to solving human-induced problems in environments ranging from coral reefs to the waters off our shores.

  • By Adi Khen

    As a first-time volunteer at the Smith lab, I got to be involved in one of the most exciting parts of data processing: drying, weighing, acidifying and, basically, slaughtering CAUs!

    Let me explain… CAU stands for Calcification Accretion Unit, or in this case a set of two stacked PVC tiles that are used to measure carbonate accretion and successional development on coral reefs. Three years ago, PhD student Levi Lewis, installed 160 CAUs across 8 different reef sites on leeward Maui. Half of the CAUs at each site were “caged,” or enclosed in a stainless steel frame to prevent herbivory, while the rest were “uncaged.” Environmental characteristics at each site, such as temperature, light, pH, salinity, and sedimentation were also measured. By installing and later removing CAUs, researchers are able to sample reef communities without causing extensive damage to the reef.

    This past summer, Levi removed all of his CAUs from the reef and brought them back to the lab. The macroalgae that had grown on the tiles, as well as the sediments that had collected on the tiles and the cryptic invertebrates that found shelter among them, were put into separate bags and frozen for future processing. All tiles were photographed for image analysis and then, our slaughterhouse was open for business.

    [caption id="attachment_3451" align="alignnone" width="300"]Innocent CAUs laying out, completely unaware of what’s about to hit them Innocent CAUs laying out, completely unaware of what’s about to hit them[/caption]

    [caption id="attachment_3452" align="alignnone" width="300"]After pouring 5% HCl on the CAUs, their carbonate instantly started dissolving After pouring 5% HCl on the CAUs, their carbonate instantly started dissolving[/caption]

    [caption id="attachment_3453" align="alignnone" width="300"]About a day later, bare CAUs sitting on top of a container of their own fleshy (macroalgae and acid) About a day later, bare CAUs sitting on top of a container of their own flesh (…y macroalgae and acid)[/caption]

    We dried the tiles in a drying oven, weighed them, let them soak in acid until all of their calcified matter dissolved, scraped them, and then dried and weighed them again (the difference between the initial and final tile masses would then represent the amount of carbonate accretion). We also filtered out the remaining fleshy matter from each tile, dried it, and weighed it to find the amount of fleshy biomass on each tile. After several months of the lab reeking of acid, we were left with about 300 clean PVC tiles, and we moved onto our next subjects: the macroalgae and invertebrates.

    Macroalgae samples were also collected from the tiles in Maui, and froze for later analysis. Well, we thawed them, sorted each CAU’s algae by type or species, dried them, and then weighed them individually. We could then compare not only the difference in macroalgal cover between sites, but also the density and diversity of the macroalgal communities.

    [caption id="attachment_3458" align="alignnone" width="300"]Microscope view of filaments of Dasya algae that had grown on one of the CAUs Microscope view of filaments of Dasya algae that had grown on one of the CAUs[/caption]

    [caption id="attachment_3459" align="alignnone" width="300"]Microscope view of the growing tip of another thin branching alga Microscope view of the growing tip of another thin branching alga[/caption]

    [caption id="attachment_3460" align="alignnone" width="300"]Microscope view of a cystocarp on Halichrysis, a leafy red alga Microscope view of a cystocarp on Halichrysis, a leafy red alga[/caption]

    As for the frozen invertebrates, we thawed them, too, sieved them into different size categories, and then identified and quantified the critters from each CAU. This would help us determine the diversity, abundance, and potential importance of cryptic invertebrates in benthic communities.

    [caption id="attachment_3455" align="alignnone" width="300"]IMG_4645 Microscope view of a stomatopod found on one of the CAUs.[/caption]

    [caption id="attachment_3456" align="alignnone" width="300"]Inverted microscope view of the same invertebrate (which I like to call, “inverted invert”) Inverted microscope view of the same invertebrate (which I like to call, “inverted invert”)[/caption]

    [caption id="attachment_3457" align="alignnone" width="225"]My sketch of the “inverted invert,” now hanging by the lab’s microscope My sketch of the “inverted invert,” now hanging by the lab’s microscope[/caption]

    These days, though our slaughterhouse is no longer in session, we’re getting ready to photoanalyze the surfaces of each of the CAUs to get a better picture of benthic community development on Maui’s reefs.

  • Clint Edwards, et al.  publication, Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects, has been selected as one of the most influential conservation papers of 2014!!  Congratulations Clint & Smith Lab!!!

    http://conservationbytes.com/2014/12/22/influential-conservation-papers-of-2014/

    [caption id="attachment_2944" align="alignnone" width="300"]Congratulations to Clint for completing his Master's! Congratulations to Clint and Jennifer![/caption]

     

  • By Abby Cannon:

    This September I left my usual seagrass habitat and helped the Khaled bin Sultan Living Oceans Foundation survey corals on the Great Barrier Reef. Somewhere in the midst of identifying all of the corals within a ten meter by one meter belt at various sites I reached the conclusion that everybody interested in corals needs to visit the Great Barrier Reef at least once.

    [caption id="attachment_3427" align="alignnone" width="274"]Green sea turtle swimming past a large thicket of Isopora coral. Green sea turtle swimming past a large thicket of Isopora coral.[/caption]

    [caption id="attachment_3425" align="alignnone" width="289"]Corals from several families growing together. Corals from several families growing together.[/caption]

    One reason the Great Barrier Reef should be on every coral aficionado’s must-see list is the amazing diversity of corals. According to J.E.N. Veron and Mary Stafford-Smith the Great Barrier Reef is home to between 300 and 500 coral species.  This gives coral admirers a much better chance of seeing something new on every dive than they would get in less-diverse locations like Hawaii and the Caribbean. Even divers who do not know much about different coral species will be impressed by the amazing range of coral colors and growth forms. I can say that I probably recognize three times as many coral genera as I did before this trip.

    [caption id="attachment_3434" align="alignnone" width="300"]A damselfish’s garden of green filamentous algae on top of a colony of Pachyseris spp. A damselfish’s garden of green filamentous algae on top of a colony of Pachyseris spp.[/caption]

    [caption id="attachment_3433" align="alignnone" width="225"]Close up view of a Leptoria spp. colony Close up view of a Leptoria spp. colony[/caption]

    Another reason to visit the Great Barrier Reef is to get a better idea of what a healthy reef looks like. Many reefs around the world have been so degraded for so long that the people who claim to know them underestimate the damage, because they have forgotten what a healthy reef looks like. The Great Barrier Reef serves as a reminder of how those reefs looked in the past and set higher goals for how they should look in the future with better management.

    Unfortunately, not even the Great Barrier Reef is immune from degradation and some of the sites we visited reflected this. Excessive sediment and nutrient pollution can favor the growth of algae over corals and interfere with the reef’s ability to recover from events like cyclones as algae rather than coral grows back. Outbreaks of crown of thorns starfish, voracious coral predators, also seem to worsen when nutrient pollution becomes excessive. If Australia wants the Great Barrier Reef to continue being the world example of a healthy reef, these problems will need to be overcome.

    [caption id="attachment_3424" align="alignnone" width="319"]Snapper hiding behind Acropora spp. Snapper hiding behind Acropora spp.[/caption]

    [caption id="attachment_3435" align="alignnone" width="300"]This reef was hit by a storm recently, but the lack of turf algae and the presence of small corals suggests it will recover. This reef was hit by a storm recently, but the lack of turf algae and the presence of small corals suggests it will recover.[/caption]

    [caption id="attachment_3429" align="aligncenter" width="300"]Crown of thorns starfish don’t usually eat soft coral, but this one is on a degraded reef, where hard coral is not available. Turf algae and sediment can be seen on dead corals. Crown of thorns starfish don’t usually eat soft coral, but this one is on a degraded reef, where hard coral is not available. Turf algae and sediment can be seen on dead corals.[/caption]

  • ThumbnailMy first summer in the field
     

    When I tell people that I spent six weeks on Maui this summer, nobody seems to believe that it wasn’t a vacation. I tell them that I was working from dawn to dark every day and […]

  • ThumbnailClinton Edwards and Clifford Kapono from the Scripps Instituition of Oceanography and UCSD, are proposing a 1 year project to visually map (think Google-Earth) the health of the coral reefs under the world’s most […]

  • ThumbnailThe 2013 Southern Line Islands Research Expedition is starting to publish results!  Check out this new paper by Smith Lab San Diego State collaborators:

    Sequencing at sea: challenges and experiences in Ion […]

  • ThumbnailThe Smith and Sandin Labs in the Center for Marine Biodiversity and Conservation have been using new diver-operated technology to capture hundreds of reef images that will become a 200m² photomosaic.

    Coral […]

  • Gordon Research Conference: Global Ocean Change Biology

    I recently had the opportunity to participate in a Gordon Research Conference. If you haven’t heard of the Gordon conferences, you should take a minute and check them out (http://www.grc.org/about.aspx). They are based on a different format than the larger scientific conferences I have been too, like Ocean Sciences or the International Coral Reef Symposium (ICRS). The conference is intended to present more open discussion of research topics, and presenters are encouraged to discuss unpublished results, with each conferee agreeing not to discuss the details of topics discussed. Further, the conference was organized around one session, with all conferees (200 in this case) in one large room. The speakers presented for roughly 30-45 minutes, followed by 20-30 minutes of open discussion with everyone.

    The conference was held at Waterville Valley Resort in New Hampshire. Being a New Englander I was excited to visit the Granite state in the height of summer. The conference was intense in the sense that we began with breakfast at 7:30 am, and finished with the final talks of the day at 9:30-10:00 pm. We started on a Sunday night, and continued until Friday morning when everyone departed after breakfast. Everyone, PI’s, government representatives, and grad students alike, ate all three meals together. We had a couple of hours in the afternoon ‘off’, where we were encouraged to continue our networking during these breaks into the great outdoors. A large group of us went hiking one afternoon, some of us tried our hand at mountain biking down the slopes of the peak at Waterville Valley ski resort. After catching our breath in the outdoors, we reconvened with poster sessions. I presented a poster on the first chapter of my dissertation entitled, “Not all algae are created equal: Differential effects of ocean acidification on coral reef algae.” I got a lot of interesting feedback on my research, and had the chance to, to talk about my research ideas with some of the top minds in the field.

    With a relatively small group of 200 people, the conference provided a less intimidating environment to meet some of my science heroes in the field of ocean global change biology. The highlight of my conference was meeting Joan Kleypas, of NOAA. Reading her earlier papers on ocean acidification effects on coral reefs was what sparked my interest in the topic and started me down the road to my PhD research. It was also incredible to meet other scientists that share similar research interests to my own and form potential collaborations for future projects.

    I came away from the GRC in Waterville Valley with renewed curiosity and enthusiasm for my dissertation research which is focused on understand how global change impacts coral reefs, through studying effects of ocean acidification on coral reef seaweeds. Although it was exhausting, it was well worth the trip to the east coast in the height of the beautiful summer!

    Maggie Johnson

    [caption id="attachment_3309" align="alignleft" width="300"]Waterville Valley, New Hampshire Waterville Valley, New Hampshire[/caption]

    [caption id="attachment_3300" align="alignright" width="300"]The view from the top during our group hike in Waterville Valley, NH. The view from the top during our group hike in Waterville Valley, NH.[/caption]

  • Career Girls, Marine Biologist Dr. Smith.

    Career Girls is an organization dedicated to providing young girls of all income levels and ethnic backgrounds with the academic tools and support they need to achieve their professional aspirations. They do this by providing a “real world” context for a child’s academic studies, specifically through interviews with positive female role models and a comprehensive collection of easy-to-follow educational resources.

    By hearing from successful women they can identify with, and learning about the educational paths these professionals took to reach their goals, female students can take direct steps toward nurturing their own intellects, skills and talents in order to create fulfilling and productive lives of their choosing.

    Today, Career Girls® is a registered trademark with over 200 role models and over 4,000 video clips. Career Girls has shared videos and collaborated with a wide variety of organizations from Girl Scouts to Young Women in Bio to the Charles H. Wright Museum of Aftrican American History in Detroit. Career Girls videos are now seen around the world on multiple platforms.

    Dr. Smith was recently featured in one of these videos, check it out!! Career Girls, Marine Biologist Dr. Smith.

    [caption id="attachment_3287" align="aligncenter" width="300"]CareerGirls_DrSmith Check out the other inspiring professional women on CareerGirls.org![/caption]

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