The beating heart of a multicorer

The current cruise marks my 29th oceanographic expedition on a research ship. Each successful expedition and operation relies heavily on the knowledge, experience and instincts of the vessel crew. When I participate in a cruise, I make it my business to learn  about about the operation of the gear we use, so that I can improve my planning efforts, and maximize my time at sea. Over the past five cruises, I have been accumulating data on what make for a perfect deployment of a deep-sea multicorer. Much of that data has been furnished by the ship’s engineer, and winch operator. Perfection of a sampling event for me means  sufficient replicate cores to conduct the entirety of our biogeochemical and microbiological examination of the sedimentary habitat. Perfection for them means  recovering the gear, maintaining safety, and providing material for scientists to work with. I  produce graphs to illustrate my results. So too does the ship’s crew. Below is a photo that speaks volumes about a “perfect” operation. And it looks very similar to the image of an echo cardiogram of a beating  heart, ready for scientific discovery.

-LJH

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Image of the winch operation station on board R/V Point Sur. The left part of the graph is the MC800 deep sea multicorer descending to 1500m depth. The drop in tension is the corer hitting bottom. Then followed by the important max tension peak, indicating the corer being pulled out of the sediment filled with mud. The right of the plot is the device being returned to surface, heavier because of the scientific samples it now carries. The whole image looks strikingly similar to an echo cardiogram.

Our Deep-Sea Treasure

As we transit between sites, I find myself reflecting on my first year of graduate school. When I was offered a graduate student position with Dr. Hamdan, I was told that my thesis work would use linear transects extending from shipwrecks to focus on investigating the biodiversity of sediment microbiomes surrounding them. At that time, I had little idea of what that would entail, but I knew I was excited to work on such a unique project. As I began to dive into my work, I learned about the shipwrecks, sediment microbiomes, and deep-sea habitats. I also realized that I’ve been entrusted with a daunting dataset: data collected over 5 years on 5 cruises at 5 shipwreck sites amounting to over 500 samples that will undergo sequencing and a litany of geochemical and physical properties analyses.

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When sitting at my computer thinking about the appropriate ways to process the dataset, it’s easy to forget about the immense work that went into sample collection. Being able to participate in some of these cruises has given me a reality check and opened my eyes to the amount of planning, time, and effort that goes into each and every sample. The process of deploying and recovering the multi-corer, extruding the cores into tubes, and then sampling the cores has caused me to treat each sample with care and respect.

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As we collect the final samples that will complete the transects, there is excitement every time the multi-corer comes on deck filled with our deep-sea treasure. Seeing the holes in our dataset disappear has given me a motivational kick to keep pursuing and tackling the difficult questions that the samples pose to us. When we return to land, I’m excited to squeeze every ounce of information out of these samples to try to uncover the story they will tell us about how these amazing cultural and scientific artifacts impact the seafloor.

  • Melissa Brock

Third Time is the Charm

Until about a week ago (when Justin Berg joined our lab- see previous post), Melissa and I have been the only students in Dr. Hamdan’s microbial ecology lab, since it moved to USM the previous year. During that time, we have sailed together on three research cruises. Although the scientific objectives are not always the same, we find that with each cruise our experiences bond us closer together as a lab, help us form new bonds with collaborating scientists, and enrich our scientific knowledge.

Being a team player is essential to accomplishing any scientific goals in the Hamdan Lab. On our June 2017 cruise, Melissa helped me collect a lot of seawater (260 liters!) from the Anona shipwreck site to use in my microcosm experiment for my thesis. I ran my experiment for 14 weeks in a cold room, and she helped me sample for hours at a time every two weeks, so that I can study marine biofilm formation and  microbially induced corrosion.

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On this cruise, I am helping Melissa collect and process sediment cores from transects at historic shipwrecks that will support her thesis on microbial biodiversity. By helping each other with our science, we not only expand our scientific knowledge, but we are also able to learn from one another. One of the things that Melissa taught me this cruise is that fanny packs (aka party packs) are actually very useful, much to our advisor’s chagrin.**

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Anybody who has been through grad school knows that it is not easy, and having a support system is important. We may not have a big lab, but we have each other to lean on, and for that I am grateful. On our third cruise, both of us are much less nervous, we are familiar with the protocols, and we are definitely having fun with our science!

-Rachel

**The views expressed on fanny packs are not the official position of the laboratory. Said advisor will never approve of the accessory – this post does not constitute endorsement.

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New Address: R/V POINT SUR

By: Justin Berg

With two feet firmly planted on land, I wondered what my first ever extended trip at sea was going to be like. I pondered the idea of being like Captain Jack from the Pirates of the Caribbean, one of the castaways in Giligan’s Island, or the very scary thought of the crew from the Perfect Storm; however, as time grew shorter and June 9th approached, I was ensured that I would be a standard researcher aboard R/V Point Sur. As I packed for life at sea, my curiosity heightened and it finally sank in that I will conduct research on the big, blue sea.

When we pulled into the port, I saw my new home for the week, R/V Point Sur. First came unpacking the bags in the bunk followed by unpacking the lab equipment. Ironically, everything was rather standard from what I expected. We configured the sediment coring station, we neatly tucked away all pipettes and loose goods, and saw BOTH beautiful MC800 multi-corer out on the deck. One of the things that I was surprised with was the necessity to tie everything down. While everything can lay dormant at the dock, life out at sea can be slightly more… unpredictable. Once everything was finished,  grabed a quick round of sushi at a local Gulfport restaurant. Bellies full, everything in place, we were at last able to have our safety briefing. For me, this was a reassuring moment that everyone was prepared and that there was no need to worry. With a positive vibe and nice weather, we waited to depart…

At 12:01 am on June 10, we took off into the Gulf of Mexico ready to conduct our research. As soon as our heads hit the pillow, everyone was vastly asleep ready to start fresh at our first site. Upon arrival at the Viosca Knoll Shipwreck, we conducted a CTD and multicore sampling to collect water and sediment to study microbial life associated with historic shipwrecks. For someone without sea legs, this was rather difficult as sea sickness started to take over. Nonetheless, processing CTD samples was an exciting first step into this exploitative field and aiding Rachel and Melissa with the multicorer was an exciting first group effort. Up to this point, this trip has passed my expectations and I can only hope the weather and sea stay as positive as the atmosphere on the boat. P.S. Who would have thought the first meal I ate on the boat was alligator!

 

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Rachel Mugge and Melissa Brock, both MS students in USM’s Department of Coastal Sciences hard at work on the multi-core sampler.

What Would Susan Do?

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Susan Williams (center), at the CERF 2015 conference with three people who will always ask “What Would Susan Do”. Left to right: Leila Hamdan, Ruth Carmichael, Susan Williams, and Janet Nestlerode.

Over the last two days, the world of aquatic science has learned of the devastating loss of Dr. Susan L. Williams, Distinguished Professor of Evolution and Ecology at University of California Davis. Susan was Director of the Bodega Marine Lab (BML) from 2000 to 2010. She also led the Coastal and Estuarine Research Federation (CERF) as President (2009-2011). It was during that time that I came to know her.

I spent significant time working with Susan to shape the future of CERF. I now know that Susan was shaping the future of me. I learned what it meant to be a leader. I saw the rewards it brought, and the toll that it takes through her efforts. In 2011, I had the privilege of teaming with Susan on a day of congressional office visits during Capitol Hill Ocean Week. We talked with staff and legislators about the scientific needs arising from the Deepwater Horizon Spill. I watched how she valued the opinions of others. How she listened to what was said with an openness that allowed her to truly “hear”. I saw how she measured her words, so that when she spoke, they had deep, and meaningful impact.

From these experiences, a role model emerged for me – someone I could emulate to be a better colleague. At the same time, the radiant light of Susan’s friendship shone on me. Along with a small group of other CERF volunteers, we forged a sisterhood of service permeated with friendship, advice, understanding and love. We met for dinner at each CERF meeting to share stories, weigh leadership challenges, get advice, vent, and LAUGH. At our last dinner in November 2017, we sat at a round table, and spoke for hours. They flew by in seconds. I had the guilty pleasure of sitting next to Susan, and left the dinner soul nourished, and ready for new opportunities. We all took away from the dinners a powerful tool: the wisdom to ask, when faced with a difficult challenge, “What Would Susan Do“.

We must ask that now, as her loss presses a great weight on us. I looked back to the words and emails we exchanged over the years. To the times when I came to her for advice, letters of support, or a course correction. In this search, I found two gifts.

First, I found that I had the presence of mind to thank her for being in my life, and for guiding my career. I wrote her “Thank you for the strengthen you give me, even when you don’t know it”. This  brought some comfort, and  reminded me how special our community of science is, and how important it is to tell each other how we appreciate each other.

I also found what Susan would do. She would learn. She passed the quote below to me, at exactly the moment I needed it, and I share it with everyone who is weighing her loss . In her memory, I ask my colleagues, friends, and any future scientist who might follow in her footsteps to do good with your science, dare to be a leader, value the opinions of everyone, and measure your words. It is What Susan Would Do.

-LJH

“The best thing for being sad,” replied Merlin, beginning to puff and blow, “is to learn something. That’s the only thing that never fails. You may grow old and trembling in your anatomies, you may lie awake at night listening to the disorder of your veins, you may miss your only love, you may see the world about you devastated by evil lunatics, or know your honour trampled in the sewers of baser minds. There is only one thing for it then — to learn. Learn why the world wags and what wags it. That is the only thing which the mind can never exhaust, never alienate, never be tortured by, never fear or distrust, and never dream of regretting. Learning is the only thing for you. Look what a lot of things there are to learn.” -E. B. White, the Once and Future King

 

GoM-SCHEMA Wins National Oceanographic Partnership Program 2017 Excellence in Partnering Award!

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Our lab is excited to receive National Oceanographic Partnership Program’s (NOPP) 2017 Excellence in Partnering Award for our work in the Gulf of Mexico – Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology (GOM-SCHEMA) project led by Dr. Leila Hamdan of the School of Ocean Science and Technology at USM, and Ms. Melanie Damour of the Bureau of Ocean Energy Management.

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The GoM-SCHEMA team with the crew of R/V Pelican in 2014 after a successful research expedition.

After the 2010 Deepwater Horizon oil spill in the Gulf of Mexico, our team of scientists from Federal agencies, academic institutions, and the private sector initiated a partnership to examine the impacts of the spill on deep water historic shipwrecks. This project examined changes in microbial biodiversity and degradation/corrosion processes at wooden- and steel-hulled historic shipwrecks in deferentially spill-impacted and un-impacted areas. The project adopted a multiscalar approach to address micro-, meso-, and macroscale impacts through microbial ecological and archaeological analyses. The GOM-SCHEMA partners brought together expertise spanning natural science, social science and technology, and created a foundation for long-term monitoring of ecosystem recovery of these unique, and non-renewable deep-sea habitats. The study partners learned across disciplines, and in doing so provided a better understanding of ocean science, and supported the science and management missions of our many partner institutions.

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Copper-sheathing from the Mica shipwreck, obtained during field work in 2014.

The study benefited from collaboration with 16 partners and funding through three agencies. Partners include the Bureau of Ocean Energy Management, Naval Research Laboratory, Bureau of Safety and Environmental Enforcement, University of Southern Mississippi, George Mason University, Oceaneering Inc., Droycon Bioconcepts Inc., the PAST Foundation, Montana State University, Louisiana Universities Marine Consortium, American University, Deep Sea Systems International, University of Georgia, University of Texas at Austin, and Woods Hole Oceanographic Institution.

GOM-SCHEMA valued team work, interdisciplinary research, and engagement of diverse communities.  We are especially proud of our efforts towards supporting women in STEM.  More than half of the leadership team, including the two lead PIs, were women. Women led all six of the oceanographic expeditions under GOM-SCHEMA. Female students, staff, and managers contributed at every level of the project, and were provided with role models and mentors.

The depth of of expertise, viewpoints and talent at all career levels that GoM-SCHEMA strove for resulted in new perspectives,  paradigms, and a truly holistic partnership to build upon. We thank and congratulate our whole team for this award, and are grateful to NOPP for supporting ocean science.

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Study leads Rob Church, Hamdan and Damour at BOEM’s Information Transfer Meeting in 2017.

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Team members Damour, Chrissy Figan, Zeima Kassahun and Hamdan after a successful ROV mission.

 

 

 

 

 

 

 

 

 

To read more about the award, visit the NOPP website.

The function of education

The function of education is to teach one to think intensively and to think critically –  MLK, Jr.

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This summer I had the special opportunity to attend the Strategies and Techniques for Analyzing Microbial Population Structure (STAMPS) course at the Marine Biological Laboratory in Woods Hole, Massachusetts. The focus of the course was to learn a variety of strategies for analyzing next-generation DNA sequences. These strategies included how to assign taxonomy, compare microbial communities, and estimate microbial diversity using statistical models.

But the most important thing that was demonstrated throughout the course was that there isn’t a “cookie cutter” analysis that will fit all datasets. Instead, it is our job to think critically about the constraints of our data and what tool or tools will best fit those constraints. While that is a huge responsibility, it is also an incredible motivator to always be aware of and learning about the advances in the field of bioinformatics.

I came back to the lab at Southern Miss excited about everything that I learned and that I will learn. This course opened my eyes to the limitations and the power that these bioinformatics tools provide. They not only enable us to make new discoveries about microbes but they also push the field of deep-sea microbial ecology a little further into the future every day. And if that’s not exciting, I don’t know what is.

  • MB