This month we published a research article in Frontiers in Marine Science. The paper “Exposure to Crude Oil and Chemical Dispersant May Impact Marine Microbial Biofilm Composition and Steel Corrosion” by Dr. Jennifer Salerno and colleagues investigated the impacts of oil and dispersant on marine biofilm communities. The paper reveals how spill contaminants interact with marine microbiomes on steel surfaces.

For the study, Salerno performed microcosm experiments  to determine community structure and function of microorganisms in biofilms on carbon steel, a common ship hull construction material. Metal loss and biofilm dynamics were monitored over four months. The paper discovered that bacterial community structure differed significantly between experiments treated with and without oil spill related contaminants.  A sustained reduction in biodiversity was observed when dispersant was present. The introduction of oil increased genes associated with sulfur metabolism, and an increase in metal loss was also observed. This study indicates that exposure to oil and dispersant could disrupt the composition and  function of biofilms colonizing the hulls of historic shipwrecks, and potentially impact the preservation of these ecological and historical resources.

Below is a photo taken during the experiment, showing off our cold room fashion.

Congratulations, Jen!

-LJH

 

 

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

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.

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.

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

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.

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.**

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.

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.” -T. H. White, the Once and Future King

 

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.

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.

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.

 

 

 

 

 

 

 

 

 

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

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

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

“We are tied to the ocean. And when we go back to the sea, whether it is to sail or to watch – we are going back from whence we came.” – JFK.

We still have much to learn about the ocean and the microbes of the deep sea. The data we collected on our most recent cruise in the Gulf of Mexico will bring us a little closer to understanding them. The scientific objective of this cruise was to collect sediment and water samples from six different historic shipwrecks so that we can continue our effort to evaluate the effects of the Deepwater Horizon spill on microbes in deep-sea sediments.  We collected the sediment cores with a multi-corer, and as you can see, we were all very excited when our cores came on deck with our deep-sea treasure.

At one point in the cruise, we had some Atlantic spotted dolphin visitors who came along, no doubt, to check up on our science.

As we settle back into life at the lab, we are grateful for our time spent out on the sea and for the time we were able to spend with our colleagues and crew. Southern Miss to the Deep!

Click the link below if you would like to see more photos from our cruise.

Point Sur Cruise PS17-26 Photo Album

The lab is preparing to head out to sea this weekend to continue our effort to evaluate the effects of the Deepwater Horizon spill on microbes in deep-sea sediments.  These are enigmatic ecosystems because of their remoteness, but we have much to learn from microbes in them about the spill, and life in the deep ocean.  These trips, and the time they afford with my students and colleagues are the best part of my work.  Each time I learn something new about the ocean, my field, and myself.

To prepare for the cruise, and to celebrate World Oceans Day, I share one of my favorite poems:

The Sea by Pablo Neruda

I need the sea because it teaches me.
I don’t know if I learn music or awareness,
if it’s a single wave or its vast existence,
or only its harsh voice or its shining
suggestion of fishes and ships.
The fact is that until I fall asleep,
in some magnetic way I move in
the university of the waves.

It’s not simply the shells crunched
as if some shivering planet
were giving signs of its gradual death;
no, I reconstruct the day out of a fragment,
the stalactite from the sliver of salt,
and the great god out of a spoonful.

What it taught me before, I keep. It’s air
ceaseless wind, water and sand.

It seems a small thing for a young person,
to have come here to live with his own fire;
nevertheless, the pulse that rose
and fell in its abyss,
the crackling of the blue cold,
the gradual wearing away of the star,
the soft unfolding of the wave
squandering snow with its foam,
the quiet power out there, sure
as a stone shrine in the depths,
replaced my world in which were growing
stubborn sorrow, gathering oblivion,
and my life changed suddenly:
as I became part of its pure movement.

Happy World Oceans Day

-LJH

The Hamdan Lab at the University of Southern Mississippi seeks a qualified and highly motivated individual for a Postdoctoral Research Scientist position. This position will support research on the effects of oil spills on benthic ecosystems in the Gulf of Mexico. Specifically sought is a Postdoc to investigate the long-term consequences of oil and chemical dispersant exposure on the preservation of 20^th century historic steel shipwreck in the deep biosphere. The individual will design and implement ROV deployable seafloor experiments to monitor microbially induced corrosion. Individuals with experience with microbiology and biogeochemistry, with specific knowledge and molecular biological techniques (DNA extraction, amplification, sequencing) are encouraged to apply. Experience and proficiency in bioinformatics and statistical analysis is desired for this position as well as proficiency with analytical chemistry techniques, including hydrocarbon analysis. Applicants must have a Ph.D. in coastal or marine sciences, geomicrobiology, biogeochemistry or similar field. The hire will be encouraged to participate in the planning and execution of oceanographic research onboard USM’s research vessel Point Sur for periods of up to two weeks at sea, and contribute to student mentoring. Excellent written and oral communication skills are needed, as well as a commitment to developing peer-reviewed manuscripts. Pending funding, the position will support the hire for 3 years, starting as early as June 2017.

About the University of Southern Mississippi

The Division of Coastal Sciences is a research and graduate education unit within the School of Ocean Science and Technology, offering programs leading to the Doctor of Philosophy and Master of Science degrees. The Division is located at the USM Gulf Coast Research Laboratory (Ocean Springs, Mississippi), a marine laboratory featuring comprehensive basic and applied research programs in coastal and marine biological sciences. Research program support includes state-of-the-art laboratory facilities and instrumentation; a fleet of small and large research vessels, including the R/V Point Sur; the GCRL Museum collection; the Center for Fisheries Research and Development; NSF I/UCRC Science Center for Marine Fisheries, and aquaculture facilities including the Thad Cochran Marine Aquaculture Center.

Founded in 1910, The University of Southern Mississippi is a comprehensive doctoral and research-driven university with a proud history and an eye on the future. As one of only 34 institutions in the nation accredited in art, dance, music and theatre, we are a haven for creativity and artistic expression. A dual-campus university, Southern Miss serves students on campuses in Hattiesburg and Long Beach, in addition to five teaching and research sites in Mississippi. We are among U.S. News & World Report’s most popular universities and recognized by The Princeton Review for our commitment to sustainability. Our Center for Undergraduate Research affords our students meaningful research opportunities, and as a proven leader in innovation, we conduct transformative research that translates into real-world solutions. In the classroom or lab, on the playing field, or in the performance hall, we strive to have a positive impact not only on our students, but also the world around us. Further information is found at www.usm.edu.

To apply for the Postdoc position, please submit via email to leila.hamdan@usm.edu:

• Cover letter outlining interest and experience in the study of microbial ecology
• Curriculum vitae
• Contact information for three references

Please see our websites for more information about USM, the Gulf Coast Research Laboratory, SOST, and studies in the Hamdan lab: https://hamdanlab.com, http://gcrl.usm.edu/,  https://www.usm.edu/school-ocean-science-and-technology/about