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

We are tied to the ocean

“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.

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

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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

I need the sea because it teaches me

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

-LJHScreen Shot 2014-08-05 at 8.30.51 PM

Postdoctoral Research Position in Marine Microbial Ecology

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 20th 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.comhttp://gcrl.usm.edu/,  https://www.usm.edu/school-ocean-science-and-technology/about

 

Student opportunity available for Fall 2017

PhD and MS Graduate Research Assistantship in Marine Microbial Ecology

Location: Division of Coastal Sciences, School of Ocean Science and Technology, University of Southern Mississippi, Ocean Springs, MS

Description:

The Hamdan Lab, in the Division of Coastal Sciences at the University of Southern Mississippi seeks an exceptional student to participate in marine microbial ecology studies in deep-sea habitats. This funded position will support independent research on the effects of oil spills on benthic ecosystems in the Gulf of Mexico. The research assistantship will support (stipend, tuition, benefits) a highly motivated PhD or MS study for up to three years beginning in Fall 2017.

A student is sought to conduct independent research that investigates microbial population structure, metabolic capability, biodiversity and biogeochemistry of benthic environments. This position will involve laboratory studies using molecular biological techniques (DNA extraction, amplification, sequencing), bioinformatics,  classical approaches to environmental microbiology (microscopy, metabolic tracers), and analytical chemistry techniques (stable carbon isotope studies, elemental analysis, bulk carbon pool analysis).

Successful applicants will have a BS or MS degree in biology, ecology, environmental science, chemistry or other relevant field. Applicants with previous experience in molecular biology, biogeochemistry or statistical analysis are encouraged to apply. Students will be required 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. The ability to work collaboratively with students, PIs and external researchers from multiple institutions and fields on interdisciplinary studies of the deep-sea is a must. Those with experience in environmental microbiology or chemistry will be given preferential consideration. Students are expected to participate in development of manuscripts for peer review.

Individuals interested in this position should contact Dr. Leila Hamdan (leila.hamdan@usm.edu), and provide a cover letter outlining specific interests and experience in the study of marine microbial ecology or biogeochemistry and a curriculum vita. Application for Fall 2017 admission at USM is required.

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

Southern Miss to the Deep- Success at the Sea Floor

A joint effort between Dr. Hamdan and Dr. Monty Graham, Director of the School of Ocean Science and Technology at USM, yielded a new slogan during our recent cruise on USM’s R/V Point Sur: “Southern Miss to the Deep!”, clever spin on the university’s slogan, “Southern Miss to the Top!”.

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Preparing to send the corrosion monitoring platforms (CMPs) developed in collaboration with colleagues at the Naval Research Lab to 1100 m in the Gulf of Mexico.

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Our CMPs adorned with USM’s new slogan and various USM stickers.

 

The  scientific objective of this cruise was to use the Remotely Operated Vehicle (ROV) Odysseus to install two corrosion monitoring platforms (CMPs) (pictured above) on the seafloor.  These will incubate for approximately a year, after which they will be recovered to study biotic and abiotic marine corrosion of metal aloys, and the recruitment of microbial biofilms.

 

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Rachel Mugge (left) and Leila Hamdan (right) securing the CMPs to the lower tray of the ROV.

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Still image captured from the ROV camera as we watched our experiments travel to the deep.  The monkey’s fists attached here help the manipulator arm handle the experiments during deployment.

 

By using the multiple cameras on the ROV, we were able to watch the ROV travel deep into the ocean, touch bottom, and began its task of deploying our experiments. While  launch and recovery of an ROV is exciting, the true value of it is to facilitate science. The concept and design of the experiment takes creativity and time, and their placement takes careful effort and team work, both of which were in supply during our cruise.

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The first CMP is placed on the sea floor.

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A curious eel swims by as the manipulator arm grapples for the knot on the second CMP.

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Our experiments will remain in place for approximately a year, when we will return to recover them.  The small circular surfaces on these experiments are what really matters.  They will contain valuable information and microorganisms that can help us learn about how metals degrade in the marine environment.

 

The ROV set both CMPs on the bottom of the Gulf at a depth of about 1,100 meters. This was my first ROV cruise (hopefully more to come) and it was exciting to see our experiments in place, the ROV Odysseus in action, and the deep sea with my own eyes.

Thanks for reading! Oh, and #SMTTDeep

RLM

Welcome Aboard!

The captain and crew greeted me with this phrase multiple times when I arrived at USM’s R/V Point Sur this afternoon, as we set to sail on a three day research cruise in the Gulf of Mexico.

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R/V Point Sur docked at the Port of Gulfport in Gulfport, MS.

During this cruise, we will use the ROV Odysseus (Pelagic Research Systems) to study the microbiology and mineralogy of corrosion near the World War II era shipwreck AnonaAnona, first discovered in 1995, will be the setting for two new long term corrosion experiments, that we hope to place on the seafloor, using the ROV’s manipulator arms. We also hope to obtain new video footage of tube worms observed on the wreck in 2014 as part of the GOM-SCHEMA study.

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The ROV Odysseus on the stern of the R/V Point Sur.

As for myself, I have settled in quite nicely. The living and working quarters aboard a ship may be cramped, but they are cozy!

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My bunk (in the chief scientist’s cabin!) aboard the R/V Point Sur.

I am thrilled to be on my first research cruise, and am eager to do some science at sea. Stay tuned for more updates!

RLM