Hamdan Lab in New York Times

We are very excited to share that our research on shipwreck microbiomes was recently featured in the New York Times! Article “Microbes Point the Way to Shipwrecks” by Katherine Kornei was published in February 2020 and highlights our newest findings from two studies presented at the Ocean Sciences Meeting 2020 in San Diego. Check out the article to find out more about steel yacht Anona, the two wooden shipwrecks we explored last summer, and their microbiomes!


Bow of Anona, sank in 1944 in the Gulf of Mexico

We are in this boat together

Artist's rendering of research vessel.

This week, the National Science Foundation (NSF) announced it selected the Gulf – Caribbean Oceanographic Consortium, cooperatively led by The University of Southern Mississippi (USM) and the Louisiana Universities Marine Consortium (LUMCON), to operate the third new oceanographic research ship to carry out regional scale research in the Gulf of Mexico, Caribbean Sea and Atlantic Ocean. We are thrilled by this announcement and this opportunity to support, enhance and expand scientific research and discovery in the Gulf and Caribbean.

Our lab had a unique insight in the process that lead to this award. I worked with a team at USM and LUMCON to develop the proposal and a vision for supporting ocean science through the use of this ship. I also had the chance to see my lab team pull together. The lab endured the development of this proposal over several months. They heard the conference calls, the “ding” of hundreds of emails, and bore witness to a horrendous stress diet (candy? did someone say candy?). Worst of all, proposal submission converged with our prep for the Microbial Stowaways cruise, leading to this very accurate Venn diagram:


Through it all, we stuck together, supported each other, and made our work matter, for our research and in support of the academic research fleet. I was honored to work on this proposal, and excited about the work ahead with UNOLS. I am overflowing with gratitude for how our lab members stuck together, worked hard, and supported this important award.

Rachel, Rachel, Anirban, Justyna and Leif, I am glad we made it through July/August. I am glad we are a team.


Microbial Stowaways Research Expedition

On June 25th, 2019, we will embark on the first research cruise for the Microbial Stowaways project, funded by NOAA’s Ocean Exploration and Research program. This expedition will take 9 days aboard USMs R/V Point Sur with ROV Odysseus on board. Our team includes 8 scientist, 2 archeologist, 4 ROV crew members, an outreach specialist, a middle-school teacher from the NOAA Teacher at Sea program, and 8 Point Sur crew members.


Main goals for this expedition are to discover and characterize two unexplored, wooden shipwrecks in the Gulf of Mexico, and investigate their role in microbial biogeography in the deep-sea. We will be collecting hours of video footage of these never before seen shipwrecks, and collecting sediment and water samples around them to explore the environment and microbiomes around these exciting habitats. We will also deploy experiments on the seafloor to study how biofilms form on surfaces in the deep-sea, a critical step which takes shipwrecks out maritime past and into the present as artificial reef ecosystems, teaming with life both visible, and invisible.

Our lab is in the middle of cruise preparations, a busy but exciting time! We are planning the cruise track, dive plan, and sampling schedule. And, importantly, taping and labeling vials for sample collection by the 100s. These expeditions depend on attention to detail, early preparation, and a lot of supplies.


On June 24th – 25th, we will be at Port of Gulfport, in Gulfport, MS doing our cruise mobilization and engaging with the Ocean Science and Technology Sea Camp students who will be visiting the ship with staff from USMs Marine Education Center. As a part of the Camp, high school students will tour R/V Point Sur. observe our preparations to go offshore and talk with us during a live telepresence event later in the week.

We will set sail by midnight on June 25th. Stay tuned for pictures and videos! Follow @HamdanLab and @Just_AquaticN on Twitter for cruise updates. SMTTDeep!

Seeking Graduate Student for Oyster Aquaculture Microbiome Study

We seek an exceptional student to participate in microbial ecological research concerning marine aquaculture. In the Gulf of Mexico there is considerable interest in developing technologies to expand the oyster industry through aquaculture. The chemical and microbiological conditions which permit survival of healthy oyster larvae and ultimately production of viable oysters are largely unknown. We invite students interested in studying the intersection of ecology and oyster aquaculture to apply for a Graduate Research Assistantship in the Division of Coastal Sciences at the University of Southern Mississippi to explore aquaculture microbiomes.

Successful applicants will have a BS or MS degree in biology, ecology, environmental science, chemistry, aquaculture or relevant field. Applicants with experience in molecular biology, biogeochemistry, larval culture or statistical analysis are encouraged to apply. Students are expected to develop manuscripts for peer review, participate in outreach, and present results in written and oral formats. This opportunity will involve collaboration with experts in marine aquaculture at the Thad Cochran Marine Aquaculture Center and provide a rich environment for learning about marine microbial ecology.

Individuals that are serious about graduate study should contact Dr. Leila Hamdan (leila.hamdan@usm.edu). Please provide a cover letter outlining specific interests and experience in the study of microbial ecology or marine aquaculture and a curriculum vita. Application for Fall  2019 admission at USM is required. Information on graduate admission requirements can be found hereThe deadline for Fall 2019 admission is April 1, 2019.

For more information about USM, the School of Ocean Science and Engineering or the Division of Coastal Sciences, please visit this site.

2018 in Photos

Towards the end of 2018, the lab became very busy developing and implementing a new study supported by the Defense Advanced Research Projects Agency’s (DARPA) Biological Technology Office. The goal of this work is to use microbiomes to tell us about the history and present of human structures on the seafloor. The project came up fast, and in August and September, all hands in the Hamdan Lab, some extra hands from the School of Ocean Science and Engineering, and some more hands from our collaborators at the MMRI at University of Mississippi worked together to design, build and test seafloor landers and experimental arrays to collect biofilms. We benefited from the support and advice of the crew of R/V Point Sur (University of Southern Mississippi’s ship), and worked closely with ocean engineers who helped us integrate our experiments with the remotely operated vehicle Odysseus (Pelagic Research Systems, Inc), which ultimately drove our experiments to depths up to 2000m deep, and placed them exactly where they needed to be to accomplish our goals. Then, in December, we went back out in the Gulf of Mexico on R/V Point Sur, and called all eight of our experiments home.

This work was incredibly hands on, extremely tiring, and required all of our imagination and “make it work” skills. It was also a huge amount of fun. You can see it on our faces in the photo albums posted below. These are long overdue, and we hope you enjoy seeing the many perspectives of marine microbial ecology and ocean engineering happening here, and appreciate the happy, smiling, science we accomplished together.

Flickr Photo Albums from 2018

September ROV Cruise https://flic.kr/s/aHskNcFvZ8

December cruise – recovering experiments https://flic.kr/s/aHsmAkHwBh

ROV stills of the Alcoa Puritan shipwreck https://www.flickr.com/gp/87030063@N08/6QP9ey

Welcoming our new Lab Manager


We are excited to have Anirban Ray join the Hamdan Lab team. Anirban completed his MS in Molecular/Microbial Ecology from BGSU, Ohio, and has a Master’s in Microbiology from Bangalore University, India. ​Anirban is experienced in the field of genome editing using the CRISPR/Cas9 system, and cutting-edge molecular methods.

Anirban joins the lab as our Lab Manager, and will support our work to study  microbiome signature of the built environment of Gulf of Mexico seafloor. He will guide our work in 16S rRNA gene sequencing and metagenomics, and help students develop new techniques to broaden our work and their expertise. We are thrilled to have him join our team.

Welcome Anirban!

Seeking Postdoctoral Researcher to Support Exploration of Shipwreck Microbiomes

We seek a postdoctoral researcher to support a 2 year project funded by NOAA’s Ocean Exploration and Research Program. The project includes the first exploration mission to two shipwrecks in the Gulf of Mexico, and discovery focused studies of their microbiomes. Individuals with experience with microbiology, biogeochemistry, and expertise in molecular ecology are encouraged to apply.Primary Duties and Responsibilities

  • Engage in a project studying seafloor microbiomes and metagenomes to characterize communities in water, sediment and biofilms.
  • Develop expertise in ecological theories regarding microbial biogeography and contribute new knowledge and ideas to this area of research.
  • Develop and apply bioinformatics tools and approaches to identify communities, relevant taxa and associations. Learn and apply machine learning tools to datasets generated during the course of the study in collaboration with project scientists from other institutions.
  • Participate in planning and executing field work on board USM’s Research Vessel Point Sur, and other oceanographic research vessels.
  • Contribute significantly to written and oral communication, including the development of peer-reviewed manuscripts, blog posts, outreach through social media, and the public outreach products designed to engage broad audiences in the study of the deep-sea.
  • Participate in student mentoring, and perform other duties as assigned by the study PI.
Minimum Qualifications
Applicants must have a Ph.D. in coastal or marine sciences, microbiology, geomicrobiology, biogeochemistry or similar field.  Applicants must also have a publication record that illustrates ability to conduct and communicate independent research as well as experience and proficiency in bioinformatics and statistical analysis.
Knowledge, Skills & Abilities

·  Proficiency with molecular biological laboratory techniques, general laboratory practice, experimental design, laboratory safety procedures. A high level of computer literacy.

·  Ability to read and interpret documents such as safety rules, operating and maintenance instructions, and procedure manuals.  Ability to write reports, correspondence and peer-reviewed manuscripts.  Ability to speak effectively before groups. Ability and interest in contributing to outreach activities.

·  Interested candidates should be self-motivated, results driven, able to take a project vision and shape it with scientific experience, and work with a team to support discovery and learning.

Preferred Qualifications  
Significant proficiency in bioinformatics and, programming experience.
To apply for the position of Post Doctoral Research Associate please click hereAll applications must be submitted through the USM career site. Please contact Leila Hamdan with specific questions.