New Publication Alert! “Deep-sea wooden shipwrecks influence sediment microbiome diversity” published in Limnology and Oceanography

We have a new article published in Limnology and Oceanography titled “Deep-sea wooden shipwrecks influence sediment microbiome diversity”. The paper, by Dr. Justyna Hampel and colleagues, investigated the influence of two historic wooden shipwrecks, from the Microbial Stowaways project, on sediment microbiomes in the deep sea.

Historic shipwrecks function as habitats for benthic organisms by providing food, refuge, and structure. They also form islands of biodiversity on the seabed, shaping microbial ecology and ecosystem processes. This study examined two wooden deep-sea shipwrecks at 525 and 1800 m water depth and probed their influence on sediment microbiomes and geochemistry. Microbiomes were investigated with 16S rRNA gene amplicon sequencing along 60 m transects extending in four directions from the hulls of the shipwrecks. Distance from shipwrecks and sediment depth both shaped microbiome structure. Archaeal alpha diversity was significantly and positively correlated with proximity to the deeper shipwreck while bacterial diversity was not to either. Archaeal community structure differed at both sites; the deeper site had a higher proportion of Bathyarchaeia and Lokiarchaeia proximate to shipwreck compared to the shallow location. Major bacterial communities were consistent at both sites, however, at the deeper site had higher abundance of Bacteroidetes, Chloroflexi, Desulfofarculales, and Desulfobacteriales. Core microbiome and differential abundance analyses revealed unique taxa nearest the shipwrecks compared to the surrounding seabed including organoheterotrophs, and cellulolytic and sulfur cycling taxa. Sediment carbon content influenced microbiome structure near the shipwrecks (5–10 m). We show that shipwrecks have a distinct sediment microbiome and form unique habitat patches on seabed, resembling those surrounding organic falls. The shipwreck influence was more pronounced at the deeper site, further from terrestrial influences, signaling shipwrecks may be a significant source of organic matter in far-shore oligotrophic settings.

The full paper is available online now! And stay tuned, the next paper from the Microbial Stowaways project is coming soon!

-RDM

Coastal Sciences Graduate Fellowship in Support of Diversity

The Department of Coastal Sciences of the University of Southern Mississippi School of Ocean Science and Engineering is pleased to announce the availability of graduate fellowships in support of diversity to prospective students seeking a M.S. or Ph.D. degree. These fellowships are awarded competitively and are intended to support the recruitment of graduate students from historically underrepresented groups in coastal and marine science who demonstrate scholarly promise. Additional information on the Department of Coastal Sciences and the Coastal Sciences graduate program are available at https://www.usm.edu/graduate-programs/coastal-sciences.php. Candidates must contact potential faculty advisors in the Department of Coastal Sciences to discuss their research and educational interests and must identify a faculty sponsor prior to submitting a fellowship application. The graduate school application fee for students applying to the Coastal Sciences Graduate Fellowship in Support of Diversity will be waived. Mississippi residents who fall under historically underrepresented groups in coastal and marine science are particularly encouraged to apply.

Application Deadline

June 30, 2021

(Spring 2022 admission to the graduate program)

Additional Information

Location: The University of Southern Mississippi Gulf Coast Research Laboratory in Ocean Springs, MS

Salary: $1,900/month (M.S.) or $1,950/month (Ph.D). Salary increases $50/month when the student advances to candidacy. Additional benefits include a tuition waiver and health insurance.

Contact: penny.isgar@usm.edu, 228.818.8887

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How to Apply

To be considered for a fellowship, applicants will be required to submit the following by the application deadline:

1. A CV

2. Official transcripts

3. A statement of purpose

4. Three letters of recommendation. (It is the responsibility of the applicant to ensure recommendation letters are submitted by the deadline.)

5. An essay that speaks to the candidate’s inclusion in one or more historically underrepresented groups in higher education. This essay is separate and in addition to the statement of purpose but should be submitted with the statement of purpose as a single PDF.

For all admission applications (undergraduate, graduate, or international) visit usm.edu/admissions.

The Essay

Applicants should use the essay to articulate how their experiences and background have influenced their career to this point (including how those experiences influenced their decision to apply for graduate school). Within this statement, applicants should provide insight about how they could contribute to a scholarly environment that values inclusivity and diversity. Applicants should also consider their potential in contributing to the inclusivity of COA, USM, and their broader field of study, as applicable. The essay should be a maximum of two pages. Applicants should use this essay to address how one or more of the following identities or experiences, and their intersections,
apply to them.
• Member of an ethnic or racial group underrepresented or marginalized in graduate education and coastal and marine science, including but not limited to Black, Indigenous (American Indian/Alaskan Native, Native Hawaiian or other Native Pacific Islander) and/or Latinx
• First-generation college student
• McNair or Mellon Mays Undergraduate Scholar
• Other identities and experiences including, but not limited to:
− Being of a gender and/or sexual orientation identity historically underrepresented
− Those who identify as a military veteran
− Those that manage a disability
− Those who have experienced housing or food insecurity
− Single parents

The candidates will be initially evaluated based on the completeness of their application, their academic records (as evidenced through their CV and transcripts), their potential to flourish in the COA program (as evidenced through their statement of purpose and letters of recommendation), and potential to contribute to diversity, equity, and inclusion in the Division of Coastal Sciences (as evidenced in their essay). The three top candidates will then be asked for an on-campus or virtual interview with faculty and students from the Division of Coastal Sciences. Preference for Mississippi residents from historically underrepresented groups in coastal and marine science may be shown if all other marks between applicants are equal.

New Publication Alert! Study revealing deep-sea shipwrecks represent island-like ecosystems for marine microbiomes published in The ISME Journal

In April, we published a research article in The ISME Journal titled “Deep-sea shipwrecks represent island-like ecosystems for marine microbiomes”. The paper, by Dr. Leila Hamdan and colleagues, investigated the influence a deep-sea shipwreck, Anona, exerts on sediment microbiomes in the deep sea.

Biogeography of macro- and micro-organisms in the deep sea is, in part, shaped by naturally occurring heterogeneous habitat features of geological and biological origin such as seeps, vents, seamounts, whale and wood-falls. Artificial features including shipwrecks and energy infrastructure shape the biogeographic patterns of macro-organisms; how they influence microorganisms is unclear. Shipwrecks may function as islands of biodiversity for microbiomes, creating a patchwork of habitats with influence radiating out into the seabed. Here we show microbiome richness and diversity increase as a function of proximity to the historic deep-sea shipwreck, Anona, in the Gulf of Mexico. Diversity and richness extinction plots provide evidence of an island effect on microbiomes. A halo of core taxa on the seabed was observed up to 200 m away from the wreck indicative of the transition zone from shipwreck habitat to the surrounding environment. Transition zones around natural habitat features are often small in area compared to what was observed at Anona, indicating shipwrecks may exert a large sphere of influence on seabed microbiomes. Historic shipwrecks are abundant, isolated habitats with global distribution, providing a means to explore contemporary processes shaping biogeography on the seafloor. This work is a case study for how built environments impact microbial biodiversity and provides new information on how arrival of material to the seafloor shapes benthic microbiomes.

Check out the full paper online! Also, check out Dr. Hamdan’s “Behind the Paper” here: https://naturemicrobiologycommunity.nature.com/posts/the-shipwreck-anona-a-microbial-island-under-sea

-RDM

A Thesis & A Thank You

I recently defended my Master’s Thesis “How Historic Shipwrecks Influence Dispersal of Deep-sea Microbiomes”. My thesis investigated how historic (> 50 years old) wooden shipwrecks influence dispersal of deep-sea microbiomes by placing introduced wood on the seafloor in near proximity (0-200 m) to wooden-hulled historic shipwrecks in the northern Gulf of Mexico (GoM). Biofilms formed on experiments were analyzed for microbiome richness, diversity, and phylogenetic composition. Richness and diversity decreased with decreasing proximity to both shipwrecks revealing historic shipwrecks may function as island-like habitats. The phylogenetic composition analysis shows strong selection by wood type for bacteria, and highlights differences in bacteria, archaea, and fungi dispersal patterns. The results of my thesis show that built structures, like shipwrecks, impact microbial biogeography in the deep sea. I will be working through the summer to publish this research.

Conducting this research was challenging, but extremely exciting. I am grateful to all the people who assisted me and helped make this thesis and my defense a success. I could not have done it without my advisor and lab mates standing with me (even through 8-foot seas on the recovery cruise for my experiments). I could not have done it without our collaborators and those who helped on the research cruises aboard USM’s R/V Point Sur. I could also not have done it without the support of my family. Thank you all. I have thoroughly enjoyed my time as a graduate student in the Hamdan Lab and at USM. #SMTTDeep

-Rachel D Moseley

A historic wooden shipwreck, Site 15470, that was discovered during the course of this thesis work.

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!

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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:

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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.

Leila

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.

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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.

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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

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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!