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.

We are Hiring! Three new positions in marine microbial ecology available

Three new positions in the lab are  available: Postdoctoral Researcher; Research Technician; Graduate Student

Consider working with us on two projects to explore the built environment’s impact on marine microbiomes. Details below:

Postdoctoral Research Associate

To apply for the position of Post Doctoral Research Associate please click hereApplicants will need to submit a curriculum vitae, a cover letter outlining their specific interest in and relevant experience for this position, and names of three references to be considered for this position. All applications must be submitted through the USM career site.

Job Summary

The Hamdan Lab in the School of Ocean Science and Engineering at the University of Southern Mississippi seeks a postdoctoral researcher to support microbiome studies of benthic ecosystems in the Gulf of Mexico. Work will focus on the built environment in the deep-sea. Individuals with experience with microbiology and biogeochemistry, with specific knowledge 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.

 

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 Engineering, 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. 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 and through Online at Southern Miss.  Since 2006, our students have collected three Truman Scholarships and 18 National Science Foundation Graduate Research Fellowships. USM students also lead Mississippi with 21 Goldwater Scholarships, an honor that recognizes the next generation of great research scientists. Our Drapeau 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. As one of only 36 institutions in the nation accredited in theatre, art and design, dance and music, we are a haven for creativity and artistic expression. 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 usm.edu.

As an Affirmative Action/Equal Employment Opportunity employer/Americans with Disabilities Act institution, The University of Southern Mississippi encourages minorities, women, veterans and persons with disabilities to apply.

 

Research Technician

To apply for the position of Research Technician, please click here.
Applicants will need to submit curriculum vitae, a cover letter outlining their specific interest in and relevant experience for this position, and names of three references to be considered for this position. All applications must be submitted through the USM career site.

Job Summary

The Hamdan Lab in the School of Ocean Science and Engineering at the University of Southern Mississippi seeks a research technician to support microbiome studies of benthic ecosystems in the Gulf of Mexico. Work will focus on the study of aquatic microbial communities and their interaction with natural and anthropogenic features. Individuals with experience with microbiology, biogeochemistry, and molecular ecology are encouraged to apply.

Primary Duties and Responsibilities

  1. Engage in projects studying seafloor microorganisms to characterize communities in water, sediment and biofilms.
  2. Develop expertise in molecular techniques and bioinformatics to support projects.
  3. Participate in planning and executing field work on board USM’s Research Vessel Point Sur, and other oceanographic research vessels.
  4. Assist with purchasing, expense tracking, laboratory inventory and organization.
  5. Participate in training of laboratory staff in laboratory practices, and develop of new analytical procedures in collaboration with PIs, postdocs and students.
  6. Contribute to written and oral communication through producing graphs and tables to summarize data and the development of reports, grants, and publications. Participate in outreach through social media, and upkeep of the lab website, and perform other duties as assigned by the study PI.
Minimum Qualifications
Applicants must have a MS degree in a related field (coastal or marine sciences, microbiology, chemistry, biogeochemistry, biology or other similar field) or a BS degree with relevant laboratory experience.

Knowledge, Skills & Abilities

·  Proficiency with standard laboratory techniques, molecular biology, laboratory safety procedures, and computer literacy.

·  Interested candidates should be organized, self-motivated, and able to work with a team to support discovery and learning.

·  Ability to read and interpret documents such as safety rules, operating and maintenance instructions, and procedure manuals.  Ability to contribute to reports, correspondence, peer-reviewed manuscripts and outreach.

Preferred Qualifications  
Experience with molecular biology practices, bioinformatics, statistical analysis and programming.

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 Engineering, 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. 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 and through Online at Southern Miss.  Since 2006, our students have collected three Truman Scholarships and 18 National Science Foundation Graduate Research Fellowships. USM students also lead Mississippi with 21 Goldwater Scholarships, an honor that recognizes the next generation of great research scientists. Our Drapeau 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. As one of only 36 institutions in the nation accredited in theatre, art and design, dance and music, we are a haven for creativity and artistic expression. 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 usm.edu.

As an Affirmative Action/Equal Employment Opportunity employer/Americans with Disabilities Act institution, The University of Southern Mississippi encourages minorities, women, veterans and persons with disabilities to apply.

 

Graduate Assistant


We seek an exceptional student to participate in marine microbial ecology studies. This position will support independent research on benthic ecosystems. The assistantship (stipend, tuition and benefits) will enable a student to participate in discovery driven research on deep-sea historic shipwreck microbiomes. This position will involve molecular biology (DNA extraction, amplification, sequencing), bioinformatics, and environmental microbiology techniques. Interested candidates must be willing to participate in laboratory and field experiments, and be motivated, enthusiastic, responsible and able to work with a team.

Successful applicants will have a BS or MS degree in biology, ecology, environmental science, chemistry or other relevant field. Applicants with experience in molecular biology, biogeochemistry or statistical analysis are encouraged to apply. Students involved in this work will participate in the planning and execution of oceanographic research onboard USM’s research vessel Point Sur. 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 marine archaeologists and geologists, and provide a rich environment for learning about marine microbial ecology.

Interested 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 marine microbial ecology and a curriculum vita. Application for Spring 2019 admission at USM is required. Information on graduate admission requirements can be found here. The deadline for Spring 2019 admission is September 1, 2018.

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 Engineering, 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.

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

 

Graduate Assistantship in Marine Microbial Ecology – Spring 2019

The Hamdan Lab in the School of Ocean Science and Engineering at the University of Southern Mississippi seeks an exceptional student to participate in marine microbial ecology studies. This position will support independent research on benthic ecosystems. The assistantship (stipend, tuition and benefits) will enable a student to participate in discovery driven research on deep-sea historic shipwreck microbiomes. This position will involve molecular biology (DNA extraction, amplification, sequencing), bioinformatics, and environmental microbiology techniques. Interested candidates must be willing to participate in laboratory and field experiments, and be motivated, enthusiastic, responsible and able to work with a team.

Successful applicants will have a BS or MS degree in biology, ecology, environmental science, chemistry or other relevant field. Applicants with experience in molecular biology, biogeochemistry or statistical analysis are encouraged to apply. Students involved in this work will participate in the planning and execution of oceanographic research onboard USM’s research vessel Point Sur. 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 marine archaeologists and geologists, and provide a rich environment for learning about marine microbial ecology.

Interested 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 marine microbial ecology and a curriculum vita. Application for Spring 2019 admission at USM is required. Information on graduate admission requirements can be found here. The deadline for Spring 2019 admission is September 1, 2018.

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 Engineering, 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.

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

_DSC1501-20180613-0052

 

Study on biofilms, oil impacts and steel corrosion published in Frontiers

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!IMG_9618

-LJH

 

 

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

IMG_5622

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.

porewater

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.

core extrusion.jpg

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.

RM_MB_pic3

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.**

RM_MB_pic1

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.

RM_MB_pic2