AUC Professor Joins a Team of Ocean Researchers in Uncovering a Series of Complicated Relationships among Marine Microbes

In a recent study published in the Proceedings of the National Academy of Sciences (PNAS), a team of ocean researchers have uncovered a series of complicated relationships among marine microbes, and these relationships appear to have critical consequences for coastal Southern Ocean food webs. Team members are scientists from the J. Craig Venter Institute (JCVI), the Scripps Institution of Oceanography (SIO) at UC San Diego, the University of Southern California (USC), and the Virginia Institute of Marine Sciences (VIMS) and The American University in Cairo (AUC). Some team members ventured to the US Antarctic Program’s McMurdo Station, located on the south tip of Ross Island and conducted expeditions over the frozen sea to the ice edge where they carefully collected water samples from the sunlit surface and returned them to the Crary lab at McMurdo, in order to perform experiments. Ahmed Moustafa, Associate Professor of Bioinformatics and Genomics at AUC, was in charge of the computational and statistical work to process, analyze and visualize the genomic data from Cairo, with the help and support of AUC’s University Technology Infrastructure (UTI) Team.The Southern Ocean around Antarctica is home to massive phytoplankton populations, and scientists have long considered their growth to be controlled largely by availability of iron and light. Now, thanks to the new study published in PNAS, the picture looks much more complicated, and a bit like a theatrical drama, packed with tension and intrigue, but starring microbes. Microscopic organisms, phytoplankton (single celled photosynthetic algae) and bacteria, which live suspended in seawater and form the base of marine food webs, underpin the success of all the inhabitants of Antarctic seas like penguins, deals and orca whales. The researchers learned that although the water appeared teeming with a particular type of phytoplankton called diatoms, the diatoms displayed cellular signatures of malnourishment. Unlike most regions of the global ocean which do not contain sufficient nitrogen or phosphorous for sustained phytoplankton growth, diatoms in the remote waters of McMurdo Sound, adjacent to the Ross Sea, were starving from lack of iron and deficiency of vitamin B12, just like the vitamin and mineral supplements humans might take with breakfast in the morning. Erin Bertrand a former JCVI and SIO researcher, now an Assistant Professor at Dalhousie University in Halifax, Nova Scotia, Canada, was lead author of the study. “Just like humans, phytoplankton require vitamins, including vitamin B12, to survive. We have shown that the phytoplankton in McMurdo Sound acquire this precious resource from a very specific group of bacteria. Those bacteria, in turn, appear to depend directly on phytoplankton to supply them with food and energy,” said Bertrand. But here is where it gets messy. The team further confirmed that a large portion of the B12 supply in the Southern Ocean appears to be produced by a particular group of gammaproteobacteria bacteria belonging to the Oceanospirllaceae. This aspect of this study was facilitated by collaboration with researchers at the University of Rhode Island (URI) and the Marine Biological Laboratory who have been conducting studies on bacteria in and around the Amundsen Sea, another region of the Southern Ocean. “Through a combination of field manipulation experiments and next-generation sequencing, we’ve obtained a new view of the microbial interactions underpinning a highly productive ecosystem,” said senior author Andrew Allen, a joint Associate Professor at SIO and JCVI. In order to analyze patterns of gene expression in the diverse assemblage of bacteria and phytoplankton, the researchers generated massive volumes of rRNA and mRNA sequence data. Ahmed Moustafa, Associate Professor of Bioinformatics and Genomics at the American University Cairo (AUC), said “We conducted large-scale phylogenomic analyses to determine the identities of the phytoplankton and bacterial populations existed in the collected samples, coupled with metatranscriptomic analyses to know which microbial groups are responsible for specific metabolic and biochemical transformations. The integration of the phylogenomic and metatranscriptomic results was instrumental in characterizing the co-occurrence and interaction modes among the members of the microbial community in the Southern Ocean.” The computational analyses were facilitated by the high-throughput computing infrastructures at AUC. Moustafa, who has been conducting research in the area of marine microbial genomics, has been collaborating with JVCI research group for the past five years. With this new understanding of the nature of these interactions and the careful balance of competitive and cooperative behaviors that exist in this key ecosystem, researchers can work towards predicting how these relationships might change in the future, as temperatures begin to rise in the Southern Ocean.

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