Fun Science FRIEDay – One microbial trash is another’s microbial treasure!

Happy FSF!

You know that old saying, the one that explains how something devalued by one person is of the utmost value to another.

Well this week we bring you an analogy of that quote in nature, and in the form of microbes.

Leishmaniasis… have you heard of it? If not, do not worry, I had not either before I began writing this piece, and subsequently almost gagged while googling “appropriate” photos to accompany this piece.  Leishmaniasis is a disease caused by the protozoan parasite Leishmana. The vector that spreads this wonderful treasure? Sand flies. If you are unfortunate enough to get this disease it can turn your skin into all manner of foul lookingness. See Exhibit A.

Exhibit A

Skin ulcer on the hand due to leishmaniasis. (Photo credit: CDC Dr. S. Martin)

Skin ulcer on the hand due to leishmaniasis. (Photo credit: CDC Dr. S. Martin)

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The Ocean Adventure: mud, robots, and ecosystems

We traveled to Cape Lookout Bight aboard the R/V Susan Hudson to sample sediment and test our homemade ROV. Along the way, we asked the research team to talk about their favorite marine ecosystems.

Let us know what your favorite marine ecosystems are in the comments below.

Beneath the Broken Ice: Playing with Mud

Megumi Shimizu is a graduate student aboard the RVIB Nathaniel B. Palmer to collect sediment samples near Antarctic Peninsula as a part of the LARISSA project. She is interested in microorganisms and biogeochemistry of marine sediments; how the metabolism of microorganisms interact with the surrounding environment and the chemical components in sediments. See her first update here.


Are you playing with mud on the research vessel?

Some people on the ship joked when they saw me processing my sediment core. Yes, I’m playing with mud in Antarctica. Sampling sediments can tell us a lot, not only what happened across geologic time scales, but also what kind of organisms are living in the sediment, microbiology, and the geochemical conditions. We are serious about collecting mud and playing with mud.

upper panel: the entire view of glove box, lower panel: Liz Bucceri working on sediment sample processing in glove box. Photo by Megumi Shimizu

upper panel: the entire view of glove box, lower panel: Liz Bucceri working on sediment sample processing in glove box. Photo by Megumi Shimizu

Nathaniel B. Palmer has three pieces of equipment to collect sediment; the megacore, kasten core, and jumbo piston core. The length you can reach below seafloor is different, 40cm, 1.5 to 6m and 24m respectively. Megacore is more suitable for biological studies since it preserves the sediment-water interface better than kasten core and jumbo piston core. Geological studies prefer Kasten core and jumbo piston core so that they can get older data from the sediment.

For my microbial lipid biomarker study, I’m taking samples from the megacore and kasten core. Along with microbial lipid and DNA, our team is collecting sediment and porewater (the water in pore spaces of sediments) to analyze geochemical properties of sediments, such as methane, sulfate, sulfide, and dissolved inorganic carbon. To maintain the condition of the sediments as close as the real environment, the sediment cores are processed under the condition of cold (~0C degree) and anoxic (no oxygen). How to make that condition? We have a special room called “The Little Antarctica”, on the ship, which is a big refrigerator containing glove box. A glove box is the transparent container with two pairs of gloves. The inside of the box is kept practically anoxic (less than 1% of oxygen. Atmospheric oxygen is ~20%).

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Beneath the Broken Ice: Megumi Shimizu on the 2012 LARISSA Campaign to the Antarctic Peninsula

Megumi Shimizu is a graduate student studying microorganisms in marine sediment. She is currently on board the RVIB Nathaniel B. Palmer exploring seafloor communities in a once ice-covered region beneath the Larsen Ice Shelf. Over the next month, she will be updating us from the field.


The RVIB Nathaniel B. Palmer. photo by Megumi Shimizu

The RVIB Nathaniel B. Palmer. photo by Megumi Shimizu

I’m a PhD student interested in microorganisms and biogeochemistry of marine sediments; how the metabolisms of microorganisms interacting with the surrounding environment, the chemical components in sediments. Microorganisms in subseafloor are universally important because of its large biomass. It is said 50% of prokaryotes are living under the seafloor. This biomass makes large carbon and nutrients reservoir, which are important in biogeochemical cycle. For example, microorganisms play the role of organic carbon decomposition in sediments, as a result, carbon dioxide and methane are produced. In contrast, carbon dioxide and methane are also consumed by microorganisms called chemolithotrophs and methanotrophs in sediments. Therefore, understanding microorganisms in sediments; who they are, what are they doing, is important to reveal the details of global biogeochemical cycle and accurate estimate of budgets (amount of elements converted to different forms of chemicals for example, amount of carbon dioxide converted into organic carbon by carbon fixation). In addition, how microbial community response to environmental changes such as climate warming is also important in terms of the influence of global elemental cycles.

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