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Mighty microbes implicated in Permian mass extinction

Ninety-six percent of marine and 70% of terrestrial species died in the Permian mass extinction, which began about 252 million years ago and lasted for over 20,000 years. Geochemistry tells us that this extinction coincided with a severe and rapid change in the Earth’s carbon cycle, but this alone could not have been the cause of the extinction. Initially it was thought that carbon dioxide released by Siberian volcanism explained this change in the carbon cycle but the volcanic outgassing was not large enough to have been responsible for this big a disruption. So if not volcanoes, what could have produced so much carbon in the atmosphere?

A new study shows that the speed and exponential growth of carbon had to be of biological origin. The study proposes that the emergence of a new group of microbes, Methanosarcina, was responsible for producing the methane in the atmosphere that led to the extinctions. At around 250 million years ago, these microbes acquired fancy new machinery, or a new metabolic pathway through lateral gene transfer that made them capable of taking advantage of the large amounts of marine carbon produced at the time and converting it to methane. This also required large amounts of nickel that was released by the volcanoes. The new source of nickel, a limiting resource in the ocean, combined with increases in marine carbon created a feeding frenzy of bacteria. Following the production of methane by Methanosarcina, other microbes, anaerobic methanotrophs, turned the methane into carbon dioxide further lowering oxygen levels in the ocean.

Today we see similar short-lived low oxygen events in the ocean, but these are driven by algal blooms. Marine algae (i.e., marine plants) are responsible for most of the photosynthesis that occurs on the planet and the resulting oxygen and marine organic carbon. Just like the plants that grow in your garden, these algae rely on nutrients to grow and reproduce. When there’s a new source of otherwise limiting nutrients, they often grow rapidly and we call this a “bloom.” As the algae use up the nutrient source, they begin to die and microbial decomposition begins. These microbes consume oxygen in the water as they feed on the algae and release hydrogen sulfide gas as they have their own population explosion. Just as scientists have observed in the fossil record for the Permian extinction, we see low oxygen levels in areas of the ocean following algal blooms and increases in microbial digestion. The hydrogen sulfide gases released during decomposition of modern algal blooms often produce mass die-offs of marine animals.

Ulva releasing life history stages

Ulva releasing microscopic life history stages. Photo by Rosemary Romero.

I study microscopic life history stages of modern bloom-forming algae, green seaweeds in particular. These life stages are similar to invertebrate larvae in that they are released into the ocean by adults and can be carried long distances by waves and currents. Last spring I set out to learn how to detect these life stages in coastal waters using their genetic code, or DNA. I was hoping that I could use this method to predict when these seaweed blooms were more likely to happen. My first challenge was to find out if I could extract DNA from these life stages. I went to the rocky intertidal at the Romberg Tiburon Center (RTC) and collected some specimens of adult Ulva, the alga responsible for most of the worlds green seaweed blooms. I brought the algal specimens back to the lab and kept them dry, dark, and cold for a week. When I submerged the algae in artificial seawater they began to release what looked like green ooze. Upon closer investigation under a microscope this ooze proved to be microscopic swimmers, Ulva's tiny planktonic life history stage! I filtered this solution of swimmers to concentrate them and stored them in the freezer for DNA extraction at a later time. Just to make sure my procedure for DNA extraction would work for green algae, I extracted DNA from as many morphologically different specimens of adult Ulva I could find at RTC. These included specimens taken in small volume from the solution of swimmers and I filtered them on the the same day. After the extraction procedure I used a method called gel electrophoresis to test if I had successfully extracted DNA from my samples. This method works by adding a fluorescent dye that will bind to any DNA present and produce a glowing band under UV light. Unfortunately, the first four times I tried this, no glowing bands resulted. After taking a few more classes and working with other scientists that have experience extracting DNA from algae, I finally had a breakthrough. I successfully extracted DNA from the adult Ulva specimens I collected in December 2013. I’m still tying to figure out what went wrong with the filters, but I went back to RTC in April 2014 to do another survey of Ulva species. By the end of this spring I will be able to test for changes in Ulva species composition across different seasons.