Scientists and Students Explore Diversity of Microbial Life on Maine’s Coast

Anyone who has driven along the coast will recognize the distinctive, sulfury odor of low tide. The mudflats from which the smell emanates may appear lifeless, but they’re anything but. In fact, that smell comes from the release of sulfide from diverse communities of microbes that make their home in the coastal mud.

“If we look at microbes in the surface ocean, most of their basic biological functions are driven by photosynthesis and oxygen respiration,” said Bigelow Laboratory Research Scientist Melody Lindsay. “I’m interested in processes that don’t require oxygen to show the full range of what microbes can do.”

Lindsay is interested in how microbes obtain energy and nutrients in extreme environments where there’s less oxygen or, in some cases, where microbes can’t tolerate any oxygen. Much of her research focuses on what’s happening in rocks and sediment in the deep sea, which could help scientists understand the fate of pollutants and carbon that fall to the seafloor. But similar extreme systems can be found closer to home.

In recent years, Lindsay has been exploring one such system just a few miles from Bigelow Laboratory’s campus in East Boothbay.

Edgecomb Eddy is a mudflat that acts as a boundary — physically and chemically — between land and the ocean. The sediments there are rich with organic matter and microbes that have adapted to the anoxic, or low oxygen, conditions. In that setting, any oxygen there is, is quickly consumed, so the microbes rely on what’s called anaerobic respiration. Rather than “breathing” oxygen, they’re getting energy from chemical reactions of compounds like sulfate, which ultimately produces the unpleasant smell.

The proximity of Edgecomb Eddy, and the relative ease of sampling there, has made it an ideal site — not only for developing new scientific tools, but also for giving students hands-on research experience.

Starting in 2020, when the pandemic put her original plans for fieldwork on hold, Lindsay began sampling at Edgecomb Eddy for a collaborative project with senior research scientists Beth Orcutt, Ramunas Stepanauskas, Nicole Poulton, and Dave Emerson, who has researched the biological communities of these mudflats for several years. The team devised a method to separate microbes out from the muddy sediment so they could sequence their genomes and figure out what they’re doing to survive.

The ultimate goal is to understand how the presence or absence of oxygen, and the stirring up of sediments by organisms like worms and clams, affects microbial productivity.

“Initially, we just wanted to look at anaerobic microbes in general,” Lindsay said. “But, as we explored the eddy, we started finding things we hadn’t seen before, and it’s been fun to have a site so nearby.”

Lindsay also realized that this could provide a close-to-home opportunity for students to learn new laboratory and field skills. Since 2021, undergraduate students in Bigelow Laboratory’s Sea Change Semester program have collected sediment cores from Edgecomb Eddy each fall as part of their biogeochemistry class. In processing those cores, they learn geochemical techniques for measuring oxygen, sulfide, and other compounds in sediment and get experience with a completely different type of ocean research.

“By the time they hit this part of their program, the students have gotten a lot of experience on our research vessel, so this is a new kind of fieldwork for them,” Lindsay said. “They get the novelty of doing something different while being exposed to some really interesting and important chemistry right in our muddy backyard.”

As she’s built out this student exercise, Lindsay has continued to analyze the samples she’s collected for her own research and combine the data with that produced by the students. Her preliminary results suggest that, as one moves deeper into the sediment, the environment transforms quickly from oxygen-rich to anoxic, and the microbial community is remarkably diverse.

Those results could provide insight as to what’s happening to the microbes living in sediments in environments that are harder to sample, including the deep sea.

“It can be difficult to dig deeper than the surface of these sediments,” Lindsay said. “What we’re starting to realize is that there is this whole host of untapped biodiversity the deeper one goes in the subsurface.”