Scientists discover dynamic microbial life in coastal sediments

Bigelow Laboratory scientists have advanced an exciting method for linking the activity of individual microbes to their unique genetic code, providing the first application of the approach to sediments. Their findings were recently published in The ISME Journal.

The method combines single cell genomics and flow cytometry to quantify individual rates of respiration for different taxa. It revealed that low-oxygen sediments from the Maine coast host a diverse microbial community that appears to thrive in an environment where they’re regularly subject to disruption from rapid temperature changes, tides, and more.

“Marine sediments are important ecosystems for active chemical cycling, and some of the most microbially diverse communities found on Earth live there,” said Melody Lindsay, a research scientist at Bigelow Laboratory who led the study. “It was a natural—and fascinating—place to advance our method for illuminating microbial activity using single-cell respiration rates.”

The paper features researchers from Bigelow Laboratory’s Single Cell Genomics Center and Center for Aquatic Cytometry, as well as several undergraduate interns who aided with field sampling and laboratory experiments.

Shallow coastal sediments help control the flow of energy and nutrients from land to ocean. Because oxygen penetrates only a few millimeters below the surface, microbes living in this environment tend to rely on chemical processes other than respiring, or “breathing,” oxygen to survive. Yet, disturbances like sedimentation and burrowing animals regularly introduce oxygen and organic matter into the subsurface environment. The team aimed to understand the impact of this mixing and physical disruption.

“We know the abundance and diversity of ocean sediment microbes is much greater than in the water column above, but we know far less about their actual functions and activities,” said Senior Research Scientist David Emerson, a co-author on the paper. “This method provides a powerful way to reveal new knowledge about a vast, and vastly understudied, part of the marine environment.”

Though scientists have traditionally measured the rates of chemical turnover and other processes for the microbial community as a whole, this larger effort is revolutionizing understanding of activity at the individual level—and how that links to genomic potential.

The revolutionary new method was developed by Bigelow Laboratory from a $6 million grant from the National Science Foundation. In 2022, the researchers first applied the method to the surface ocean, showing how a tiny proportion of microbes consume most of the oxygen. Last year, they tested it with samples from an aquifer deep below Death Valley, illustrating the applicability of the method in low-biomass environments with limited oxygen.

For the current study, the team once again used flow cytometry, staining cells with a chemical called RedoxSensor Green. The intensity at which stained cells light up under a laser correlates with the rate at which those cells are respiring. The DNA of each individual cell was then sequenced to understand the relationship between its activity rate and what it’s programmed to do. This combined technique enables researchers to get a snapshot of the microbial biodiversity and determine which species are the most abundant and active.

“The Single Cell Genomics Center is the world’s first facility capable of large-scale studies of microbial genomes and activities at the ultimate resolution in biology: individual cells,” said Ramunas Stepanauaskas, the director of the center and a co-author on the study. “It is exciting that this unique technology enabled us to shed light on these important ecological processes and truly amazing biological diversity in an environment that is so abundant yet so underexplored.”

To test the ability of microbes to adapt to disruption, which was a new aspect of the project, the team added different amounts of oxygen and laminarin, an abundant carbohydrate produced by brown algae and some phytoplankton common along Maine’s coast.

“By perturbing the system in a manner that has real-world relevance, we can determine the effects of, say, a worm burying into the sediment bringing oxygen or seaweed degrading at the bottom of a mudflat,” Lindsay said.

The findings demonstrate that sulfate-reducers from the Chloroflexota phylum were by far the most active cells in the sediments, though not the most abundant. The researchers also found that adding even small concentrations of oxygen and laminarin stimulated respiration. Chloroflexota cells are metabolically diverse, capable of using both oxygen and other chemical processes. That “genetic flexibility,” Lindsay suggested, may explain why they dominate.

“We went in with the hypothesis that oxygen would poison everything, but it turns out that cells are good at withstanding it and even taking advantage of it,” Lindsay said. “It suggests that the microbial community living in this capricious environment is more resilient than initially thought.”

The findings underscore the incredible range of microorganisms living in these extreme environments—and the value of a cell-by-cell approach for interrogating that diversity.

To that end, the team is currently working to expand their understanding of Maine’s coastal sediments. Using “kickstarter” funding from Bigelow Laboratory, they have begun examining deeper samples from the same study sites using the same experimental design, to observe how the microbial community changes with depth.

At the same time, they are continuing to refine the method for increasingly extreme environments, applying it to sediment collected through the International Ocean Discovery Program more than a kilometer below the Mid-Atlantic ridge, an environment which hosts orders of magnitude fewer cells.

“The advantage of this single-cell approach, enabled by the Center for Aquatic Cytometry and Single Cell Genomics Center, is we can target low-biomass environments where there are so few cells it would be impossible to make a measurement otherwise,” Lindsay said. “My dream is to get a flow cytometer on a mission like NASA’s Europa lander, so we can use this technique to detect possible metabolic activity on other worlds.”