Scientists discover dynamic microbial life in coastal sediments

Bigelow Laboratory Scientists advances stimulating methods for linking the activities of individual microorganisms to their own genetic codes, offering the first application of an approach to sediment. Their findings were recently published in the ISME Journal.

This method combines single cell genomics and flow cytometry to quantify individual respiratory rates for different taxa. It revealed that hypoxic deposits on Maine coasts host diverse microbial communities that appear to thrive in environments that regularly target disruptions from rapid temperature changes, tides, and more.

“Marine sediments are an important ecosystem for active chemical cycling, and some of the most microbial-diverse communities found on the planet live there,” said Melody Lindsay, a research scientist at Bigelow Laboratory. “It was a natural and fascinating place to advance how to use single-cell respiratory rates to light microbial activity.”

This paper features researchers from the Bigelow Laboratory’s Single Cell Genomics Center and the Aquatic Cell Measurement Center, as well as several undergraduate interns who supported field sampling and laboratory experiments.

Shallow coastal sediments help to control energy and nutrient flow from land to sea. Because oxygen penetrates just a few millimeters below the surface, microorganisms living in this environment tend to rely on chemical processes other than breathing oxygen or “breathing.” However, turbulence, like sedimentation and burrowing animals, regularly introduces oxygen and organic matter into the underground environment. The team sought to understand the effects of this mixing and physical disruption.

“We know that the abundance and diversity of marine sediment microorganisms is much greater than the above water column, but we know that there is much less in terms of actual function and activity,” says senior research scientist David Emerson, co-author of the paper. “This method provides a powerful way to uncover new knowledge about the vast and highly studied parts of the marine environment.”

Scientists have traditionally measured the percentage of chemical turnover and other processes across microbial communities, but this major effort is to innovate how they understand their activity at an individual level and how they link to their genome potential.

An innovative new method was developed by Bigelow Laboratory from a $6 million grant from the National Science Foundation. In 2022, researchers first applied the method to the surface seas, showing how a small portion of the microorganism consumes most of the oxygen. Last year they tested it on samples of aquifers deep in Death Valley, demonstrating the applicability of the method in low-biomas environments where oxygen is limited.

In the current study, the team again used flow cytometry to stain a chemical called redox sensor green. The intensity illuminated by cells stained under the laser correlates with the rate at which those cells respiratory. The DNA of individual cells was then sequenced to understand the relationship between their activity rate and its programmedness. This combined approach allows researchers to take snapshots of microbial biodiversity and determine which species are most abundant and active.

“The Single Sergenomics Centre is the world’s first facility that allows for large-scale research into microbial genomes and activities at the ultimate resolution of biology. “It is exciting to see this unique technology shed light on these important ecological processes and truly incredible biological diversity in a highly abundant yet unexposed environment.”

To test the microbial ability to adapt to the new aspect of the project, the disruption, the team added varying amounts of oxygen and laminalin.

“By disrupting the system in a way that is relevant in the real world, we can determine the effectiveness of worms buried in sediments, for example, to break down oxygen and seaweed at the bottom of the mud flat,” Lindsay said.

Findings show that sulfate reducing agents from the phylum Chlorofectota were the most active cells in the sediment, but not the most abundant. Researchers also found that adding oxygen and even laminarin concentrations stimulates breathing. Chlorofectota cells are metabolically diverse and can use both oxygen and other chemical processes. Lindsay may explain why they dominate, as suggested by “genetic flexibility.”

“We hypothesized that oxygen poisons everything, but we found that cells can withstand it and even take advantage of it,” Lindsay said. “This suggests that microbial communities living in this whimsical environment are more resilient than initially thought.”

The findings highlight the incredible range of microorganisms living in these extreme environments. It highlights the value of a cell-by-cell approach to interrogating its diversity.

To that end, the team is currently working to expand understanding of Maine’s coastal sediment. Using “Kickstarter” funds from Bigelow Laboratory, we began to look at deeper samples from the same research site using the same experimental design to observe how microbial communities change with depth.

At the same time, they continue to refine their methods of extreme environments, applying them to sediments collected from the International Marine Discovery Program, more than a km below the mid-Atlantic ridge.

“The advantage of this single-cell approach, enabled by the Aquatic Cell Measurement Center and the Single-Cell Genomics Center, is that it allows you to target low-biomass environments where measurements cannot be made because there are so few cells,” Lindsay said. “My dream is to get a flow cytometer on a mission like NASA’s Europa Lander, so I can use this technique to detect possible metabolic activities in other worlds.”