Endospores Rival Growing Cells in Ocean Sediments

A survey of ocean sediments from around the world finds that dormant bacterial endospores are about as common as slow-growing cells, and make up a significant portion of the total microbial biomass, especially in deeper sediments.

A diverse group of bacteria called Firmicutes, which can be found in human infections, fermented foods, and a variety of natural environments, have a bacterial superpower. When facing tough times, they transform into tough, seed-like endospores and go dormant until conditions improve, sometimes for millions of years. Endospores don’t need nutrients and are resistant to UV radiation, hot and cold temperatures, and dehydration. They are so tough, they’re even resistant to the methods commonly used to count and identify cells. As a result, scientists often have overlooked bacterial endospores when cataloguing bacterial life in the subsurface.

Once DCO scientists started looking however, they found endospores in ocean sediments all over the world. In a new paper [1] in Science Advances, researchers report that the number of endospores in ocean sediments is similar to the number of slow-growing “vegetative” cells, and they become more dominant with depth. The project involved numerous Deep Life Community members, including Lars Wörmer, Bernhard Viehweger, Martin Könneke, Kai-Uwe Hinrichs (all at MARUM – Center for Marine Environmental Sciences at the University of Bremen, Germany), Marshall Bowles (Louisiana Universities Marine Consortium, USA), and Tatsuhiko Hoshino, Yuki Morono, and Fumio Inagaki (all at Japan Agency for Marine-Earth Science and Technology, Japan).

Endospores 1
These spore-forming bacteria grew from samples collected from more than 100 meters beneath the seafloor off Peru’s coast (Ocean Drilling Program Leg 201 Site 1227, Hole A 12H-3, 102.4 mbsf). The vegetative cells glow blue due to a florescent dye, while the endospores appear as bright round balls. Credit: Fumio Inagaki, JAMSTEC

“Globally, endospores might be as abundant as vegetative cells, which is something that we didn’t expect,” said Wörmer. “I think this was a piece that was missing in our understanding of the deep biosphere.” Typically, endospores are smaller than vegetative cells and are encased in several protective layers. The deeply buried endospores don’t react with most stains used to visualize vegetative cells under the microscope, and won’t crack open during most bacterial DNA extraction protocols.

Wörmer first got involved with the project when he met Inagaki at the second DCO International Science Meeting in Munich, Germany in 2015. Inagaki’s group had more than 300 sediment samples collected from different environments all over the world through various scientific ocean drilling expeditions. It was the ideal data set for looking at global endospore populations. Previously, scientists had counted endospores only in North Sea sediments and in the continental shelf off the coast of Peru.

To detect endospores, Wörmer relied on a biomarker called dipicolinic acid (DPA). Vegetative cells don’t make DPA, but in endospores the compound makes up around 10 percent of their weight. By quantifying the DPA in samples, Wörmer and his colleagues could estimate the number of endospores they contained.

Based on DPA concentrations, the researchers estimate that the top kilometer of ocean sediments worldwide holds between 25 and 190 octillion endospores, which represent about 4.6 to 35 billion tons of carbon. The biomass of endospores may even be larger than that of vegetative cells in the sediments, which they estimate to be 1.2 to 1.8 billion tons. 

Expedition 347
Credit: B.B. Jorgensen, ECORD/IODP

The youngest sediments had the greatest abundance of endospores, with the numbers decreasing with depth. The top endospores likely washed in from land or settled out of the water column. In sediments older than about 10000 years, however, the numbers decline more slowly, suggesting that after thousands of years, only the hardiest endospores have survived and they’re in it for the long haul.

The researchers suspect that these older, tougher endospores exist as a “seed bank” in the deep sediments. Just like a plant seed bank, this reservoir of endospores can preserve genetic diversity until they encounter a more favorable environment where they can reactivate and reproduce.

Now that researchers have identified this formerly invisible population as a major component of the subseafloor biomass in sediments, they’ll need to determine what, if anything, they are doing there. Next, Wörmer plans to investigate the ecological role endospores play in the environment and how often they come out of hibernation. “We have quantified them,” said Wörmer. “Now we have to ask ourselves, ‘What are they are contributing to the deep biosphere?’” 


Main image: Core recovered during IODP Expedition 347. Credit: I. Marshall, ECORD/IODP

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